2010-05-31  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog: updated changelog
	* NEWS: update NEWS
	* ChangeLog: updated changelog
	* Makefile.template, configure: compile fixes for osx

2010-05-30  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog: updated changelog

2010-05-28  Soeren Sonnenburg <sonne@debian.org>

	* NEWS: update news

2010-05-27  Alexander Binder <alexander.binder@first.fraunhofer.de>

	* libshogun/classifier/mkl/MKLMultiClass.cpp,
	  libshogun/classifier/mkl/MKLMultiClass.h,
	  libshogun/classifier/mkl/MKLMultiClassGradient.cpp: MKL
	  Multiclass: added debug output, for L1 norm check of duality gap
	  now performed instead of weight

2010-05-27  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* libshogun/kernel/SpectrumRBFKernel.cpp: minor fix

2010-05-24  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* libshogun/kernel/SpectrumRBFKernel.cpp,
	  libshogun/kernel/SpectrumRBFKernel.h: Fusion of RBF and Spectrum
	  kernel

2010-05-14  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/StringFeatures.h: fix minor memory leak and
	  bug in append features
	* libshogun/features/StringFeatures.h: fix uninited memory read in
	  histogram normalization
	* libshogun/lib/File.cpp, libshogun/lib/File.h: add close() to file
	  to force close before destruction

2010-05-12  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/mkl/MKLMultiClassGradient.cpp,
	  libshogunui/GUIKernel.cpp: enable scatter kernel from matlab
	  interface

2010-05-10  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/StringFeatures.h, libshogun/lib/AsciiFile.cpp:
	  add append_features function for CStringFeatures as inputs and
	  impl. load/save for bytes

2010-05-09  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* libshogun/kernel/SpectrumMismatchRBFKernel.cpp: A
	  src/libshogun/kernel/SpectrumMismatchRBFKernel.cpp
	* configure, libshogun/kernel/SpectrumMismatchRBFKernel.h: missing
	  file
	* libshogunui/GUIKernel.cpp, libshogunui/GUIKernel.h,
	  libshogunui/SGInterface.cpp: matlab gui for WEIGHTEDDEGREERBF and
	  SPECTRUMMISMATCHRBF
	* libshogun/kernel/Kernel.cpp, libshogun/kernel/Kernel.h,
	  libshogun/kernel/WeightedDegreeRBFKernel.cpp,
	  libshogun/kernel/WeightedDegreeRBFKernel.h: minor changes to
	  CWeightedDegreeRBFKernel and CKernel for WeightedDegreeRBFKernel

2010-05-07  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/StringFeatures.h: add function to concatenate
	  features
	* libshogun/features/StringFeatures.h, modular/Features.i: add
	  functions to compute histogram/random features for it

2010-05-04  Alexander Binder <alexander.binder@first.fraunhofer.de>

	* libshogun/kernel/PyramidChi2.cpp, libshogun/kernel/PyramidChi2.h,
	  libshogunui/GUIClassifier.cpp: GUIclassifier.cpp: mklnorm
	  parameter now affects CMKLMultiClass
	  updated examples for MKL Multiclass
	  worked on PYChi2kernel
	* libshogun/classifier/mkl/MKLMultiClass.cpp,
	  libshogun/classifier/mkl/MKLMultiClass.h,
	  libshogun/classifier/mkl/MKLMultiClassGLPK.h,
	  libshogun/classifier/mkl/MKLMultiClassGradient.cpp,
	  libshogun/classifier/mkl/MKLMultiClassGradient.h,
	  libshogun/classifier/mkl/MKLMultiClassOptimizationBase.cpp,
	  libshogun/classifier/mkl/MKLMultiClassOptimizationBase.h: iadded
	  Lp norm MKL for MKL multiclass

2010-05-03  Alexander Binder <alexander.binder@first.fraunhofer.de>

	* libshogun/kernel/PyramidChi2.h: updated documentation

2010-05-03  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* modular/Kernel.i: added WDK that considers additional properties
	  of amino acids (swig)
	* libshogun/kernel/WeightedDegreeRBFKernel.cpp,
	  libshogun/kernel/WeightedDegreeRBFKernel.h: added WDK that
	  considers additional properties of amino acids

2010-05-03  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/kernel/LinearKernel.cpp,
	  libshogun/kernel/SparseLinearKernel.cpp: fix sparse linear
	  kernel's add_to_normal *sigh*

2010-05-02  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/kernel/CustomKernel.cpp,
	  libshogun/kernel/CustomKernel.h, libshogun/lib/Parameter.cpp,
	  libshogun/lib/Parameter.h, modular/Kernel.i,
	  python_modular/swig_typemaps.i: allow also floats etc as input
	  for custom kernel

2010-04-16  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/SVM.cpp, libshogun/classifier/svm/SVM.h,
	  libshogun/lib/DataType.h, libshogun/lib/File.h,
	  libshogun/lib/Parameter.h: move datatype enum into a separate
	  file and introduce parameters with SVM C as example

2010-04-15  Soeren Sonnenburg <sonne@debian.org>

	* .generate_link_dependencies.py, modular/SGBase.i,
	  octave_modular/sg_print_functions.cpp,
	  r_modular/sg_print_functions.cpp: update link dependency
	  generator script to work with .so as suffix and get octave/r
	  modular interfaces back to work
	* Makefile.template, configure: try to get python-dbg to work...

2010-04-14  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, configure: adjust .so suffix for python and apply yaroslavs
	  patch to use distutils to figure out libs & co
	* libshogun/features/Labels.cpp, libshogun/features/Labels.h,
	  modular/Features.i: apply patch from Amir Saffari to add label
	  confidences

2010-04-12  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, libshogun/evaluation/PerformanceMeasures.cpp,
	  libshogun/evaluation/PerformanceMeasures.h: fix race condition in
	  perf measures
	* NEWS: update for 0.9.3

2010-04-05  Soeren Sonnenburg <sonne@debian.org>

	* configure: really fix static libshogunui linking problem
	* configure: fix static linking of libshogunui

2010-03-31  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/distributions/histogram, libshogun/distributions/hmm:
	  make -> $(MAKE)

2010-03-30  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog: updated changelog
	* libshogun/features/CombinedDotFeatures.h,
	  libshogun/features/DotFeatures.h,
	  libshogun/features/HashedWDFeatures.h,
	  libshogun/features/HashedWDFeaturesTransposed.h,
	  libshogun/features/SimpleFeatures.h,
	  libshogun/features/SparseFeatures.h,
	  libshogun/features/SparsePolyFeatures.h,
	  libshogun/features/StringFeatures.h,
	  libshogun/kernel/MultitaskKernelTreeNormalizer.h,
	  libshogun/kernel/PyramidChi2.h, libshogun/lib/AsciiFile.h,
	  libshogun/lib/BinaryFile.h, libshogun/lib/File.h,
	  libshogun/lib/HDF5File.h, libshogun/lib/Hash.h: - many further
	  documentation improvements
	  - fix installation of libshogun examples
	* ChangeLog: updated changelog
	* libshogun/lib/AsciiFile.cpp, libshogun/lib/AsciiFile.h,
	  libshogun/lib/BinaryFile.cpp, libshogun/lib/BinaryFile.h,
	  libshogun/lib/File.cpp, libshogun/lib/File.h,
	  libshogun/lib/HDF5File.cpp, libshogun/lib/HDF5File.h: more
	  documentation
	* .version.sh, libshogun/classifier/svm/LaRank.h,
	  libshogun/features/CombinedDotFeatures.h,
	  libshogun/features/DotFeatures.h,
	  libshogun/features/HashedWDFeaturesTransposed.h,
	  libshogun/features/ImplicitWeightedSpecFeatures.h,
	  libshogun/features/SNPFeatures.h,
	  libshogun/features/SimpleFeatures.h,
	  libshogun/features/SparseFeatures.h,
	  libshogun/features/StringFeatures.h,
	  libshogun/features/WDFeatures.h,
	  libshogun/kernel/KernelNormalizer.h: add a gazillion of
	  docstrings
	* Makefile.template, configure,
	  libshogun/features/StringFeatures.h: workaround a compile failure
	  on osx
	* Makefile, Makefile.template: tests run through finally
	* Makefile.template: don't kill default paths
	* libshogun/lib/AsciiFile.cpp, libshogun/lib/HDF5File.cpp: don't
	  transpose ascii (really really don't) and remove debug code from
	  hdf5
	* NEWS, configure: shogun octave-modular works reliably until one
	  exits octave. however octave
	  crashes upon exit. disable octave modular by default until
	  swig/octave fix the
	  crasher when *unloading* modules.
	* .version.sh, libshogun/lib/HDF5File.cpp,
	  libshogun/lib/HDF5File.h: r/w support of hdf5 matrices/vectors
	* Makefile.template: set LD_LIBRARY_PATH w/ matlab
	* libshogun/lib/HDF5File.cpp, libshogun/lib/HDF5File.h: hdf5 vector
	  and matrix read support plus proper error handling

2010-03-29  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/lib/HDF5File.cpp, libshogun/lib/HDF5File.h,
	  libshogun/lib/Mathematics.cpp: non-standard boolean type
	  detection, print function for ulong vectors
	* NEWS, libshogun/lib/HDF5File.cpp: drafty hdf5 read support for
	  vectors

2010-03-29  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun, libshogun/base, libshogun/classifier/svm,
	  libshogun/distributions/histogram, libshogun/distributions/hmm,
	  libshogun/lib/common.h: additional boost::serialization code
	* libshogun/kernel/Kernel.h,
	  libshogun/kernel/MultitaskKernelMaskPairNormalizer.h,
	  modular/Kernel.i: added MultitaskKernelMaskPairNormalizer
	* libshogun/classifier/svm/DomainAdaptationSVM.cpp,
	  libshogun/classifier/svm/DomainAdaptationSVM.h: added optional
	  train factor
	* libshogun/classifier/mkl/MKL.cpp: fixed minor bug
	* libshogun/features/Alphabet.cpp, libshogun/features/Alphabet.h,
	  libshogun/features/Features.cpp, libshogun/features/Features.h,
	  libshogun/features/StringFeatures.cpp: further work on
	  serialization code
	* libshogun/kernel/MultitaskKernelMaskNormalizer.h,
	  libshogun/kernel/MultitaskKernelMklNormalizer.h,
	  libshogun/kernel/MultitaskKernelNormalizer.h,
	  libshogun/kernel/MultitaskKernelPlifNormalizer.h,
	  libshogun/kernel/MultitaskKernelTreeNormalizer.h: completed
	  documentation for multitask mkl code

2010-03-29  Soeren Sonnenburg <sonne@debian.org>

	* configure, libshogun/lib/AsciiFile.cpp,
	  libshogun/lib/AsciiFile.h, libshogun/lib/BinaryFile.cpp,
	  libshogun/lib/BinaryFile.h, libshogun/lib/File.cpp,
	  libshogun/lib/File.h, libshogun/lib/HDF5File.cpp,
	  libshogun/lib/HDF5File.h: start integration of hdf5 file support
	* cmdline/CmdLineInterface.cpp,
	  libshogun/features/SparseFeatures.h, libshogun/lib/AsciiFile.cpp,
	  libshogun/lib/AsciiFile.h, libshogun/lib/BinaryFile.cpp,
	  libshogun/lib/BinaryFile.h, libshogun/lib/File.h: load/write of
	  sparse features of arbitrary type

2010-03-28  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/Labels.cpp, libshogun/features/Labels.h,
	  libshogun/lib/AsciiFile.cpp: support loading/writing of labels
	* libshogun/lib/BinaryFile.cpp, libshogun/lib/File.h: set/get
	  functions for vectors/strings

2010-03-27  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/lib/BinaryFile.cpp: implement binary vector GET
	  function

2010-03-26  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/lib/BinaryFile.cpp, libshogun/lib/BinaryFile.h,
	  libshogun/lib/File.h: support for basic reading/writing of binary
	  matrices
	* libshogun/lib/BinaryFile.cpp, libshogun/lib/BinaryFile.h,
	  modular/Library.i: template for binary i/o
	* libshogun/kernel/Kernel.cpp, modular/Library.i: ascii file i/o
	  seems to work now
	* libshogun/features/StringFeatures.h, libshogun/lib/AsciiFile.cpp:
	  fix erraneous close when file is not opened and warnings caused
	  by wrong fprintf format strings
	* libshogun/lib/AsciiFile.h: all features read from ascii files are
	  transposed now (one example == one line): so change examples
	  accordingly
	* cmdline/CmdLineInterface.cpp, libshogun/lib/AsciiFile.cpp,
	  libshogun/lib/AsciiFile.h, libshogun/lib/BinaryFile.h,
	  libshogun/lib/File.cpp, libshogun/lib/File.h,
	  libshogunui/SGInterface.cpp, libshogunui/SGInterface.h:
	  consolidate i/o functions

2010-03-25  Soeren Sonnenburg <sonne@debian.org>

	* cmdline/CmdLineInterface.cpp, libshogun/lib/AsciiFile.cpp,
	  libshogun/lib/AsciiFile.h: implement loading of dense matrices
	* cmdline/CmdLineInterface.cpp, libshogun/distance/Distance.cpp,
	  libshogun/distance/Distance.h, libshogun/features/DotFeatures.h,
	  libshogun/features/Features.cpp, libshogun/features/Features.h,
	  libshogun/features/Labels.cpp, libshogun/features/Labels.h,
	  libshogun/features/SimpleFeatures.h,
	  libshogun/features/SparseFeatures.h,
	  libshogun/features/StringFeatures.h, libshogun/kernel/Kernel.cpp,
	  libshogun/kernel/Kernel.h, libshogun/lib/AsciiFile.cpp,
	  libshogun/lib/AsciiFile.h, libshogun/lib/BinaryFile.cpp,
	  libshogun/lib/BinaryFile.h, libshogun/lib/File.cpp,
	  libshogun/lib/File.h, libshogun/lib/HDF5File.h,
	  libshogun/lib/LibSVMFile.h, libshogunui/GUIDistance.cpp,
	  libshogunui/GUIFeatures.cpp, libshogunui/GUIKernel.cpp,
	  libshogunui/GUILabels.cpp, libshogunui/SGInterface.cpp,
	  libshogunui/SGInterface.h: inital (dysfunctional) commit starting
	  to use the generalized access functions in CFile

2010-03-22  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/kernel/PolyKernel.cpp: poly kernel was correct / fixes
	  brown paper back commit

2010-03-19  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/SVM.h: add function to retrieve tube
	  epsilon
	* libshogun/kernel/Kernel.cpp, libshogun/kernel/Kernel.h,
	  libshogun/kernel/KernelNormalizer.h,
	  libshogun/kernel/MultitaskKernelMklNormalizer.h: minor whitespace
	  cleanup & init kernel normalizer when features are already
	  available
	* libshogun/features/Alphabet.cpp, libshogun/features/Alphabet.h,
	  libshogun/features/SNPFeatures.cpp,
	  libshogun/features/StringFeatures.h: - add error handling on
	  load_ascii_file
	  - add SNP alphabet
	  - require SNP alphabet in SNP features
	* libshogun/features/DotFeatures.h,
	  libshogun/features/SNPFeatures.cpp,
	  libshogun/features/SNPFeatures.h: add snp feature exampel

2010-03-18  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/SNPFeatures.cpp,
	  libshogun/features/SNPFeatures.h,
	  libshogun/kernel/SNPStringKernel.h, modular/Features.i: start
	  implementing SNP features
	* libshogun/features/Alphabet.cpp, libshogun/features/Alphabet.h,
	  libshogun/features/StringFeatures.h, libshogunui/SGInterface.cpp:
	  include RAWDIGITS etc alphabets and generalize load_dna_file to
	  load_ascii_file in stringfreatures
	* libshogun/features/Alphabet.cpp, libshogun/features/Alphabet.h,
	  libshogun/kernel/PolyMatchStringKernel.h: add DIGIT and DIGIT2
	  alphabet
	* .version.sh: apply patch from Yaroslav Halchenko that adds
	  versions when building within a git-svn tracked source

2010-03-17  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/kernel/GaussianMatchStringKernel.cpp,
	  libshogun/kernel/GaussianMatchStringKernel.h,
	  libshogun/kernel/Kernel.h,
	  libshogun/kernel/PolyMatchStringKernel.cpp,
	  libshogun/kernel/PolyMatchStringKernel.h, modular/Kernel.i:
	  integrate hagens gaussian match str kernel
	* libshogun/features/CombinedDotFeatures.h: fix use of combined
	  weight

2010-03-11  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/kernel/PolyKernel.cpp: fix bug in poly kernel when
	  inhomog. kernel was used

2010-03-10  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/LaRank.h, modular/Kernel.i: - fix a
	  crasher in LaRank
	  - fix set_subkernel_weights

2010-03-03  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp, libshogunui/SGInterface.cpp: --
	  included a check that the size of the segment_mask corresponds to
	  the size of
	  the observation matrix. To do that I had to set the observation
	  matrix before the
	  segment_mask in all interfaces

2010-03-02  Soeren Sonnenburg <sonne@debian.org>

	* INSTALL, libshogunui/SGInterface.cpp: update docu/install
	  instructions based on vojtechs comments

2010-03-01  Soeren Sonnenburg <sonne@debian.org>

	* INSTALL, configure: explain which python packages need to be
	  installed and fix configure to fail when python is requrested but
	  not installed
	* libshogun/preproc/LogPlusOne.h: fix typo
	* configure: forget about python when it is not properly installed
	* configure: proper python2.4 detection...
	* libshogun/lib/io.cpp, libshogun/lib/io.h,
	  libshogunui/SGInterface.cpp: really disable all syntax
	  highlighting, even for error messages
	* configure: don't enable python-static when python is not
	  available

2010-02-26  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/lib/io.cpp, libshogunui/SGInterface.cpp: - disable line
	  prefixes (that were on by default)
	  - mention how syntax highlighting can be disabled (for poor
	  matlab gui users ;)
	* libshogun/distributions/Distribution.h,
	  libshogun/distributions/LinearHMM.cpp: fix reference counting for
	  linear hmms/distributions set/get_features
	* libshogun/features/SimpleFeatures.h: hopefully fix access of
	  feature vectors in matrices >2GB (but still with no more than
	  2^31 features/ 2^31 examples)

2010-02-25  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/classifier/LPBoost.h, libshogun/classifier/LPM.h,
	  libshogun/classifier/SubGradientLPM.h,
	  libshogun/classifier/svm/LibLinear.h,
	  libshogun/classifier/svm/SVM.h,
	  libshogun/classifier/svm/SVMLin.h,
	  libshogun/classifier/svm/SVMOcas.h,
	  libshogun/classifier/svm/SVMSGD.h,
	  libshogun/classifier/svm/SubGradientSVM.h,
	  libshogun/classifier/svm/WDSVMOcas.h: renamed set_C(c1, c2) to
	  set_C(c_neg, c_pos) to make it self-explanatory

2010-02-25  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/SVM_libsvm.cpp: avoid bias messing
	  around when bias is disabled and return 0 immediately
	* libshogun/classifier/svm/SVM_libsvm.cpp: add support for
	  disabling bias for libsvm - thanks Chih-Jen Lin for the code
	* libshogun/features/SimpleFeatures.h: fix a bug when returned
	  matrices are >4GB
	* libshogun/classifier/svm/LibSVM.cpp: minor cleanup
	* libshogun/features/SimpleFeatures.h: fix crasher in out of memory
	  condigiton

2010-02-24  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/kernel/ScatterKernelNormalizer.h, modular/Kernel.i: add
	  scatter kernel normalizer for scattersvm
	* libshogun/base/SGObject.cpp,
	  libshogun/classifier/svm/LibLinear.cpp,
	  libshogun/classifier/svm/LibLinear.h,
	  libshogun/classifier/svm/SVM_libsvm.cpp,
	  libshogun/classifier/svm/Tron.cpp,
	  libshogun/classifier/svm/Tron.h: support setting of maximum
	  number of iterations for liblinear and include time limit

2010-02-23  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/MultiClassSVM.h: add function to fetch
	  multiclass type
	* libshogun/classifier/svm/MultiClassSVM.cpp: no longer assign
	  labels to sub-svms

2010-02-22  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/SimpleFeatures.h,
	  libshogun/features/WDFeatures.cpp,
	  libshogun/features/WDFeatures.h, modular/Features.i: add an
	  option to set custom weights / normalization const in wd features
	* libshogun/classifier/svm/LibLinear.cpp: add todo snippet for
	  liblinear multiclass
	* libshogun/classifier/LinearClassifier.h,
	  libshogun/classifier/svm/LibLinear.cpp, libshogun/lib/io.cpp: fix
	  bias handling in liblinear L1_*, turn on file/error nr for error
	  msg's
	* NEWS, libshogun/base/SGObject.cpp, libshogun/base/SGObject.h,
	  libshogun/base/init.cpp, libshogun/base/init.h,
	  libshogun/classifier/svm/LibLinear.cpp: add set/get io object
	  functions and update news

2010-02-19  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/SimpleFeatures.h,
	  libshogun/kernel/MultitaskKernelMklNormalizer.h,
	  libshogun/kernel/MultitaskKernelTreeNormalizer.h,
	  modular/Kernel.i: - fix multitaskkernelnormalizer inclusion order
	  - add function to simplefeatures to obtain fm directly from
	  dotfeatures

2010-02-19  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/kernel/Kernel.h: fixed multiple friend
	* modular/Kernel.i, modular/SGBase.i: updated interfaces for MT
	  kernels
	* libshogun/base/SGObject.h: included some stl containers
	* libshogun/kernel/MultitaskKernelMklNormalizer.h,
	  libshogun/kernel/MultitaskKernelPlifNormalizer.h,
	  libshogun/kernel/MultitaskKernelTreeNormalizer.h,
	  libshogun/kernel/WeightedDegreeStringKernel.cpp,
	  libshogun/kernel/WeightedDegreeStringKernel.h: further work on MT
	  kernels
	* libshogun/kernel/Kernel.cpp, libshogun/kernel/Kernel.h: added MT
	  normalizers as friends
	* libshogun/kernel/KernelNormalizer.h: added kernel_normalizer type
	  enum

2010-02-19  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/TransposedWDFeatures.cpp,
	  libshogun/features/TransposedWDFeatures.h, modular/Features.i:
	  remove transposed wd features
	* libshogun/features/TransposedWDFeatures.cpp,
	  libshogun/features/TransposedWDFeatures.h,
	  libshogun/features/WDFeatures.cpp, modular/Features.i: add
	  transposed wd features

2010-02-19  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp, libshogun/structure/Plif.cpp: --
	  new example description + some additional debug code

2010-02-19  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/regression/svr/LibSVR.cpp: set max train time for
	  libsvr

2010-02-18  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/kernel/MultitaskKernelMaskNormalizer.h,
	  libshogun/kernel/MultitaskKernelTreeNormalizer.h: added mask
	  normalizer and improved tree normalizer

2010-02-16  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/StringFeatures.h: fix string feature transpose
	  function
	* libshogun/features/StringFeatures.h: fix get_transposed() in
	  string features
	* configure, libshogun/features/ImplicitWeightedSpecFeatures.cpp,
	  libshogun/features/ImplicitWeightedSpecFeatures.h,
	  libshogun/features/WDFeatures.cpp,
	  libshogun/features/WDFeatures.h: implement feature iterator for
	  wd and spectrum kernel features
	* Makefile, libshogun/classifier/svm/LibLinear.cpp,
	  libshogun/features/CombinedDotFeatures.cpp,
	  libshogun/features/CombinedDotFeatures.h,
	  libshogun/features/ImplicitWeightedSpecFeatures.h,
	  libshogun/features/SimpleFeatures.h,
	  libshogun/features/SparseFeatures.h,
	  libshogun/features/WDFeatures.h: integreate sparse feature
	  iterator in combined dot features
	* libshogun/classifier/svm/LibLinear.cpp,
	  libshogun/features/SimpleFeatures.h,
	  libshogun/features/SparseFeatures.h: L1 based liblinear methods
	  work now

2010-02-15  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/LibLinear.cpp,
	  libshogun/features/SimpleFeatures.h,
	  libshogun/features/SparseFeatures.h: fix transpose functions
	* libshogun/classifier/svm/LibLinear.cpp, modular/Features.i:
	  modify L1 parts of liblinear to use new interface
	* libshogun/features/CombinedDotFeatures.h,
	  libshogun/features/DotFeatures.h,
	  libshogun/features/ExplicitSpecFeatures.h,
	  libshogun/features/FKFeatures.cpp,
	  libshogun/features/HashedWDFeatures.h,
	  libshogun/features/HashedWDFeaturesTransposed.h,
	  libshogun/features/ImplicitWeightedSpecFeatures.cpp,
	  libshogun/features/ImplicitWeightedSpecFeatures.h,
	  libshogun/features/PolyFeatures.h,
	  libshogun/features/SimpleFeatures.h,
	  libshogun/features/SparseFeatures.h,
	  libshogun/features/SparsePolyFeatures.h,
	  libshogun/features/WDFeatures.h: add an iterator to enable
	  traversing non-zero components of (sparse) feature vectors

2010-02-12  Soeren Sonnenburg <sonne@debian.org>

	* Makefile, Makefile.template, libshogun/signals: fix makefile to
	  install examples

2010-02-09  Soeren Sonnenburg <sonne@debian.org>

	* configure: support Renesas SH architectures (thanks Nobuhiro
	  Iwamatsu for the patch)
	* libshogun/classifier/Classifier.h: fix a potential crasher in
	  get_labels()

2010-02-06  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/mkl/MKL.cpp, libshogun/classifier/mkl/MKL.h:
	  apply ryotas patch for elastic net lambda setting in libshogun
	* libshogunui/GUIClassifier.cpp, libshogunui/GUIClassifier.h,
	  libshogunui/GUICommands.h, libshogunui/SGInterface.cpp,
	  libshogunui/SGInterface.h: apply ryotas patch for setting the
	  lambda elastic net parameter in static interface

2010-02-03  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/SimpleFeatures.h: add transposed fkt
	* libshogun/features/SparseFeatures.h,
	  libshogun/features/StringFeatures.h: add functions to transpose
	  strings/sparse features

2010-02-01  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/HashedWDFeatures.h,
	  libshogun/features/ImplicitWeightedSpecFeatures.h,
	  libshogun/features/SparsePolyFeatures.h,
	  libshogun/features/WDFeatures.h: try to do some reasonable
	  estimates of nnz in a number of dotfeatures

2010-01-31  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/SparsePolyFeatures.cpp: compute hash
	  incrementally
	* libshogun/features/SparsePolyFeatures.cpp,
	  libshogun/features/SparsePolyFeatures.h: fix sparse dot features
	  + hashing
	* NEWS, libshogun/features/SparsePolyFeatures.cpp: dim fix, update
	  NEWS
	* libshogun/features/PolyFeatures.h,
	  libshogun/features/SparseFeatures.h,
	  libshogun/features/SparsePolyFeatures.cpp,
	  libshogun/features/SparsePolyFeatures.h, modular/Features.i: add
	  sparse poly features dotfeatures

2010-01-27  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/kernel/WeightedDegreeStringKernel.cpp,
	  libshogunui/SGInterface.cpp: fix a too strict error check

2010-01-26  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/LibLinear.cpp,
	  libshogun/classifier/svm/Tron.cpp: enable progress w/ liblinear

2010-01-25  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/HashedWDFeaturesTransposed.cpp: bugfix in sub
	  idx
	* libshogun/features/DotFeatures.cpp,
	  libshogun/features/HashedWDFeaturesTransposed.cpp: bugfixes -
	  sub_index needs to be NULL
	* libshogun/classifier/svm/SVM_linear.cpp,
	  libshogun/features/CombinedDotFeatures.cpp,
	  libshogun/features/CombinedDotFeatures.h,
	  libshogun/features/DotFeatures.cpp,
	  libshogun/features/DotFeatures.h,
	  libshogun/features/HashedWDFeaturesTransposed.cpp,
	  libshogun/features/HashedWDFeaturesTransposed.h: introduce
	  dense_dot_range_subset()

2010-01-24  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/DotFeatures.cpp,
	  libshogun/features/HashedWDFeaturesTransposed.cpp,
	  libshogun/features/HashedWDFeaturesTransposed.h: properly
	  parallelize hashedwdfeatures

2010-01-23  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/CombinedDotFeatures.cpp: fix a bug in combined
	  dot features dense_dot_range
	* libshogun/features/DotFeatures.cpp,
	  libshogun/features/DotFeatures.h,
	  libshogun/features/HashedWDFeatures.cpp,
	  libshogun/features/HashedWDFeaturesTransposed.cpp,
	  libshogun/features/WDFeatures.cpp: get transposed wd features to
	  work correctly
	* libshogun/classifier/svm/SVM_linear.cpp,
	  libshogun/classifier/svm/Tron.cpp: use dot() instead of loop

2010-01-22  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/CombinedDotFeatures.cpp: fix combined dot
	  dense range
	* libshogun/features/CombinedDotFeatures.cpp,
	  libshogun/features/CombinedDotFeatures.h,
	  libshogun/kernel/Kernel.h: fix compile error with multitask
	  kernel and add dense_dot_range call to combined dot features
	* libshogun/features/HashedWDFeaturesTransposed.cpp: offset fixes

2010-01-22  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/kernel/MultitaskKernelNormalizer.h,
	  libshogun/kernel/MultitaskKernelTreeNormalizer.h: fixed a few
	  issues

2010-01-22  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/HashedWDFeaturesTransposed.cpp,
	  libshogun/features/HashedWDFeaturesTransposed.h,
	  libshogun/features/StringFeatures.h: wip commit
	* libshogun/features/HashedWDFeaturesTransposed.cpp,
	  libshogun/features/HashedWDFeaturesTransposed.h,
	  libshogun/features/StringFeatures.h, modular/Features.i: add
	  transposed wd features
	* NEWS, libshogun/classifier/Classifier.h,
	  libshogun/classifier/mkl/MKL.cpp, libshogun/classifier/mkl/MKL.h,
	  libshogunui/GUIClassifier.cpp, libshogunui/SGInterface.cpp,
	  libshogunui/SGInterface.h: - integrate Ryotas elastic net mkl and
	  wrap liblinear in static interfaces.
	  - update NEWS accordingly

2010-01-21  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/HashedWDFeatures.h,
	  libshogun/features/WDFeatures.h: add get_normalization const
	  fucntion
	* libshogun/features/HashedWDFeatures.cpp,
	  libshogun/features/HashedWDFeatures.h,
	  libshogun/features/WDFeatures.cpp,
	  libshogun/features/WDFeatures.h: in hash wd features, precompute
	  seed taking into account previous start_degree-1 nt and allow
	  external setting of normalization const to be able to concat
	  wdfeatures and hashedwdfeatures
	* libshogun/features/DotFeatures.cpp,
	  libshogun/features/DotFeatures.h, libshogun/lib/Time.h: fix
	  benchmarking for parallel tests
	* libshogun/classifier/svm/SVM_linear.cpp: use dense_dot_range()
	  which effectively parallelizes liblinear
	* libshogun/features/HashedWDFeatures.cpp: fix crasher, forgotten
	  to mask hash to bitsize

2010-01-20  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/HashedWDFeatures.cpp,
	  libshogun/features/HashedWDFeatures.h: use incremental hash
	* libshogun/lib/Hash.cpp, libshogun/lib/Hash.h: add incremental
	  murmur like hash
	* libshogun/features/DotFeatures.h: fix crasher and beautify bench
	  outputs
	* libshogun/classifier/svm/LibLinear.cpp,
	  libshogun/features/DotFeatures.h, libshogun/lib/Time.h: add
	  functions to benchmark dotfeatures
	* libshogun/classifier/svm/LibLinear.cpp,
	  libshogun/classifier/svm/LibLinear.h,
	  libshogun/classifier/svm/SVM_linear.cpp,
	  libshogun/classifier/svm/SVM_linear.h,
	  libshogun/features/SparseFeatures.h: merge liblinear 1.51:
	  currently solvers for
	  
	  L2R_LR
	  L2R_L2LOSS_SVC_DUAL
	  L2R_L2LOSS_SVC
	  L2R_L1LOSS_SVC_DUAL
	  
	  work.
	  
	  MCSVM_CS, L1R_L2LOSS_SVC, L1R_LR require further work.

2010-01-19  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/HashedWDFeatures.cpp,
	  libshogun/features/WDFeatures.cpp: fix a minor memory leak and
	  offs and normalization for start_degree>0
	* libshogun/features/HashedWDFeatures.cpp,
	  libshogun/features/HashedWDFeatures.h: fix off by one counter
	* libshogun/features/HashedWDFeatures.cpp,
	  libshogun/features/HashedWDFeatures.h: fixes + add debug output

2010-01-18  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/HashedWDFeatures.cpp: further fixes
	* libshogun/features/HashedWDFeatures.cpp: fix argument ordering
	  and use start
	* libshogun/features/HashedWDFeatures.cpp,
	  libshogun/features/HashedWDFeatures.h, libshogun/lib/Hash.h,
	  modular/Features.i: implement hashed wd features
	* libshogun/lib/Hash.h: fix typo - murmUr

2010-01-16  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/structure/DynProg.h: remove segment loss functions that
	  only appear in headers - fixes compilation

2010-01-14  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, libshogun/lib/Trie.h: fix typo, update news

2010-01-11  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* libshogun/genomic_signals/TrainPredMaster.cpp,
	  libshogun/genomic_signals/TrainPredMaster.cpp.orig,
	  libshogunui/GUISignals.cpp, libshogunui/GUISignals.cpp.orig,
	  libshogunui/GUISignals.h, libshogunui/SGInterface.cpp,
	  libshogunui/SGInterface.h: Hack to get it to work without the
	  missing file(s) in genomic_signals

2010-01-11  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/mkl/MKL.h: fix typos

2010-01-10  Soeren Sonnenburg <sonne@debian.org>

	* modular/Classifier.doxy, modular/Clustering.doxy,
	  modular/Distance.doxy, modular/Distribution.doxy,
	  modular/Evaluation.doxy, modular/Features.doxy,
	  modular/Kernel.doxy, modular/Library.doxy, modular/PreProc.doxy,
	  modular/Regression.doxy, modular/Structure.doxy: disable search
	  engine for doxygen 1.6.2 (fixes build failures)

2010-01-08  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/genomic_signals/KernelParam.cpp,
	  libshogun/genomic_signals/KernelParam.h,
	  libshogun/genomic_signals/SignalModel.cpp,
	  libshogun/genomic_signals/SignalModel.h,
	  libshogun/genomic_signals/TrainPredMaster.cpp,
	  libshogun/genomic_signals/TrainPredMaster.h,
	  libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/GUISignals.cpp, libshogunui/GUISignals.h,
	  libshogunui/SGInterface.cpp: -- cleanup
	* libshogun/genomic_signals,
	  libshogun/genomic_signals/KernelParam.cpp,
	  libshogun/genomic_signals/KernelParam.h,
	  libshogun/genomic_signals/SignalModel.cpp,
	  libshogun/genomic_signals/SignalModel.h,
	  libshogun/genomic_signals/TrainPredMaster.cpp,
	  libshogun/genomic_signals/TrainPredMaster.h,
	  libshogun/signals/KernelParam.cpp,
	  libshogun/signals/KernelParam.h,
	  libshogun/signals/SignalModel.cpp,
	  libshogun/signals/SignalModel.h,
	  libshogun/signals/TrainPredMaster.cpp,
	  libshogun/signals/TrainPredMaster.h: -- rename to avooid
	  confusion with Unix signals
	* libshogunui/GUICommands.h: -- new commands for the SGInterface
	* libshogun/signals, libshogun/signals/KernelParam.cpp,
	  libshogun/signals/KernelParam.h,
	  libshogun/signals/SignalModel.cpp,
	  libshogun/signals/SignalModel.h,
	  libshogun/signals/TrainPredMaster.cpp,
	  libshogun/signals/TrainPredMaster.h, libshogunui/GUISignals.cpp,
	  libshogunui/GUISignals.h, libshogunui/SGInterface.cpp,
	  libshogunui/SGInterface.h: -- first new classes for the signal
	  prediction pipeline
	  
	  Conflicts:
	  
	  trunk/src/libshogun/signals/TrainPredMaster.cpp
	  trunk/src/libshogun/signals/TrainPredMaster.h
	  trunk/src/libshogunui/GUISignals.cpp
	  trunk/src/libshogunui/GUISignals.h
	* libshogun/structure/PlifMatrix.cpp, libshogunui/GUIStructure.h,
	  libshogunui/SGInterface.cpp: -- more work on memory leaks
	* libshogun/structure/PlifMatrix.cpp,
	  libshogun/structure/PlifMatrix.h, libshogunui/GUICommands.h,
	  libshogunui/GUIStructure.h, libshogunui/SGInterface.cpp,
	  libshogunui/SGInterface.h: -- fixed more memory leaks
	  looks quite good now
	* libshogun/structure/PlifMatrix.cpp,
	  libshogun/structure/PlifMatrix.h, libshogunui/SGInterface.cpp: --
	  fixed some more mem leaks

2010-01-08  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/kernel/MultitaskKernelTreeNormalizer.h: Parameterized
	  MTL Kernel Normalizer

2010-01-07  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h:
	  (hopefully) fixed a bug in best_path/long transitions

2010-01-06  Soeren Sonnenburg <sonne@debian.org>

	* cmdline/CmdLineInterface.cpp: write out floating point scalars to
	  file for cmdline interface
	* libshogun/kernel/SNPStringKernel.cpp,
	  libshogun/kernel/SNPStringKernel.h: fix name

2010-01-05  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* libshogun/lib/MemoryMappedFile.h: reactivated 32bit access
	  operator
	* libshogun/lib/MemoryMappedFile.h: better?

2009-12-30  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/LibSVMMultiClass.cpp,
	  libshogun/classifier/svm/LibSVMOneClass.cpp: time limit also for
	  libsvm oneclass/multiclass
	* libshogun/classifier/svm/LibSVM.cpp,
	  libshogun/classifier/svm/SVM_libsvm.cpp,
	  libshogun/classifier/svm/SVM_libsvm.h: let libsvm respect
	  max_train_time
	* NEWS, libshogunui/GUIKernel.cpp: fix a bug in static interfaces
	  that could make testing fail when not directly done after
	  training

2009-12-27  Soeren Sonnenburg <sonne@debian.org>

	* configure: R compile fixes; however matlab/R won't work until
	  cygwin gets mingw support of gcc4.x
	* Makefile.template, configure: further compile fixes for
	  cygwin1.7: works now cleanly for octave,python,python_modular:
	  note upon install issue
	  
	  make install DESTDIR=
	  
	  otherwise installation will fail (cygwin has problems with double
	  '/', i.e. '//' in paths)

2009-12-26  Soeren Sonnenburg <sonne@debian.org>

	* Makefile.template, configure, octave/OctaveInterface.cpp: build
	  fixes for win32/cygwin1.7: octave, python & cmdline work now

2009-12-25  Soeren Sonnenburg <sonne@debian.org>

	* configure, libshogun/base/Version.h, libshogun/lib/Mathematics.h:
	  compile fixes for cygwin
	* libshogun/base/Version.h: update copyright to 2010

2009-12-09  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp: -- fixed delete delete[]
	  mismatch

2009-12-04  Soeren Sonnenburg <sonne@debian.org>

	* configure, libshogun/structure/DynProg.h: fix compilation of
	  dynprog in python modular (the structure needs to be global
	  to be recognized by swig)
	* libshogun/classifier/svm/LibLinear.cpp: potentially fix sign flip
	  occurring with liblinear
	* libshogun/classifier/svm/LibSVM.cpp: formatting changes

2009-12-02  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/SegmentLoss.h: -- fixed problem with loss
	  that turned up using the mask for alternative regions
	* libshogun/structure/SegmentLoss.h: -- modified semgent loss such
	  that it is similar to
	  the old segment loss used for nGasp
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h:
	  -- integrated different versions of dynamic program and loss
	  implementations via ifdefs to compare the different loss types
	  and debug the DynProg

2009-11-25  Soeren Sonnenburg <sonne@debian.org>

	* octave/OctaveInterface.cpp: fix compile error occuring with
	  octave

2009-11-24  Soeren Sonnenburg <sonne@debian.org>

	* libshogunui/GUIKernel.cpp: potentially fix custom kernel init
	  problem in static interfaces
	* octave/OctaveInterface.cpp: improve error output when getting
	  vectors

2009-11-23  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* matlab/MatlabInterface.cpp: trial to fix matlab interface for
	  matlab R2009a

2009-11-20  Soeren Sonnenburg <sonne@debian.org>

	* matlab/MatlabInterface.cpp: potentially improve vector shape
	  error message (untested)
	* configure: fix cplex detection on amd64 machines

2009-11-19  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/kernel/SNPStringKernel.cpp,
	  libshogun/kernel/SNPStringKernel.h: make SNP kernel LIK like
	* libshogun/distributions/HMM.cpp: fix observations...

2009-11-17  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/kernel/SNPStringKernel.cpp,
	  libshogun/kernel/SNPStringKernel.h: fixes...

2009-11-17  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/SegmentLoss.cpp: -- bugfix: nucleotide loss
	  produced negative results
	* libshogun/structure/DynProg.cpp: -- dead code removed

2009-11-16  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, libshogun/kernel/SNPStringKernel.cpp,
	  libshogun/kernel/SNPStringKernel.h, modular/Kernel.i: add SNP
	  kernel
	* libshogun/classifier/LinearClassifier.h,
	  libshogun/classifier/SubGradientLPM.cpp,
	  libshogun/classifier/svm/SVMLin.cpp,
	  libshogun/classifier/svm/SubGradientSVM.cpp,
	  libshogunui/SGInterface.cpp: fix set_w() for linear classifiers,
	  thanks to Александр Горбань for the report

2009-11-16  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/classifier/svm/CPLEXSVM.cpp: fixed compilation problem
	* libshogun/kernel/MultitaskKernelNormalizer.h: minor change
	* libshogun/kernel/KernelNormalizer.h,
	  libshogun/kernel/MultitaskKernelNormalizer.h: working
	  implementation of the MultitaskKernel by means of a
	  KernelNormalizer

2009-11-16  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog: updated changelog
	* Makefile.template, libshogun/classifier/svm/LaRank.h,
	  libshogun/features/StringFeatures.h: - fix type mismatch in
	  larank
	  - fix documentation in stringfeatures
	  - fix compilation of examples upon make check-examples
	* ChangeLog: updated changelog
	* Makefile.template: fix a compile failure occuring with the
	  upcoming binutils-gold
	  - workaround quality only though.
	* NEWS: update news

2009-11-14  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/LaRank.cpp,
	  libshogun/classifier/svm/LaRank.h, libshogun/lib/Mathematics.h,
	  libshogun/lib/Time.h: use shogun types in LaRank and cleanup /
	  reorder code

2009-11-13  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/kernel/MultitaskKernelNormalizer.h, modular/Kernel.i:
	  moved MultitaskKernel functionality into a kernel normalizer

2009-11-13  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/kernel/MultitaskKernel.cpp,
	  libshogun/kernel/MultitaskKernel.h, modular/Kernel.i: remove
	  multitask kernel
	* libshogun/classifier/mkl/MKL.cpp, libshogunui/GUIClassifier.cpp:
	  - fix a crasher occurring with MKL and interleaved optimization
	  - fix bug #143 thanks Thomas Fillon for the patch

2009-11-12  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/LaRank.cpp,
	  libshogun/classifier/svm/LaRank.h: larank finally seems to work
	  reliably
	* configure, libshogun/classifier/svm/LaRank.cpp,
	  libshogun/classifier/svm/LaRank.h: -don't warn on deprecated
	  functions
	  -get larank to work in most cases

2009-11-10  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/KNN.cpp, libshogun/classifier/KNN.h,
	  modular/Classifier.i: add a function that returns all k-NN
	  solutions for 1...k
	* libshogun/kernel/Kernel.h: improve get_kernel_matrix progress
	  feedback

2009-11-09  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/SparseFeatures.h: some sparse features don't
	  come *sorted* with features in ascending order.
	  introduce sort_features() function to remedy this and call it by
	  default when
	  loading svmlight files
	* libshogun/classifier/KNN.cpp, libshogun/lib/io.cpp,
	  libshogun/lib/io.h: - code beautifications in KNN
	  - in io progress: measure current time not cpu runtime (as this
	  will always stay the same even when more processors are used)
	* libshogun/classifier/DistanceMachine.cpp,
	  libshogun/classifier/DistanceMachine.h: whitespace cleanups
	* libshogun/classifier/KNN.cpp: KNN fix crash when labels are not
	  set
	* libshogun/classifier/svm/LaRank.cpp,
	  libshogun/classifier/svm/SVM_libsvm.cpp,
	  libshogun/features/StringFileFeatures.h,
	  libshogun/kernel/PyramidChi2.h, libshogun/lib/io.h,
	  libshogun/preproc/DecompressString.h: fix a number of warnings
	* libshogun/classifier/KernelMachine.cpp,
	  libshogun/classifier/svm/SVM_libsvm.cpp, modular/Classifier.i:
	  fix two memory leaks

2009-11-08  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/kernel/Kernel.h: spelling fix explicitly
	* libshogun/distributions/LinearHMM.h,
	  libshogun/features/CombinedDotFeatures.h,
	  libshogun/features/CombinedFeatures.h,
	  libshogun/features/Features.h, libshogun/kernel/Kernel.h,
	  libshogun/kernel/WeightedDegreeStringKernel.h,
	  libshogun/structure/Plif.h, python_modular/swig_typemaps.i: fix a
	  few spelling mistakes as pointed out by lintian
	* libshogun/kernel/CustomKernel.cpp,
	  libshogun/kernel/CustomKernel.h: add convenience constructor for
	  custom kernel

2009-11-07  Soeren Sonnenburg <sonne@debian.org>

	* CONTRIBUTIONS, NEWS: include chinese documentation on make
	  update-webpage and update news and contributors

2009-11-06  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/kernel/Kernel.h: compute matrix in a parallel way upon
	  get_kernel_matrix()

2009-11-06  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/kernel/MultitaskKernel.cpp,
	  libshogun/kernel/MultitaskKernel.h: added has_features()
	* libshogun/kernel/MultitaskKernel.h: added get_kernel_type
	* libshogun/kernel/MultitaskKernel.cpp,
	  libshogun/kernel/MultitaskKernel.h: added get_feature_type,
	  get_feature_class
	* libshogun/kernel/MultitaskKernel.cpp,
	  libshogun/kernel/MultitaskKernel.h: added missing include

2009-11-06  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/kernel/MultitaskKernel.cpp,
	  libshogun/kernel/MultitaskKernel.h: use ASSERT instead of assert

2009-11-06  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/kernel/MultitaskKernel.cpp,
	  libshogun/kernel/MultitaskKernel.h: added MultitaskKernel
	* modular/Kernel.i: added swig interface for MultitaskKernel

2009-11-06  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/kernel/Kernel.h: simplify kernel computation, proper
	  progress and cancel
	* libshogun/kernel/Kernel.cpp: potentially more correct svr fix :)
	* libshogun/kernel/Kernel.cpp, libshogun/kernel/Kernel.h,
	  libshogun/lib/io.cpp, libshogun/lib/io.h,
	  libshogun/regression/svr/SVR_light.cpp: - modify io functions:
	  using obj.io.enable_file_and_line() it is now possible to
	  prefix all of shogun's output with filename and line number
	  (where the printing
	  takes place). this allows for better tracing of where an error
	  actually occured
	  - fix problem with svr light + kernel access
	* Makefile, Makefile.template, libshogun/features/StringFeatures.h,
	  libshogun/kernel/CombinedKernel.cpp,
	  libshogun/kernel/CustomKernel.cpp,
	  libshogun/kernel/CustomKernel.h, libshogun/kernel/Kernel.cpp,
	  libshogun/kernel/Kernel.h, libshogun/regression/KRR.cpp,
	  libshogunui/SGInterface.cpp: - remove
	  get_kernel_matrix_{real,shortreal} and get_kernel_matrix() code
	  duplication
	  and use a template function instead, adjust callers accordingly
	  - fix combined kernel init w/ svmlight
	  - call make clean in libshogun examples on check-examples and
	  always use
	  $(MAKE) to get things work on non-gnumake systems

2009-11-05  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/preproc/DecompressString.h: forgot to add decompress
	  preproc
	* NEWS, libshogun/features/StringFeatures.h,
	  libshogun/features/StringFileFeatures.h,
	  libshogun/kernel/CombinedKernel.cpp,
	  libshogun/kernel/CombinedKernel.h, libshogun/kernel/Kernel.cpp,
	  libshogun/kernel/Kernel.h, libshogun/lib/Compressor.cpp,
	  libshogun/lib/Compressor.h, libshogun/preproc/PreProc.h,
	  libshogun/preproc/SortUlongString.h, libshogunui/GUIPreProc.cpp,
	  libshogunui/SGInterface.cpp, modular/PreProc.i,
	  python_modular/swig_typemaps.i: - hopefully really fix
	  combined/custom kernel num_vec_lhs etc
	  - add example on how to use compression features of all kinds
	  - add decompression preproc
	  - fix preproc processing in string features: now preprocs are
	  allowed to return
	  strings of arbitrary length. This requires to always return
	  copies of the
	  (processed) string / caching is currently not implemented.
	  - change get_string_features and typemap accordingly: strings are
	  now copied
	  first within libshogun and then again to python etc: while this
	  results in
	  memory overhead (1 string is always duplicated), it works
	  correcly with
	  preprocessors.
	  - update NEWS
	* libshogun/kernel/CustomKernel.h: range check no loner necessary
	  (is taken care of in CKernel)
	* libshogun/classifier/svm/SVM_light.cpp,
	  libshogun/classifier/svm/SVM_light.h,
	  libshogun/kernel/Kernel.cpp, libshogun/kernel/Kernel.h,
	  libshogunui/GUIClassifier.cpp: intrusive change to get combined
	  kernels with only custom kernels to work in svr

2009-11-04  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/kernel/CombinedKernel.h,
	  libshogun/kernel/CustomKernel.h, libshogun/kernel/Kernel.h,
	  libshogunui/GUIClassifier.cpp: fix a few init problems with
	  combined/custom kernel
	* libshogun/features/StringFeatures.h,
	  libshogun/lib/Compressor.cpp: (de)compression works now for other
	  compressors too
	* configure: really fix python 2.6 / 2.5 paths
	* configure: fail when any of the modular interfaces is enabled but
	  swig is not found or too old
	* configure: add python 2.6 and cplex 12 detection
	* libshogun/features/StringFeatures.h,
	  libshogun/lib/Compressor.cpp, libshogun/lib/Compressor.h,
	  modular/Library.i: add load_compressed/save_compressed - seems to
	  work ok for UNCOMPRESSED, LZO, GZIP

2009-11-03  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/StringFeatures.h,
	  libshogun/lib/Compressor.cpp, libshogun/lib/Compressor.h,
	  libshogun/lib/Signal.h: add save_compressed and load_compressed
	  functions to features
	* libshogunui/GUIKernel.cpp: don't init kernel when no features are
	  available (assume kernel does not need
	  to be inited)
	* libshogun/lib/Compressor.cpp, libshogun/lib/Compressor.h: add
	  compression code + docu for gzip, bzip2, lzo and lzma
	* configure, libshogun/lib/Compressor.h,
	  libshogunui/SGInterface.cpp: fix compilation in static interfaces
	  and add lzma detection / partial support

2009-11-02  Soeren Sonnenburg <sonne@debian.org>

	* configure, libshogun/lib/Compressor.h: add lzo/gzip/bzip2
	  compression / decompression support
	* libshogun/features/StringFeatures.h,
	  libshogun/kernel/RegulatoryModulesStringKernel.cpp: add preproc
	  functionality to string features
	* NEWS, configure, libshogun/classifier/PluginEstimate.cpp,
	  libshogun/classifier/svm/WDSVMOcas.cpp,
	  libshogun/classifier/svm/WDSVMOcas.h,
	  libshogun/distance/CanberraWordDistance.cpp,
	  libshogun/distance/HammingWordDistance.cpp,
	  libshogun/distance/ManhattanWordDistance.cpp,
	  libshogun/distributions/HMM.cpp, libshogun/distributions/HMM.h,
	  libshogun/distributions/Histogram.cpp,
	  libshogun/distributions/LinearHMM.cpp,
	  libshogun/features/ExplicitSpecFeatures.cpp,
	  libshogun/features/ImplicitWeightedSpecFeatures.cpp,
	  libshogun/features/StringFeatures.h,
	  libshogun/features/WDFeatures.cpp,
	  libshogun/kernel/CommUlongStringKernel.cpp,
	  libshogun/kernel/CommWordStringKernel.cpp,
	  libshogun/kernel/FixedDegreeStringKernel.cpp,
	  libshogun/kernel/HistogramWordStringKernel.cpp,
	  libshogun/kernel/LinearStringKernel.cpp,
	  libshogun/kernel/LocalAlignmentStringKernel.cpp,
	  libshogun/kernel/LocalityImprovedStringKernel.cpp,
	  libshogun/kernel/MatchWordStringKernel.cpp,
	  libshogun/kernel/OligoStringKernel.cpp,
	  libshogun/kernel/PolyMatchStringKernel.cpp,
	  libshogun/kernel/PolyMatchWordStringKernel.cpp,
	  libshogun/kernel/RegulatoryModulesStringKernel.cpp,
	  libshogun/kernel/SalzbergWordStringKernel.cpp,
	  libshogun/kernel/SimpleLocalityImprovedStringKernel.cpp,
	  libshogun/kernel/WeightedCommWordStringKernel.cpp,
	  libshogun/kernel/WeightedDegreePositionStringKernel.cpp,
	  libshogun/kernel/WeightedDegreeStringKernel.cpp,
	  libshogun/preproc/SortUlongString.cpp,
	  libshogun/preproc/SortWordString.cpp: - add free argument to
	  string features' get_feature_vector.
	  - configure detection of ultra fast lzo (de-)compression
	* libshogun/classifier/svm/LaRank.cpp,
	  libshogun/classifier/svm/LaRank.h, libshogun/kernel/Kernel.cpp: a
	  little larank progess: now starts and crashes

2009-10-31  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/StringFileFeatures.h: fix a crasher when
	  invalid chars occur in the file
	* NEWS, libshogun/features/StringFeatures.cpp,
	  libshogun/features/StringFeatures.h,
	  libshogun/features/StringFileFeatures.h,
	  libshogun/lib/Mathematics.h, libshogun/lib/MemoryMappedFile.h,
	  modular/Features.i: add StringFileFeatures (file based memory
	  mapped string features)

2009-10-30  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/LaRank.cpp,
	  libshogun/classifier/svm/LaRank.h,
	  libshogun/classifier/svm/kcache.cpp,
	  libshogun/classifier/svm/kcache.h: fix compilation of modular
	  interfaces by moving (at least temporarily) laranks kcache into
	  larank
	* libshogunui/GUIClassifier.cpp: enable testing for one class mkl,
	  thanks gorden jemwa

2009-10-27  Soeren Sonnenburg <sonne@debian.org>

	* configure: fill in x86_32 and fail when cplex is forefully
	  enabled but not found

2009-10-26  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/Classifier.h,
	  libshogun/classifier/svm/LaRank.cpp,
	  libshogun/classifier/svm/LaRank.h,
	  libshogun/classifier/svm/kcache.cpp,
	  libshogun/classifier/svm/kcache.h, libshogun/kernel/Kernel.cpp,
	  libshogunui/GUIClassifier.cpp, libshogunui/SGInterface.cpp,
	  modular/Classifier.i: integrate fast (one-pass) multiclass svm
	  (LaRank) - only compiles for now

2009-10-25  Soeren Sonnenburg <sonne@debian.org>

	* configure: let octave not write history on configure

2009-10-23  Soeren Sonnenburg <sonne@debian.org>

	* NEWS: now really prepare for the future :)
	* NEWS: revert news
	* NEWS: update news for things to come
	* ChangeLog: updated changelog
	* ChangeLog: updated changelog
	* libshogun/kernel/PyramidChi2.cpp: remove a static allocation and
	  replace with new/delete

2009-10-23  Alexander Binder <alexander.binder@first.fraunhofer.de>

	* libshogun/kernel/PyramidChi2.cpp, libshogun/kernel/PyramidChi2.h:
	  refurbished PyrmidChi2 kernel

2009-10-23  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog: updated changelog
	* libshogun/kernel/WeightedDegreeStringKernel.cpp,
	  libshogunui/GUIKernel.h, libshogunui/SGInterface.cpp: get
	  mkl_pseudo_dna example to run again
	* NEWS, README, libshogun/features/StringFeatures.h: update NEWS
	  and README and add minor debug code to stringfeatures
	* libshogun/classifier/svm/GMNPSVM.cpp,
	  libshogun/classifier/svm/GMNPSVM.h: document missing parameter
	  and rename member variable base_alphas to m_base_alphas

2009-10-23  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/classifier/Classifier.cpp,
	  libshogun/classifier/Classifier.h,
	  libshogun/classifier/KernelMachine.cpp,
	  libshogun/classifier/KernelMachine.h: modified code for
	  serialization support
	* libshogun/classifier/Classifier.h: minor change
	* libshogun/kernel/GaussianKernel.cpp,
	  libshogun/kernel/GaussianKernel.h, libshogun/kernel/Kernel.cpp,
	  libshogun/kernel/Kernel.h, libshogun/kernel/SimpleKernel.cpp,
	  libshogun/kernel/SimpleKernel.h: added default constructors to
	  some kernels to enable boost serialization. Works now for
	  Gaussian kernel.

2009-10-22  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/features/SimpleFeatures.cpp: enabled serialization
	  support for simple features by registering class
	* libshogun/kernel/WeightedDegreeStringKernel.h: wdk now
	  deserializes
	* libshogun/kernel/WeightedDegreeStringKernel.h: fixed typo
	* libshogun/kernel/Kernel.h: not saving lhs/rhs in base class atm
	* libshogun/features/Alphabet.cpp, libshogun/features/Alphabet.h:
	  adjusted load/save_construct_data to namespaces
	* libshogun/kernel/WeightedDegreeStringKernel.cpp,
	  libshogun/kernel/WeightedDegreeStringKernel.h: adjusted
	  load/save_construct_data to namespaces

2009-10-21  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* INSTALL: -- fixed typo

2009-10-21  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/lib/SimpleFile.h: fix a bug in file (wrong cast of
	  int64 to int)

2009-10-21  Alexander Binder <alexander.binder@first.fraunhofer.de>

	* libshogun/classifier/mkl/MKLMultiClass.cpp,
	  libshogun/classifier/mkl/MKLMultiClass.h,
	  libshogun/classifier/mkl/MKLMultiClass2glpk.cpp,
	  libshogun/classifier/mkl/MKLMultiClass2glpk.h,
	  libshogun/classifier/mkl/MKLMultiClassGLPK.cpp,
	  libshogun/classifier/mkl/MKLMultiClassGLPK.h: moved
	  MKLMulticlass2glpk.{h,cpp} to MKLMultiClassGLPK.{h.cpp} and
	  updated dependencies

2009-10-21  Soeren Sonnenburg <sonne@debian.org>

	* INSTALL: mention doxygen 1.6.0 as requirement for docs
	* configure: test for doxygen version 1.6.0 or higher
	* NEWS, libshogun/classifier/mkl/MKLMultiClass.cpp,
	  libshogun/classifier/mkl/MKLMultiClass2glpk.cpp: move code to
	  disable verbose glpk output into MKLMultiClass2glpkg.cpp

2009-10-21  Alexander Binder <alexander.binder@first.fraunhofer.de>

	* libshogun/classifier/mkl/MKLMultiClass.h,
	  libshogun/classifier/mkl/MKLMultiClass2glpk.h,
	  libshogun/classifier/svm/GMNPSVM.h: updated documentation

2009-10-21  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/DynProg.h: -- more comments

2009-10-20  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* modular/SGBase.i: std_string now mapped correctly (again)

2009-10-20  Soeren Sonnenburg <sonne@debian.org>

	* modular/SGBase.i: enable pythoncode only with python

2009-10-20  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/base/SGObject.cpp, libshogun/classifier/Classifier.cpp,
	  libshogun/classifier/KernelMachine.cpp,
	  libshogun/classifier/svm/LibSVM.cpp,
	  libshogun/classifier/svm/SVM.cpp,
	  libshogun/features/Alphabet.cpp, libshogun/features/Alphabet.h,
	  libshogun/features/Features.h,
	  libshogun/features/StringFeatures.h,
	  libshogun/kernel/WeightedDegreeStringKernel.cpp,
	  libshogun/kernel/WeightedDegreeStringKernel.h: some modifications
	  to get shogun to compile with serialization enabled

2009-10-20  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/Classifier.cpp,
	  libshogun/classifier/KernelMachine.cpp,
	  libshogun/classifier/svm/SVM.cpp,
	  libshogun/features/Alphabet.cpp, libshogun/features/Features.cpp,
	  libshogun/features/Labels.cpp,
	  libshogun/features/StringFeatures.cpp,
	  libshogun/kernel/WeightedDegreeStringKernel.cpp,
	  libshogun/lib/common.h: fix a couple of issues with serialization
	* libshogun/base/SGObject.h, libshogun/classifier/Classifier.cpp,
	  libshogun/classifier/Classifier.h,
	  libshogun/classifier/KernelMachine.cpp,
	  libshogun/classifier/KernelMachine.h,
	  libshogun/classifier/svm/DomainAdaptationSVM.cpp,
	  libshogun/classifier/svm/DomainAdaptationSVM.h,
	  libshogun/classifier/svm/SVM.cpp, libshogun/classifier/svm/SVM.h,
	  libshogun/classifier/svm/SVM_light.cpp,
	  libshogun/classifier/svm/SVM_light.h,
	  libshogun/features/Alphabet.h, libshogun/features/DotFeatures.h,
	  libshogun/features/Features.h, libshogun/features/Labels.h,
	  libshogun/features/RealFileFeatures.h,
	  libshogun/features/SimpleFeatures.h,
	  libshogun/features/StringFeatures.h,
	  libshogun/kernel/GaussianKernel.h, libshogun/kernel/Kernel.h,
	  libshogun/kernel/SimpleKernel.h, libshogun/kernel/StringKernel.h,
	  libshogun/kernel/WeightedDegreeStringKernel.h,
	  libshogun/lib/common.h: use global namespace for boost

2009-10-20  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/features/StringFeatures.h, libshogun/lib/common.h:
	  changes to seralization respecting namespaces

2009-10-20  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/SimpleFeatures.h: document align

2009-10-20  Christian Gehl <Christian.Gehl@first.fraunhofer.de>

	* libshogun/clustering/KMeans.cpp: changed KMeans to handle all
	  distances with feature type F_DREAL:
	  D_BRAYCURTIS, D_CANBERRA, D_CHEBYSHEW, D_CHISQUARE, D_COSINE,
	  D_EUCLIDIAN, D_GEODESIC, D_JENSEN, D_MANHATTAN, D_MINKOWSKI,
	  D_SPARSEEUCLIDIAN,D_TANIMOTO
	* libshogun/classifier/DistanceMachine.cpp,
	  libshogun/classifier/DistanceMachine.h,
	  libshogun/classifier/KNN.cpp: changed method name in
	  DistanceMachine

2009-10-20  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/lib/Hash.h, libshogun/structure/DynProg.h,
	  libshogun/structure/PlifMatrix.h: don't document all structures
	* configure, libshogunui/GUIClassifier.cpp,
	  matlab/MatlabInterface.cpp: generate webpages with examples

2009-10-19  Christian Gehl <Christian.Gehl@first.fraunhofer.de>

	* libshogun/classifier/KNN.cpp: changed computation of distance
	  values
	* libshogun/classifier/DistanceMachine.cpp,
	  libshogun/classifier/DistanceMachine.h: added distances method
	  (pthread)
	* libshogun/distance/Distance.cpp, libshogun/distance/Distance.h:
	  added replace_rhs method to temporary replace rhs

2009-10-19  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/classifier/svm/LibSVM.cpp,
	  libshogun/classifier/svm/LibSVMMultiClass.cpp,
	  libshogun/classifier/svm/SVM_libsvm.cpp,
	  libshogun/classifier/svm/SVM_libsvm.h: initialized pv and C to
	  avoid problem with multiclass svm

2009-10-19  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/kernel/PyramidChi2.h, libshogun/lib/DynInt.h: updated
	  example
	* NEWS, libshogun/classifier/PluginEstimate.cpp,
	  libshogun/classifier/PluginEstimate.h,
	  libshogun/distributions/GHMM.cpp, libshogun/distributions/GHMM.h,
	  libshogun/distributions/HMM.cpp, libshogun/distributions/HMM.h,
	  libshogun/distributions/Histogram.cpp,
	  libshogun/distributions/Histogram.h,
	  libshogun/distributions/LinearHMM.cpp,
	  libshogun/distributions/LinearHMM.h,
	  libshogun/distributions/histogram, libshogun/distributions/hmm,
	  libshogun/features/FKFeatures.h,
	  libshogun/features/TOPFeatures.h, libshogunui/GUIHMM.h,
	  modular/Distribution.i, python_modular/swig_typemaps.i: - move
	  HMM.h etc into distributions
	  - comment log_derivative computation to speed up running of
	  examples
	  - fix sparse features, now everything (except multicalss svm)
	  works again in
	  all interfaces
	  - update news
	* Makefile.template, configure,
	  libshogun/classifier/mkl/MKLMultiClass2glpk.h,
	  libshogun/classifier/svm/SVM_libsvm.cpp,
	  libshogun/distributions/Distribution.h,
	  libshogun/distributions/histogram/Histogram.cpp,
	  libshogun/distributions/histogram/Histogram.h,
	  modular/Features.i, octave_modular/swig_typemaps.i,
	  python_modular/sg_print_functions.cpp: get modular string featurs
	  back to work in modular interface, compile with -fvirtual

2009-10-18  Soeren Sonnenburg <sonne@debian.org>

	* Makefile.template, configure, libshogun/base/SGObject.h,
	  libshogun/classifier/Classifier.h,
	  libshogun/classifier/DistanceMachine.h,
	  libshogun/classifier/KernelMachine.h, libshogun/classifier/LDA.h,
	  libshogun/classifier/LinearClassifier.h,
	  libshogun/classifier/svm/WDSVMOcas.h,
	  libshogun/distance/CanberraMetric.h,
	  libshogun/distance/Distance.h,
	  libshogun/distance/HammingWordDistance.h,
	  libshogun/distance/SparseEuclidianDistance.h,
	  libshogun/distributions/Distribution.h,
	  libshogun/distributions/histogram/Histogram.h,
	  libshogun/distributions/hmm/HMM.h,
	  libshogun/evaluation/PerformanceMeasures.h,
	  libshogun/features/CombinedDotFeatures.h,
	  libshogun/features/CombinedFeatures.h,
	  libshogun/features/FKFeatures.h, libshogun/features/Features.h,
	  libshogun/features/SparseFeatures.h,
	  libshogun/features/StringFeatures.h,
	  libshogun/features/TOPFeatures.h, libshogun/kernel/AUCKernel.h,
	  libshogun/kernel/CombinedKernel.h,
	  libshogun/kernel/CommUlongStringKernel.h,
	  libshogun/kernel/DistanceKernel.h,
	  libshogun/kernel/HistogramWordStringKernel.h,
	  libshogun/kernel/Kernel.h, libshogun/kernel/PyramidChi2.h,
	  libshogun/kernel/SparseGaussianKernel.h, libshogun/lib/File.h,
	  libshogun/preproc/PreProc.h, libshogun/structure/DynProg.h,
	  libshogun/structure/PlifMatrix.h,
	  libshogun/structure/SegmentLoss.h, modular/Features.i,
	  modular/Library.i, modular/SGBase.i,
	  octave_modular/swig_typemaps.i, python_modular/swig_typemaps.i,
	  r_modular/swig_typemaps.i: get modular interfaces back to work
	* libshogunui/GUIClassifier.cpp, libshogunui/GUIClassifier.h,
	  libshogunui/SGInterface.cpp: use a new train function for mkl
	  multiclass in ui

2009-10-18  Alexander Binder <alexander.binder@first.fraunhofer.de>

	* libshogun/classifier/mkl/MKLMultiClass.cpp,
	  libshogunui/GUIClassifier.cpp, libshogunui/SGInterface.cpp: fixed
	  a bug in GUIClassifier.cpp, CMKLMultiClass is now called via
	  train_Svm() and not train_mkl because it is not derived from CMKL
	  in order to avoid multiple inheritance

2009-10-18  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/Classifier.h,
	  libshogun/classifier/svm/MCSVM.cpp,
	  libshogun/classifier/svm/MCSVM.h,
	  libshogun/classifier/svm/ScatterSVM.cpp,
	  libshogun/classifier/svm/ScatterSVM.h,
	  libshogunui/GUIClassifier.cpp, libshogunui/SGInterface.cpp,
	  modular/Classifier.i: rename MCSVM to scattersvm / mark it
	  experiemntal

2009-10-18  Alexander Binder <alexander.binder@first.fraunhofer.de>

	* libshogun/classifier/mkl/MKLMultiClass.cpp,
	  libshogun/classifier/mkl/MKLMultiClass.h,
	  libshogunui/GUIClassifier.cpp: temporary check in
	* matlab/MatlabInterface.h: added
	  using namespace shogun;
	  in order to fix a compitle time error from this file
	* libshogun/classifier/mkl/MKLMultiClass.cpp,
	  libshogun/classifier/mkl/MKLMultiClass.h,
	  libshogun/classifier/mkl/MKLMultiClass2glpk.cpp,
	  libshogun/classifier/mkl/MKLMultiClass2glpk.h: format changes

2009-10-17  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/base/SGObject.cpp, libshogun/base/SGObject.h,
	  libshogun/base/init.cpp, libshogun/base/init.h,
	  libshogun/classifier/svm/SVM_libsvm.cpp,
	  libshogun/classifier/svm/SVM_libsvm.h,
	  libshogun/classifier/svm/SVM_linear.cpp,
	  libshogun/classifier/svm/SVM_linear.h,
	  libshogun/classifier/svm/Tron.h,
	  libshogun/classifier/svm/gpdt.cpp,
	  libshogun/classifier/svm/gpdt.h,
	  libshogun/classifier/svm/gpdtsolve.cpp,
	  libshogun/classifier/svm/gpdtsolve.h,
	  libshogun/classifier/svm/gpm.cpp, libshogun/classifier/svm/gpm.h,
	  libshogun/classifier/svm/libocas.cpp,
	  libshogun/classifier/svm/libocas.h,
	  libshogun/classifier/svm/libocas_common.h,
	  libshogun/classifier/svm/pr_loqo.cpp,
	  libshogun/classifier/svm/pr_loqo.h,
	  libshogun/classifier/svm/qpssvmlib.cpp,
	  libshogun/classifier/svm/qpssvmlib.h,
	  libshogun/classifier/svm/ssl.cpp, libshogun/classifier/svm/ssl.h,
	  libshogun/clustering/KMeans.cpp,
	  libshogun/kernel/LocalAlignmentStringKernel.cpp,
	  libshogun/kernel/LocalAlignmentStringKernel.h,
	  libshogun/lib/Signal.h, libshogun/lib/io.h,
	  libshogun/lib/lapack.cpp, libshogun/lib/lapack.h,
	  libshogun/lib/memory.h, modular/Library.i, modular/SGBase.i: move
	  remaining classes/functions/variables into shogun namespace

2009-10-16  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/mkl/MKLMultiClass2glpk.h,
	  libshogun/lib/Mathematics.h: minor documentation fixes
	* libshogun/classifier/LPBoost.cpp, libshogun/classifier/LPBoost.h,
	  libshogun/classifier/LPM.cpp, libshogun/classifier/LPM.h,
	  libshogun/classifier/LinearClassifier.h,
	  libshogun/classifier/SubGradientLPM.cpp,
	  libshogun/classifier/SubGradientLPM.h,
	  libshogun/classifier/svm/CPLEXSVM.cpp,
	  libshogun/classifier/svm/CPLEXSVM.h,
	  libshogun/kernel/AUCKernel.h, libshogun/lib/Cplex.cpp,
	  libshogun/lib/Cplex.h, libshogun/lib/DynInt.h,
	  libshogun/lib/GCArray.h, libshogun/lib/IndirectObject.h,
	  libshogunui/GUIClassifier.cpp: namespaces for the remaining
	  classes

2009-10-16  Alexander Binder <alexander.binder@first.fraunhofer.de>

	* libshogun/classifier/mkl/MKLMultiClass.h: final modifications
	  after namespace changes
	* libshogun/classifier/mkl/MKLMultiClass.cpp,
	  libshogun/classifier/mkl/MKLMultiClass.h,
	  libshogun/classifier/mkl/MKLMultiClass2glpk.cpp,
	  libshogun/classifier/mkl/MKLMultiClass2glpk.h:

2009-10-16  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, libshogun/kernel/DiceKernelNormalizer.h,
	  libshogun/kernel/TanimotoKernelNormalizer.h,
	  libshogun/kernel/WeightedDegreePositionStringKernel.cpp,
	  libshogun/kernel/WeightedDegreePositionStringKernel.h,
	  libshogun/lib/BinaryStream.h, libshogun/lib/BitString.h,
	  libshogun/preproc/LogPlusOne.cpp, libshogun/preproc/LogPlusOne.h,
	  libshogun/preproc/NormOne.cpp, libshogun/preproc/NormOne.h,
	  libshogun/preproc/PCACut.cpp, libshogun/preproc/PCACut.h,
	  libshogun/preproc/PreProc.h,
	  libshogun/preproc/PruneVarSubMean.cpp,
	  libshogun/preproc/PruneVarSubMean.h,
	  libshogun/preproc/SortUlongString.cpp,
	  libshogun/preproc/SortUlongString.h,
	  libshogun/preproc/SortWordString.cpp,
	  libshogun/preproc/SortWordString.h, libshogunui/GUIPreProc.cpp,
	  libshogunui/GUIPreProc.h, libshogunui/SGInterface.cpp,
	  libshogunui/SGInterface.h, modular/Distance.i,
	  modular/Features.i, modular/Kernel.i, modular/Library.i,
	  modular/PreProc.i, modular/SGBase.i: - modular interfaces compile
	  now (at least)
	  - remove load/save_init in preprocs
	* cmdline/CmdLineInterface.cpp, cmdline/CmdLineInterface.h,
	  libshogun/kernel/RidgeKernelNormalizer.h,
	  libshogun/kernel/VarianceKernelNormalizer.h,
	  libshogun/preproc/SparsePreProc.h, libshogunui/GUIClassifier.h,
	  libshogunui/GUIDistance.cpp, libshogunui/GUIDistance.h,
	  libshogunui/GUIFeatures.cpp, libshogunui/GUIFeatures.h,
	  libshogunui/GUIHMM.cpp, libshogunui/GUIHMM.h,
	  libshogunui/GUIKernel.cpp, libshogunui/GUIKernel.h,
	  libshogunui/GUILabels.cpp, libshogunui/GUILabels.h,
	  libshogunui/GUIMath.cpp, libshogunui/GUIMath.h,
	  libshogunui/GUIPluginEstimate.cpp,
	  libshogunui/GUIPluginEstimate.h, libshogunui/GUIPreProc.cpp,
	  libshogunui/GUIPreProc.h, libshogunui/GUIStructure.cpp,
	  libshogunui/GUIStructure.h, libshogunui/GUITime.cpp,
	  libshogunui/GUITime.h, libshogunui/SGInterface.h,
	  octave/OctaveInterface.h, python/PythonInterface.cpp,
	  python/PythonInterface.h, r/RInterface.h: get static interfaces
	  back to work
	* libshogun/features/FeatureTypes.h: move feature types into
	  separate file
	* libshogun/base/Parallel.cpp, libshogun/base/Parallel.h,
	  libshogun/base/SGObject.cpp, libshogun/base/SGObject.h,
	  libshogun/base/Version.cpp, libshogun/base/Version.h,
	  libshogun/base/init.cpp, libshogun/base/init.h,
	  libshogun/classifier/Classifier.cpp,
	  libshogun/classifier/Classifier.h,
	  libshogun/classifier/DistanceMachine.cpp,
	  libshogun/classifier/DistanceMachine.h,
	  libshogun/classifier/KNN.cpp, libshogun/classifier/KNN.h,
	  libshogun/classifier/KernelMachine.cpp,
	  libshogun/classifier/KernelMachine.h,
	  libshogun/classifier/KernelPerceptron.cpp,
	  libshogun/classifier/KernelPerceptron.h,
	  libshogun/classifier/LDA.cpp, libshogun/classifier/LDA.h,
	  libshogun/classifier/LinearClassifier.cpp,
	  libshogun/classifier/LinearClassifier.h,
	  libshogun/classifier/Perceptron.cpp,
	  libshogun/classifier/Perceptron.h,
	  libshogun/classifier/PluginEstimate.cpp,
	  libshogun/classifier/PluginEstimate.h,
	  libshogun/classifier/mkl/MKL.cpp, libshogun/classifier/mkl/MKL.h,
	  libshogun/classifier/mkl/MKLClassification.cpp,
	  libshogun/classifier/mkl/MKLClassification.h,
	  libshogun/classifier/mkl/MKLMultiClass.cpp,
	  libshogun/classifier/mkl/MKLMultiClass.h,
	  libshogun/classifier/mkl/MKLOneClass.cpp,
	  libshogun/classifier/mkl/MKLOneClass.h,
	  libshogun/classifier/svm/DomainAdaptationSVM.cpp,
	  libshogun/classifier/svm/DomainAdaptationSVM.h,
	  libshogun/classifier/svm/GMNPSVM.cpp,
	  libshogun/classifier/svm/GMNPSVM.h,
	  libshogun/classifier/svm/GNPPSVM.cpp,
	  libshogun/classifier/svm/GNPPSVM.h,
	  libshogun/classifier/svm/GPBTSVM.cpp,
	  libshogun/classifier/svm/GPBTSVM.h,
	  libshogun/classifier/svm/LibLinear.cpp,
	  libshogun/classifier/svm/LibLinear.h,
	  libshogun/classifier/svm/LibSVM.cpp,
	  libshogun/classifier/svm/LibSVM.h,
	  libshogun/classifier/svm/LibSVMMultiClass.cpp,
	  libshogun/classifier/svm/LibSVMMultiClass.h,
	  libshogun/classifier/svm/LibSVMOneClass.cpp,
	  libshogun/classifier/svm/LibSVMOneClass.h,
	  libshogun/classifier/svm/MCSVM.cpp,
	  libshogun/classifier/svm/MCSVM.h,
	  libshogun/classifier/svm/MPDSVM.cpp,
	  libshogun/classifier/svm/MPDSVM.h,
	  libshogun/classifier/svm/MultiClassSVM.cpp,
	  libshogun/classifier/svm/MultiClassSVM.h,
	  libshogun/classifier/svm/SVM.cpp, libshogun/classifier/svm/SVM.h,
	  libshogun/classifier/svm/SVMLin.cpp,
	  libshogun/classifier/svm/SVMLin.h,
	  libshogun/classifier/svm/SVMOcas.cpp,
	  libshogun/classifier/svm/SVMOcas.h,
	  libshogun/classifier/svm/SVMSGD.cpp,
	  libshogun/classifier/svm/SVMSGD.h,
	  libshogun/classifier/svm/SVM_libsvm.cpp,
	  libshogun/classifier/svm/SVM_libsvm.h,
	  libshogun/classifier/svm/SVM_light.cpp,
	  libshogun/classifier/svm/SVM_light.h,
	  libshogun/classifier/svm/SVM_linear.h,
	  libshogun/classifier/svm/SubGradientSVM.cpp,
	  libshogun/classifier/svm/SubGradientSVM.h,
	  libshogun/classifier/svm/Tron.cpp,
	  libshogun/classifier/svm/Tron.h,
	  libshogun/classifier/svm/WDSVMOcas.cpp,
	  libshogun/classifier/svm/WDSVMOcas.h,
	  libshogun/classifier/svm/gmnplib.cpp,
	  libshogun/classifier/svm/gmnplib.h,
	  libshogun/classifier/svm/gnpplib.cpp,
	  libshogun/classifier/svm/gnpplib.h,
	  libshogun/classifier/svm/gpdt.h,
	  libshogun/classifier/svm/libocas.cpp,
	  libshogun/classifier/svm/pr_loqo.cpp,
	  libshogun/classifier/svm/qpbsvmlib.cpp,
	  libshogun/classifier/svm/qpbsvmlib.h,
	  libshogun/classifier/svm/qpssvmlib.cpp,
	  libshogun/classifier/svm/ssl.cpp, libshogun/classifier/svm/ssl.h,
	  libshogun/clustering/Hierarchical.cpp,
	  libshogun/clustering/Hierarchical.h,
	  libshogun/clustering/KMeans.cpp, libshogun/clustering/KMeans.h,
	  libshogun/distance/BrayCurtisDistance.cpp,
	  libshogun/distance/BrayCurtisDistance.h,
	  libshogun/distance/CanberraMetric.cpp,
	  libshogun/distance/CanberraMetric.h,
	  libshogun/distance/CanberraWordDistance.cpp,
	  libshogun/distance/CanberraWordDistance.h,
	  libshogun/distance/ChebyshewMetric.cpp,
	  libshogun/distance/ChebyshewMetric.h,
	  libshogun/distance/ChiSquareDistance.cpp,
	  libshogun/distance/ChiSquareDistance.h,
	  libshogun/distance/CosineDistance.cpp,
	  libshogun/distance/CosineDistance.h,
	  libshogun/distance/Distance.cpp, libshogun/distance/Distance.h,
	  libshogun/distance/EuclidianDistance.cpp,
	  libshogun/distance/EuclidianDistance.h,
	  libshogun/distance/GeodesicMetric.cpp,
	  libshogun/distance/GeodesicMetric.h,
	  libshogun/distance/HammingWordDistance.cpp,
	  libshogun/distance/HammingWordDistance.h,
	  libshogun/distance/JensenMetric.cpp,
	  libshogun/distance/JensenMetric.h,
	  libshogun/distance/ManhattanMetric.cpp,
	  libshogun/distance/ManhattanMetric.h,
	  libshogun/distance/ManhattanWordDistance.cpp,
	  libshogun/distance/ManhattanWordDistance.h,
	  libshogun/distance/MinkowskiMetric.cpp,
	  libshogun/distance/MinkowskiMetric.h,
	  libshogun/distance/RealDistance.h,
	  libshogun/distance/SimpleDistance.h,
	  libshogun/distance/SparseDistance.h,
	  libshogun/distance/SparseEuclidianDistance.cpp,
	  libshogun/distance/SparseEuclidianDistance.h,
	  libshogun/distance/StringDistance.h,
	  libshogun/distance/TanimotoDistance.cpp,
	  libshogun/distance/TanimotoDistance.h,
	  libshogun/distributions/Distribution.cpp,
	  libshogun/distributions/Distribution.h,
	  libshogun/distributions/histogram/Histogram.cpp,
	  libshogun/distributions/histogram/Histogram.h,
	  libshogun/distributions/hmm/GHMM.cpp,
	  libshogun/distributions/hmm/GHMM.h,
	  libshogun/distributions/hmm/HMM.cpp,
	  libshogun/distributions/hmm/HMM.h,
	  libshogun/distributions/hmm/LinearHMM.cpp,
	  libshogun/distributions/hmm/LinearHMM.h,
	  libshogun/evaluation/PerformanceMeasures.cpp,
	  libshogun/evaluation/PerformanceMeasures.h,
	  libshogun/features/Alphabet.cpp, libshogun/features/Alphabet.h,
	  libshogun/features/AttributeFeatures.cpp,
	  libshogun/features/AttributeFeatures.h,
	  libshogun/features/CombinedDotFeatures.cpp,
	  libshogun/features/CombinedDotFeatures.h,
	  libshogun/features/CombinedFeatures.cpp,
	  libshogun/features/CombinedFeatures.h,
	  libshogun/features/DotFeatures.cpp,
	  libshogun/features/DotFeatures.h,
	  libshogun/features/DummyFeatures.h,
	  libshogun/features/ExplicitSpecFeatures.cpp,
	  libshogun/features/ExplicitSpecFeatures.h,
	  libshogun/features/FKFeatures.cpp,
	  libshogun/features/FKFeatures.h, libshogun/features/Features.cpp,
	  libshogun/features/Features.h,
	  libshogun/features/ImplicitWeightedSpecFeatures.cpp,
	  libshogun/features/ImplicitWeightedSpecFeatures.h,
	  libshogun/features/Labels.cpp, libshogun/features/Labels.h,
	  libshogun/features/PolyFeatures.cpp,
	  libshogun/features/PolyFeatures.h,
	  libshogun/features/RealFileFeatures.cpp,
	  libshogun/features/RealFileFeatures.h,
	  libshogun/features/SimpleFeatures.h,
	  libshogun/features/SparseFeatures.h,
	  libshogun/features/StringFeatures.h,
	  libshogun/features/TOPFeatures.cpp,
	  libshogun/features/TOPFeatures.h,
	  libshogun/features/WDFeatures.cpp,
	  libshogun/features/WDFeatures.h, libshogun/kernel/AUCKernel.cpp,
	  libshogun/kernel/AUCKernel.h,
	  libshogun/kernel/AvgDiagKernelNormalizer.h,
	  libshogun/kernel/Chi2Kernel.cpp, libshogun/kernel/Chi2Kernel.h,
	  libshogun/kernel/CombinedKernel.cpp,
	  libshogun/kernel/CombinedKernel.h,
	  libshogun/kernel/CommUlongStringKernel.cpp,
	  libshogun/kernel/CommUlongStringKernel.h,
	  libshogun/kernel/CommWordStringKernel.cpp,
	  libshogun/kernel/CommWordStringKernel.h,
	  libshogun/kernel/ConstKernel.cpp, libshogun/kernel/ConstKernel.h,
	  libshogun/kernel/CustomKernel.cpp,
	  libshogun/kernel/CustomKernel.h, libshogun/kernel/DiagKernel.cpp,
	  libshogun/kernel/DiagKernel.h,
	  libshogun/kernel/DistanceKernel.cpp,
	  libshogun/kernel/DistanceKernel.h,
	  libshogun/kernel/FirstElementKernelNormalizer.h,
	  libshogun/kernel/FixedDegreeStringKernel.cpp,
	  libshogun/kernel/FixedDegreeStringKernel.h,
	  libshogun/kernel/GaussianKernel.cpp,
	  libshogun/kernel/GaussianKernel.h,
	  libshogun/kernel/GaussianShiftKernel.cpp,
	  libshogun/kernel/GaussianShiftKernel.h,
	  libshogun/kernel/GaussianShortRealKernel.cpp,
	  libshogun/kernel/GaussianShortRealKernel.h,
	  libshogun/kernel/HistogramWordStringKernel.cpp,
	  libshogun/kernel/HistogramWordStringKernel.h,
	  libshogun/kernel/IdentityKernelNormalizer.h,
	  libshogun/kernel/Kernel.cpp, libshogun/kernel/Kernel.h,
	  libshogun/kernel/KernelNormalizer.h,
	  libshogun/kernel/LinearByteKernel.cpp,
	  libshogun/kernel/LinearByteKernel.h,
	  libshogun/kernel/LinearKernel.cpp,
	  libshogun/kernel/LinearKernel.h,
	  libshogun/kernel/LinearStringKernel.cpp,
	  libshogun/kernel/LinearStringKernel.h,
	  libshogun/kernel/LinearWordKernel.cpp,
	  libshogun/kernel/LinearWordKernel.h,
	  libshogun/kernel/LocalAlignmentStringKernel.cpp,
	  libshogun/kernel/LocalAlignmentStringKernel.h,
	  libshogun/kernel/LocalityImprovedStringKernel.cpp,
	  libshogun/kernel/LocalityImprovedStringKernel.h,
	  libshogun/kernel/MatchWordStringKernel.cpp,
	  libshogun/kernel/MatchWordStringKernel.h,
	  libshogun/kernel/OligoStringKernel.cpp,
	  libshogun/kernel/OligoStringKernel.h,
	  libshogun/kernel/PolyKernel.cpp, libshogun/kernel/PolyKernel.h,
	  libshogun/kernel/PolyMatchStringKernel.cpp,
	  libshogun/kernel/PolyMatchStringKernel.h,
	  libshogun/kernel/PolyMatchWordStringKernel.cpp,
	  libshogun/kernel/PolyMatchWordStringKernel.h,
	  libshogun/kernel/PyramidChi2.cpp, libshogun/kernel/PyramidChi2.h,
	  libshogun/kernel/RegulatoryModulesStringKernel.cpp,
	  libshogun/kernel/RegulatoryModulesStringKernel.h,
	  libshogun/kernel/SalzbergWordStringKernel.cpp,
	  libshogun/kernel/SalzbergWordStringKernel.h,
	  libshogun/kernel/SigmoidKernel.cpp,
	  libshogun/kernel/SigmoidKernel.h,
	  libshogun/kernel/SimpleKernel.h,
	  libshogun/kernel/SimpleLocalityImprovedStringKernel.cpp,
	  libshogun/kernel/SimpleLocalityImprovedStringKernel.h,
	  libshogun/kernel/SparseGaussianKernel.cpp,
	  libshogun/kernel/SparseGaussianKernel.h,
	  libshogun/kernel/SparseKernel.h,
	  libshogun/kernel/SparseLinearKernel.cpp,
	  libshogun/kernel/SparseLinearKernel.h,
	  libshogun/kernel/SparsePolyKernel.cpp,
	  libshogun/kernel/SparsePolyKernel.h,
	  libshogun/kernel/SqrtDiagKernelNormalizer.h,
	  libshogun/kernel/StringKernel.h,
	  libshogun/kernel/TensorProductPairKernel.cpp,
	  libshogun/kernel/TensorProductPairKernel.h,
	  libshogun/kernel/WeightedCommWordStringKernel.cpp,
	  libshogun/kernel/WeightedCommWordStringKernel.h,
	  libshogun/kernel/WeightedDegreePositionStringKernel.cpp,
	  libshogun/kernel/WeightedDegreePositionStringKernel.h,
	  libshogun/kernel/WeightedDegreeStringKernel.cpp,
	  libshogun/kernel/WeightedDegreeStringKernel.h,
	  libshogun/lib/Array.h, libshogun/lib/Array2.h,
	  libshogun/lib/Array3.h, libshogun/lib/Cache.h,
	  libshogun/lib/DynamicArray.h, libshogun/lib/File.cpp,
	  libshogun/lib/File.h, libshogun/lib/Hash.cpp,
	  libshogun/lib/Hash.h, libshogun/lib/List.h,
	  libshogun/lib/Mathematics.cpp, libshogun/lib/Mathematics.h,
	  libshogun/lib/MemoryMappedFile.h, libshogun/lib/Set.h,
	  libshogun/lib/ShogunException.cpp,
	  libshogun/lib/ShogunException.h, libshogun/lib/Signal.cpp,
	  libshogun/lib/Signal.h, libshogun/lib/SimpleFile.h,
	  libshogun/lib/Time.cpp, libshogun/lib/Time.h,
	  libshogun/lib/Trie.cpp, libshogun/lib/Trie.h,
	  libshogun/lib/io.cpp, libshogun/lib/io.h,
	  libshogun/lib/lapack.cpp, libshogun/lib/memory.cpp,
	  libshogun/preproc/LogPlusOne.cpp, libshogun/preproc/LogPlusOne.h,
	  libshogun/preproc/NormDerivativeLem3.cpp,
	  libshogun/preproc/NormDerivativeLem3.h,
	  libshogun/preproc/NormOne.cpp, libshogun/preproc/NormOne.h,
	  libshogun/preproc/PCACut.cpp, libshogun/preproc/PCACut.h,
	  libshogun/preproc/PreProc.cpp, libshogun/preproc/PreProc.h,
	  libshogun/preproc/PruneVarSubMean.cpp,
	  libshogun/preproc/PruneVarSubMean.h,
	  libshogun/preproc/SimplePreProc.h,
	  libshogun/preproc/SortUlongString.cpp,
	  libshogun/preproc/SortUlongString.h,
	  libshogun/preproc/SortWordString.cpp,
	  libshogun/preproc/SortWordString.h,
	  libshogun/preproc/SparsePreProc.h,
	  libshogun/preproc/StringPreProc.h, libshogun/regression/KRR.cpp,
	  libshogun/regression/KRR.h, libshogun/regression/Regression.h,
	  libshogun/regression/svr/LibSVR.cpp,
	  libshogun/regression/svr/LibSVR.h,
	  libshogun/regression/svr/MKLRegression.cpp,
	  libshogun/regression/svr/MKLRegression.h,
	  libshogun/regression/svr/SVR_light.cpp,
	  libshogun/regression/svr/SVR_light.h,
	  libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogun/structure/IntronList.cpp,
	  libshogun/structure/IntronList.h, libshogun/structure/Plif.cpp,
	  libshogun/structure/Plif.h, libshogun/structure/PlifArray.cpp,
	  libshogun/structure/PlifArray.h, libshogun/structure/PlifBase.h,
	  libshogun/structure/PlifMatrix.cpp,
	  libshogun/structure/PlifMatrix.h,
	  libshogun/structure/SegmentLoss.cpp,
	  libshogun/structure/SegmentLoss.h, modular/SGBase.i,
	  python_modular/sg_print_functions.cpp: WARNING DON'T SVN UP, this
	  introduces namespaces in libshogun and as a consequence breaks
	  *all* static+modular interfaces

2009-10-16  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/classifier/svm/SVM.cpp: fixed warning
	* libshogun/classifier/svm/LibSVM.cpp,
	  libshogun/classifier/svm/LibSVM.h,
	  libshogun/classifier/svm/SVM_libsvm.cpp,
	  libshogun/classifier/svm/SVM_libsvm.h: ported code of custom
	  linear term enabled LibSVM to trunk

2009-10-16  Alexander Binder <alexander.binder@first.fraunhofer.de>

	* libshogun/classifier/mkl/MKLMultiClass.cpp,
	  libshogun/classifier/mkl/MKLMultiClass.h: added some comments to
	  main class
	* libshogun/classifier/mkl/MKLMultiClass.cpp,
	  libshogun/classifier/mkl/MKLMultiClass.h: started to clean it up,
	  not finished yet

2009-10-16  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/regression/svr/SVR_light.cpp: adjusted to new
	  linear_term format
	* libshogun/classifier/svm/DomainAdaptationSVM.cpp,
	  libshogun/classifier/svm/DomainAdaptationSVM.h,
	  libshogun/classifier/svm/SVM.cpp, libshogun/classifier/svm/SVM.h,
	  libshogun/classifier/svm/SVM_light.cpp,
	  libshogun/classifier/svm/SVM_light.h: moved linear_term
	  (including getter/setter) from SVM_light to base class SVM, as
	  the code will also be used by LibSVM
	* libshogun/base/SGObject.h: included STL
	* modular/SGBase.i: included bindings for STL structures
	  (std::vector)

2009-10-16  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/features/PolyFeatures.h, libshogun/structure/DynProg.h,
	  libshogun/structure/PlifArray.h, libshogun/structure/PlifBase.h,
	  libshogun/structure/PlifMatrix.h: -- documented something more

2009-10-16  Soeren Sonnenburg <sonne@debian.org>

	* NEWS: update news
	* libshogun/classifier/SubGradientLPM.cpp,
	  libshogun/classifier/svm/SVM_libsvm.cpp,
	  libshogun/classifier/svm/SubGradientSVM.cpp,
	  libshogun/classifier/svm/SubGradientSVM.h,
	  libshogun/classifier/svm/qpbsvmlib.cpp,
	  libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h:
	  remove a couple of global symbols (make them class
	  specific/static)
	* libshogun/classifier/svm/GMNPSVM.cpp: fix train function (w/
	  labels)
	* modular/SGBase.i: remove accidentally commited debug code
	* NEWS, libshogun/classifier/Classifier.cpp,
	  libshogun/classifier/Classifier.h, libshogun/classifier/KNN.cpp,
	  libshogun/classifier/KNN.h,
	  libshogun/classifier/KernelMachine.cpp,
	  libshogun/classifier/KernelMachine.h,
	  libshogun/classifier/LinearClassifier.cpp,
	  libshogun/classifier/LinearClassifier.h,
	  libshogun/classifier/PluginEstimate.cpp,
	  libshogun/classifier/PluginEstimate.h,
	  libshogun/classifier/mkl/MKLMultiClass.cpp,
	  libshogun/classifier/mkl/MKLMultiClass.h,
	  libshogun/classifier/svm/MultiClassSVM.cpp,
	  libshogun/classifier/svm/MultiClassSVM.h,
	  libshogun/classifier/svm/WDSVMOcas.cpp,
	  libshogun/classifier/svm/WDSVMOcas.h,
	  libshogun/clustering/Hierarchical.h,
	  libshogun/clustering/KMeans.h, libshogun/regression/KRR.cpp,
	  libshogun/regression/KRR.h, libshogunui/GUIClassifier.cpp,
	  libshogunui/GUIClassifier.h, libshogunui/GUIPluginEstimate.cpp,
	  libshogunui/GUIPluginEstimate.h, modular/SGBase.i: make the
	  classifier classify function pure virtual

2009-10-15  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/mkl/MKLMultiClass.cpp,
	  libshogun/classifier/mkl/MKLMultiClass.h,
	  libshogun/lib/Mathematics.h: minor style improvements; add
	  twonorm function
	* configure, libshogun/base/SGObject.h,
	  libshogun/classifier/Classifier.h,
	  libshogun/classifier/mkl/MKLMultiClass.cpp,
	  libshogun/classifier/mkl/MKLMultiClass.h,
	  libshogun/classifier/mkl/MKLMulticlass.h,
	  libshogun/classifier/svm/SVM_light.cpp,
	  libshogun/classifier/svm/gmnpmkl.cpp,
	  libshogun/classifier/svm/gmnpmkl.h,
	  libshogunui/GUIClassifier.cpp, libshogunui/SGInterface.cpp,
	  modular/Classifier.i, shogun: integrate multi class mkl into
	  static and modular interfaces

2009-10-15  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/classifier/svm/DA_SVM.cpp,
	  libshogun/classifier/svm/DA_SVM.h,
	  libshogun/classifier/svm/DomainAdaptationSVM.cpp,
	  libshogun/classifier/svm/DomainAdaptationSVM.h: renamed DA_SVM
	  files
	* libshogun/classifier/svm/DA_SVM.cpp,
	  libshogun/classifier/svm/DA_SVM.h: renaming of class DA_SVM to
	  DomainAdaptationSVM
	* libshogun/classifier/svm/DA_SVM.cpp,
	  libshogun/classifier/svm/DA_SVM.h: DA_SVM fully documented

2009-10-15  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp: -- sorry, forgot to remove some
	  old code
	* shogun/structure/PlifMatrix.h: -- remove file with wrong path
	  from git repo
	* libshogun/features/PolyFeatures.h,
	  libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogun/structure/Plif.h, libshogun/structure/PlifMatrix.h,
	  libshogun/structure/SegmentLoss.h, shogun, shogun/structure,
	  shogun/structure/PlifMatrix.h: -- commented everything on the
	  list you gave me Soeren
	* libshogun/structure/DynProg.cpp: apply bugfix

2009-10-15  Soeren Sonnenburg <sonne@debian.org>

	* configure, libshogun/base/SGObject.h,
	  libshogun/features/Features.cpp, libshogun/lib/List.h,
	  libshogun/preproc/PreProc.h, libshogunui/GUIPreProc.cpp,
	  r_modular/swig_typemaps.i: get r-modular interface back to work
	  (when reference counting is disabled)

2009-10-15  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/classifier/svm/DA_SVM.cpp,
	  libshogun/classifier/svm/DA_SVM.h: fixed warnings

2009-10-15  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/mkl/MKL.h: fix typo in mkl doc
	* Makefile.template, configure,
	  libshogun/classifier/KernelMachine.h,
	  libshogun/classifier/mkl/MKL.h,
	  libshogun/classifier/mkl/MKLClassification.h,
	  libshogun/classifier/mkl/MKLOneClass.h,
	  libshogun/classifier/svm/SVM_libsvm.h,
	  libshogun/clustering/Hierarchical.cpp,
	  libshogun/clustering/Hierarchical.h,
	  libshogun/features/SparseFeatures.h,
	  libshogun/features/WDFeatures.h,
	  libshogun/kernel/RegulatoryModulesStringKernel.h,
	  libshogun/kernel/VarianceKernelNormalizer.h,
	  libshogun/lib/Hash.h, libshogun/lib/SimpleFile.h,
	  libshogun/regression/svr/MKLRegression.h,
	  libshogun/structure/DynProg.cpp: document most of the remaining
	  parts
	* libshogun/classifier/mkl/MKLClassification.h,
	  libshogun/classifier/mkl/MKLOneClass.h,
	  libshogun/regression/svr/MKLRegression.h: document mkl properly

2009-10-14  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/classifier/svm/DA_SVM.cpp: unit test working for
	  arbitrary B parameter

2009-10-14  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/Alphabet.h, libshogun/lib/BinaryStream.h,
	  libshogun/lib/BitString.h, libshogun/lib/Hash.cpp,
	  libshogun/lib/Hash.h, libshogun/lib/MemoryMappedFile.h,
	  libshogun/lib/Set.h, libshogun/lib/SimpleFile.h,
	  modular/Library.i: document a bit more and add murmur hash

2009-10-14  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/classifier/svm/DA_SVM.cpp,
	  libshogun/classifier/svm/DA_SVM.h: more elegant formulation of
	  DA_SVM, which should support several stacked SVMs
	* libshogun/classifier/svm/DA_SVM.cpp,
	  libshogun/classifier/svm/DA_SVM.h: verified version of DA_SVM for
	  one level of classifiers

2009-10-12  Soeren Sonnenburg <sonne@debian.org>

	* configure: show octave api version that is used
	* libshogun/classifier/svm/MCSVM.cpp,
	  libshogun/classifier/svm/MCSVM.h: rename result to outputs to
	  resolve conflict in r_modular

2009-10-12  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* modular/Classifier.i: made DA_SVM available to bindings
	* libshogun/features/Features.h: typo
	* libshogun/classifier/KernelMachine.h: commented out duplicated
	  serialization code, will have to be ironed out later
	* libshogun/classifier/Classifier.h: added enum for DA_SVM
	* libshogun/classifier/svm/SVM.h: removed SVM_model from
	  serialization code
	* libshogun/classifier/svm/DA_SVM.cpp,
	  libshogun/classifier/svm/DA_SVM.h: added SVMLight based
	  implementation of Domain Adaptive SVM

2009-10-12  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/KernelMachine.h: fix get_support_vectors
	* libshogun/lib/memory.h: move ifdef up
	* libshogun/classifier/LPBoost.cpp, libshogun/classifier/LPM.cpp,
	  libshogun/classifier/SubGradientLPM.cpp,
	  libshogun/classifier/svm/CPLEXSVM.cpp, libshogun/lib/common.h,
	  libshogun/lib/memory.h, libshogunui/SGInterface.cpp,
	  libshogunui/SGInterface.h: compile fixes for cplex based methods
	* Makefile.template, libshogun/classifier/svm/WDSVMOcas.cpp: - fix
	  permission error in init_shogun octave modular
	  - fix crasher in wdsvmocas

2009-10-06  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/KernelMachine.cpp,
	  libshogun/classifier/KernelMachine.h,
	  libshogun/classifier/svm/SVM.cpp,
	  libshogun/classifier/svm/SVM_light.cpp: fix compilation alpha
	  variable naming clash
	* libshogun/classifier/KernelMachine.cpp,
	  libshogun/classifier/KernelMachine.h,
	  libshogun/classifier/svm/SVM.cpp, libshogun/classifier/svm/SVM.h:
	  move model and classify functionality from SVM to KernelMachine
	* libshogun/regression/KRR.h, modular/Classifier.i: seems like
	  parameter-overloading functions must be defined in the uppermost
	  class to be visible for swig. define for KRR accordingly.
	* libshogun/classifier/Classifier.h, libshogun/classifier/KNN.cpp,
	  libshogun/classifier/KNN.h,
	  libshogun/classifier/KernelMachine.cpp,
	  libshogun/classifier/KernelPerceptron.cpp,
	  libshogun/classifier/KernelPerceptron.h,
	  libshogun/classifier/LDA.cpp, libshogun/classifier/LDA.h,
	  libshogun/classifier/LPBoost.h, libshogun/classifier/LPM.h,
	  libshogun/classifier/Perceptron.cpp,
	  libshogun/classifier/Perceptron.h,
	  libshogun/classifier/PluginEstimate.cpp,
	  libshogun/classifier/PluginEstimate.h,
	  libshogun/classifier/SubGradientLPM.h,
	  libshogun/classifier/mkl/MKL.cpp, libshogun/classifier/mkl/MKL.h,
	  libshogun/classifier/svm/CPLEXSVM.h,
	  libshogun/classifier/svm/GMNPSVM.cpp,
	  libshogun/classifier/svm/GMNPSVM.h,
	  libshogun/classifier/svm/GNPPSVM.cpp,
	  libshogun/classifier/svm/GNPPSVM.h,
	  libshogun/classifier/svm/GPBTSVM.cpp,
	  libshogun/classifier/svm/GPBTSVM.h,
	  libshogun/classifier/svm/LibLinear.cpp,
	  libshogun/classifier/svm/LibLinear.h,
	  libshogun/classifier/svm/LibSVM.cpp,
	  libshogun/classifier/svm/LibSVM.h,
	  libshogun/classifier/svm/LibSVMMultiClass.cpp,
	  libshogun/classifier/svm/LibSVMMultiClass.h,
	  libshogun/classifier/svm/LibSVMOneClass.cpp,
	  libshogun/classifier/svm/LibSVMOneClass.h,
	  libshogun/classifier/svm/MCSVM.cpp,
	  libshogun/classifier/svm/MCSVM.h,
	  libshogun/classifier/svm/MPDSVM.cpp,
	  libshogun/classifier/svm/MPDSVM.h,
	  libshogun/classifier/svm/SVMLin.cpp,
	  libshogun/classifier/svm/SVMLin.h,
	  libshogun/classifier/svm/SVMOcas.cpp,
	  libshogun/classifier/svm/SVMOcas.h,
	  libshogun/classifier/svm/SVMSGD.cpp,
	  libshogun/classifier/svm/SVMSGD.h,
	  libshogun/classifier/svm/SVM_light.cpp,
	  libshogun/classifier/svm/SVM_light.h,
	  libshogun/classifier/svm/SubGradientSVM.cpp,
	  libshogun/classifier/svm/SubGradientSVM.h,
	  libshogun/classifier/svm/WDSVMOcas.cpp,
	  libshogun/classifier/svm/WDSVMOcas.h,
	  libshogun/classifier/svm/gmnpmkl.cpp,
	  libshogun/classifier/svm/gmnpmkl.h,
	  libshogun/clustering/Hierarchical.h,
	  libshogun/clustering/KMeans.cpp, libshogun/clustering/KMeans.h,
	  libshogun/distributions/Distribution.h,
	  libshogun/distributions/hmm/GHMM.cpp,
	  libshogun/distributions/hmm/GHMM.h,
	  libshogun/distributions/hmm/HMM.cpp,
	  libshogun/distributions/hmm/HMM.h,
	  libshogun/distributions/hmm/LinearHMM.cpp,
	  libshogun/distributions/hmm/LinearHMM.h,
	  libshogun/regression/KRR.cpp, libshogun/regression/KRR.h,
	  libshogun/regression/svr/LibSVR.cpp,
	  libshogun/regression/svr/LibSVR.h,
	  libshogun/regression/svr/SVR_light.cpp,
	  libshogun/regression/svr/SVR_light.h: transition
	  classifiers/regressors/clustering methods to work with training
	  data passed on method->train(data);

2009-10-05  Soeren Sonnenburg <sonne@debian.org>

	* cmdline/CmdLineInterface.cpp, libshogun/classifier/Classifier.h,
	  libshogun/classifier/DistanceMachine.cpp,
	  libshogun/classifier/DistanceMachine.h,
	  libshogun/classifier/KNN.cpp, libshogun/classifier/KNN.h,
	  libshogun/classifier/KernelMachine.cpp,
	  libshogun/classifier/KernelMachine.h,
	  libshogun/classifier/KernelPerceptron.h,
	  libshogun/classifier/LinearClassifier.cpp,
	  libshogun/classifier/LinearClassifier.h,
	  libshogun/classifier/PluginEstimate.cpp,
	  libshogun/classifier/PluginEstimate.h,
	  libshogun/classifier/svm/SVM.h,
	  libshogun/classifier/svm/SVM_light.cpp,
	  libshogun/clustering/Hierarchical.h,
	  libshogun/clustering/KMeans.h,
	  libshogun/distance/DistanceMachine.cpp,
	  libshogun/distance/DistanceMachine.h,
	  libshogun/kernel/KernelMachine.cpp,
	  libshogun/kernel/KernelMachine.h, libshogun/regression/KRR.h,
	  libshogun/regression/svr/SVR_light.cpp, modular/Classifier.i,
	  modular/Clustering.i, modular/Regression.i: - move
	  distance/kernelmachine into classifier
	  - add classify function for classifiers
	* libshogun/regression/KRR.h: fix comment

2009-10-02  Soeren Sonnenburg <sonne@debian.org>

	* NEWS: update NEWS and use a more sane value for C
	* libshogun/features/Features.h, libshogun/kernel/Kernel.cpp,
	  libshogun/kernel/Kernel.h: remove unused mindy define
	* libshogunui/GUIKernel.cpp, modular/Features.i: remove further
	  mindy cruft
	* configure, libshogun/features/MindyGramFeatures.cpp,
	  libshogun/features/MindyGramFeatures.h,
	  libshogun/kernel/MindyGramKernel.cpp,
	  libshogun/kernel/MindyGramKernel.h, libshogunui/GUIFeatures.h,
	  libshogunui/GUIKernel.cpp, libshogunui/GUIKernel.h,
	  libshogunui/SGInterface.cpp, modular/Features.i,
	  modular/Kernel.i: remove mindy support

2009-10-02  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp,
	  libshogun/structure/IntronList.h,
	  libshogun/structure/SegmentLoss.h: unused variables removed and
	  documentation added for new functions
	* libshogun/structure/DynProg.cpp: -- two important bugfixes:
	  suboptimal paths and invalid write
	  1. for the transition to the sequence_end state long transitions
	  could not be
	  used since the corresponding table entry was computed after the
	  maximization step
	  This resulted in suboptimal path predictions.
	  2. fixed invalid write in case of predictions that used all
	  candidate positons
	  in their prediction path
	* libshogun/structure/DynProg.cpp,
	  libshogun/structure/IntronList.cpp: -- bugfix related to the
	  dynamic programm with long transitions
	* libshogun/structure/DynProg.cpp: some more debug output

2009-10-02  Soeren Sonnenburg <sonne@debian.org>

	* configure: remove mindy support
	* configure: fix minor errors in configure that prevented octave to
	  work on solaris
	* cmdline/CmdLineInterface.cpp: fix accidental error killing
	  cmdline interface i/o

2009-09-30  Soeren Sonnenburg <sonne@debian.org>

	* configure: fix error in octave detection script
	* Makefile, cmdline/CmdLineInterface.cpp, configure,
	  libshogun/features/Alphabet.h,
	  libshogun/features/PolyFeatures.cpp,
	  libshogun/features/StringFeatures.h,
	  libshogun/kernel/WeightedDegreePositionStringKernel.cpp,
	  libshogun/lib/Mathematics.h, libshogun/lib/common.h,
	  libshogun/lib/io.cpp, libshogun/lib/io.h,
	  libshogun/structure/DynProg.cpp, libshogunui/GUIClassifier.cpp,
	  libshogunui/SGInterface.cpp: get shogun
	  (libshogun,libshgounui,cmdline) to compile under solaris again
	* libshogunui/GUIKernel.cpp, libshogunui/SGInterface.cpp: get tests
	  running again

2009-09-29  Soeren Sonnenburg <sonne@debian.org>

	* libshogunui/GUIClassifier.cpp, libshogunui/GUIClassifier.h,
	  libshogunui/GUIKernel.cpp, libshogunui/SGInterface.cpp: fix
	  examples for new interface / make KRR and custom kernel work
	  again

2009-09-25  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, libshogun/classifier/mkl, libshogun/classifier/mkl/MKL.cpp,
	  libshogun/classifier/mkl/MKL.h,
	  libshogun/classifier/mkl/MKLClassification.cpp,
	  libshogun/classifier/mkl/MKLClassification.h,
	  libshogun/classifier/mkl/MKLMulticlass.h,
	  libshogun/classifier/mkl/MKLOneClass.cpp,
	  libshogun/classifier/mkl/MKLOneClass.h,
	  libshogun/classifier/svm/MKL.cpp, libshogun/classifier/svm/MKL.h,
	  libshogun/classifier/svm/MKLClassification.cpp,
	  libshogun/classifier/svm/MKLClassification.h,
	  libshogun/classifier/svm/MKLMulticlass.h,
	  libshogun/classifier/svm/MKLOneClass.cpp,
	  libshogun/classifier/svm/MKLOneClass.h,
	  libshogun/classifier/svm/SVM.cpp,
	  libshogun/distance/BrayCurtisDistance.cpp,
	  libshogun/distance/BrayCurtisDistance.h,
	  libshogun/distance/CanberraMetric.cpp,
	  libshogun/distance/CanberraMetric.h,
	  libshogun/distance/CanberraWordDistance.cpp,
	  libshogun/distance/CanberraWordDistance.h,
	  libshogun/distance/ChebyshewMetric.cpp,
	  libshogun/distance/ChebyshewMetric.h,
	  libshogun/distance/ChiSquareDistance.cpp,
	  libshogun/distance/ChiSquareDistance.h,
	  libshogun/distance/CosineDistance.cpp,
	  libshogun/distance/CosineDistance.h,
	  libshogun/distance/Distance.h,
	  libshogun/distance/EuclidianDistance.cpp,
	  libshogun/distance/EuclidianDistance.h,
	  libshogun/distance/GeodesicMetric.cpp,
	  libshogun/distance/GeodesicMetric.h,
	  libshogun/distance/HammingWordDistance.cpp,
	  libshogun/distance/HammingWordDistance.h,
	  libshogun/distance/JensenMetric.cpp,
	  libshogun/distance/JensenMetric.h,
	  libshogun/distance/ManhattanMetric.cpp,
	  libshogun/distance/ManhattanMetric.h,
	  libshogun/distance/ManhattanWordDistance.cpp,
	  libshogun/distance/ManhattanWordDistance.h,
	  libshogun/distance/MinkowskiMetric.cpp,
	  libshogun/distance/MinkowskiMetric.h,
	  libshogun/distance/SparseEuclidianDistance.cpp,
	  libshogun/distance/SparseEuclidianDistance.h,
	  libshogun/distance/TanimotoDistance.cpp,
	  libshogun/distance/TanimotoDistance.h,
	  libshogun/kernel/AUCKernel.cpp, libshogun/kernel/AUCKernel.h,
	  libshogun/kernel/Chi2Kernel.cpp, libshogun/kernel/Chi2Kernel.h,
	  libshogun/kernel/CombinedKernel.h,
	  libshogun/kernel/CommUlongStringKernel.cpp,
	  libshogun/kernel/CommUlongStringKernel.h,
	  libshogun/kernel/CommWordStringKernel.cpp,
	  libshogun/kernel/CommWordStringKernel.h,
	  libshogun/kernel/ConstKernel.cpp, libshogun/kernel/ConstKernel.h,
	  libshogun/kernel/CustomKernel.cpp,
	  libshogun/kernel/CustomKernel.h, libshogun/kernel/DiagKernel.cpp,
	  libshogun/kernel/DiagKernel.h,
	  libshogun/kernel/DistanceKernel.cpp,
	  libshogun/kernel/DistanceKernel.h,
	  libshogun/kernel/FixedDegreeStringKernel.cpp,
	  libshogun/kernel/FixedDegreeStringKernel.h,
	  libshogun/kernel/GaussianKernel.cpp,
	  libshogun/kernel/GaussianKernel.h,
	  libshogun/kernel/GaussianShortRealKernel.cpp,
	  libshogun/kernel/GaussianShortRealKernel.h,
	  libshogun/kernel/HistogramWordStringKernel.cpp,
	  libshogun/kernel/HistogramWordStringKernel.h,
	  libshogun/kernel/Kernel.h, libshogun/kernel/LinearByteKernel.cpp,
	  libshogun/kernel/LinearByteKernel.h,
	  libshogun/kernel/LinearKernel.cpp,
	  libshogun/kernel/LinearKernel.h,
	  libshogun/kernel/LinearStringKernel.cpp,
	  libshogun/kernel/LinearStringKernel.h,
	  libshogun/kernel/LinearWordKernel.cpp,
	  libshogun/kernel/LinearWordKernel.h,
	  libshogun/kernel/LocalAlignmentStringKernel.h,
	  libshogun/kernel/LocalityImprovedStringKernel.cpp,
	  libshogun/kernel/LocalityImprovedStringKernel.h,
	  libshogun/kernel/MatchWordStringKernel.cpp,
	  libshogun/kernel/MatchWordStringKernel.h,
	  libshogun/kernel/MindyGramKernel.cpp,
	  libshogun/kernel/MindyGramKernel.h,
	  libshogun/kernel/OligoStringKernel.h,
	  libshogun/kernel/PolyKernel.cpp, libshogun/kernel/PolyKernel.h,
	  libshogun/kernel/PolyMatchStringKernel.cpp,
	  libshogun/kernel/PolyMatchStringKernel.h,
	  libshogun/kernel/PolyMatchWordStringKernel.cpp,
	  libshogun/kernel/PolyMatchWordStringKernel.h,
	  libshogun/kernel/PyramidChi2.cpp, libshogun/kernel/PyramidChi2.h,
	  libshogun/kernel/RegulatoryModulesStringKernel.cpp,
	  libshogun/kernel/RegulatoryModulesStringKernel.h,
	  libshogun/kernel/SalzbergWordStringKernel.cpp,
	  libshogun/kernel/SalzbergWordStringKernel.h,
	  libshogun/kernel/SigmoidKernel.cpp,
	  libshogun/kernel/SigmoidKernel.h,
	  libshogun/kernel/SimpleLocalityImprovedStringKernel.cpp,
	  libshogun/kernel/SimpleLocalityImprovedStringKernel.h,
	  libshogun/kernel/SparseGaussianKernel.cpp,
	  libshogun/kernel/SparseGaussianKernel.h,
	  libshogun/kernel/SparseLinearKernel.cpp,
	  libshogun/kernel/SparseLinearKernel.h,
	  libshogun/kernel/SparsePolyKernel.cpp,
	  libshogun/kernel/SparsePolyKernel.h,
	  libshogun/kernel/TensorProductPairKernel.cpp,
	  libshogun/kernel/TensorProductPairKernel.h,
	  libshogun/kernel/WeightedDegreePositionStringKernel.cpp,
	  libshogun/kernel/WeightedDegreePositionStringKernel.h,
	  libshogun/kernel/WeightedDegreeStringKernel.cpp,
	  libshogun/kernel/WeightedDegreeStringKernel.h,
	  libshogun/lib/io.h, libshogun/regression/svr/MKLRegression.h,
	  libshogun/structure/IntronList.h,
	  libshogun/structure/SegmentLoss.h, libshogunui/GUIClassifier.cpp,
	  libshogunui/GUICommands.h, libshogunui/GUIDistance.cpp,
	  libshogunui/GUIDistance.h, libshogunui/GUIKernel.cpp,
	  libshogunui/GUIKernel.h, libshogunui/SGInterface.cpp,
	  modular/Classifier.i, modular/Regression.i, modular/Structure.i:
	  - when training kernel/distance machines it is no longer
	  necessary to call sg('init_kernel', 'TRAIN') or 'TEST'. this is
	  now done internally.
	  - sg('get_kernel_matrix') now has an extra argument, i.e.
	  sg('get_kernel_matrix', 'TRAIN')
	  - remove the unused {load,save}_{kernel,distance}_init functions
	  in Kernels and Distances
	  - move the mkl Code into libshogun/classifier/mkl
	  - integrate the new structure code into python
	  - add a macro to display a deprecated message ( SG_DEPRECATED )

2009-09-24  Soeren Sonnenburg <sonne@debian.org>

	* NEWS: target news :)

2009-09-23  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* libshogun/features/StringFeatures.cpp: example for serialization
	* libshogun/classifier/Classifier.cpp,
	  libshogun/classifier/Classifier.h,
	  libshogun/classifier/svm/SVM.cpp, libshogun/classifier/svm/SVM.h,
	  libshogun/classifier/svm/SVM_light.cpp,
	  libshogun/classifier/svm/SVM_light.h,
	  libshogun/features/DotFeatures.h,
	  libshogun/features/Features.cpp, libshogun/features/Labels.cpp,
	  libshogun/features/Labels.h,
	  libshogun/features/RealFileFeatures.h,
	  libshogun/features/SimpleFeatures.h,
	  libshogun/features/StringFeatures.h,
	  libshogun/kernel/GaussianKernel.h, libshogun/kernel/Kernel.h,
	  libshogun/kernel/KernelMachine.cpp,
	  libshogun/kernel/KernelMachine.h,
	  libshogun/kernel/SimpleKernel.h, libshogun/kernel/StringKernel.h,
	  libshogun/kernel/WeightedDegreeStringKernel.cpp,
	  libshogun/kernel/WeightedDegreeStringKernel.h: awesome.
	  Serialization merged successfully (at least for some classes).
	* .generate_link_dependencies.py, libshogun/base/SGObject.cpp,
	  libshogun/base/SGObject.h, libshogun/features/Alphabet.cpp,
	  libshogun/features/Alphabet.h, libshogun/features/Features.h,
	  libshogun/features/StringFeatures.h, modular/SGBase.i: Initial
	  version of serialization support for Alphabet and StringFeatures

2009-09-23  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/SVM_light.cpp,
	  libshogun/classifier/svm/SVM_light.h,
	  libshogun/features/Labels.cpp,
	  libshogun/regression/svr/SVR_light.cpp,
	  libshogun/regression/svr/SVR_light.h, modular/Classifier.i: add
	  option to set linear term in svm light

2009-09-22  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/evaluation/PerformanceMeasures.cpp,
	  libshogun/evaluation/PerformanceMeasures.h: fix a number of
	  integer range overflows in perf measures
	* configure: fix bug in configure ignoring --cxx and --cc options

2009-09-21  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/MCSVM.cpp,
	  libshogun/classifier/svm/MCSVM.h: fixes for testing rule
	* configure: space between ! and darwin
	* NEWS: update NEWS/README
	* libshogun/classifier/svm/MCSVM.cpp,
	  libshogun/classifier/svm/MCSVM.h,
	  libshogun/classifier/svm/SVM_libsvm.cpp,
	  libshogun/classifier/svm/SVM_libsvm.h: implement new testing rule
	  for mcsvm (using bias)

2009-09-20  Soeren Sonnenburg <sonne@debian.org>

	* configure: don't use wordsize = 64bit on darwin/leopard

2009-09-17  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/LibSVM.cpp,
	  libshogun/classifier/svm/LibSVMMultiClass.cpp,
	  libshogun/classifier/svm/LibSVMOneClass.cpp,
	  libshogun/classifier/svm/MCSVM.cpp,
	  libshogun/classifier/svm/SVM_libsvm.cpp,
	  libshogun/classifier/svm/SVM_libsvm.h,
	  libshogun/regression/svr/LibSVR.cpp: enable bias computation in
	  mcsvm prepare other libsvm based svms for disabling bias
	* NEWS, libshogun/classifier/svm/SVM_libsvm.cpp: implement correct
	  bias and objective computation for mcsvm
	* libshogunui/SGInterface.cpp: remove debug code

2009-09-15  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/MCSVM.cpp,
	  libshogun/classifier/svm/SVM_libsvm.cpp: add further progress
	  output
	* libshogun/classifier/svm/SVM_libsvm.cpp: remove obsolete
	  calculations of Gmaxn*

2009-09-13  Soeren Sonnenburg <sonne@debian.org>

	* octave/OctaveInterface.cpp, octave/OctaveInterface.h: revert
	  include path fix / it was correct

2009-09-10  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp: * bug fix in dp related to long
	  transitions and loss

2009-09-08  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp: enable long transitions for
	  auxiliary data in feature generation function
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogun/structure/SegmentLoss.cpp,
	  libshogun/structure/SegmentLoss.h, libshogunui/SGInterface.cpp:
	  Revert "changed type of linear features from float64 to float32
	  to save mem"
	  
	  This reverts commit 81a6816cda389a2e52ac5f0f9fee7ce820980b94.
	  
	  Conflicts:
	  
	  trunk/src/libshogun/structure/DynProg.cpp
	* libshogun/structure/DynProg.cpp: fix invalid write

2009-09-05  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogun/structure/SegmentLoss.cpp,
	  libshogun/structure/SegmentLoss.h, libshogunui/SGInterface.cpp:
	  changed type of lineat features from float64 to float32 to save
	  mem

2009-09-04  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/GUICommands.h, libshogunui/SGInterface.cpp,
	  libshogunui/SGInterface.h: -- new sg interface function for
	  settings related to the long transition approximation

2009-09-03  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp,
	  libshogun/structure/SegmentLoss.h: * solved the segment loss
	  additivity problem

2009-09-02  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp,
	  libshogun/structure/SegmentLoss.cpp,
	  libshogun/structure/SegmentLoss.h: * fixed bug in debug code
	  * still non-additivity issues in loss
	* libshogun/structure/DynProg.cpp: seems to work now
	* libshogun/structure/DynProg.cpp,
	  libshogun/structure/SegmentLoss.cpp: * long introns should work
	  without loss
	  * still some additivity issues with the segment loss

2009-09-02  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp,
	  libshogun/structure/SegmentLoss.cpp: -- segment loss is now
	  additive, at least for my small example

2009-09-02  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp: pre cleanup

2009-09-01  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* libshogun/lib/BitString.h, libshogun/structure/DynProg.cpp: *
	  version with long introns. Tested for a few cases without loss
	  * still inconsistent when using loss
	  
	  * fixed some minor issues in BitString.h (a while ago)

2009-09-01  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp,
	  libshogun/structure/SegmentLoss.cpp: -- segment loss seems to be
	  OK now
	  the prediction for my example was the same, but
	  the loss is slightly different (110 vs. 108)
	  only one example tested
	* libshogun/structure/DynProg.cpp,
	  libshogun/structure/SegmentLoss.cpp, libshogunui/SGInterface.cpp:
	  -- some more debug code
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogun/structure/SegmentLoss.cpp,
	  libshogun/structure/SegmentLoss.h, libshogunui/SGInterface.cpp,
	  octave/OctaveInterface.cpp, octave/OctaveInterface.h: -- new loss
	  calculation leads to similar but not equal results
	  still some bugs left
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogun/structure/SegmentLoss.cpp,
	  libshogun/structure/SegmentLoss.h, libshogunui/SGInterface.cpp:
	  -- main functionality is there
	* libshogun/structure/DynProg.cpp,
	  libshogun/structure/SegmentLoss.cpp,
	  libshogun/structure/SegmentLoss.h, libshogunui/SGInterface.cpp:
	  -- precompute segment loss and move code for that to a new class

2009-08-28  Soeren Sonnenburg <sonne@debian.org>

	* matlab/MatlabInterface.cpp, matlab/MatlabInterface.h: revert path
	  changes. they are indeed correct

2009-08-28  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* matlab/MatlabInterface.cpp, matlab/MatlabInterface.h: adapted
	  paths of header files

2009-08-25  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/features/PolyFeatures.cpp,
	  libshogun/features/PolyFeatures.h, libshogunui/SGInterface.cpp:
	  -- the dot feature for the polynomial kernel can now be
	  normalized

2009-08-25  Soeren Sonnenburg <sonne@debian.org>

	* libshogunui/SGInterface.cpp: impl. get_features for other
	  dot_features

2009-08-25  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/features/Features.h,
	  libshogun/features/PolyFeatures.cpp,
	  libshogun/features/PolyFeatures.h, libshogunui/SGInterface.cpp,
	  libshogunui/SGInterface.h, modular/Features.i: -- implemented dot
	  feature for polynomial kernel
	* libshogunui/SGInterface.cpp: -- some needless code removed
	* libshogunui/SGInterface.cpp: -- several mem leaks fixed

2009-08-24  Soeren Sonnenburg <sonne@debian.org>

	* configure, libshogun/lib/Mathematics.h: further sunos magic

2009-08-23  Soeren Sonnenburg <sonne@debian.org>

	* configure: split up python modular examples

2009-08-19  Soeren Sonnenburg <sonne@debian.org>

	* configure, libshogun/lib/common.h: a few sunos fixes.
	* libshogunui/GUIClassifier.cpp: fix for get_classifier
	* NEWS, libshogunui/SGInterface.cpp: potentiallyfix one class mkl

2009-08-18  Soeren Sonnenburg <sonne@debian.org>

	* libshogunui/SGInterface.cpp: add missing include
	* NEWS: update NEWS
	* libshogunui/GUICommands.h, libshogunui/SGInterface.cpp,
	  libshogunui/SGInterface.h: implement set_linear_classifier

2009-08-16  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog: updated changelog
	* libshogun/regression/svr/MKLRegression.cpp: another compile fix
	* libshogun/classifier/svm/MKLClassification.cpp: fix compile error
	  w/o svmlight
	* ChangeLog: updated changelog
	* NEWS: update news to release date

2009-08-15  Soeren Sonnenburg <sonne@debian.org>

	* configure, libshogunui/SGInterface.cpp, modular/Regression.i,
	  r/RInterface.cpp: - on darwin use ${_prefix} in library path
	  - fix MKL modular inclusion
	  - fix examples for new syntax and a related regression for
	  WD/SPEC features
	* modular/Classifier.i, modular/Regression.i: enable new MKL for
	  python modular
	* ChangeLog: updated changelog
	* NEWS: remove legacy examples and update documentation/examples

2009-08-14  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/lib/BitString.h: function to set word in bitstring
	* libshogun/classifier/svm/MKL.cpp, libshogun/classifier/svm/MKL.h,
	  libshogun/kernel/CombinedKernel.h: fix another memory leak
	  occurring only with interleaved MKL

2009-08-13  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/Alphabet.cpp, libshogun/features/Alphabet.h:
	  add BINARY alphabet
	* libshogun/classifier/svm/MKL.cpp: fix another minor memory leak
	  occurring with mkl

2009-08-11  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/MKL.cpp,
	  libshogun/regression/svr/SVR_light.cpp: fix further leaks related
	  to multiple kernels and mkl
	* libshogun/classifier/svm/SVM_light.cpp,
	  libshogun/kernel/CombinedKernel.cpp, libshogun/lib/List.h: fix a
	  memory leak occurring with svm light linadd and multiple kernels

2009-08-10  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/Labels.cpp: be really strict on two-class
	  labeling test, throw an error if label +1 or -1 or not found or
	  labels!=+/-1 are found

2009-08-02  Soeren Sonnenburg <sonne@debian.org>

	* octave/OctaveInterface.cpp: memory tracing still does not work
	  with octave...
	* libshogun/base/SGObject.h, libshogun/base/init.cpp,
	  libshogun/lib/Set.h, libshogun/lib/memory.cpp,
	  libshogun/lib/memory.h, libshogunui/GUICommands.h,
	  libshogunui/SGInterface.cpp, libshogunui/SGInterface.h,
	  matlab/MatlabInterface.cpp, octave/OctaveInterface.cpp: memory
	  tracing finally works ( sg('whos') ), it requires the new/delete
	  etc operators to be defined/implemented in the
	  matlab.cpp/octave.cpp otherwise the standard operators
	  (std:new,...) are used
	* configure, libshogun/lib/DynamicArray.h, libshogun/lib/Set.h,
	  libshogun/lib/memory.cpp, libshogun/lib/memory.h,
	  libshogunui/GUICommands.h, libshogunui/SGInterface.cpp: add
	  memory alloc tracing (configure --enable-trace-memory-allocs) and
	  add new command "who" in static interfaces to list shogun alloc'd
	  objects and their sizes. note that current implementation is very
	  inefficient - only use for debugging purposes.
	* libshogun/features/Features.cpp, libshogun/kernel/Kernel.cpp,
	  libshogunui/SGInterface.cpp: new loglevel ALL/ GCDEBUG (to debug
	  memory leaks)
	* libshogun/classifier/KNN.cpp, libshogun/classifier/LPBoost.cpp,
	  libshogun/classifier/svm/MKL.cpp,
	  libshogun/classifier/svm/SVM.cpp,
	  libshogun/classifier/svm/SVMSGD.cpp,
	  libshogun/classifier/svm/Tron.cpp,
	  libshogun/classifier/svm/gpdtsolve.cpp,
	  libshogun/features/DotFeatures.cpp, libshogun/kernel/Kernel.cpp,
	  libshogun/kernel/RegulatoryModulesStringKernel.cpp,
	  libshogun/kernel/RegulatoryModulesStringKernel.h: add several
	  cancel_computation() checks

2009-07-31  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, libshogun/kernel/RegulatoryModulesStringKernel.cpp,
	  libshogun/kernel/RegulatoryModulesStringKernel.h: several fixes
	  in RMK
	* libshogun/classifier/svm/MKL.cpp: fix potential memory leak in
	  MKL
	* libshogun/lib/BinaryStream.h, libshogun/lib/Mathematics.h: fix a
	  bug in binary search and add a read_next function to binary
	  stream

2009-07-30  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/kernel/Kernel.h,
	  libshogun/kernel/RegulatoryModulesStringKernel.cpp,
	  libshogun/kernel/RegulatoryModulesStringKernel.h,
	  modular/Kernel.i: initial rmk import

2009-07-29  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/lib/BinaryStream.h: add open/close functions and
	  default constructor

2009-07-25  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/MKL.cpp,
	  libshogun/kernel/WeightedDegreeStringKernel.h, r/RInterface.cpp:
	  get mkl examples for python/r back to work
	* libshogun/classifier/svm/MKL.cpp,
	  libshogun/kernel/CommWordStringKernel.h,
	  libshogun/kernel/Kernel.h,
	  libshogun/kernel/RidgeKernelNormalizer.h,
	  libshogun/lib/BinaryStream.h, libshogunui/GUIKernel.cpp,
	  libshogunui/GUIKernel.h, libshogunui/SGInterface.cpp,
	  modular/Kernel.i: - implement ridge kernel normalizer and include
	  in static/modular if's
	  - minor fixes to binary stream

2009-07-24  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/lib/BinaryStream.h: remove empty line

2009-07-24  Alexander Zien <Alexander.Zien@tuebingen.mpg.de>

	* libshogun/classifier/svm/MKL.cpp: MKL: more more debug output

2009-07-23  Alexander Zien <Alexander.Zien@tuebingen.mpg.de>

	* libshogun/classifier/svm/MKL.cpp: MKL: again, more debug output
	* libshogun/classifier/svm/MKL.cpp: MKL: even more debug ouput
	* libshogun/classifier/svm/MKL.cpp: MKL: more debugging output
	* libshogun/classifier/svm/MKL.cpp: MKL: added assertions and
	  debug-printfs for strange bug in direct reported by Marius
	* libshogun/classifier/svm/MKL.cpp:

2009-07-23  Soeren Sonnenburg <sonne@debian.org>

	* libshogunui/SGInterface.cpp: fix wrong call to bias enabled
	  instead of interleaved_enabled
	* libshogun/classifier/svm/MKL.cpp: compute obj. based on new beta
	* libshogun/lib/BinaryStream.h: binary mmap alike stream

2009-07-22  Soeren Sonnenburg <sonne@debian.org>

	* modular/Classifier.i, modular/Regression.i: mkl for modular
	  interfaces
	* libshogunui/GUIClassifier.cpp, libshogunui/GUIClassifier.h,
	  libshogunui/SGInterface.cpp: compile fixes
	* NEWS, libshogunui/GUIClassifier.cpp, libshogunui/GUIClassifier.h,
	  libshogunui/GUICommands.h, libshogunui/SGInterface.cpp,
	  libshogunui/SGInterface.h: implement set_constraint_generator (to
	  allow for arbitrary svm's in mkl wrapper)
	* libshogun/classifier/svm/MKL.cpp, libshogun/classifier/svm/MKL.h:
	  fix crasher with CPLEX

2009-07-21  Soeren Sonnenburg <sonne@debian.org>

	* libshogunui/GUIClassifier.cpp: compile fix when svmlikght is
	  disabled
	* libshogun/classifier/svm/MKL.cpp: another cplex related compile
	  fix
	* libshogun/classifier/svm/MKL.cpp: compile fix when cplex is
	  available
	* libshogun/classifier/Classifier.h,
	  libshogun/classifier/svm/MKL.cpp, libshogun/classifier/svm/MKL.h,
	  libshogun/classifier/svm/MKLClassification.cpp,
	  libshogun/classifier/svm/MKLClassification.h,
	  libshogun/classifier/svm/MKLOneClass.cpp,
	  libshogun/classifier/svm/MKLOneClass.h,
	  libshogun/classifier/svm/MKLRegression.cpp,
	  libshogun/classifier/svm/MKLRegression.h,
	  libshogun/classifier/svm/OneClassMKL.cpp,
	  libshogun/classifier/svm/OneClassMKL.h,
	  libshogun/regression/svr/MKLRegression.cpp,
	  libshogun/regression/svr/MKLRegression.h,
	  libshogunui/GUIClassifier.cpp, libshogunui/GUIClassifier.h,
	  libshogunui/GUICommands.h, libshogunui/SGInterface.cpp,
	  libshogunui/SGInterface.h: set reasonable defaults(?), enable all
	  potential mkl solvers and add gui command to enable interleaved
	  optimization
	* libshogun/classifier/Classifier.h,
	  libshogun/classifier/svm/MKL.cpp, libshogun/classifier/svm/MKL.h,
	  libshogun/classifier/svm/MKLClassification.cpp,
	  libshogun/classifier/svm/MKLClassification.h,
	  libshogun/classifier/svm/MKLRegression.cpp,
	  libshogun/classifier/svm/MKLRegression.h,
	  libshogun/classifier/svm/OneClassMKL.cpp,
	  libshogun/classifier/svm/OneClassMKL.h: add oneclass mkl
	* libshogun/base/Version.h, libshogun/classifier/svm/MKL.cpp,
	  libshogun/classifier/svm/MKL.h,
	  libshogun/classifier/svm/MKLClassification.cpp,
	  libshogun/classifier/svm/MKLClassification.h,
	  libshogun/classifier/svm/MKLRegression.cpp,
	  libshogun/classifier/svm/MKLRegression.h,
	  libshogun/classifier/svm/SVM_light.cpp,
	  libshogun/classifier/svm/SVM_light.h,
	  libshogun/regression/svr/SVR_light.cpp,
	  libshogun/regression/svr/SVR_light.h,
	  libshogunui/GUIClassifier.cpp: mkl regression works again

2009-07-18  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, libshogun/classifier/svm/MKL.cpp,
	  libshogun/classifier/svm/MKL.h,
	  libshogun/classifier/svm/MKLClassification.cpp,
	  libshogun/classifier/svm/MKLClassification.h,
	  libshogun/classifier/svm/MKLRegression.cpp,
	  libshogun/classifier/svm/MKLRegression.h,
	  libshogun/classifier/svm/SVM_light.cpp,
	  libshogun/regression/svr/SVR_light.cpp,
	  libshogun/regression/svr/SVR_light.h: restructure MKL framework:
	  core routines are the same for regression/classification...

2009-07-17  Soeren Sonnenburg <sonne@debian.org>

	* ., .r-install.sh, cmdline, cmdline/CmdLineInterface.cpp,
	  cmdline/CmdLineInterface.h, cmdline/cmdline.cpp, libshogun/base,
	  libshogun/classifier, libshogun/classifier/svm/CPLEXSVM.cpp,
	  libshogun/classifier/svm/MKL.h,
	  libshogun/classifier/svm/MKLClassification.cpp,
	  libshogun/classifier/svm/MKLClassification.h,
	  libshogun/classifier/svm/MKLRegression.h,
	  libshogun/classifier/svm/MPDSVM.cpp,
	  libshogun/classifier/svm/SVM.cpp, libshogun/classifier/svm/SVM.h,
	  libshogun/classifier/svm/SVM_light.cpp, libshogun/clustering,
	  libshogun/distance, libshogun/distributions,
	  libshogun/evaluation, libshogun/features,
	  libshogun/features/ExplicitSpecFeatures.cpp,
	  libshogun/features/ExplicitSpecFeatures.h, libshogun/kernel,
	  libshogun/kernel/CommWordStringKernel.h,
	  libshogun/kernel/FirstElementKernelNormalizer.h,
	  libshogun/kernel/HistogramWordStringKernel.cpp,
	  libshogun/kernel/HistogramWordStringKernel.h,
	  libshogun/kernel/Kernel.h,
	  libshogun/kernel/MatchWordStringKernel.cpp,
	  libshogun/kernel/MatchWordStringKernel.h,
	  libshogun/kernel/PolyMatchWordStringKernel.cpp,
	  libshogun/kernel/PolyMatchWordStringKernel.h,
	  libshogun/kernel/SalzbergWordStringKernel.cpp,
	  libshogun/kernel/SalzbergWordStringKernel.h,
	  libshogun/kernel/VarianceKernelNormalizer.h, libshogun/lib,
	  libshogun/preproc, libshogun/regression, libshogun/structure,
	  libshogunui/GUIClassifier.cpp, libshogunui/GUIClassifier.h,
	  libshogunui/GUICommands.h, libshogunui/GUIDistance.cpp,
	  libshogunui/GUIDistance.h, libshogunui/GUIFeatures.cpp,
	  libshogunui/GUIFeatures.h, libshogunui/GUIHMM.cpp,
	  libshogunui/GUIHMM.h, libshogunui/GUIKernel.cpp,
	  libshogunui/GUIKernel.h, libshogunui/GUILabels.cpp,
	  libshogunui/GUILabels.h, libshogunui/GUIMath.cpp,
	  libshogunui/GUIMath.h, libshogunui/GUIPluginEstimate.cpp,
	  libshogunui/GUIPluginEstimate.h, libshogunui/GUIPreProc.cpp,
	  libshogunui/GUIPreProc.h, libshogunui/GUIStructure.cpp,
	  libshogunui/GUIStructure.h, libshogunui/GUITime.cpp,
	  libshogunui/GUITime.h, libshogunui/SGInterface.cpp,
	  libshogunui/SGInterface.h, libshogunui/SyntaxHighLight.h, matlab,
	  matlab/MatlabInterface.cpp, matlab/MatlabInterface.h, modular,
	  modular/Classifier.doxy, modular/Classifier.i,
	  modular/Clustering.doxy, modular/Clustering.i,
	  modular/Distance.doxy, modular/Distance.i,
	  modular/Distribution.doxy, modular/Distribution.i,
	  modular/Evaluation.doxy, modular/Evaluation.i,
	  modular/Features.doxy, modular/Features.i, modular/Kernel.doxy,
	  modular/Kernel.i, modular/Library.doxy, modular/Library.i,
	  modular/PreProc.doxy, modular/PreProc.i, modular/Regression.doxy,
	  modular/Regression.i, modular/Structure.doxy,
	  modular/Structure.i, octave, octave/OctaveInterface.cpp,
	  octave/OctaveInterface.h, octave_modular,
	  octave_modular/swig_typemaps.i, python,
	  python/PythonInterface.cpp, python/PythonInterface.h,
	  python_modular, python_modular/swig_typemaps.i, r,
	  r/RInterface.cpp, r/RInterface.h, r_modular,
	  r_modular/swig_typemaps.i:

2009-07-16  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/MKL.cpp,
	  libshogun/classifier/svm/MKLClassification.cpp,
	  libshogun/classifier/svm/SVM.cpp,
	  libshogun/classifier/svm/SVM_light.cpp,
	  libshogun/classifier/svm/SVM_light.h,
	  libshogunui/GUIClassifier.cpp: interleaved mkl seems to work now
	  :)
	* libshogun/classifier/svm/MKLClassification.cpp,
	  libshogun/classifier/svm/MKLClassification.h,
	  libshogun/classifier/svm/SVM_light.cpp,
	  libshogun/classifier/svm/SVM_light.h: wip checkin

2009-07-15  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/MKL.h: fix comment
	* libshogun/classifier/svm/MKL.cpp, libshogun/classifier/svm/MKL.h,
	  libshogun/classifier/svm/SVM.cpp, libshogun/classifier/svm/SVM.h:
	  pass mkl obj in callback function
	* libshogun/classifier/svm/MKL.cpp, libshogun/classifier/svm/MKL.h,
	  libshogun/classifier/svm/MKLClassification.cpp,
	  libshogun/classifier/svm/MKLClassification.h,
	  libshogun/classifier/svm/MKLRegression.cpp,
	  libshogun/classifier/svm/MKLRegression.h,
	  libshogun/classifier/svm/SVM.h: add a helper callback function
	  that takes an MKL object, sumw and suma as input, finally
	  compiles and works again w/ wrapper
	* libshogun/classifier/svm/MKL.cpp, libshogun/classifier/svm/MKL.h,
	  libshogun/classifier/svm/MKLClassification.cpp,
	  libshogun/classifier/svm/SVM.h: wip commit

2009-07-14  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/MKL.cpp,
	  libshogun/classifier/svm/MKLClassification.cpp,
	  libshogun/classifier/svm/SVM_light.cpp: remove debug code, minor
	  cleanup
	* libshogun/classifier/svm/MKL.cpp, libshogun/classifier/svm/MKL.h,
	  libshogun/classifier/svm/MKLClassification.cpp,
	  libshogun/classifier/svm/MKLClassification.h,
	  libshogun/classifier/svm/MKLRegression.cpp,
	  libshogun/classifier/svm/MKLRegression.h,
	  libshogun/lib/Mathematics.cpp, libshogun/lib/Mathematics.h:
	  1-norm mkl wrapper optimization via glpk works now
	* libshogun/classifier/svm/MKL.cpp, libshogun/classifier/svm/MKL.h,
	  libshogun/classifier/svm/MKLClassification.h,
	  libshogun/classifier/svm/MKLRegression.h,
	  libshogunui/GUIClassifier.cpp, libshogunui/GUIClassifier.h,
	  libshogunui/SGInterface.cpp: mkl with nop wrapper works

2009-07-13  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp: fixed conflict

2009-07-13  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/MKL.cpp, libshogun/classifier/svm/MKL.h:
	  further WIP towards general MKL wrapping

2009-06-29  Soeren Sonnenburg <sonne@debian.org>

	* configure: encode full libpath in case of darwin

2009-06-26  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp: + removed several bugs:
	  - set_element arguments were in incorrect order
	  - copy_array/ free_array flags were set incorrectly in some
	  Array2s
	  - get_{states,scores,positions} did not copy the array structures

2009-06-25  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/kernel/LinearKernel.h: fix typo in doc

2009-06-22  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/SGInterface.cpp, modular/Structure.i: + added missing
	  typemap for set_content_type_array
	  + added asertions
	* libshogun/structure/DynProg.cpp, modular/Structure.i,
	  python_modular/swig_typemaps.i: + fixed typemap for 3d array
	  observation_matrix
	  + added typemap for compute plif matrix

2009-06-19  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogun/structure/IntronList.cpp,
	  libshogun/structure/IntronList.h, libshogunui/SGInterface.cpp: --
	  intron lists can be used now...
	  output reduced

2009-06-18  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp, libshogunui/SGInterface.cpp:
	  double free fixed and output reduced
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/SGInterface.cpp: -- moved some computations that were
	  duplicated in SGInterface into DynProg.cpp

2009-06-16  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/SGInterface.cpp: bug fixes
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h:
	  removed member variables that were not in use any more
	* libshogunui/SGInterface.cpp: compile fixes
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogun/structure/IntronList.cpp,
	  libshogun/structure/IntronList.h, libshogunui/SGInterface.cpp: --
	  setting all_pos and seq_len in the begining as member variables
	  avoids passing them all the time
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogun/structure/IntronList.cpp,
	  libshogun/structure/IntronList.h, libshogunui/SGInterface.cpp:
	  started to include Intron Lists in DynProg

2009-06-15  Soeren Sonnenburg <sonne@debian.org>

	* libshogunui/SGInterface.cpp: fix get_kernel_weights being
	  transposed to set_kernel_weights
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/SGInterface.cpp, modular/Structure.i: convert
	  set_observation_matrix() to use 3d-array
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/SGInterface.cpp: split up precompute_content_values

2009-06-15  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/DynProg.h: rename m_seq in DynProg.h as well
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/SGInterface.cpp: -- renamed m_seq ->
	  m_observation_matrix
	  and the function set_seq -> set_observation_matrix
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/SGInterface.cpp: -- feature matrix was not set in in
	  best_path_trans_deriv interface
	  -- third dimension of feature matrix was ignored
	* libshogun/structure/PlifMatrix.cpp: fix typo
	* libshogun/structure/PlifMatrix.cpp: -- bugfix: penalties were
	  written into the limits array
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h:
	  -- removed functions that were not used any more.
	  Most of them were related to content svm predictions.
	  They became useless because these predictions are now
	  done in a separate step before the decoding.

2009-06-15  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* modular/Structure.i: + added typemap to wrap
	  pm.compute_signal_plifs(...

2009-06-15  Soeren Sonnenburg <sonne@debian.org>

	* octave/OctaveInterface.cpp, octave/OctaveInterface.h: get things
	  to work with octave 3.2 and elwms
	* configure, octave/OctaveInterface.cpp: compile fixes for octave
	  3.2
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h:
	  remove obsolete find_values_till_pos functions

2009-06-12  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/lib/Hash.h, libshogunui/SGInterface.cpp: collection of
	  hash functions in CHash
	* libshogun/lib/Hash.cpp, libshogun/lib/Hash.h,
	  libshogun/lib/Mathematics.cpp, libshogun/lib/Mathematics.h: add
	  crc32 and md5 string hashing functions
	* libshogun/structure/PlifMatrix.cpp,
	  libshogun/structure/PlifMatrix.h, modular/Structure.i: introduce
	  dummy parameter maxlen
	* libshogun/classifier/svm/MKLClassification.h,
	  libshogun/regression/svr/SVR_light.cpp, modular/Structure.i: -
	  fill in typemaps
	  - minor compile fixes w/ cplex

2009-06-12  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* modular/Structure.i: + added PlifMatrix rename/includes

2009-06-12  Soeren Sonnenburg <sonne@debian.org>

	* NEWS: update news
	* Makefile.template: upon make install of elwms don't install files
	  into R/octave/python if these interfaces were not configured

2009-06-11  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/structure/PlifMatrix.cpp,
	  libshogun/structure/PlifMatrix.h, libshogunui/SGInterface.cpp:
	  get rid of struct monster function. things are fully split up now
	  and should work under modular interfaces (given typemaps are
	  added at few places...)
	* libshogun/structure/PlifMatrix.cpp,
	  libshogun/structure/PlifMatrix.h, libshogunui/SGInterface.cpp:
	  remove plif_ids, min and max_values from set_plif_struct
	* libshogun/features/StringFeatures.h,
	  libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogun/structure/PlifMatrix.cpp,
	  libshogun/structure/PlifMatrix.h, libshogunui/SGInterface.cpp:
	  start to split up set_plif_struct, move
	  get_zero_terminated_string_copy as static function into
	  StringFeatures
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogun/structure/PlifMatrix.h, libshogunui/GUIStructure.cpp,
	  libshogunui/SGInterface.cpp: git rid of the PlifArray** arguments
	  in compute_nbest_path / *trans_deriv
	* libshogun/lib/Array.h, libshogun/structure/PlifMatrix.cpp,
	  libshogun/structure/PlifMatrix.h, libshogunui/GUIStructure.cpp,
	  libshogunui/GUIStructure.h, libshogunui/SGInterface.cpp: extract
	  plif related functions from GUIStructure into new class
	  PlifMatrix

2009-06-10  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogun/structure/Plif.cpp, libshogun/structure/Plif.h,
	  libshogunui/GUIStructure.cpp, libshogunui/SGInterface.cpp: -
	  remove the output arguments from best_path* functions and use
	  member variables to store the results and seperate get_*
	  functions to obtain the output member variables
	  - properly initialize output member variables
	  - rename function best_path_trans to compute_nbest_paths() and
	  remove templated implementation
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h:
	  remove best_path prefix
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/SGInterface.cpp: remove sparse args from
	  best_path_trans and move the templated function into the .h file
	  (yes that is the policy ... should get rid of templates)
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/SGInterface.cpp: remove orf_info form
	  best_path_trans{,_derif}
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/SGInterface.cpp: remove orf_info from best_path_trans
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/SGInterface.cpp: get rid of seq argument in
	  best_path_trans
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/SGInterface.cpp: move wordstr creation into DynProg
	* libshogun/features/Alphabet.h,
	  libshogun/features/StringFeatures.h,
	  libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h:
	  remove code duplication and move translate_from_single_order to
	  Alphabet and make dynprog and stringfeatures use this
	* libshogun/classifier/svm/MKL.cpp,
	  libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/SGInterface.cpp: genestr, genestr_num and length are
	  no longer passed as arguments (internally functions use m_genestr
	  instead)
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/SGInterface.cpp: - introduce function
	  set_gene_string(char* s, int32_t len) (no longer 2d!)
	  - remove function set_genestr_len, length is obtained from
	  gene_string anyway
	  - get rid of all the m_step m_call variables, no one knows which
	  values they should take anyway
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h:
	  merge member variables dict_weight and m_dict_weight
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h:
	  removed member variable m_dict_weights_array, still works

2009-06-09  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/SGInterface.cpp, libshogunui/SGInterface.h: - remove
	  obsolete best_path_2struct/simple functions
	  - prefix all member variables with m_ (except for dict_weights)
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h:
	  replace N -> m_N
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h:
	  further m_ prefixing
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h:
	  further m_ prefixing
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogun/structure/IntronList.cpp.o: continue m_ prefixing

2009-06-09  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogun/structure/IntronList.cpp,
	  libshogun/structure/IntronList.cpp.o,
	  libshogun/structure/IntronList.h, libshogunui/GUICommands.h,
	  libshogunui/SGInterface.cpp, libshogunui/SGInterface.h: -- new
	  class IntronList created
	  stores a list of supported introns for efficient access during
	  the dynamic programm
	  --functions of the class tested with valgrind

2009-06-09  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h: -
	  remove inline functions
	  - start prefixing member variables with m_ (first m_max_a_id )
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h:
	  fix some obvious mixups between parameters p_N and N etc and make
	  all variables protected
	* libshogun/classifier/svm/SVM_libsvm.cpp: compile fixes for
	  line-search...

2009-06-08  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/SVM_libsvm.cpp: potentially speed up
	  multi-class svm working set selection

2009-06-03  Soeren Sonnenburg <sonne@debian.org>

	* python/PythonInterface.cpp: fix rare compilation error
	* libshogun/kernel/CombinedKernel.cpp: fix custom kernel init

2009-06-02  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/kernel/CombinedKernel.h: fix off by one bug
	* libshogun/base/SGObject.h, libshogun/classifier/svm/MKL.cpp,
	  libshogun/lib/io.cpp, libshogun/lib/io.h,
	  libshogunui/GUIKernel.cpp, libshogunui/SGInterface.cpp,
	  libshogunui/SGInterface.h: now features can be embedded into
	  WORD/ULONG immediately without the need for an extra convert cmd,
	  e.g.
	  
	  sg('add_features','TRAIN',{x},'DNAWORD', 3, 'from_position_list',
	  4, int32([0,1,2,3,4]));

2009-06-01  Soeren Sonnenburg <sonne@debian.org>

	* libshogunui/GUIKernel.cpp: fix a crasher when set_kernel is used
	  followed by add_kernel
	* CONTRIBUTIONS, libshogunui/GUICommands.h,
	  libshogunui/GUIFeatures.cpp, libshogunui/GUIFeatures.h,
	  libshogunui/SGInterface.cpp, libshogunui/SGInterface.h: remove
	  commands from_position_list and slide_window and move
	  functionallity into set/add_features, e.g.:
	  
	  x='CATCTGACGTCAGGTACGTACGGCGTGGGCATCATG';
	  sg('add_features','TRAIN',{x},'DNA', 'slide_window', 4, 1,0);
	  sg('add_features','TRAIN',{x},'DNA', 'from_position_list', 4,
	  int32([0,1,2,3,4]), 1);

2009-05-31  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/MCSVM.cpp,
	  libshogun/classifier/svm/MKLClassification.cpp,
	  libshogun/classifier/svm/MultiClassSVM.cpp,
	  libshogun/classifier/svm/SVM_libsvm.cpp,
	  libshogunui/SGInterface.cpp: fix a couple of memory leaks

2009-05-30  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp: disabled some experimental code
	* libshogun/classifier/svm/MKL.cpp,
	  libshogun/classifier/svm/MKLClassification.cpp: compile fixes ...

2009-05-29  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/MKL.cpp: further mkl restructuring

2009-05-28  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/MCSVM.cpp,
	  libshogun/classifier/svm/MultiClassSVM.h,
	  libshogun/classifier/svm/SVM_libsvm.cpp,
	  libshogunui/GUIClassifier.cpp: MCSVM seems to work OK now
	* libshogun/classifier/svm/MCSVM.cpp: add debug code
	* libshogun/classifier/svm/MCSVM.cpp,
	  libshogun/classifier/svm/MCSVM.h,
	  libshogun/classifier/svm/MultiClassSVM.h,
	  libshogun/classifier/svm/SVM_libsvm.cpp: more on testing
	* libshogun/classifier/svm/MCSVM.cpp,
	  libshogun/classifier/svm/SVM_libsvm.cpp: first attempt on
	  implementing mc-testing
	* libshogun/classifier/svm/MCSVM.cpp,
	  libshogun/classifier/svm/MultiClassSVM.h,
	  libshogun/classifier/svm/SVM_libsvm.cpp: starting work on passing
	  the classifier back to shogun for testing
	* modular/Kernel.i: wrap set_subkernel_weights

2009-05-27  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/Classifier.h,
	  libshogun/classifier/svm/MCSVM.h,
	  libshogun/classifier/svm/SVM_libsvm.cpp,
	  libshogunui/GUIClassifier.cpp, libshogunui/SGInterface.cpp,
	  modular/Classifier.i: progress output / bugfixes for MCSVM
	* libshogun/classifier/svm/MCSVM.cpp,
	  libshogun/classifier/svm/MCSVM.h: mcsvm entry class
	* libshogun/classifier/svm/LibSVM.cpp,
	  libshogun/classifier/svm/LibSVM.h,
	  libshogun/classifier/svm/LibSVMMultiClass.cpp,
	  libshogun/classifier/svm/LibSVMMultiClass.h,
	  libshogun/classifier/svm/LibSVMNU.cpp,
	  libshogun/classifier/svm/LibSVMNU.h,
	  libshogun/classifier/svm/SVM_libsvm.cpp,
	  libshogun/classifier/svm/SVM_libsvm.h,
	  libshogunui/GUIClassifier.cpp, modular/Classifier.i: merge MCSVM
	  from multiclass branch
	* NEWS, libshogun/classifier/svm/MKLClassification.cpp,
	  libshogun/classifier/svm/MKLClassification.h,
	  libshogun/classifier/svm/MKLRegression.cpp,
	  libshogun/classifier/svm/MKLRegression.h,
	  libshogun/classifier/svm/SVM_libsvm.h,
	  libshogunui/GUIClassifier.cpp, libshogunui/GUIClassifier.h,
	  libshogunui/GUICommands.h, libshogunui/SGInterface.cpp,
	  libshogunui/SGInterface.h: get things to compile again and change
	  svm_one_class_nu to svm_nu
	* libshogun/classifier/Classifier.h,
	  libshogun/classifier/svm/SVM_libsvm.cpp,
	  libshogunui/GUIClassifier.cpp: starting to port mc svm, *don't
	  use, won't compile*

2009-05-26  Soeren Sonnenburg <sonne@debian.org>

	* NEWS: change soname
	* libshogun/classifier/svm/LibSVMMultiClass.cpp,
	  libshogun/classifier/svm/LibSVMMultiClass.h,
	  libshogun/classifier/svm/SVM_libsvm.h,
	  libshogunui/GUIClassifier.cpp: allow nu svm for multiclass

2009-05-22  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* libshogunui/SGInterface.cpp: mem leak fixed

2009-05-22  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/SVM_libsvm.cpp: fix typo
	* libshogun/classifier/svm/SVM_libsvm.cpp: remove debug code
	* libshogun/lib/Array2.h: a default constructor (as this change
	  implements) is needed to get the modular interfaces to compile
	* libshogun/classifier/svm/SVM_libsvm.cpp,
	  libshogunui/SGInterface.cpp: fix libsvmnu

2009-05-22  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp: fixed finite renaming
	* libshogun/structure/DynProg.cpp:
	* libshogun/features/SparseFeatures.h, libshogun/lib/Array.h,
	  libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/GUICommands.h, libshogunui/GUIStructure.cpp,
	  libshogunui/GUIStructure.h, libshogunui/SGInterface.cpp,
	  libshogunui/SGInterface.h: implemented support for sparse seq
	  arrays (untested)
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/GUIStructure.cpp, libshogunui/GUIStructure.h,
	  libshogunui/SGInterface.cpp, octave/OctaveInterface.cpp: cleanups
	  and memory leak fixes

2009-05-22  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/LibSVMNU.cpp,
	  libshogun/classifier/svm/MKLRegression.h, libshogun/lib/Array.h,
	  libshogun/lib/Array2.h, libshogunui/GUIClassifier.cpp,
	  libshogunui/SGInterface.cpp, modular/Classifier.i: lots of
	  compile fixes (dynprog still does not work with modular IF's)

2009-05-20  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/Classifier.h,
	  libshogun/classifier/svm/LibSVMNU.cpp,
	  libshogun/classifier/svm/LibSVMNU.h,
	  libshogunui/GUIClassifier.cpp, libshogunui/GUIClassifier.h,
	  modular/Classifier.i: add NU LibSVM
	* configure: fix mmxext etc detection
	* configure: merge mplayers recent configure cpu flag detection
	* configure: fix core2 detection
	* configure: this should speedup things a lot for core2 and other
	  recent cpus - fix cpu detection logic

2009-05-18  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp: still buggy...
	* libshogun/structure/DynProg.cpp: version without loss seems to
	  work now.
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogun/structure/Plif.cpp, libshogun/structure/Plif.h,
	  libshogun/structure/PlifArray.cpp,
	  libshogun/structure/PlifArray.h, libshogun/structure/PlifBase.h,
	  libshogunui/SGInterface.cpp: first part of long transitions code
	* libshogun/lib/Array.h, libshogun/lib/Array2.h,
	  libshogun/lib/Array3.h, libshogun/structure/DynProg.cpp:
	  intermediate code ...

2009-05-18  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/Alphabet.h: fix documentation, DNA is only
	  A,C,G,T

2009-05-17  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* libshogun/lib/Array.h, libshogun/structure/DynProg.cpp,
	  libshogun/structure/DynProg.h: first changes towards a faster
	  DynProg + conflict resolution
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h:
	* libshogun/structure/DynProg.cpp, libshogun/structure/Plif.h,
	  libshogunui/GUIStructure.cpp: one bug fix related to plifs
	  prepared some extensions

2009-05-14  Soeren Sonnenburg <sonne@debian.org>

	* modular/Library.i: add memorymapped file

2009-05-08  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/MKL.cpp, libshogun/classifier/svm/MKL.h,
	  libshogun/classifier/svm/MKLClassification.cpp,
	  libshogun/classifier/svm/MKLClassification.h,
	  libshogun/classifier/svm/SVM_light.cpp: broken, but compiles at
	  least
	* libshogun/classifier/svm/MKL.cpp, libshogun/classifier/svm/MKL.h,
	  libshogun/classifier/svm/MKLClassification.cpp,
	  libshogun/classifier/svm/SVM.cpp, libshogun/classifier/svm/SVM.h:
	  further restructuring

2009-05-06  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/MKL.cpp, libshogun/classifier/svm/MKL.h,
	  libshogun/classifier/svm/MKLClassification.cpp,
	  libshogun/classifier/svm/MKLClassification.h: work in progress
	* configure: suppress error on configure

2009-05-05  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/MKL.cpp,
	  libshogun/classifier/svm/MKLClassification.cpp: back to broken
	* libshogunui/GUIClassifier.cpp: fix for one class nu svm, thanks
	  to motoaki kawanabe
	* NEWS, libshogun/classifier/svm/MKL.cpp,
	  libshogun/classifier/svm/MKL.h, libshogunui/GUIClassifier.cpp:
	  get things back to compile
	* libshogun/classifier/svm/MKL.cpp, libshogun/classifier/svm/MKL.h,
	  libshogun/classifier/svm/MKLClassification.h,
	  libshogun/classifier/svm/MKLMulticlass.h,
	  libshogun/classifier/svm/MKLRegression.cpp,
	  libshogun/classifier/svm/MKLRegression.h,
	  libshogun/classifier/svm/SVM.cpp, libshogun/classifier/svm/SVM.h,
	  libshogun/classifier/svm/SVM_light.cpp,
	  libshogun/classifier/svm/SVM_light.h,
	  libshogun/regression/svr/SVR_light.cpp,
	  libshogun/regression/svr/SVR_light.h: start cleaning up the MKL
	  mess(tm), DON'T CURRENTLY USE
	* libshogun/classifier/svm/MKL.h: start to work on generic MKL
	  class

2009-05-04  Alexander Zien <Alexander.Zien@tuebingen.mpg.de>

	* libshogun/classifier/svm/SVM_light.cpp: fixed a bug in MKL newton

2009-05-04  Soeren Sonnenburg <sonne@debian.org>

	* libshogunui/SGInterface.cpp: fix description

2009-05-02  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog: updated changelog
	* NEWS: update NEWS
	* Makefile.template: get some of the test to compile and actually
	  run on OSX :)
	* configure: don't fail when gnu sed is in path on osx
	* Makefile.template, configure: set include paths, libpaths to
	  allow testing of libshogun examples in non standard dirs, add
	  ldflags to allow custom
	* ChangeLog: updated changelog
	* Makefile, Makefile.template: prefix make tests with
	  LD_LIBRARY_PATH
	* libshogun/lib/GCArray.h: fix docu
	* libshogun/lib/Mathematics.h: workaround broke compilation here :(
	* ChangeLog: updated changelog
	* NEWS: new release tomorrow if things build under osx with this
	  workaround
	* libshogun/lib/Mathematics.h: it seems that we get clashes with
	  the standard template library...

2009-05-01  Cheng Soon Ong <chengsoon.ong@tuebingen.mpg.de>

	* libshogun/classifier/svm/SVM.h,
	  libshogun/classifier/svm/SVM_light.cpp: Count the number of times
	  beta is updated in MKL

2009-04-29  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/lib/GCArray.h, modular/Library.i: throw away operator
	  overloading and use get + set and add an example. things compile
	  now again.
	* libshogun/classifier/svm/SVM_light.cpp,
	  libshogun/classifier/svm/ssl.cpp,
	  libshogun/distributions/hmm/HMM.cpp,
	  libshogun/features/Alphabet.h,
	  libshogun/features/ImplicitWeightedSpecFeatures.h,
	  libshogun/features/SimpleFeatures.h,
	  libshogun/features/StringFeatures.h, libshogun/lib/GCArray.h,
	  libshogun/lib/Mathematics.h, libshogun/structure/DynProg.cpp,
	  libshogunui/GUIStructure.cpp: define is_infinity, is_nan,
	  is_finite in CMath and make others use it, closer to compiling
	  (GCArray still fails...)

2009-04-28  Soeren Sonnenburg <sonne@debian.org>

	* modular/Library.i: put GCArray into .i file
	* libshogun/structure/Plif.h: remove erreaneously introduced plif
	  functiosn
	* libshogun/lib/GCArray.h, libshogun/structure/DynProg.cpp,
	  libshogun/structure/Plif.cpp, libshogun/structure/Plif.h,
	  libshogunui/GUIStructure.cpp: - introduce garbage collecting
	  array (GCArray)
	  - cleanup Plifs: never ever delete[] arrays in core functions.
	  assume intial size (or size that is set using set_plif_length) is
	  correct

2009-04-26  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/lib/Mathematics.h: use isfinite everywhere as this is
	  in the C99 standard
	* Makefile.template: fix warnings on build dependencies for python
	  modular on mac
	* configure: build fixes for osx
	* configure: python extensions always have an .so suffix on *nix
	  and darwin as well

2009-04-23  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/KNN.cpp,
	  libshogun/distance/MinkowskiMetric.cpp: use test data size when
	  computing outputs in KNN

2009-04-21  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* libshogun/lib/BitString.h, libshogun/lib/Mathematics.h: minor
	  modifications and some testcode.
	* python_modular/swig_typemaps.i:

2009-04-18  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/lib/BitString.h, libshogun/lib/IndirectObject.h:
	  finally bitstring/indirect objects work together

2009-04-16  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/lib/BitString.h:
	* libshogun/lib/BitString.h: add example on how to access indirect
	  objects

2009-04-14  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/lib/IndirectObject.cpp, libshogun/lib/IndirectObject.h:
	  declare static variable in header file

2009-04-13  Soeren Sonnenburg <sonne@debian.org>

	* modular/Structure.i: apply nd-array typemap
	* libshogun/lib/IndirectObject.cpp, libshogun/lib/IndirectObject.h:
	  create an indirect object - allows for quicksort etc only
	  modifying an index list
	* python_modular/swig_typemaps.i: input typemap for N-dimensional
	  python arrays
	* configure: fix syntax errors in script

2009-04-12  Soeren Sonnenburg <sonne@debian.org>

	* .r-install.sh, Makefile, Makefile.template, configure: potential
	  install fixes for OSX

2009-04-11  Soeren Sonnenburg <sonne@debian.org>

	* NEWS: improve tutorial

2009-04-10  Soeren Sonnenburg <sonne@debian.org>

	* configure, libshogun/classifier/svm/libocas.cpp,
	  libshogun/classifier/svm/libocas_common.h,
	  libshogun/classifier/svm/qpssvmlib.cpp: use -funroll-loops and
	  CMath::{max,min,abs}
	* libshogun/lib/BitString.h, libshogun/lib/DynInt.h,
	  libshogun/lib/Mathematics.h: move displaybits to lib/Mathematics,
	  further work on bitstring

2009-04-08  Soeren Sonnenburg <sonne@debian.org>

	* configure, libshogun/lib/lapack.cpp: compile fixes for darwin
	* NEWS: update NEWS

2009-04-08  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* libshogunui/SGInterface.cpp: more memleaks fixed
	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/GUIStructure.cpp, libshogunui/GUIStructure.h,
	  libshogunui/SGInterface.cpp: fixed some memory leaks

2009-04-07  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/StringFeatures.h: compile fixes for modular
	  interfaces

2009-04-05  Soeren Sonnenburg <sonne@debian.org>

	* configure: don't set -undefined error on OSX as this conflicts
	  with R and other builds
	* libshogun/features/StringFeatures.h, libshogun/lib/BitString.h:
	  add bitstring to efficiently represent huge strings

2009-04-03  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/StringFeatures.h: provide function to
	  translate embedded bits back to string

2009-04-02  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/StringFeatures.h: speed up embedding
	* libshogun/features/Alphabet.h,
	  libshogun/features/StringFeatures.h: add inplace remapping for
	  fastq files
	* libshogun/features/StringFeatures.h, libshogun/lib/DynInt.h: fix
	  bitshift ops

2009-04-01  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/lib/Time.cpp: time outputs should use SG_PRINT
	* libshogun/features/Alphabet.cpp, libshogun/features/Alphabet.h,
	  libshogun/features/StringFeatures.h, libshogun/lib/DynInt.h: add
	  dynamic size integers and support for them in
	  stringfeatures/alphabet
	* libshogun/features/StringFeatures.h: fast fasta file reading
	* libshogun/features/Alphabet.cpp, libshogun/features/Alphabet.h,
	  libshogun/features/StringFeatures.h,
	  libshogun/lib/MemoryMappedFile.h, libshogun/lib/SimpleFile.h:
	  fast reading of fastq files

2009-03-31  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, libshogun/lib/Mathematics.h: always use the central element
	  as pivot element. it speeds up things when the array is already
	  sorted.

2009-03-30  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/lib/Mathematics.h: - speed up qsort by factor of 2
	  - also provide convenience function for parallel qsort, to be
	  called like CMath::parallel_qsort_index<uint64_t>(a, b, LEN,
	  num_threads), gets quite some further speedup here

2009-03-27  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, libshogun/base/Parallel.h, libshogun/base/SGObject.h,
	  libshogun/base/Version.h, libshogun/classifier/svm/SVMSGD.h,
	  libshogun/classifier/svm/Tron.h,
	  libshogun/classifier/svm/gmnplib.h,
	  libshogun/classifier/svm/gnpplib.h,
	  libshogun/classifier/svm/qpbsvmlib.h,
	  libshogun/distributions/hmm/GHMM.h,
	  libshogun/distributions/hmm/LinearHMM.h,
	  libshogun/evaluation/PerformanceMeasures.cpp,
	  libshogun/evaluation/PerformanceMeasures.h,
	  libshogun/features/Alphabet.h,
	  libshogun/features/AttributeFeatures.h,
	  libshogun/features/Labels.h,
	  libshogun/features/MindyGramFeatures.h,
	  libshogun/kernel/OligoStringKernel.h, libshogun/lib/Array.h,
	  libshogun/lib/Array2.h, libshogun/lib/Array3.h,
	  libshogun/lib/Cache.h, libshogun/lib/Cplex.h,
	  libshogun/lib/DynamicArray.h, libshogun/lib/File.h,
	  libshogun/lib/List.h, libshogun/lib/Signal.h,
	  libshogun/lib/SimpleFile.h, libshogun/lib/Time.h,
	  libshogun/lib/Trie.h, libshogun/structure/DynProg.h,
	  libshogun/structure/Plif.h, modular/Evaluation.i: - Make sure
	  that all destructors are declared virtual.
	  - get_name function was undefined in Evaluation causing the
	  PerformanceMeasures class to be defunct.

2009-03-23  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog, NEWS: updated changelog

2009-03-22  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/Alphabet.h,
	  libshogun/features/SimpleFeatures.h,
	  libshogun/features/SparseFeatures.h,
	  libshogun/features/StringFeatures.h, libshogun/lib/Mathematics.h,
	  libshogun/lib/common.h, modular/Features.i,
	  python_modular/swig_typemaps.i: long double can be 96 or 128 bits
	  so name it floatmax_t
	* libshogunui/GUIClassifier.cpp: fix norm printing
	* .authors, .r-install.sh, AUTHORS, NEWS,
	  libshogun/base/Parallel.h, libshogun/base/SGObject.cpp,
	  libshogun/base/SGObject.h, libshogun/base/Version.h,
	  libshogun/classifier/Classifier.cpp,
	  libshogun/classifier/Classifier.h, libshogun/classifier/KNN.cpp,
	  libshogun/classifier/KNN.h,
	  libshogun/classifier/KernelPerceptron.cpp,
	  libshogun/classifier/KernelPerceptron.h,
	  libshogun/classifier/LDA.cpp, libshogun/classifier/LDA.h,
	  libshogun/classifier/LPBoost.cpp, libshogun/classifier/LPBoost.h,
	  libshogun/classifier/LPM.cpp, libshogun/classifier/LPM.h,
	  libshogun/classifier/LinearClassifier.h,
	  libshogun/classifier/Perceptron.cpp,
	  libshogun/classifier/Perceptron.h,
	  libshogun/classifier/PluginEstimate.h,
	  libshogun/classifier/SubGradientLPM.cpp,
	  libshogun/classifier/SubGradientLPM.h,
	  libshogun/classifier/svm/CPLEXSVM.cpp,
	  libshogun/classifier/svm/CPLEXSVM.h,
	  libshogun/classifier/svm/GMNPSVM.h,
	  libshogun/classifier/svm/GNPPSVM.h,
	  libshogun/classifier/svm/GPBTSVM.cpp,
	  libshogun/classifier/svm/GPBTSVM.h,
	  libshogun/classifier/svm/LibLinear.cpp,
	  libshogun/classifier/svm/LibLinear.h,
	  libshogun/classifier/svm/LibSVM.cpp,
	  libshogun/classifier/svm/LibSVM.h,
	  libshogun/classifier/svm/LibSVMMultiClass.cpp,
	  libshogun/classifier/svm/LibSVMMultiClass.h,
	  libshogun/classifier/svm/LibSVMOneClass.cpp,
	  libshogun/classifier/svm/LibSVMOneClass.h,
	  libshogun/classifier/svm/MPDSVM.cpp,
	  libshogun/classifier/svm/MPDSVM.h,
	  libshogun/classifier/svm/MultiClassSVM.cpp,
	  libshogun/classifier/svm/MultiClassSVM.h,
	  libshogun/classifier/svm/SVM.cpp, libshogun/classifier/svm/SVM.h,
	  libshogun/classifier/svm/SVMLin.cpp,
	  libshogun/classifier/svm/SVMLin.h,
	  libshogun/classifier/svm/SVMOcas.cpp,
	  libshogun/classifier/svm/SVMOcas.h,
	  libshogun/classifier/svm/SVMSGD.h,
	  libshogun/classifier/svm/SVM_libsvm.cpp,
	  libshogun/classifier/svm/SVM_libsvm.h,
	  libshogun/classifier/svm/SVM_light.cpp,
	  libshogun/classifier/svm/SVM_light.h,
	  libshogun/classifier/svm/SVM_linear.cpp,
	  libshogun/classifier/svm/SVM_linear.h,
	  libshogun/classifier/svm/SubGradientSVM.cpp,
	  libshogun/classifier/svm/SubGradientSVM.h,
	  libshogun/classifier/svm/Tron.h,
	  libshogun/classifier/svm/WDSVMOcas.cpp,
	  libshogun/classifier/svm/WDSVMOcas.h,
	  libshogun/classifier/svm/gmnplib.h,
	  libshogun/classifier/svm/gmnpmkl.h,
	  libshogun/classifier/svm/gnpplib.h,
	  libshogun/classifier/svm/gpdt.cpp,
	  libshogun/classifier/svm/gpdt.h,
	  libshogun/classifier/svm/gpdtsolve.cpp,
	  libshogun/classifier/svm/gpdtsolve.h,
	  libshogun/classifier/svm/libocas.cpp,
	  libshogun/classifier/svm/libocas.h,
	  libshogun/classifier/svm/pr_loqo.cpp,
	  libshogun/classifier/svm/pr_loqo.h,
	  libshogun/classifier/svm/qpbsvmlib.cpp,
	  libshogun/classifier/svm/qpbsvmlib.h,
	  libshogun/classifier/svm/ssl.h,
	  libshogun/clustering/Hierarchical.cpp,
	  libshogun/clustering/Hierarchical.h,
	  libshogun/clustering/KMeans.cpp, libshogun/clustering/KMeans.h,
	  libshogun/distance/BrayCurtisDistance.cpp,
	  libshogun/distance/BrayCurtisDistance.h,
	  libshogun/distance/CanberraMetric.cpp,
	  libshogun/distance/CanberraMetric.h,
	  libshogun/distance/CanberraWordDistance.cpp,
	  libshogun/distance/CanberraWordDistance.h,
	  libshogun/distance/ChebyshewMetric.cpp,
	  libshogun/distance/ChebyshewMetric.h,
	  libshogun/distance/ChiSquareDistance.cpp,
	  libshogun/distance/ChiSquareDistance.h,
	  libshogun/distance/CosineDistance.cpp,
	  libshogun/distance/CosineDistance.h,
	  libshogun/distance/Distance.cpp, libshogun/distance/Distance.h,
	  libshogun/distance/DistanceMachine.cpp,
	  libshogun/distance/DistanceMachine.h,
	  libshogun/distance/EuclidianDistance.cpp,
	  libshogun/distance/EuclidianDistance.h,
	  libshogun/distance/GeodesicMetric.cpp,
	  libshogun/distance/GeodesicMetric.h,
	  libshogun/distance/HammingWordDistance.cpp,
	  libshogun/distance/HammingWordDistance.h,
	  libshogun/distance/JensenMetric.cpp,
	  libshogun/distance/JensenMetric.h,
	  libshogun/distance/ManhattanMetric.cpp,
	  libshogun/distance/ManhattanMetric.h,
	  libshogun/distance/ManhattanWordDistance.cpp,
	  libshogun/distance/ManhattanWordDistance.h,
	  libshogun/distance/MinkowskiMetric.cpp,
	  libshogun/distance/MinkowskiMetric.h,
	  libshogun/distance/RealDistance.h,
	  libshogun/distance/SimpleDistance.h,
	  libshogun/distance/SparseDistance.h,
	  libshogun/distance/SparseEuclidianDistance.cpp,
	  libshogun/distance/SparseEuclidianDistance.h,
	  libshogun/distance/StringDistance.h,
	  libshogun/distance/TanimotoDistance.cpp,
	  libshogun/distance/TanimotoDistance.h,
	  libshogun/distributions/Distribution.cpp,
	  libshogun/distributions/Distribution.h,
	  libshogun/distributions/histogram/Histogram.cpp,
	  libshogun/distributions/histogram/Histogram.h,
	  libshogun/distributions/hmm/GHMM.cpp,
	  libshogun/distributions/hmm/GHMM.h,
	  libshogun/distributions/hmm/HMM.cpp,
	  libshogun/distributions/hmm/HMM.h,
	  libshogun/distributions/hmm/LinearHMM.cpp,
	  libshogun/distributions/hmm/LinearHMM.h,
	  libshogun/evaluation/PerformanceMeasures.cpp,
	  libshogun/evaluation/PerformanceMeasures.h,
	  libshogun/features/Alphabet.cpp, libshogun/features/Alphabet.h,
	  libshogun/features/AttributeFeatures.h,
	  libshogun/features/ByteFeatures.cpp,
	  libshogun/features/ByteFeatures.h,
	  libshogun/features/CharFeatures.cpp,
	  libshogun/features/CharFeatures.h,
	  libshogun/features/CombinedDotFeatures.h,
	  libshogun/features/CombinedFeatures.cpp,
	  libshogun/features/CombinedFeatures.h,
	  libshogun/features/DotFeatures.cpp,
	  libshogun/features/DotFeatures.h,
	  libshogun/features/DummyFeatures.h,
	  libshogun/features/ExplicitSpecFeatures.h,
	  libshogun/features/FKFeatures.cpp,
	  libshogun/features/FKFeatures.h, libshogun/features/Features.cpp,
	  libshogun/features/Features.h,
	  libshogun/features/ImplicitWeightedSpecFeatures.h,
	  libshogun/features/IntFeatures.cpp,
	  libshogun/features/IntFeatures.h, libshogun/features/Labels.cpp,
	  libshogun/features/Labels.h,
	  libshogun/features/MindyGramFeatures.cpp,
	  libshogun/features/MindyGramFeatures.h,
	  libshogun/features/RealFeatures.cpp,
	  libshogun/features/RealFeatures.h,
	  libshogun/features/RealFileFeatures.cpp,
	  libshogun/features/RealFileFeatures.h,
	  libshogun/features/ShortFeatures.cpp,
	  libshogun/features/ShortFeatures.h,
	  libshogun/features/ShortRealFeatures.cpp,
	  libshogun/features/ShortRealFeatures.h,
	  libshogun/features/SimpleFeatures.h,
	  libshogun/features/SparseFeatures.h,
	  libshogun/features/StringFeatures.cpp,
	  libshogun/features/StringFeatures.h,
	  libshogun/features/TOPFeatures.cpp,
	  libshogun/features/TOPFeatures.h,
	  libshogun/features/WDFeatures.h,
	  libshogun/features/WordFeatures.cpp,
	  libshogun/features/WordFeatures.h,
	  libshogun/kernel/AUCKernel.cpp, libshogun/kernel/AUCKernel.h,
	  libshogun/kernel/AvgDiagKernelNormalizer.h,
	  libshogun/kernel/Chi2Kernel.cpp, libshogun/kernel/Chi2Kernel.h,
	  libshogun/kernel/CombinedKernel.cpp,
	  libshogun/kernel/CombinedKernel.h,
	  libshogun/kernel/CommUlongStringKernel.cpp,
	  libshogun/kernel/CommUlongStringKernel.h,
	  libshogun/kernel/CommWordStringKernel.cpp,
	  libshogun/kernel/CommWordStringKernel.h,
	  libshogun/kernel/ConstKernel.cpp, libshogun/kernel/ConstKernel.h,
	  libshogun/kernel/CustomKernel.cpp,
	  libshogun/kernel/CustomKernel.h, libshogun/kernel/DiagKernel.cpp,
	  libshogun/kernel/DiagKernel.h,
	  libshogun/kernel/DiceKernelNormalizer.h,
	  libshogun/kernel/DistanceKernel.cpp,
	  libshogun/kernel/DistanceKernel.h,
	  libshogun/kernel/FirstElementKernelNormalizer.h,
	  libshogun/kernel/FixedDegreeStringKernel.cpp,
	  libshogun/kernel/FixedDegreeStringKernel.h,
	  libshogun/kernel/GaussianKernel.cpp,
	  libshogun/kernel/GaussianKernel.h,
	  libshogun/kernel/GaussianShiftKernel.cpp,
	  libshogun/kernel/GaussianShiftKernel.h,
	  libshogun/kernel/GaussianShortRealKernel.cpp,
	  libshogun/kernel/GaussianShortRealKernel.h,
	  libshogun/kernel/HistogramWordStringKernel.cpp,
	  libshogun/kernel/HistogramWordStringKernel.h,
	  libshogun/kernel/IdentityKernelNormalizer.h,
	  libshogun/kernel/Kernel.cpp, libshogun/kernel/Kernel.h,
	  libshogun/kernel/KernelMachine.cpp,
	  libshogun/kernel/KernelMachine.h,
	  libshogun/kernel/KernelNormalizer.h,
	  libshogun/kernel/LinearByteKernel.cpp,
	  libshogun/kernel/LinearByteKernel.h,
	  libshogun/kernel/LinearKernel.cpp,
	  libshogun/kernel/LinearKernel.h,
	  libshogun/kernel/LinearStringKernel.cpp,
	  libshogun/kernel/LinearStringKernel.h,
	  libshogun/kernel/LinearWordKernel.cpp,
	  libshogun/kernel/LinearWordKernel.h,
	  libshogun/kernel/LocalAlignmentStringKernel.h,
	  libshogun/kernel/LocalityImprovedStringKernel.cpp,
	  libshogun/kernel/LocalityImprovedStringKernel.h,
	  libshogun/kernel/MatchWordStringKernel.cpp,
	  libshogun/kernel/MatchWordStringKernel.h,
	  libshogun/kernel/MindyGramKernel.cpp,
	  libshogun/kernel/MindyGramKernel.h,
	  libshogun/kernel/OligoKernel.cpp, libshogun/kernel/OligoKernel.h,
	  libshogun/kernel/OligoStringKernel.cpp,
	  libshogun/kernel/OligoStringKernel.h,
	  libshogun/kernel/PolyKernel.cpp, libshogun/kernel/PolyKernel.h,
	  libshogun/kernel/PolyMatchStringKernel.cpp,
	  libshogun/kernel/PolyMatchStringKernel.h,
	  libshogun/kernel/PolyMatchWordStringKernel.cpp,
	  libshogun/kernel/PolyMatchWordStringKernel.h,
	  libshogun/kernel/PyramidChi2.cpp, libshogun/kernel/PyramidChi2.h,
	  libshogun/kernel/SalzbergWordStringKernel.cpp,
	  libshogun/kernel/SalzbergWordStringKernel.h,
	  libshogun/kernel/SigmoidKernel.cpp,
	  libshogun/kernel/SigmoidKernel.h,
	  libshogun/kernel/SimpleKernel.h,
	  libshogun/kernel/SimpleLocalityImprovedStringKernel.cpp,
	  libshogun/kernel/SimpleLocalityImprovedStringKernel.h,
	  libshogun/kernel/SparseGaussianKernel.cpp,
	  libshogun/kernel/SparseGaussianKernel.h,
	  libshogun/kernel/SparseKernel.h,
	  libshogun/kernel/SparseLinearKernel.cpp,
	  libshogun/kernel/SparseLinearKernel.h,
	  libshogun/kernel/SparsePolyKernel.cpp,
	  libshogun/kernel/SparsePolyKernel.h,
	  libshogun/kernel/SqrtDiagKernelNormalizer.h,
	  libshogun/kernel/StringKernel.h,
	  libshogun/kernel/TanimotoKernelNormalizer.h,
	  libshogun/kernel/TensorProductPairKernel.cpp,
	  libshogun/kernel/TensorProductPairKernel.h,
	  libshogun/kernel/WeightedCommWordStringKernel.cpp,
	  libshogun/kernel/WeightedCommWordStringKernel.h,
	  libshogun/kernel/WeightedDegreePositionStringKernel.cpp,
	  libshogun/kernel/WeightedDegreePositionStringKernel.h,
	  libshogun/kernel/WeightedDegreeStringKernel.cpp,
	  libshogun/kernel/WeightedDegreeStringKernel.h,
	  libshogun/lib/Array.h, libshogun/lib/Array2.h,
	  libshogun/lib/Array3.h, libshogun/lib/Cache.h,
	  libshogun/lib/Cplex.h, libshogun/lib/DynamicArray.h,
	  libshogun/lib/File.h, libshogun/lib/List.h,
	  libshogun/lib/Mathematics.h, libshogun/lib/ShogunException.h,
	  libshogun/lib/Signal.h, libshogun/lib/SimpleFile.h,
	  libshogun/lib/Time.h, libshogun/lib/Trie.h,
	  libshogun/lib/common.h, libshogun/lib/io.cpp, libshogun/lib/io.h,
	  libshogun/lib/lapack.h, libshogun/preproc/LogPlusOne.cpp,
	  libshogun/preproc/LogPlusOne.h,
	  libshogun/preproc/NormDerivativeLem3.cpp,
	  libshogun/preproc/NormDerivativeLem3.h,
	  libshogun/preproc/NormOne.cpp, libshogun/preproc/NormOne.h,
	  libshogun/preproc/PCACut.cpp, libshogun/preproc/PCACut.h,
	  libshogun/preproc/PreProc.cpp, libshogun/preproc/PreProc.h,
	  libshogun/preproc/PruneVarSubMean.cpp,
	  libshogun/preproc/PruneVarSubMean.h,
	  libshogun/preproc/SimplePreProc.h,
	  libshogun/preproc/SortUlongString.cpp,
	  libshogun/preproc/SortUlongString.h,
	  libshogun/preproc/SortWordString.cpp,
	  libshogun/preproc/SortWordString.h,
	  libshogun/preproc/SparsePreProc.h,
	  libshogun/preproc/StringPreProc.h, libshogun/regression/KRR.cpp,
	  libshogun/regression/KRR.h, libshogun/regression/Regression.h,
	  libshogun/regression/svr/LibSVR.cpp,
	  libshogun/regression/svr/LibSVR.h,
	  libshogun/regression/svr/SVR_light.cpp,
	  libshogun/regression/svr/SVR_light.h,
	  libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogun/structure/Plif.cpp, libshogun/structure/Plif.h,
	  libshogun/structure/PlifArray.cpp,
	  libshogun/structure/PlifArray.h, libshogun/structure/PlifBase.h,
	  libshogunui/GUIClassifier.cpp, libshogunui/GUIDistance.cpp,
	  libshogunui/GUIFeatures.cpp, libshogunui/GUIFeatures.h,
	  libshogunui/GUIKernel.cpp, libshogunui/GUIPreProc.cpp,
	  libshogunui/SGInterface.cpp, modular/Features.i,
	  modular/Kernel.i, octave_modular/swig_typemaps.i,
	  python_modular/swig_typemaps.i: - Support all data types from
	  python_modular: dense, scipy-sparse
	  csc_sparse matrices and strings of type bool, char,
	  (u)int{8,16,32,64},
	  float{32,64,96}. In addition, individual vectors/strings can now
	  be
	  obtained and even changed. See
	  examples/python_modular/features_*.py
	  for examples.
	  - AUC maximization now works with arbitrary kernel SVMs.
	  - Documentation updates, many examples have been polished.
	  - Slightly speedup Oligo kernel.
	  - Fix reading strings from directory (f.load_from_directory()).
	  - Update copyright to 2009.
	  - Remove {Char,Short,Word,Int,Real}Features and only ever use the
	  templated SimpleFeatures.
	  - Split up examples in examples/python_modular to separate files.
	  - Now use s.set_features(strs) instead of
	  s.set_string_features(strs)
	  to set string features.
	  - The meaning of the width parameter for the Oligo Kernel
	  changed, the
	  OligoKernel has been renamed to OligoStringKernel.

2009-03-11  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/Labels.cpp: equivalant logic transformation

2009-03-10  Soeren Sonnenburg <sonne@debian.org>

	* .relpath.py, Makefile.template, modular/Classifier.i: compile
	  fixes / make installation path relative

2009-03-08  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog: updated changelog
	* ChangeLog: updated changelog
	* NEWS, libshogun/classifier/Classifier.h,
	  libshogun/classifier/KNN.h,
	  libshogun/classifier/KernelPerceptron.h,
	  libshogun/classifier/LDA.h, libshogun/classifier/LPBoost.h,
	  libshogun/classifier/LPM.h,
	  libshogun/classifier/LinearClassifier.h,
	  libshogun/classifier/Perceptron.h,
	  libshogun/classifier/PluginEstimate.cpp,
	  libshogun/classifier/PluginEstimate.h,
	  libshogun/classifier/SubGradientLPM.h,
	  libshogun/classifier/svm/GMNPSVM.h,
	  libshogun/classifier/svm/gmnplib.h,
	  libshogun/classifier/svm/gmnpmkl.h,
	  libshogun/classifier/svm/gnpplib.h,
	  libshogun/distance/DistanceMachine.h,
	  libshogun/features/AttributeFeatures.h,
	  libshogun/kernel/KernelMachine.h, libshogun/lib/Cplex.h: update
	  documentation

2009-03-05  Soeren Sonnenburg <sonne@debian.org>

	* configure, libshogun/base/SGObject.h: whitespace code cleanup +
	  docu
	* .authors, configure, libshogunui/GUICommands.h,
	  libshogunui/SGInterface.cpp, libshogunui/SGInterface.h,
	  matlab/MatlabInterface.cpp, matlab/MatlabInterface.h,
	  octave/OctaveInterface.cpp, octave/OctaveInterface.h,
	  python/PythonInterface.cpp, python/PythonInterface.h,
	  r/RInterface.cpp, r/RInterface.h: add chris to authors and get
	  python,... to R interface to work

2009-03-05  Christian Widmer <cwidmer@tuebingen.mpg.de>

	* configure, libshogun/base/SGObject.cpp,
	  libshogun/base/SGObject.h, libshogun/classifier/svm/SVM_libsvm.h,
	  r/RInterface.h: first piece of serialization support ported to a
	  non-ancient version of shogun, default=off
	* configure: checks for boost_serialization

2009-03-04  Soeren Sonnenburg <sonne@debian.org>

	* matlab/MatlabInterface.cpp, octave/OctaveInterface.cpp,
	  octave/OctaveInterface.h, python/PythonInterface.cpp,
	  r/RInterface.cpp: run octave embedded quietly
	* octave/OctaveInterface.cpp: x to octave now fully working for x
	  in r,python and I guess even matlab

2009-03-03  Soeren Sonnenburg <sonne@debian.org>

	* configure, libshogun/features/RealFeatures.h: -fvirtual seems to
	  break things
	* configure, libshogun/kernel/CombinedKernel.cpp,
	  libshogun/kernel/CombinedKernel.h,
	  libshogun/lib/ShogunException.cpp,
	  libshogun/lib/ShogunException.h, modular/Kernel.i: add function
	  to get sub kernel weights and fix clash in exceptions by
	  introducing a virtual functions as suggested in
	  http://sourceforge.net/mailarchive/message.php?msg_name=48DF377F.2050407%40salilab.org
	* Makefile.template, configure, libshogunui/GUICommands.h,
	  libshogunui/SGInterface.cpp, libshogunui/SGInterface.h,
	  matlab/MatlabInterface.cpp, matlab/MatlabInterface.h,
	  octave/OctaveInterface.cpp, octave/OctaveInterface.h,
	  python/PythonInterface.cpp, python/PythonInterface.h,
	  r/RInterface.cpp, r/RInterface.h: python,... to octave

2009-03-02  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, cmdline/CmdLineInterface.cpp, cmdline/CmdLineInterface.h,
	  libshogunui/SGInterface.cpp, libshogunui/SGInterface.h,
	  matlab/MatlabInterface.cpp, matlab/MatlabInterface.h,
	  octave/OctaveInterface.cpp, octave/OctaveInterface.h,
	  python/PythonInterface.cpp, python/PythonInterface.h,
	  r/RInterface.cpp, r/RInterface.h: implement dummy attribute
	  struct hooks, fix examples

2009-03-01  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/AttributeFeatures.cpp,
	  libshogun/features/AttributeFeatures.h,
	  libshogun/features/CombinedFeatures.h,
	  libshogun/lib/DynamicArray.h, libshogunui/SGInterface.h,
	  modular/Features.i: add attribute features
	* libshogun/kernel/Kernel.cpp: fix a bug in get_kernel_matrix
	* libshogun/classifier/svm/SVM.cpp, libshogun/kernel/Kernel.cpp:
	  allow kernels with NULL as features
	* configure: disable elwms when interfaces are given
	* libshogun/features/CombinedFeatures.cpp,
	  libshogun/features/CombinedFeatures.h,
	  libshogun/kernel/CombinedKernel.cpp,
	  libshogun/kernel/CombinedKernel.h,
	  libshogun/kernel/CustomKernel.h, libshogun/kernel/Kernel.h,
	  libshogun/regression/svr/SVR_light.cpp,
	  libshogunui/GUIKernel.cpp, matlab/MatlabInterface.cpp: fix error
	  printing in matlab, combined kernel needs an init when custom
	  features are used
	* Makefile.template, cmdline/CmdLineInterface.cpp, elwms/Makefile:
	  don't set verbosity in examples, fix compilation error in cmdline
	  if and remove elwms Makefile
	* .r-install.sh, INSTALL, Makefile.template, NEWS, configure,
	  elwms/Makefile, elwms/elwms.cpp, libshogun/base/SGObject.h,
	  libshogun/features/StringFeatures.h, libshogun/kernel/Kernel.cpp,
	  libshogunui/SGInterface.cpp, libshogunui/SGInterface.h,
	  matlab/MatlabInterface.cpp, octave/OctaveInterface.cpp,
	  python/PythonInterface.cpp, r/RInterface.cpp: - rename elwms
	  interface from sg to elwms (to avoid naming conflicts with other
	  interfaces) and properly integrate it into ./configure and the
	  standard install procedure
	  - update NEWS and INSTALL accordingly and support the whole
	  spectrum of types from scalars to strings in translation
	* libshogun/base/Version.h: 2008 -> 2009
	* octave/OctaveInterface.cpp: also accept scalars as vec/matrix
	* elwms/elwms.cpp, matlab/MatlabInterface.cpp,
	  octave/OctaveInterface.cpp, python/PythonInterface.cpp,
	  r/RInterface.cpp: - don't actually print anything on SG_ERROR (as
	  it throws an exception anyway - so only print the error then)
	  - fix a clash in R and octave error function (in elwms
	  interface), also don't require result to be a dictionary, make it
	  a tuple

2009-02-28  Soeren Sonnenburg <sonne@debian.org>

	* configure, elwms/Makefile, matlab/MatlabInterface.cpp,
	  r/RInterface.cpp: dynamically load the python libs to global
	  context
	  (since matlab/R don't load them automagically they fail due to
	  missing
	  symbols), do at least try to get the python version right
	* elwms/Makefile, elwms/elwms.cpp, libshogunui/SGInterface.cpp,
	  libshogunui/SGInterface.h, matlab/MatlabInterface.cpp,
	  matlab/MatlabInterface.h, octave/OctaveInterface.cpp,
	  octave/OctaveInterface.h, python/PythonInterface.cpp,
	  python/PythonInterface.h, r/RInterface.cpp, r/RInterface.h: get
	  the run_python command to work in r,octave and matlab, also
	  release memory of converted matrices
	* libshogunui/SGInterface.cpp, libshogunui/SGInterface.h,
	  octave/OctaveInterface.cpp, python/PythonInterface.cpp,
	  python/PythonInterface.h: octave to python translator now
	  functional

2009-02-27  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, elwms/Makefile, libshogunui/GUICommands.h,
	  libshogunui/SGInterface.cpp, libshogunui/SGInterface.h,
	  octave/OctaveInterface.cpp, octave/OctaveInterface.h: add
	  run_python command to the eierlegendewollmilchsau which will
	  translate octave variables into python variables, execute python
	  code and translate the variables back into octave *currently
	  returning a matrix works*
	* NEWS, elwms, elwms/Makefile, elwms/elwms.cpp,
	  libshogunui/SGInterface.cpp, octave/OctaveInterface.h: -
	  *taddaaa* I hereby proudly present THE EIERLEGENDEWOLLMILCHSAU
	  (elwms), that is a *single file* that constitutes a interfaces to
	  python, octave, R and matlab all at the same time - yes now one
	  shoe^H^H^H^Hfile that fits all.
	  - minor warning fixes in interface, update NEWS
	* libshogun/classifier/Classifier.cpp,
	  libshogun/classifier/svm/MultiClassSVM.cpp,
	  libshogun/classifier/svm/SVM.cpp,
	  libshogun/classifier/svm/gmnpmkl.cpp,
	  libshogun/kernel/CombinedKernel.cpp,
	  libshogun/kernel/CombinedKernel.h,
	  libshogun/kernel/CustomKernel.cpp,
	  libshogun/kernel/CustomKernel.h, libshogun/kernel/Kernel.h,
	  libshogun/kernel/KernelMachine.cpp: sole combined kernel based on
	  custom kernels no longer requires features nor init

2009-02-27  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp: fixed compile errors in debug
	  code

2009-02-27  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp, libshogunui/SGInterface.cpp: --
	  bugfix: precompute stop codons for precomp interface as well
	* libshogunui/SGInterface.cpp: - double declaration removed
	* libshogun/structure/DynProg.cpp, libshogunui/SGInterface.cpp: -
	  some SG_PRINTs removed
	  - changed function init_content_svm_value_array such that all
	  arguments are now passed,
	  instead of using member variables

2009-02-26  Soeren Sonnenburg <sonne@debian.org>

	* octave/OctaveInterface.cpp: fix size?
	* octave/OctaveInterface.cpp, octave/OctaveInterface.h: potentially
	  get nd arrays to work
	* Makefile.template: fix install

2009-02-25  Soeren Sonnenburg <sonne@debian.org>

	* configure: this adds checks to configure that does not allow
	  building using an illegal
	  config, e.g. --interfaces=python_modular will trigger an error
	  since libshogun
	  is missing, --interfaces=libshogun,python_modular will work
	  nicely etc
	* Makefile.template: always call ldconfig and create symlinks to
	  soname/library name manually
	* NEWS, libshogunui/GUIClassifier.cpp, libshogunui/GUIKernel.cpp,
	  libshogunui/GUIKernel.h, libshogunui/SGInterface.cpp,
	  libshogunui/SGInterface.h: this changes the syntax of the custom
	  kernel. a simple
	  
	  sg('set_kernel', 'CUSTOM', km, 'FULL2DIAG');
	  
	  is enough now too in static interfaces, no features nor init
	  required

2009-02-24  Soeren Sonnenburg <sonne@debian.org>

	* .generate_link_dependencies.py, Makefile.template, configure:
	  configure / make should work now when libshogun / libshogunui are
	  installed but the local libshogun/libshogunui directories are
	  missing
	* libshogun/base/Parallel.cpp, libshogun/base/Parallel.h,
	  libshogun/base/SGObject.cpp, libshogun/base/Version.cpp,
	  libshogun/base/Version.h, libshogun/base/init.cpp,
	  libshogun/classifier/svm/SVM.cpp, libshogun/lib/Array.h,
	  libshogun/lib/Array2.h, libshogun/lib/Array3.h,
	  libshogun/lib/Cache.h, libshogun/lib/Cplex.cpp,
	  libshogun/lib/Cplex.h, libshogun/lib/File.cpp,
	  libshogun/lib/File.h, libshogun/lib/List.h,
	  libshogun/lib/Mathematics.cpp, libshogun/lib/ShogunException.cpp,
	  libshogun/lib/ShogunException.h, libshogun/lib/Signal.cpp,
	  libshogun/lib/SimpleFile.h, libshogun/lib/Time.cpp,
	  libshogun/lib/Time.h, libshogun/lib/Trie.cpp,
	  libshogun/lib/Trie.h, libshogun/lib/io.cpp, libshogun/lib/io.h,
	  libshogun/lib/lapack.cpp, libshogun/lib/lapack.h,
	  libshogun/lib/memory.cpp, libshogun/lib/memory.h: update
	  copyright to 2009 in lib and base
	* libshogun/base/SGObject.h: ifdef pthread mutex handling
	* Makefile, configure: test if variables are set and then uninstall
	  things, undo changes in configure

2009-02-24  Cheng Soon Ong <chengsoon.ong@tuebingen.mpg.de>

	* Makefile, Makefile.template, configure: Hack for cleaning up
	  installed shogun, make uninstall

2009-02-24  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/kernel/CombinedKernel.cpp: this should not skip over
	  custom kernels on init (so users don't need to assign
	  features to custom kernels in combined features)

2009-02-23  Soeren Sonnenburg <sonne@debian.org>

	* configure: fix an error in configure that always de-selected
	  matlab
	* configure: potentially fix a compile error for people that have
	  libshogun headers installed in the same path as they are
	  installing to
	* libshogun/base/SGObject.h, libshogun/kernel/CombinedKernel.cpp,
	  libshogun/kernel/CommWordStringKernel.cpp,
	  libshogun/kernel/CommWordStringKernel.h,
	  libshogun/kernel/Kernel.cpp: fix a tricky to trigger tricky to
	  find bug occurring only with num_threads > 1 linadd enabled
	  kernels in the combined kernel: reference counts require mutex
	  locking to avoid accidental destruction of objects.
	* python_modular/swig_typemaps.i: removed some crappy lines
	  introducing a compile failure in python_modular
	* python_modular/swig_typemaps.i: work on sparse features for
	  python
	* README.developer, README.soname: minor reformatting
	* INSTALL, README.developer, README.soname, libshogun/base/init.h,
	  libshogun/classifier/svm/SVM_light.h: polish documentation

2009-02-22  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, modular/AUCKernel.i, modular/Alphabet.i, modular/Array.i,
	  modular/Array2.i, modular/Array3.i,
	  modular/AvgDiagKernelNormalizer.i, modular/BrayCurtisDistance.i,
	  modular/ByteFeatures.i, modular/Cache.i,
	  modular/CanberraMetric.i, modular/CanberraWordDistance.i,
	  modular/CharFeatures.i, modular/ChebyshewMetric.i,
	  modular/Chi2Kernel.i, modular/ChiSquareDistance.i,
	  modular/Classifier.i, modular/Clustering.i,
	  modular/CombinedDotFeatures.i, modular/CombinedFeatures.i,
	  modular/CombinedKernel.i, modular/CommUlongStringKernel.i,
	  modular/CommWordStringKernel.i, modular/ConstKernel.i,
	  modular/CosineDistance.i, modular/CustomKernel.i,
	  modular/DiagKernel.i, modular/DiceKernelNormalizer.i,
	  modular/Distance.i, modular/DistanceKernel.i,
	  modular/DistanceMachine.i, modular/Distribution.i,
	  modular/DotFeatures.i, modular/DummyFeatures.i,
	  modular/DynProg.i, modular/DynamicArray.i,
	  modular/EuclidianDistance.i, modular/Evaluation.i,
	  modular/ExplicitSpecFeatures.i, modular/FKFeatures.i,
	  modular/Features.i, modular/File.i,
	  modular/FixedDegreeStringKernel.i, modular/GHMM.i,
	  modular/GMNPSVM.i, modular/GNPPSVM.i, modular/GPBTSVM.i,
	  modular/GaussianKernel.i, modular/GaussianShiftKernel.i,
	  modular/GaussianShortRealKernel.i, modular/GeodesicMetric.i,
	  modular/HMM.i, modular/HammingWordDistance.i,
	  modular/Hierarchical.i, modular/Histogram.i,
	  modular/HistogramWordStringKernel.i,
	  modular/IdentityKernelNormalizer.i,
	  modular/ImplicitWeightedSpecFeatures.i, modular/IntFeatures.i,
	  modular/JensenMetric.i, modular/KMeans.i, modular/KNN.i,
	  modular/KRR.i, modular/Kernel.i, modular/KernelMachine.i,
	  modular/KernelNormalizer.i, modular/KernelPerceptron.i,
	  modular/LDA.i, modular/LPBoost.i, modular/LPM.i,
	  modular/Labels.i, modular/LibLinear.i, modular/LibSVM.i,
	  modular/LibSVMMultiClass.i, modular/LibSVMOneClass.i,
	  modular/LibSVR.i, modular/Library.i, modular/LinearByteKernel.i,
	  modular/LinearClassifier.i, modular/LinearHMM.i,
	  modular/LinearKernel.i, modular/LinearStringKernel.i,
	  modular/LinearWordKernel.i, modular/List.i,
	  modular/LocalAlignmentStringKernel.i,
	  modular/LocalityImprovedStringKernel.i, modular/LogPlusOne.i,
	  modular/MPDSVM.i, modular/ManhattanMetric.i,
	  modular/ManhattanWordDistance.i, modular/MatchWordStringKernel.i,
	  modular/Mathematics.i, modular/MindyGramFeatures.i,
	  modular/MindyGramKernel.i, modular/MinkowskiMetric.i,
	  modular/MultiClassSVM.i, modular/NormDerivativeLem3.i,
	  modular/NormOne.i, modular/OligoKernel.i, modular/PCACut.i,
	  modular/Parallel.i, modular/Perceptron.i,
	  modular/PerformanceMeasures.i, modular/Plif.i,
	  modular/PlifArray.i, modular/PlifBase.i,
	  modular/PluginEstimate.i, modular/PolyKernel.i,
	  modular/PolyMatchStringKernel.i,
	  modular/PolyMatchWordStringKernel.i, modular/PreProc.i,
	  modular/PruneVarSubMean.i, modular/PyramidChi2.i,
	  modular/RealDistance.i, modular/RealFeatures.i,
	  modular/RealFileFeatures.i, modular/Regression.i,
	  modular/SGBase.i, modular/SGObject.i, modular/SVM.i,
	  modular/SVMLin.i, modular/SVMOcas.i, modular/SVMSGD.i,
	  modular/SVM_light.i, modular/SVR_light.i,
	  modular/SalzbergWordStringKernel.i, modular/ShogunException.i,
	  modular/ShortFeatures.i, modular/ShortRealFeatures.i,
	  modular/SigmoidKernel.i, modular/Signal.i,
	  modular/SimpleDistance.i, modular/SimpleFeatures.i,
	  modular/SimpleFile.i, modular/SimpleKernel.i,
	  modular/SimpleLocalityImprovedStringKernel.i,
	  modular/SimplePreProc.i, modular/SortUlongString.i,
	  modular/SortWordString.i, modular/SparseDistance.i,
	  modular/SparseEuclidianDistance.i, modular/SparseFeatures.i,
	  modular/SparseGaussianKernel.i, modular/SparseKernel.i,
	  modular/SparseLinearKernel.i, modular/SparsePolyKernel.i,
	  modular/SparsePreProc.i, modular/SqrtDiagKernelNormalizer.i,
	  modular/StringDistance.i, modular/StringFeatures.i,
	  modular/StringKernel.i, modular/StringPreProc.i,
	  modular/Structure.i, modular/SubGradientLPM.i,
	  modular/SubGradientSVM.i, modular/TOPFeatures.i,
	  modular/TanimotoDistance.i, modular/TanimotoKernelNormalizer.i,
	  modular/TensorProductPairKernel.i, modular/Time.i,
	  modular/Trie.i, modular/Version.i, modular/WDFeatures.i,
	  modular/WDSVMOcas.i, modular/WeightedCommWordStringKernel.i,
	  modular/WeightedDegreePositionStringKernel.i,
	  modular/WeightedDegreeStringKernel.i, modular/WordFeatures.i,
	  modular/common.i, modular/init.i, modular/io.i, modular/lapack.i,
	  octave_modular/swig_typemaps.i, python_modular/swig_typemaps.i,
	  r_modular/swig_typemaps.i: merge swig interface files
	* libshogun/classifier/Classifier.h,
	  libshogun/features/CombinedDotFeatures.h,
	  libshogun/features/DotFeatures.h,
	  libshogun/features/ExplicitSpecFeatures.h,
	  libshogun/features/ImplicitWeightedSpecFeatures.h,
	  libshogun/features/SimpleFeatures.h,
	  libshogun/features/WDFeatures.h,
	  libshogun/kernel/CombinedKernel.h,
	  libshogun/kernel/CommWordStringKernel.h,
	  libshogun/kernel/DiceKernelNormalizer.h,
	  libshogun/kernel/Kernel.h, libshogun/lib/io.h,
	  libshogun/structure/DynProg.h: add lots of documentation and fix
	  a naming collision w/ kernel normalizers

2009-02-20  Soeren Sonnenburg <sonne@debian.org>

	* NEWS: start some tutorial
	* configure: an attempt to allow building of modular if's only
	* ChangeLog: updated changelog
	* ChangeLog: updated changelog
	* NEWS: preparing for release

2009-02-19  Soeren Sonnenburg <sonne@debian.org>

	* configure, libshogun/lib/Signal.h, modular/init.i: remove broken
	  ocas and wdocas tests on DNA, disable bias in vanilla ocas test,
	  disable r_modular by default (as long as garbage collections is
	  dysfunctional it better stays like this)
	* Makefile.template: add check scripts for libshogun based examples

2009-02-18  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/distributions/hmm/HMM.h, modular/Classifier.i,
	  modular/Clustering.i, modular/Distance.i, modular/Distribution.i,
	  modular/Evaluation.i, modular/Features.i, modular/Kernel.i,
	  modular/Library.i, modular/PreProc.i, modular/Regression.i,
	  modular/Structure.i, modular/init.i,
	  octave_modular/sg_print_functions.cpp,
	  python_modular/sg_print_functions.cpp,
	  r_modular/sg_print_functions.cpp: fix building of modular
	  interfaces

2009-02-16  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/classifier/svm/GMNPSVM.cpp,
	  libshogun/classifier/svm/MultiClassSVM.cpp,
	  libshogun/classifier/svm/gmnpmkl.cpp,
	  libshogun/classifier/svm/gmnpmkl.h: set_svm has to do SG_REF

2009-02-16  Alexander Binder <alexander.binder@first.fraunhofer.de>

	* libshogun/classifier/svm/GMNPSVM.cpp,
	  libshogun/classifier/svm/MultiClassSVM.cpp,
	  libshogun/classifier/svm/gmnpmkl.cpp: adapted to new version of
	  SG_REF/SG_UNREF scheme,gnmpmkltester is now leakfree

2009-02-16  Cheng Soon Ong <chengsoon.ong@tuebingen.mpg.de>

	* configure: Swap link order for atlas based on
	  http://math-atlas.sourceforge.net/errata.html#LINK

2009-02-16  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/SGInterface.cpp: fix typo
	* libshogunui/SGInterface.cpp: fix problem with direct passing of
	  precomputed linear feature arrays

2009-02-14  Soeren Sonnenburg <sonne@debian.org>

	* README.developer: add introduction on how to develop shogun
	  extensions and/or use libshogun
	* libshogun/kernel/CombinedKernel.cpp,
	  libshogun/kernel/CombinedKernel.h: remove convenience constructor
	  as it won't allow us to check whether number of kernels matches
	  number of features

2009-02-13  Alexander Binder <alexander.binder@first.fraunhofer.de>

	* libshogun/classifier/svm/gmnpmkl.h: bugfix in .h: added correct
	  path to an include
	  .cpp : modified for new shogun, version does not work yet

2009-02-13  Soeren Sonnenburg <sonne@debian.org>

	* Makefile.template: fix include brackets
	* Makefile.template, configure: test for SED specific -i flag
	* configure: fix typo
	* Makefile.template: fix make install on osx
	* Makefile.template, cmdline/CmdLineInterface.cpp, configure:
	  several compile fixes for osx
	* libshogun/base/init.cpp, libshogun/base/init.h: ci forgotten
	  files

2009-02-13  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp, libshogunui/SGInterface.cpp: --
	  bugfix: deleted DynProg object to early
	  -> now valgrind is happy
	  
	  -- Error handling with more informative outputs

2009-02-13  Soeren Sonnenburg <sonne@debian.org>

	* Makefile.template, configure, matlab/MatlabInterface.cpp,
	  octave/OctaveInterface.cpp, python/PythonInterface.cpp,
	  r/RInterface.cpp: finally get all interfaces to dynamically use
	  libshogun
	* Makefile.template, configure, libshogun/base/SGObject.cpp,
	  libshogun/base/SGObject.h, libshogun/base/Version.h,
	  libshogun/lib/Mathematics.h, libshogun/lib/Signal.cpp,
	  libshogun/lib/Signal.h, libshogun/lib/io.cpp, libshogun/lib/io.h,
	  matlab/MatlabInterface.cpp, matlab/MatlabInterface.h,
	  matlab/matlab.cpp, matlab/matlab.h, octave/OctaveInterface.cpp,
	  octave/OctaveInterface.h, octave/octave.cpp, octave/octave.h,
	  python/PythonInterface.cpp, python/PythonInterface.h,
	  python/python.cpp, python/python.h, r/RInterface.cpp,
	  r/RInterface.h, r/r.cpp, r/r.h: libshogun now has global pointers
	  to function callbacks instead of unresolved symbols

2009-02-12  Soeren Sonnenburg <sonne@debian.org>

	* configure: get configure to work for modular interfaces again
	* ChangeLog, NEWS: fix top-level make, update news and changelog
	* libshogun/distributions/hmm/HMM.cpp,
	  libshogun/distributions/hmm/HMM.h: get parallel HMM code to work
	  again (it actually never really worked...)
	* NEWS, configure, libshogun/distributions/hmm/HMM.cpp,
	  libshogun/distributions/hmm/HMM.h: remove NOVIT test in HMM which
	  increases code readability by factor 10, remove cruft from
	  configure and update NEWS
	* libshogun/classifier/svm/SVM_libsvm.cpp,
	  libshogun/classifier/svm/SVM_libsvm.h: update copyright
	* libshogun/classifier/svm/SVM_libsvm.cpp: update to libsvm 2.88
	* configure: remove further cruft
	* libshogun/distributions/hmm/HMM.cpp: fix a bug that screwed up
	  HMM training introduced in shogun 0.5.0 (!)
	* configure: remove HAVE_SWIG / USE_SWIG cruft
	* libshogun/distributions/hmm/HMM.cpp,
	  libshogun/distributions/hmm/HMM.h, libshogun/lib/Mathematics.h,
	  libshogun/lib/Signal.cpp: support ctrl+c in hmm training
	* README.soname: add document explaining when to change .soname
	* configure, libshogun/distributions/hmm/HMM.cpp,
	  libshogun/distributions/hmm/HMM.h, libshogun/lib/Mathematics.cpp,
	  libshogun/lib/Mathematics.h: use logcache/parallel hmm structures
	  per default

2009-02-11  Soeren Sonnenburg <sonne@debian.org>

	* libshogun/features/StringFeatures.h: use a different logic to aid
	  re-use of alphabet objects
	* Makefile.template, libshogun/distributions/histogram/Histogram.h,
	  libshogun/features/StringFeatures.h: add a little more debug
	  output and make make install possible for subdirs
	* Makefile, Makefile.template, configure,
	  libshogun/features/StringFeatures.h,
	  python_modular/swig_typemaps.i: dynamically detect library name
	  suffixes, and perform some symlink soname magic
	  add wrappers for run-testsuite, check-examples and make install
	  in Makefile.template.
	  
	  make set_features (in string features) protected. add a typemap
	  that allows FILE* conversion from python files
	* Makefile.template, configure: it turns out that install does not
	  preserve symbolic links, use ln & ldconfig instead

2009-02-10  Soeren Sonnenburg <sonne@debian.org>

	* configure, libshogun/lib/Mathematics.h: further compile fixes for
	  osx
	* Makefile.template, libshogun/lib/io.h: call ldconfig on make
	  install (for libshogun*) and make get_name function in io non
	  virtual

2009-02-10  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogunui/SGInterface.cpp: accidentally removed a function

2009-02-10  Soeren Sonnenburg <sonne@debian.org>

	* octave_modular/octave.cpp: remove obsolete file
	* configure: ignore -w454

2009-02-09  Soeren Sonnenburg <sonne@debian.org>

	* octave/sg_print_functions.cpp: remove cruft

2009-02-09  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* libshogun/structure/DynProg.cpp, libshogun/structure/DynProg.h,
	  libshogunui/GUICommands.h, libshogunui/SGInterface.h: new
	  functions for direct access of the precomputed content feature
	  arrays

2009-02-09  Soeren Sonnenburg <sonne@debian.org>

	* Makefile.template: allow building without doxygen
	* INSTALL: update description to match new layout
	* .r-install.sh: fix install source paths

2009-02-08  Soeren Sonnenburg <sonne@debian.org>

	* Makefile.template: add lib path for r file compilation
	* octave_modular/sg_print_functions.cpp: add forgotten file
	* .generate_link_dependencies.py, Makefile.template,
	  octave/sg_print_functions.cpp, octave_modular/octave.cpp,
	  python_modular/sg_print_functions.cpp,
	  r_modular/sg_print_functions.cpp: add print functions for modular
	  interfaces and let .so files in modular if's depend on them
	* .r-install.sh, Makefile.template,
	  libshogun/features/CombinedDotFeatures.h,
	  libshogun/features/DotFeatures.h, r/.r-install.sh: move
	  r-install.sh to top level src dir and fix typo in doc for
	  dotfeatures, add doc targets for all interfaces
	* Makefile.template: fix path to examples/testsuite
	* Makefile.template: fix doxyfile and reference generation for
	  static interfaces, rename modular interfaces to use underscore
	  (octave _ modular)
	* Makefile, Makefile.template: add make doc, make test target for
	  modular interfaces
	* configure, libshogun/classifier/LPBoost.h,
	  libshogun/classifier/LPM.h,
	  libshogun/classifier/SubGradientLPM.h: fix compilation when cplex
	  is available, check for obsolete swig versions and disable
	  r-modular / octave-modular accordingly
	* libshogun/classifier/svm/SVM_light.cpp: improve convergence
	  behaviour of newton q-norm mkl
	* configure: fix suffixes
	* Makefile.template: remove unecessary deps
	* Makefile.template: remove trailing .
	* configure: use -fPIC per default
	* Makefile.template: r_modular needs further deps, create
	  lib/versionstring.h in libshogun
	* configure: don't check for unreachable code (for now)
	* .generate_link_dependencies.py, Makefile.template: compiles for
	  all interfaces now
	* Makefile.template, configure, octave_modular/octave_typemaps.i,
	  octave_modular/swig_typemaps.i, python_modular/python_typemaps.i,
	  python_modular/swig_typemaps.i, r/r.h, r_modular/r_typemaps.i,
	  r_modular/swig_typemaps.i: rename language specific typemaps /
	  add lang specific code to typemaps, configure and makefile for
	  swig.
	* modular/Clustering.i, modular/Structure.i: fix include paths
	* .generate_link_dependencies.py, Makefile.template, configure,
	  libshogun/classifier/Classifier.doxy,
	  libshogun/classifier/svm/GMNPSVM.i,
	  libshogun/classifier/svm/GNPPSVM.i,
	  libshogun/classifier/svm/GPBTSVM.i,
	  libshogun/classifier/svm/LibLinear.i,
	  libshogun/classifier/svm/LibSVM.i,
	  libshogun/classifier/svm/LibSVMMultiClass.i,
	  libshogun/classifier/svm/LibSVMOneClass.i,
	  libshogun/classifier/svm/MPDSVM.i,
	  libshogun/classifier/svm/MultiClassSVM.i,
	  libshogun/classifier/svm/SVM.i,
	  libshogun/classifier/svm/SVMLin.i,
	  libshogun/classifier/svm/SVMOcas.i,
	  libshogun/classifier/svm/SVMSGD.i,
	  libshogun/classifier/svm/SVM_light.i,
	  libshogun/classifier/svm/SubGradientSVM.i,
	  libshogun/classifier/svm/WDSVMOcas.i,
	  libshogun/clustering/Clustering.doxy,
	  libshogun/distance/Distance.doxy,
	  libshogun/distributions/Distribution.doxy,
	  libshogun/distributions/histogram/Histogram.i,
	  libshogun/distributions/hmm/GHMM.i,
	  libshogun/distributions/hmm/HMM.i,
	  libshogun/distributions/hmm/LinearHMM.i,
	  libshogun/evaluation/Evaluation.doxy,
	  libshogun/features/Features.doxy, libshogun/kernel/Kernel.doxy,
	  libshogun/lib/Library.doxy, libshogun/preproc/PreProc.doxy,
	  libshogun/regression/Regression.doxy,
	  libshogun/regression/svr/LibSVR.i,
	  libshogun/regression/svr/SVR_light.i,
	  libshogun/structure/Structure.doxy, modular/AUCKernel.i,
	  modular/Alphabet.i, modular/Array.i, modular/Array2.i,
	  modular/Array3.i, modular/AvgDiagKernelNormalizer.i,
	  modular/ByteFeatures.i, modular/Cache.i, modular/CharFeatures.i,
	  modular/Chi2Kernel.i, modular/Classifier.doxy,
	  modular/Classifier.i, modular/Clustering.doxy,
	  modular/Clustering.i, modular/CombinedDotFeatures.i,
	  modular/CombinedFeatures.i, modular/CombinedKernel.i,
	  modular/CommUlongStringKernel.i, modular/CommWordStringKernel.i,
	  modular/ConstKernel.i, modular/CustomKernel.i,
	  modular/DiagKernel.i, modular/DiceKernelNormalizer.i,
	  modular/Distance.doxy, modular/Distance.i,
	  modular/DistanceKernel.i, modular/DistanceMachine.i,
	  modular/Distribution.doxy, modular/Distribution.i,
	  modular/DotFeatures.i, modular/DummyFeatures.i,
	  modular/DynProg.i, modular/DynamicArray.i,
	  modular/EuclidianDistance.i, modular/Evaluation.doxy,
	  modular/Evaluation.i, modular/ExplicitSpecFeatures.i,
	  modular/FKFeatures.i, modular/Features.doxy, modular/Features.i,
	  modular/File.i, modular/FixedDegreeStringKernel.i,
	  modular/GHMM.i, modular/GMNPSVM.i, modular/GNPPSVM.i,
	  modular/GPBTSVM.i, modular/GaussianKernel.i,
	  modular/GaussianShiftKernel.i, modular/GaussianShortRealKernel.i,
	  modular/GeodesicMetric.i, modular/HMM.i,
	  modular/HammingWordDistance.i, modular/Hierarchical.i,
	  modular/Histogram.i, modular/HistogramWordStringKernel.i,
	  modular/IdentityKernelNormalizer.i,
	  modular/ImplicitWeightedSpecFeatures.i, modular/IntFeatures.i,
	  modular/JensenMetric.i, modular/KMeans.i, modular/KNN.i,
	  modular/KRR.i, modular/Kernel.doxy, modular/Kernel.i,
	  modular/KernelMachine.i, modular/KernelNormalizer.i,
	  modular/Labels.i, modular/LibLinear.i, modular/LibSVM.i,
	  modular/LibSVMMultiClass.i, modular/LibSVMOneClass.i,
	  modular/LibSVR.i, modular/Library.doxy, modular/Library.i,
	  modular/LinearByteKernel.i, modular/LinearClassifier.i,
	  modular/LinearHMM.i, modular/LinearKernel.i,
	  modular/LinearStringKernel.i, modular/LinearWordKernel.i,
	  modular/List.i, modular/LocalAlignmentStringKernel.i,
	  modular/LocalityImprovedStringKernel.i, modular/LogPlusOne.i,
	  modular/MPDSVM.i, modular/ManhattanMetric.i,
	  modular/ManhattanWordDistance.i, modular/MatchWordStringKernel.i,
	  modular/Mathematics.i, modular/MindyGramFeatures.i,
	  modular/MindyGramKernel.i, modular/MinkowskiMetric.i,
	  modular/MultiClassSVM.i, modular/NormDerivativeLem3.i,
	  modular/NormOne.i, modular/OligoKernel.i, modular/PCACut.i,
	  modular/PerformanceMeasures.i, modular/Plif.i,
	  modular/PlifArray.i, modular/PlifBase.i, modular/PolyKernel.i,
	  modular/PolyMatchStringKernel.i,
	  modular/PolyMatchWordStringKernel.i, modular/PreProc.doxy,
	  modular/PreProc.i, modular/PruneVarSubMean.i,
	  modular/PyramidChi2.i, modular/RealDistance.i,
	  modular/RealFeatures.i, modular/RealFileFeatures.i,
	  modular/Regression.doxy, modular/Regression.i, modular/SVM.i,
	  modular/SVMLin.i, modular/SVMOcas.i, modular/SVMSGD.i,
	  modular/SVM_light.i, modular/SVR_light.i,
	  modular/SalzbergWordStringKernel.i, modular/ShogunException.i,
	  modular/ShortFeatures.i, modular/ShortRealFeatures.i,
	  modular/SigmoidKernel.i, modular/Signal.i,
	  modular/SimpleDistance.i, modular/SimpleFeatures.i,
	  modular/SimpleFile.i, modular/SimpleKernel.i,
	  modular/SimpleLocalityImprovedStringKernel.i,
	  modular/SimplePreProc.i, modular/SortUlongString.i,
	  modular/SortWordString.i, modular/SparseDistance.i,
	  modular/SparseEuclidianDistance.i, modular/SparseFeatures.i,
	  modular/SparseGaussianKernel.i, modular/SparseKernel.i,
	  modular/SparseLinearKernel.i, modular/SparsePolyKernel.i,
	  modular/SparsePreProc.i, modular/SqrtDiagKernelNormalizer.i,
	  modular/StringDistance.i, modular/StringFeatures.i,
	  modular/StringKernel.i, modular/StringPreProc.i,
	  modular/Structure.doxy, modular/Structure.i,
	  modular/SubGradientSVM.i, modular/TOPFeatures.i,
	  modular/TanimotoDistance.i, modular/TanimotoKernelNormalizer.i,
	  modular/TensorProductPairKernel.i, modular/Time.i,
	  modular/Trie.i, modular/Version.i, modular/WDFeatures.i,
	  modular/WDSVMOcas.i, modular/WeightedCommWordStringKernel.i,
	  modular/WeightedDegreePositionStringKernel.i,
	  modular/WeightedDegreeStringKernel.i, modular/WordFeatures.i,
	  modular/common.i, modular/io.i, modular/lapack.i,
	  modular/octave_typemaps.i, modular/python_typemaps.i,
	  modular/r_typemaps.i, modular/swig_typemaps.i, octave_modular,
	  octave_modular/octave_typemaps.i, python_modular,
	  python_modular/python_typemaps.i, r_modular,
	  r_modular/r_typemaps.i: move further .i files to src/modular and
	  adjust inclusion paths and scripts. move language specific .i
	  files into language dirs

2009-02-07  Soeren Sonnenburg <sonne@debian.org>

	* .r-install.sh, Makefile, Makefile.template, configure,
	  libshogun/regression/svr/SVR_light.cpp, r/.r-install.sh: enable
	  svmlight, get make install and make tests to work
	* Makefile, Makefile.template: fix a misplace endif, quieten output
	* configure, interfaces: don't fail when matlab is not found remove
	  cruft
	* Makefile, Makefile.template, cmdline,
	  cmdline/CmdLineInterface.cpp, cmdline/CmdLineInterface.h,
	  cmdline/cmdline.cpp, configure, interfaces/cmdline,
	  interfaces/lib, interfaces/matlab, interfaces/modular,
	  interfaces/octave, interfaces/python, interfaces/r,
	  libshogun/Makefile, libshogun/lib/Signal.h, libshogunui/Makefile,
	  matlab, matlab/MatlabInterface.cpp, matlab/MatlabInterface.h,
	  matlab/matlab.cpp, matlab/matlab.h, modular, octave,
	  octave/OctaveInterface.cpp, octave/OctaveInterface.h,
	  octave/octave.cpp, octave/octave.h, python,
	  python/PythonInterface.cpp, python/PythonInterface.h,
	  python/python.cpp, python/python.h, r, r/RInterface.cpp,
	  r/RInterface.h, r/r.cpp, r/r.h: building of libshogun{,ui} and
	  static interfaces works now

2009-02-05  Soeren Sonnenburg <sonne@debian.org>

	* Makefile, configure, interfaces/Makefile, interfaces/cmdline,
	  interfaces/cmdline/CmdLineInterface.cpp,
	  interfaces/cmdline/CmdLineInterface.h,
	  interfaces/lib/cmdline.cpp, interfaces/lib/matlab.cpp,
	  interfaces/lib/matlab.h, interfaces/lib/octave.cpp,
	  interfaces/lib/octave.h, interfaces/lib/python.cpp,
	  interfaces/lib/r.cpp, interfaces/lib/r.h, interfaces/matlab,
	  interfaces/matlab/MatlabInterface.cpp,
	  interfaces/matlab/MatlabInterface.h, interfaces/octave,
	  interfaces/octave/OctaveInterface.cpp,
	  interfaces/octave/OctaveInterface.h, interfaces/python,
	  interfaces/python/PythonInterface.cpp,
	  interfaces/python/PythonInterface.h, interfaces/r,
	  interfaces/r/RInterface.cpp, interfaces/r/RInterface.h,
	  interfaces/static, libshogunui/Makefile: further restructuring
	* Makefile, NEWS, configure, interfaces/Makefile,
	  interfaces/static/CmdLineInterface.cpp,
	  interfaces/static/CmdLineInterface.h,
	  interfaces/static/SGInterface.cpp,
	  interfaces/static/SGInterface.h,
	  interfaces/static/SyntaxHighLight.h, libshogun/Makefile,
	  libshogunui/GUIClassifier.cpp, libshogunui/GUIClassifier.h,
	  libshogunui/GUICommands.h, libshogunui/GUIDistance.cpp,
	  libshogunui/GUIDistance.h, libshogunui/GUIFeatures.cpp,
	  libshogunui/GUIFeatures.h, libshogunui/GUIHMM.cpp,
	  libshogunui/GUIHMM.h, libshogunui/GUIKernel.cpp,
	  libshogunui/GUIKernel.h, libshogunui/GUILabels.cpp,
	  libshogunui/GUILabels.h, libshogunui/GUIMath.cpp,
	  libshogunui/GUIMath.h, libshogunui/GUIPluginEstimate.cpp,
	  libshogunui/GUIPluginEstimate.h, libshogunui/GUIPreProc.cpp,
	  libshogunui/GUIPreProc.h, libshogunui/GUIStructure.cpp,
	  libshogunui/GUIStructure.h, libshogunui/GUITime.cpp,
	  libshogunui/GUITime.h, libshogunui/Makefile,
	  libshogunui/SGInterface.cpp, libshogunui/SGInterface.h,
	  libshogunui/SyntaxHighLight.h: more progress on new
	  configure/make system

2009-02-04  Soeren Sonnenburg <sonne@debian.org>

	* configure: further improve configure
	* Makefile, NEWS, configure, interfaces/lib,
	  interfaces/lib/cmdline.cpp, interfaces/lib/matlab.cpp,
	  interfaces/lib/matlab.h, interfaces/lib/octave.cpp,
	  interfaces/lib/octave.h, interfaces/lib/python.cpp,
	  interfaces/lib/python.h, interfaces/lib/r.cpp,
	  interfaces/lib/r.h, libshogun/Makefile, libshogun/base/Version.h,
	  libshogun/lib/Cplex.h, libshogun/lib/Signal.cpp,
	  libshogun/lib/cmdline.cpp, libshogun/lib/io.cpp,
	  libshogun/lib/matlab.cpp, libshogun/lib/matlab.h,
	  libshogun/lib/octave.cpp, libshogun/lib/octave.h,
	  libshogun/lib/python.cpp, libshogun/lib/python.h,
	  libshogun/lib/r.cpp, libshogun/lib/r.h,
	  libshogun/structure/Plif.h: move libshogun/lib/matlab.{cpp,h} etc
	  to interfaces/lib

2009-02-01  Soeren Sonnenburg <sonne@debian.org>

	* guilib, interface: remove obsolete dirs
	* guilib/GUIClassifier.cpp, guilib/GUIClassifier.h,
	  guilib/GUICommands.h, guilib/GUIDistance.cpp,
	  guilib/GUIDistance.h, guilib/GUIFeatures.cpp,
	  guilib/GUIFeatures.h, guilib/GUIHMM.cpp, guilib/GUIHMM.h,
	  guilib/GUIKernel.cpp, guilib/GUIKernel.h, guilib/GUILabels.cpp,
	  guilib/GUILabels.h, guilib/GUIMath.cpp, guilib/GUIMath.h,
	  guilib/GUIPluginEstimate.cpp, guilib/GUIPluginEstimate.h,
	  guilib/GUIPreProc.cpp, guilib/GUIPreProc.h,
	  guilib/GUIStructure.cpp, guilib/GUIStructure.h,
	  guilib/GUITime.cpp, guilib/GUITime.h,
	  interface/CmdLineInterface.cpp, interface/CmdLineInterface.h,
	  interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/OctaveInterface.cpp, interface/OctaveInterface.h,
	  interface/PythonInterface.cpp, interface/PythonInterface.h,
	  interface/RInterface.cpp, interface/RInterface.h,
	  interface/SGInterface.cpp, interface/SGInterface.h,
	  interface/SyntaxHighLight.h,
	  interfaces/static/CmdLineInterface.cpp,
	  interfaces/static/CmdLineInterface.h,
	  interfaces/static/MatlabInterface.cpp,
	  interfaces/static/MatlabInterface.h,
	  interfaces/static/OctaveInterface.cpp,
	  interfaces/static/OctaveInterface.h,
	  interfaces/static/PythonInterface.cpp,
	  interfaces/static/PythonInterface.h,
	  interfaces/static/RInterface.cpp, interfaces/static/RInterface.h,
	  interfaces/static/SGInterface.cpp,
	  interfaces/static/SGInterface.h,
	  interfaces/static/SyntaxHighLight.h,
	  libshogunui/GUIClassifier.cpp, libshogunui/GUIClassifier.h,
	  libshogunui/GUICommands.h, libshogunui/GUIDistance.cpp,
	  libshogunui/GUIDistance.h, libshogunui/GUIFeatures.cpp,
	  libshogunui/GUIFeatures.h, libshogunui/GUIHMM.cpp,
	  libshogunui/GUIHMM.h, libshogunui/GUIKernel.cpp,
	  libshogunui/GUIKernel.h, libshogunui/GUILabels.cpp,
	  libshogunui/GUILabels.h, libshogunui/GUIMath.cpp,
	  libshogunui/GUIMath.h, libshogunui/GUIPluginEstimate.cpp,
	  libshogunui/GUIPluginEstimate.h, libshogunui/GUIPreProc.cpp,
	  libshogunui/GUIPreProc.h, libshogunui/GUIStructure.cpp,
	  libshogunui/GUIStructure.h, libshogunui/GUITime.cpp,
	  libshogunui/GUITime.h: move things into static interfaces
	* base, classifier, clustering, distance, distributions,
	  evaluation, features, kernel, lib, libshogun/base,
	  libshogun/base/Parallel.i, libshogun/base/SGObject.i,
	  libshogun/base/Version.i, libshogun/classifier,
	  libshogun/classifier/Classifier.i, libshogun/classifier/KNN.i,
	  libshogun/classifier/KernelPerceptron.i,
	  libshogun/classifier/LDA.i, libshogun/classifier/LPBoost.i,
	  libshogun/classifier/LPM.i,
	  libshogun/classifier/LinearClassifier.i,
	  libshogun/classifier/Perceptron.i,
	  libshogun/classifier/PluginEstimate.i,
	  libshogun/classifier/SubGradientLPM.i, libshogun/clustering,
	  libshogun/clustering/Clustering.i,
	  libshogun/clustering/Hierarchical.i,
	  libshogun/clustering/KMeans.i, libshogun/distance,
	  libshogun/distance/BrayCurtisDistance.i,
	  libshogun/distance/CanberraMetric.i,
	  libshogun/distance/CanberraWordDistance.i,
	  libshogun/distance/ChebyshewMetric.i,
	  libshogun/distance/ChiSquareDistance.i,
	  libshogun/distance/CosineDistance.i,
	  libshogun/distance/Distance.i,
	  libshogun/distance/DistanceMachine.i,
	  libshogun/distance/EuclidianDistance.i,
	  libshogun/distance/GeodesicMetric.i,
	  libshogun/distance/HammingWordDistance.i,
	  libshogun/distance/JensenMetric.i,
	  libshogun/distance/ManhattanMetric.i,
	  libshogun/distance/ManhattanWordDistance.i,
	  libshogun/distance/MinkowskiMetric.i,
	  libshogun/distance/RealDistance.i,
	  libshogun/distance/SimpleDistance.i,
	  libshogun/distance/SparseDistance.i,
	  libshogun/distance/SparseEuclidianDistance.i,
	  libshogun/distance/StringDistance.i,
	  libshogun/distance/TanimotoDistance.i, libshogun/distributions,
	  libshogun/distributions/Distribution.i, libshogun/evaluation,
	  libshogun/evaluation/Evaluation.i,
	  libshogun/evaluation/PerformanceMeasures.i, libshogun/features,
	  libshogun/features/Alphabet.i, libshogun/features/ByteFeatures.i,
	  libshogun/features/CharFeatures.i,
	  libshogun/features/CombinedDotFeatures.i,
	  libshogun/features/CombinedFeatures.i,
	  libshogun/features/DotFeatures.i,
	  libshogun/features/DummyFeatures.i,
	  libshogun/features/ExplicitSpecFeatures.i,
	  libshogun/features/FKFeatures.i, libshogun/features/Features.i,
	  libshogun/features/ImplicitWeightedSpecFeatures.i,
	  libshogun/features/IntFeatures.i, libshogun/features/Labels.i,
	  libshogun/features/MindyGramFeatures.i,
	  libshogun/features/RealFeatures.i,
	  libshogun/features/RealFileFeatures.i,
	  libshogun/features/ShortFeatures.i,
	  libshogun/features/ShortRealFeatures.i,
	  libshogun/features/SimpleFeatures.i,
	  libshogun/features/SparseFeatures.i,
	  libshogun/features/StringFeatures.i,
	  libshogun/features/TOPFeatures.i,
	  libshogun/features/WDFeatures.i,
	  libshogun/features/WordFeatures.i, libshogun/kernel,
	  libshogun/kernel/AUCKernel.i,
	  libshogun/kernel/AvgDiagKernelNormalizer.i,
	  libshogun/kernel/Chi2Kernel.i, libshogun/kernel/CombinedKernel.i,
	  libshogun/kernel/CommUlongStringKernel.i,
	  libshogun/kernel/CommWordStringKernel.i,
	  libshogun/kernel/ConstKernel.i, libshogun/kernel/CustomKernel.i,
	  libshogun/kernel/DiagKernel.i,
	  libshogun/kernel/DiceKernelNormalizer.i,
	  libshogun/kernel/DistanceKernel.i,
	  libshogun/kernel/FixedDegreeStringKernel.i,
	  libshogun/kernel/GaussianKernel.i,
	  libshogun/kernel/GaussianShiftKernel.i,
	  libshogun/kernel/GaussianShortRealKernel.i,
	  libshogun/kernel/HistogramWordStringKernel.i,
	  libshogun/kernel/IdentityKernelNormalizer.i,
	  libshogun/kernel/Kernel.i, libshogun/kernel/KernelMachine.i,
	  libshogun/kernel/KernelNormalizer.i,
	  libshogun/kernel/LinearByteKernel.i,
	  libshogun/kernel/LinearKernel.i,
	  libshogun/kernel/LinearStringKernel.i,
	  libshogun/kernel/LinearWordKernel.i,
	  libshogun/kernel/LocalAlignmentStringKernel.i,
	  libshogun/kernel/LocalityImprovedStringKernel.i,
	  libshogun/kernel/MatchWordStringKernel.i,
	  libshogun/kernel/MindyGramKernel.i,
	  libshogun/kernel/OligoKernel.i, libshogun/kernel/PolyKernel.i,
	  libshogun/kernel/PolyMatchStringKernel.i,
	  libshogun/kernel/PolyMatchWordStringKernel.i,
	  libshogun/kernel/PyramidChi2.i,
	  libshogun/kernel/SalzbergWordStringKernel.i,
	  libshogun/kernel/SigmoidKernel.i,
	  libshogun/kernel/SimpleKernel.i,
	  libshogun/kernel/SimpleLocalityImprovedStringKernel.i,
	  libshogun/kernel/SparseGaussianKernel.i,
	  libshogun/kernel/SparseKernel.i,
	  libshogun/kernel/SparseLinearKernel.i,
	  libshogun/kernel/SparsePolyKernel.i,
	  libshogun/kernel/SqrtDiagKernelNormalizer.i,
	  libshogun/kernel/StringKernel.i,
	  libshogun/kernel/TanimotoKernelNormalizer.i,
	  libshogun/kernel/TensorProductPairKernel.i,
	  libshogun/kernel/WeightedCommWordStringKernel.i,
	  libshogun/kernel/WeightedDegreePositionStringKernel.i,
	  libshogun/kernel/WeightedDegreeStringKernel.i, libshogun/lib,
	  libshogun/lib/Array.i, libshogun/lib/Array2.i,
	  libshogun/lib/Array3.i, libshogun/lib/Cache.i,
	  libshogun/lib/DynamicArray.i, libshogun/lib/File.i,
	  libshogun/lib/Library.i, libshogun/lib/List.i,
	  libshogun/lib/Mathematics.i, libshogun/lib/ShogunException.i,
	  libshogun/lib/Signal.i, libshogun/lib/SimpleFile.i,
	  libshogun/lib/Time.i, libshogun/lib/Trie.i,
	  libshogun/lib/common.i, libshogun/lib/io.i,
	  libshogun/lib/lapack.i, libshogun/lib/octave_typemaps.i,
	  libshogun/lib/python_typemaps.i, libshogun/lib/r_typemaps.i,
	  libshogun/lib/swig_typemaps.i, libshogun/preproc,
	  libshogun/preproc/LogPlusOne.i,
	  libshogun/preproc/NormDerivativeLem3.i,
	  libshogun/preproc/NormOne.i, libshogun/preproc/PCACut.i,
	  libshogun/preproc/PreProc.i, libshogun/preproc/PruneVarSubMean.i,
	  libshogun/preproc/SimplePreProc.i,
	  libshogun/preproc/SortUlongString.i,
	  libshogun/preproc/SortWordString.i,
	  libshogun/preproc/SparsePreProc.i,
	  libshogun/preproc/StringPreProc.i, libshogun/regression,
	  libshogun/regression/KRR.i, libshogun/regression/Regression.i,
	  libshogun/structure, libshogun/structure/DynProg.i,
	  libshogun/structure/Plif.i, libshogun/structure/PlifArray.i,
	  libshogun/structure/PlifBase.i, libshogun/structure/Structure.i,
	  preproc, regression, structure: move things into libshogun
	* base/Parallel.i, base/SGObject.i, base/Version.i,
	  classifier/Classifier.i, classifier/KNN.i,
	  classifier/KernelPerceptron.i, classifier/LDA.i,
	  classifier/LPBoost.i, classifier/LPM.i,
	  classifier/LinearClassifier.i, classifier/Perceptron.i,
	  classifier/PluginEstimate.i, classifier/SubGradientLPM.i,
	  clustering/Clustering.i, clustering/Hierarchical.i,
	  clustering/KMeans.i, distance/BrayCurtisDistance.i,
	  distance/CanberraMetric.i, distance/CanberraWordDistance.i,
	  distance/ChebyshewMetric.i, distance/ChiSquareDistance.i,
	  distance/CosineDistance.i, distance/Distance.i,
	  distance/DistanceMachine.i, distance/EuclidianDistance.i,
	  distance/GeodesicMetric.i, distance/HammingWordDistance.i,
	  distance/JensenMetric.i, distance/ManhattanMetric.i,
	  distance/ManhattanWordDistance.i, distance/MinkowskiMetric.i,
	  distance/RealDistance.i, distance/SimpleDistance.i,
	  distance/SparseDistance.i, distance/SparseEuclidianDistance.i,
	  distance/StringDistance.i, distance/TanimotoDistance.i,
	  distributions/Distribution.i, evaluation/Evaluation.i,
	  evaluation/PerformanceMeasures.i, features/Alphabet.i,
	  features/ByteFeatures.i, features/CharFeatures.i,
	  features/CombinedDotFeatures.i, features/CombinedFeatures.i,
	  features/DotFeatures.i, features/DummyFeatures.i,
	  features/ExplicitSpecFeatures.i, features/FKFeatures.i,
	  features/Features.i, features/ImplicitWeightedSpecFeatures.i,
	  features/IntFeatures.i, features/Labels.i,
	  features/MindyGramFeatures.i, features/RealFeatures.i,
	  features/RealFileFeatures.i, features/ShortFeatures.i,
	  features/ShortRealFeatures.i, features/SimpleFeatures.i,
	  features/SparseFeatures.i, features/StringFeatures.i,
	  features/TOPFeatures.i, features/WDFeatures.i,
	  features/WordFeatures.i, interfaces, interfaces/modular,
	  interfaces/modular/AUCKernel.i, interfaces/modular/Alphabet.i,
	  interfaces/modular/Array.i, interfaces/modular/Array2.i,
	  interfaces/modular/Array3.i,
	  interfaces/modular/AvgDiagKernelNormalizer.i,
	  interfaces/modular/BrayCurtisDistance.i,
	  interfaces/modular/ByteFeatures.i, interfaces/modular/Cache.i,
	  interfaces/modular/CanberraMetric.i,
	  interfaces/modular/CanberraWordDistance.i,
	  interfaces/modular/CharFeatures.i,
	  interfaces/modular/ChebyshewMetric.i,
	  interfaces/modular/Chi2Kernel.i,
	  interfaces/modular/ChiSquareDistance.i,
	  interfaces/modular/Classifier.i, interfaces/modular/Clustering.i,
	  interfaces/modular/CombinedDotFeatures.i,
	  interfaces/modular/CombinedFeatures.i,
	  interfaces/modular/CombinedKernel.i,
	  interfaces/modular/CommUlongStringKernel.i,
	  interfaces/modular/CommWordStringKernel.i,
	  interfaces/modular/ConstKernel.i,
	  interfaces/modular/CosineDistance.i,
	  interfaces/modular/CustomKernel.i,
	  interfaces/modular/DiagKernel.i,
	  interfaces/modular/DiceKernelNormalizer.i,
	  interfaces/modular/Distance.i,
	  interfaces/modular/DistanceKernel.i,
	  interfaces/modular/DistanceMachine.i,
	  interfaces/modular/Distribution.i,
	  interfaces/modular/DotFeatures.i,
	  interfaces/modular/DummyFeatures.i, interfaces/modular/DynProg.i,
	  interfaces/modular/DynamicArray.i,
	  interfaces/modular/EuclidianDistance.i,
	  interfaces/modular/Evaluation.i,
	  interfaces/modular/ExplicitSpecFeatures.i,
	  interfaces/modular/FKFeatures.i, interfaces/modular/Features.i,
	  interfaces/modular/File.i,
	  interfaces/modular/FixedDegreeStringKernel.i,
	  interfaces/modular/GaussianKernel.i,
	  interfaces/modular/GaussianShiftKernel.i,
	  interfaces/modular/GaussianShortRealKernel.i,
	  interfaces/modular/GeodesicMetric.i,
	  interfaces/modular/HammingWordDistance.i,
	  interfaces/modular/Hierarchical.i,
	  interfaces/modular/HistogramWordStringKernel.i,
	  interfaces/modular/IdentityKernelNormalizer.i,
	  interfaces/modular/ImplicitWeightedSpecFeatures.i,
	  interfaces/modular/IntFeatures.i,
	  interfaces/modular/JensenMetric.i, interfaces/modular/KMeans.i,
	  interfaces/modular/KNN.i, interfaces/modular/KRR.i,
	  interfaces/modular/Kernel.i, interfaces/modular/KernelMachine.i,
	  interfaces/modular/KernelNormalizer.i,
	  interfaces/modular/KernelPerceptron.i, interfaces/modular/LDA.i,
	  interfaces/modular/LPBoost.i, interfaces/modular/LPM.i,
	  interfaces/modular/Labels.i, interfaces/modular/Library.i,
	  interfaces/modular/LinearByteKernel.i,
	  interfaces/modular/LinearClassifier.i,
	  interfaces/modular/LinearKernel.i,
	  interfaces/modular/LinearStringKernel.i,
	  interfaces/modular/LinearWordKernel.i, interfaces/modular/List.i,
	  interfaces/modular/LocalAlignmentStringKernel.i,
	  interfaces/modular/LocalityImprovedStringKernel.i,
	  interfaces/modular/LogPlusOne.i,
	  interfaces/modular/ManhattanMetric.i,
	  interfaces/modular/ManhattanWordDistance.i,
	  interfaces/modular/MatchWordStringKernel.i,
	  interfaces/modular/Mathematics.i,
	  interfaces/modular/MindyGramFeatures.i,
	  interfaces/modular/MindyGramKernel.i,
	  interfaces/modular/MinkowskiMetric.i,
	  interfaces/modular/NormDerivativeLem3.i,
	  interfaces/modular/NormOne.i, interfaces/modular/OligoKernel.i,
	  interfaces/modular/PCACut.i, interfaces/modular/Parallel.i,
	  interfaces/modular/Perceptron.i,
	  interfaces/modular/PerformanceMeasures.i,
	  interfaces/modular/Plif.i, interfaces/modular/PlifArray.i,
	  interfaces/modular/PlifBase.i,
	  interfaces/modular/PluginEstimate.i,
	  interfaces/modular/PolyKernel.i,
	  interfaces/modular/PolyMatchStringKernel.i,
	  interfaces/modular/PolyMatchWordStringKernel.i,
	  interfaces/modular/PreProc.i,
	  interfaces/modular/PruneVarSubMean.i,
	  interfaces/modular/PyramidChi2.i,
	  interfaces/modular/RealDistance.i,
	  interfaces/modular/RealFeatures.i,
	  interfaces/modular/RealFileFeatures.i,
	  interfaces/modular/Regression.i, interfaces/modular/SGObject.i,
	  interfaces/modular/SalzbergWordStringKernel.i,
	  interfaces/modular/ShogunException.i,
	  interfaces/modular/ShortFeatures.i,
	  interfaces/modular/ShortRealFeatures.i,
	  interfaces/modular/SigmoidKernel.i, interfaces/modular/Signal.i,
	  interfaces/modular/SimpleDistance.i,
	  interfaces/modular/SimpleFeatures.i,
	  interfaces/modular/SimpleFile.i,
	  interfaces/modular/SimpleKernel.i,
	  interfaces/modular/SimpleLocalityImprovedStringKernel.i,
	  interfaces/modular/SimplePreProc.i,
	  interfaces/modular/SortUlongString.i,
	  interfaces/modular/SortWordString.i,
	  interfaces/modular/SparseDistance.i,
	  interfaces/modular/SparseEuclidianDistance.i,
	  interfaces/modular/SparseFeatures.i,
	  interfaces/modular/SparseGaussianKernel.i,
	  interfaces/modular/SparseKernel.i,
	  interfaces/modular/SparseLinearKernel.i,
	  interfaces/modular/SparsePolyKernel.i,
	  interfaces/modular/SparsePreProc.i,
	  interfaces/modular/SqrtDiagKernelNormalizer.i,
	  interfaces/modular/StringDistance.i,
	  interfaces/modular/StringFeatures.i,
	  interfaces/modular/StringKernel.i,
	  interfaces/modular/StringPreProc.i,
	  interfaces/modular/Structure.i,
	  interfaces/modular/SubGradientLPM.i,
	  interfaces/modular/TOPFeatures.i,
	  interfaces/modular/TanimotoDistance.i,
	  interfaces/modular/TanimotoKernelNormalizer.i,
	  interfaces/modular/TensorProductPairKernel.i,
	  interfaces/modular/Time.i, interfaces/modular/Trie.i,
	  interfaces/modular/Version.i, interfaces/modular/WDFeatures.i,
	  interfaces/modular/WeightedCommWordStringKernel.i,
	  interfaces/modular/WeightedDegreePositionStringKernel.i,
	  interfaces/modular/WeightedDegreeStringKernel.i,
	  interfaces/modular/WordFeatures.i, interfaces/modular/common.i,
	  interfaces/modular/io.i, interfaces/modular/lapack.i,
	  interfaces/modular/octave_typemaps.i,
	  interfaces/modular/python_typemaps.i,
	  interfaces/modular/r_typemaps.i,
	  interfaces/modular/swig_typemaps.i, interfaces/static,
	  kernel/AUCKernel.i, kernel/AvgDiagKernelNormalizer.i,
	  kernel/Chi2Kernel.i, kernel/CombinedKernel.i,
	  kernel/CommUlongStringKernel.i, kernel/CommWordStringKernel.i,
	  kernel/ConstKernel.i, kernel/CustomKernel.i, kernel/DiagKernel.i,
	  kernel/DiceKernelNormalizer.i, kernel/DistanceKernel.i,
	  kernel/FixedDegreeStringKernel.i, kernel/GaussianKernel.i,
	  kernel/GaussianShiftKernel.i, kernel/GaussianShortRealKernel.i,
	  kernel/HistogramWordStringKernel.i,
	  kernel/IdentityKernelNormalizer.i, kernel/Kernel.i,
	  kernel/KernelMachine.i, kernel/KernelNormalizer.i,
	  kernel/LinearByteKernel.i, kernel/LinearKernel.i,
	  kernel/LinearStringKernel.i, kernel/LinearWordKernel.i,
	  kernel/LocalAlignmentStringKernel.i,
	  kernel/LocalityImprovedStringKernel.i,
	  kernel/MatchWordStringKernel.i, kernel/MindyGramKernel.i,
	  kernel/OligoKernel.i, kernel/PolyKernel.i,
	  kernel/PolyMatchStringKernel.i,
	  kernel/PolyMatchWordStringKernel.i, kernel/PyramidChi2.i,
	  kernel/SalzbergWordStringKernel.i, kernel/SigmoidKernel.i,
	  kernel/SimpleKernel.i,
	  kernel/SimpleLocalityImprovedStringKernel.i,
	  kernel/SparseGaussianKernel.i, kernel/SparseKernel.i,
	  kernel/SparseLinearKernel.i, kernel/SparsePolyKernel.i,
	  kernel/SqrtDiagKernelNormalizer.i, kernel/StringKernel.i,
	  kernel/TanimotoKernelNormalizer.i,
	  kernel/TensorProductPairKernel.i,
	  kernel/WeightedCommWordStringKernel.i,
	  kernel/WeightedDegreePositionStringKernel.i,
	  kernel/WeightedDegreeStringKernel.i, lib/Array.i, lib/Array2.i,
	  lib/Array3.i, lib/Cache.i, lib/DynamicArray.i, lib/File.i,
	  lib/Library.i, lib/List.i, lib/Mathematics.i,
	  lib/ShogunException.i, lib/Signal.i, lib/SimpleFile.i,
	  lib/Time.i, lib/Trie.i, lib/common.i, lib/io.i, lib/lapack.i,
	  lib/octave_typemaps.i, lib/python_typemaps.i, lib/r_typemaps.i,
	  lib/swig_typemaps.i, libshogun, libshogunui,
	  preproc/LogPlusOne.i, preproc/NormDerivativeLem3.i,
	  preproc/NormOne.i, preproc/PCACut.i, preproc/PreProc.i,
	  preproc/PruneVarSubMean.i, preproc/SimplePreProc.i,
	  preproc/SortUlongString.i, preproc/SortWordString.i,
	  preproc/SparsePreProc.i, preproc/StringPreProc.i,
	  regression/KRR.i, regression/Regression.i, structure/DynProg.i,
	  structure/Plif.i, structure/PlifArray.i, structure/PlifBase.i,
	  structure/Structure.i: begin restructuring of code
	* base/Parallel.i, base/SGObject.i, base/Version.i,
	  classifier/Classifier.i, classifier/KNN.i,
	  classifier/KernelPerceptron.i, classifier/LDA.i,
	  classifier/LPBoost.i, classifier/LPM.i,
	  classifier/LinearClassifier.i, classifier/Perceptron.i,
	  classifier/PluginEstimate.i, classifier/SubGradientLPM.i,
	  clustering/Clustering.i, clustering/Hierarchical.i,
	  clustering/KMeans.i, distance/BrayCurtisDistance.i,
	  distance/CanberraMetric.i, distance/CanberraWordDistance.i,
	  distance/ChebyshewMetric.i, distance/ChiSquareDistance.i,
	  distance/CosineDistance.i: the .i files need
	  <shogun/path/to/file> as they now base on libshogun
	* Makefile: also erase libshogun.a on clean
	* classifier/svm/gmnpmkl.h, lib/Array.h: add get_name function to
	  gmnpmkl wrappers - fixes compilation when glpk is not available

2009-01-31  Soeren Sonnenburg <sonne@debian.org>

	* features/CombinedFeatures.cpp, guilib/GUIFeatures.h,
	  guilib/GUIKernel.cpp, kernel/CombinedKernel.cpp,
	  kernel/CombinedKernel.h: all things except HMM work
	  stably+leak-free in static cmdline if
	* clustering/KMeans.cpp, distance/Distance.h,
	  interface/SGInterface.cpp: clustering and distances are now leak
	  free
	* base/SGObject.h, classifier/KNN.h, classifier/KernelPerceptron.h,
	  classifier/LDA.h, classifier/Perceptron.h,
	  classifier/PluginEstimate.h, classifier/svm/GMNPSVM.h,
	  classifier/svm/GNPPSVM.h, classifier/svm/GPBTSVM.h,
	  classifier/svm/LibLinear.h, classifier/svm/LibSVM.h,
	  classifier/svm/LibSVMMultiClass.h,
	  classifier/svm/LibSVMOneClass.h, classifier/svm/MPDSVM.h,
	  classifier/svm/SVM.h, classifier/svm/SVMLin.h,
	  classifier/svm/SVMOcas.h, classifier/svm/SVMSGD.h,
	  classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h,
	  classifier/svm/SubGradientSVM.h, classifier/svm/Tron.h,
	  classifier/svm/WDSVMOcas.h, classifier/svm/gmnplib.h,
	  classifier/svm/gnpplib.h, classifier/svm/gpdtsolve.h,
	  classifier/svm/qpbsvmlib.h, clustering/Hierarchical.h,
	  clustering/KMeans.h, distance/BrayCurtisDistance.h,
	  distance/CanberraMetric.h, distance/CanberraWordDistance.h,
	  distance/ChebyshewMetric.h, distance/ChiSquareDistance.h,
	  distance/CosineDistance.h, distance/Distance.h,
	  distance/EuclidianDistance.h, distance/GeodesicMetric.h,
	  distance/HammingWordDistance.h, distance/JensenMetric.h,
	  distance/ManhattanMetric.h, distance/ManhattanWordDistance.h,
	  distance/MinkowskiMetric.h, distance/SparseEuclidianDistance.h,
	  distance/TanimotoDistance.h, distributions/hmm/HMM.h,
	  distributions/hmm/LinearHMM.h, features/Alphabet.h,
	  features/ByteFeatures.h, features/CharFeatures.h,
	  features/CombinedDotFeatures.h, features/CombinedFeatures.cpp,
	  features/CombinedFeatures.h, features/DummyFeatures.h,
	  features/ExplicitSpecFeatures.h, features/FKFeatures.h,
	  features/ImplicitWeightedSpecFeatures.h, features/IntFeatures.h,
	  features/Labels.h, features/MindyGramFeatures.h,
	  features/RealFeatures.h, features/RealFileFeatures.h,
	  features/ShortFeatures.h, features/ShortRealFeatures.h,
	  features/SimpleFeatures.h, features/SparseFeatures.h,
	  features/StringFeatures.h, features/TOPFeatures.h,
	  features/WDFeatures.h, features/WordFeatures.h,
	  guilib/GUIClassifier.h, guilib/GUIDistance.h,
	  guilib/GUIFeatures.cpp, guilib/GUIFeatures.h, guilib/GUIHMM.h,
	  guilib/GUIKernel.cpp, guilib/GUIKernel.h, guilib/GUILabels.h,
	  guilib/GUIMath.h, guilib/GUIPluginEstimate.h,
	  guilib/GUIPreProc.h, guilib/GUIStructure.h, guilib/GUITime.h,
	  interface/CmdLineInterface.h, interface/MatlabInterface.h,
	  interface/OctaveInterface.h, interface/PythonInterface.h,
	  interface/RInterface.h, interface/SGInterface.cpp,
	  kernel/AUCKernel.h, kernel/AvgDiagKernelNormalizer.h,
	  kernel/Chi2Kernel.h, kernel/CombinedKernel.cpp,
	  kernel/CombinedKernel.h, kernel/CommUlongStringKernel.h,
	  kernel/CommWordStringKernel.h, kernel/ConstKernel.h,
	  kernel/CustomKernel.h, kernel/DiagKernel.h,
	  kernel/DistanceKernel.h, kernel/FirstElementKernelNormalizer.h,
	  kernel/FixedDegreeStringKernel.h, kernel/GaussianKernel.h,
	  kernel/GaussianShiftKernel.h, kernel/GaussianShortRealKernel.h,
	  kernel/HistogramWordStringKernel.h,
	  kernel/IdentityKernelNormalizer.h, kernel/LinearByteKernel.h,
	  kernel/LinearKernel.h, kernel/LinearStringKernel.h,
	  kernel/LinearWordKernel.h, kernel/LocalAlignmentStringKernel.h,
	  kernel/LocalityImprovedStringKernel.h,
	  kernel/MatchWordStringKernel.h, kernel/MindyGramKernel.h,
	  kernel/OligoKernel.h, kernel/PolyKernel.h,
	  kernel/PolyMatchStringKernel.h,
	  kernel/PolyMatchWordStringKernel.h, kernel/PyramidChi2.h,
	  kernel/SalzbergWordStringKernel.h, kernel/SigmoidKernel.h,
	  kernel/SimpleLocalityImprovedStringKernel.h,
	  kernel/SparseGaussianKernel.h, kernel/SparseLinearKernel.h,
	  kernel/SparsePolyKernel.h, kernel/SqrtDiagKernelNormalizer.h,
	  kernel/TensorProductPairKernel.h,
	  kernel/WeightedCommWordStringKernel.h,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.h, lib/Cache.h,
	  lib/DynamicArray.h, lib/File.h, lib/List.h, lib/Mathematics.h,
	  lib/SimpleFile.h, lib/Time.h, lib/Trie.h, regression/KRR.h,
	  regression/svr/LibSVR.h, regression/svr/SVR_light.cpp,
	  regression/svr/SVR_light.h, structure/DynProg.h,
	  structure/Plif.h, structure/PlifArray.h: fixes for many further
	  memory leaks
	* features/Features.cpp, features/SimpleFeatures.h,
	  features/StringFeatures.h, guilib/GUIFeatures.h,
	  guilib/GUIHMM.cpp, interface/SGInterface.cpp, lib/List.h: fix
	  further memory leaks
	* classifier/svm/LibLinear.cpp, classifier/svm/MPDSVM.h,
	  classifier/svm/MultiClassSVM.cpp, classifier/svm/SVMLin.cpp,
	  classifier/svm/SVMOcas.cpp, classifier/svm/SVMSGD.cpp,
	  features/StringFeatures.h, guilib/GUIClassifier.cpp,
	  guilib/GUIKernel.cpp, interface/CmdLineInterface.cpp,
	  interface/SGInterface.cpp, kernel/WeightedDegreeStringKernel.cpp,
	  regression/svr/SVR_light.cpp: classifier and regression methods
	  are leak free now
	* classifier/LinearClassifier.h, classifier/svm/GPBTSVM.cpp,
	  classifier/svm/SVMOcas.cpp, clustering/Hierarchical.h,
	  guilib/GUIClassifier.cpp, guilib/GUIKernel.cpp: fix further leaks
	  in get_classifier
	* classifier/svm/Optimizer.cpp, classifier/svm/Optimizer.h,
	  classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h,
	  regression/svr/SVR_light.cpp: fix another leak and get rid of
	  extra svmlight specific prloqo interface files
	* NEWS, base/SGObject.h, classifier/KNN.h,
	  classifier/KernelPerceptron.h, classifier/LDA.h,
	  classifier/Perceptron.h, classifier/PluginEstimate.h,
	  classifier/svm/GPBTSVM.h, classifier/svm/LibLinear.h,
	  classifier/svm/LibSVM.h, classifier/svm/LibSVMMultiClass.h,
	  classifier/svm/LibSVMOneClass.h, classifier/svm/MPDSVM.h,
	  classifier/svm/SVM.h, classifier/svm/SVMLin.h,
	  classifier/svm/SVMOcas.h, classifier/svm/SVMSGD.h,
	  classifier/svm/SVM_light.h, classifier/svm/SubGradientSVM.h,
	  classifier/svm/Tron.h, classifier/svm/WDSVMOcas.h,
	  classifier/svm/gmnplib.h, classifier/svm/gnpplib.h,
	  classifier/svm/gpdtsolve.h, classifier/svm/qpbsvmlib.h,
	  clustering/Hierarchical.h, clustering/KMeans.h,
	  distributions/hmm/HMM.h, distributions/hmm/LinearHMM.h,
	  features/Alphabet.h, features/ByteFeatures.h,
	  features/CharFeatures.h, features/CombinedDotFeatures.h,
	  features/CombinedFeatures.h, features/DummyFeatures.h,
	  features/ExplicitSpecFeatures.h, features/FKFeatures.h,
	  features/ImplicitWeightedSpecFeatures.h, features/IntFeatures.h,
	  features/Labels.h, features/MindyGramFeatures.h,
	  features/RealFeatures.h, features/RealFileFeatures.h,
	  features/ShortFeatures.h, features/ShortRealFeatures.h,
	  features/SimpleFeatures.h, features/SparseFeatures.h,
	  features/StringFeatures.h, features/TOPFeatures.h,
	  features/WDFeatures.h, features/WordFeatures.h,
	  guilib/GUIClassifier.h, guilib/GUIDistance.h,
	  guilib/GUIFeatures.h, guilib/GUIHMM.h, guilib/GUIKernel.h,
	  guilib/GUILabels.h, guilib/GUIMath.h, guilib/GUIPluginEstimate.h,
	  guilib/GUIPreProc.h, guilib/GUIStructure.cpp,
	  guilib/GUIStructure.h, guilib/GUITime.h,
	  interface/CmdLineInterface.cpp, interface/CmdLineInterface.h,
	  interface/MatlabInterface.h, interface/OctaveInterface.h,
	  interface/PythonInterface.h, interface/RInterface.h,
	  interface/SGInterface.cpp, kernel/AvgDiagKernelNormalizer.h,
	  kernel/FirstElementKernelNormalizer.h, kernel/GaussianKernel.h,
	  kernel/IdentityKernelNormalizer.h, kernel/Kernel.h,
	  kernel/SqrtDiagKernelNormalizer.h, lib/Array.h, lib/Array2.h,
	  lib/Array3.h, lib/Cache.h, lib/Cplex.h, lib/DynamicArray.h,
	  lib/File.h, lib/List.h, lib/Mathematics.h, lib/Signal.h,
	  lib/SimpleFile.h, lib/Time.h, lib/Trie.h, lib/io.h,
	  preproc/LogPlusOne.h, preproc/NormOne.h, preproc/PCACut.h,
	  preproc/PruneVarSubMean.h, preproc/SortUlongString.h,
	  preproc/SortWordString.h, regression/KRR.h, structure/DynProg.h,
	  structure/Plif.cpp, structure/Plif.h, structure/PlifArray.h:
	  implement basis function get_name() for all SGObject derived
	  objects. this increadibly aids memory leak tracing
	* base/SGObject.h, distance/Distance.cpp, distance/Distance.h,
	  distributions/hmm/HMM.cpp, distributions/hmm/HMM.h,
	  features/CombinedFeatures.cpp, guilib/GUIClassifier.cpp,
	  guilib/GUIDistance.cpp, guilib/GUIFeatures.cpp,
	  guilib/GUIFeatures.h, guilib/GUIKernel.cpp, guilib/GUILabels.h,
	  guilib/GUIPreProc.cpp, guilib/GUIPreProc.h,
	  interface/SGInterface.cpp, kernel/Kernel.cpp,
	  kernel/SimpleLocalityImprovedStringKernel.cpp, lib/List.h: fix
	  many memory leaks and crashers due to missing SG_REF/UNREFs

2009-01-30  Soeren Sonnenburg <sonne@debian.org>

	* base/SGObject.h, features/StringFeatures.h,
	  guilib/GUIClassifier.cpp, guilib/GUIDistance.cpp,
	  guilib/GUIFeatures.cpp, guilib/GUIFeatures.h, guilib/GUIHMM.cpp,
	  guilib/GUIKernel.cpp, guilib/GUILabels.cpp, guilib/GUILabels.h,
	  guilib/GUIPluginEstimate.cpp, guilib/GUIPreProc.cpp,
	  guilib/GUIStructure.cpp, guilib/GUIStructure.h,
	  guilib/GUITime.cpp, interface/SGInterface.cpp, lib/List.h:
	  convert everything from delete to use SG_UNREF
	* base/Parallel.cpp, base/Version.cpp, lib/io.cpp: fix uninited
	  refcounts
	* base/Parallel.cpp, base/Parallel.h, base/SGObject.cpp,
	  base/SGObject.h, base/Version.h, classifier/svm/SVM.cpp,
	  classifier/svm/SVM_light.cpp, classifier/svm/WDSVMOcas.cpp,
	  clustering/KMeans.cpp, distributions/hmm/HMM.cpp,
	  features/DotFeatures.cpp, features/StringFeatures.h,
	  guilib/GUIDistance.cpp, guilib/GUIFeatures.cpp,
	  guilib/GUIPreProc.cpp, interface/CmdLineInterface.cpp,
	  interface/MatlabInterface.cpp, interface/OctaveInterface.cpp,
	  interface/PythonInterface.cpp, interface/RInterface.cpp,
	  interface/SGInterface.cpp, kernel/CombinedKernel.cpp,
	  kernel/Kernel.cpp, kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.cpp, lib/DynamicArray.h,
	  lib/Mathematics.cpp, lib/Mathematics.h, lib/Signal.cpp,
	  lib/Signal.h, lib/io.cpp, lib/io.h, lib/python.cpp, lib/r.h,
	  regression/svr/SVR_light.cpp, structure/DynProg.cpp: - convert
	  all classes to use new io -> sg_io /parallel/version global
	  objects
	  - remove all interface specific cruft from anything not under
	  interface / guilib
	  - introduce finite() in lib/Mathematics.h
	* base/SGObject.cpp, base/SGObject.h, classifier/svm/gmnpmkl.cpp,
	  kernel/Kernel.cpp, lib/io.h: broken commit DON'T USE
	* structure/Plif.h: remove obsolete code
	* structure/Plif.cpp: remove obsolete code
	* lib/Signal.cpp, lib/Signal.h, lib/cmdline.cpp, lib/io.cpp,
	  lib/io.h, lib/matlab.cpp, lib/octave.cpp, lib/python.cpp,
	  lib/r.cpp: This attempts to get rid of the language specific code
	  in lib/io.{h,cpp} and lib/Signal.{cpp,h}.
	  
	  To this end every interface has to define a couple of global
	  functions called
	  sg_print_{message,warning,error} and sg_cancel_computations. The
	  printing
	  functions are called whenever anything is writting to the screen
	  (and don't
	  raise exceptions or anything).
	  
	  The cancel function is called to allow an interface to check for
	  the occurrance
	  of a signal and to set the immediate cancel flag. It will be
	  called from
	  core/busy loops only. This is to fix the varius segmentation
	  faults caused by
	  throwing exceptions within signal handlers (which are illegal -
	  not in the
	  standard).
	* Makefile: on make install don't install gui/interface headers for
	  libshogun
	* classifier/svm/SVM_light.cpp: trap a division by zero

2009-01-29  Soeren Sonnenburg <sonne@debian.org>

	* NEWS: update news

2009-01-28  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/WDSVMOcas.cpp: potentially fix the same things for
	  WDSVMOcas
	* classifier/svm/SVMOcas.cpp, classifier/svm/WDSVMOcas.cpp,
	  classifier/svm/WDSVMOcas.h, guilib/GUIClassifier.cpp: bias
	  finally works for svmocas
	* NEWS: update NEWS
	* features/DotFeatures.cpp: compile fix
	* features/DotFeatures.cpp, features/DotFeatures.h,
	  features/DotFeatures.i: impl. method to obtain feature space
	* features/ImplicitWeightedSpecFeatures.cpp: fix same bug also in
	  implicit wd spec features
	* features/WDFeatures.cpp: fix crasher in WDFeatures and error: use
	  from_degree again
	* classifier/svm/SVMOcas.cpp: compile fixes related to ocas + bias
	* classifier/svm/SVMOcas.cpp, classifier/svm/SVMOcas.h: bias 4
	* classifier/svm/SVMOcas.cpp: bias 3
	* classifier/svm/SVMOcas.cpp, classifier/svm/SVMOcas.h: bias 2
	* classifier/svm/SVMOcas.cpp: bias 1
	* features/CombinedDotFeatures.i, features/DotFeatures.i,
	  features/ExplicitSpecFeatures.i,
	  features/ImplicitWeightedSpecFeatures.i, features/WDFeatures.i:
	  rename classes to remove C prefix
	* classifier/svm/LibSVMOneClass.cpp, classifier/svm/SVM_libsvm.cpp:
	  get printing functions right
	* classifier/svm/LibSVM.cpp, classifier/svm/LibSVMMultiClass.cpp,
	  classifier/svm/LibSVMOneClass.cpp, classifier/svm/Optimizer.cpp,
	  classifier/svm/SVMOcas.cpp, classifier/svm/SVM_libsvm.cpp,
	  classifier/svm/SVM_light.cpp, classifier/svm/gpdt.cpp,
	  classifier/svm/gpdtsolve.cpp, interface/SGInterface.cpp,
	  lib/Trie.cpp, regression/svr/LibSVR.cpp,
	  regression/svr/SVR_light.cpp, structure/DynProg.cpp,
	  structure/Plif.cpp, structure/Plif.h, structure/PlifArray.h,
	  structure/PlifBase.h: remove all printf based functions and
	  replace them with appropriate SG_PRINT functions
	* classifier/svm/gmnpmkl.h: potential compile fix
	* features/ImplicitWeightedSpecFeatures.cpp: minor cleanup
	* INSTALL, README: fix isntall/readme
	* classifier/svm/SVM_light.cpp: use dual simplex/presolving and fix
	  a memleak and wrong constraint for glpk-mkl

2009-01-27  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM_light.cpp, features/StringFeatures.h: add
	  debug code to figure out what goes wrong when this assertion
	  triggers

2009-01-25  Soeren Sonnenburg <sonne@debian.org>

	* features/DotFeatures.cpp: disable progress output
	* interface/SGInterface.cpp, kernel/Kernel.cpp: fix tppk bugs
	* NEWS, classifier/svm/gmnpmkl.cpp: fix a warning in
	  getsumofsignfreealphas in multiclass MKL, update NEWS
	* classifier/svm/SVM_light.cpp, guilib/GUIKernel.cpp,
	  guilib/GUIKernel.h, interface/SGInterface.cpp,
	  kernel/AUCKernel.cpp, kernel/Kernel.h, kernel/Kernel.i,
	  kernel/TensorProductPairKernel.cpp,
	  kernel/TensorProductPairKernel.h,
	  kernel/TensorProductPairKernel.i: implement tppk

2009-01-23  Alexander Binder <alexander.binder@first.fraunhofer.de>

	* classifier/svm/gmnpmkl.cpp, classifier/svm/gmnpmkl.h: moved
	  testing routine from gnmpmkl{.h,.cpp} into examples

2009-01-23  Soeren Sonnenburg <sonne@debian.org>

	* CONTRIBUTIONS, NEWS, classifier/svm/gmnpmkl.cpp,
	  classifier/svm/gmnpmkl.h: minor code beatutifications, update
	  NEWS and list of contributors

2009-01-22  Alexander Binder <alexander.binder@first.fraunhofer.de>

	* classifier/Classifier.h, classifier/svm/GMNPSVM.cpp,
	  classifier/svm/GMNPSVM.h, classifier/svm/gmnpmkl.cpp,
	  classifier/svm/gmnpmkl.h: implemented GLPK-based L1 MKL for the
	  multiclass svm GMNPSVM

2009-01-22  Soeren Sonnenburg <sonne@debian.org>

	* classifier/LinearClassifier.cpp, features/DotFeatures.cpp,
	  features/DotFeatures.h: parallel output computation

2009-01-21  Soeren Sonnenburg <sonne@debian.org>

	* features/CombinedDotFeatures.cpp, features/CombinedDotFeatures.h,
	  guilib/GUICommands.h, interface/SGInterface.cpp,
	  interface/SGInterface.h: allow getting of subfeature weights
	* features/CombinedDotFeatures.cpp, features/CombinedDotFeatures.h,
	  features/DotFeatures.h, features/WDFeatures.cpp,
	  guilib/GUICommands.h, interface/SGInterface.cpp,
	  interface/SGInterface.h: let the wd feature space also use
	  sqrt(weights) (to be symmetric and consisten with spec features)
	  and
	  add a weight to each dotfeature object to allow weighting of the
	  subfeatures of a combineddotfeature object
	* features/ImplicitWeightedSpecFeatures.cpp,
	  features/ImplicitWeightedSpecFeatures.h,
	  kernel/WeightedCommWordStringKernel.cpp: implement normalization
	  support for implicitwspecfeatures and modify weightedcommwords
	  internal representation to be equivalent (breaks code that relies
	  on the normal vector of the weightedcommwordstringkernel - but I
	  guess nothing like this has been spotted in the wild yet)
	* features/CombinedDotFeatures.cpp, features/Features.cpp,
	  features/StringFeatures.h, interface/SGInterface.cpp: now
	  add_todotfeatures works with WD/WSPEC

2009-01-20  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* kernel/WeightedDegreePositionStringKernel.cpp: * disabled a few
	  checks for set_WD_postion_weights_lhs and _rhs.
	  * now check whether lhs==rhs, and if so, then use
	  position_weights_lhs instead of _rhs.
	* interface/SGInterface.cpp: Don't understand the logic for
	  set_WD_position_weights .. did not work for me.. fiddled around,
	  but did not change anything
	* structure/PlifBase.h: abstract print function
	* structure/Plif.h: print function
	* structure/PlifArray.h:

2009-01-20  Alexander Zien <Alexander.Zien@tuebingen.mpg.de>

	* classifier/svm/SVM_light.cpp:

2009-01-20  Soeren Sonnenburg <sonne@debian.org>

	* features/StringFeatures.h: fix reading in string features < 1MB
	  in size
	* INSTALL, interface/SGInterface.cpp, interface/SGInterface.h:
	  change syntax to allow diverse features to be created from
	  strings
	* classifier/svm/SVM_light.h: compile fix
	* classifier/svm/SVM_light.cpp, configure: update glpk detection
	  (include term_out test)
	* NEWS, features/ExplicitSpecFeatures.h, features/Features.h,
	  features/ImplicitWeightedSpecFeatures.cpp,
	  features/ImplicitWeightedSpecFeatures.h,
	  features/StringFeatures.h, interface/SGInterface.cpp: weighted
	  spectrum features work now :)

2009-01-19  Alexander Zien <Alexander.Zien@tuebingen.mpg.de>

	* classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h:
	  implemented Newton chunking MKL for q>1
	  seems to run stably and fast

2009-01-19  Soeren Sonnenburg <sonne@debian.org>

	* features/ImplicitWeightedSpecFeatures.cpp,
	  features/WDFeatures.cpp: WDFeatures do work now :)
	* features/ExplicitSpecFeatures.cpp,
	  features/ExplicitSpecFeatures.h, features/ExplicitSpecFeatures.i,
	  features/Features.i, features/ImplicitWeightedSpecFeatures.cpp,
	  features/ImplicitWeightedSpecFeatures.h,
	  features/ImplicitWeightedSpecFeatures.i,
	  features/SpecFeatures.cpp, features/SpecFeatures.h,
	  features/SpecFeatures.i, guilib/GUIFeatures.cpp,
	  guilib/GUIFeatures.h: Impl. of spec features is too memory
	  demanding, rename to ExplicitSpecFeatures
	  and introduce ImplicitWeightedSpecFeatures for weighted spectrum
	  kernel that
	  requires the same inputs as the weightedcommwordkernel but only
	  2x as much memory (not 2**8 times ...)
	* features/SpecFeatures.cpp, features/SpecFeatures.h,
	  guilib/GUIFeatures.cpp, guilib/GUIFeatures.h,
	  interface/SGInterface.cpp: support standard spec kernel
	  normalization
	* features/SpecFeatures.cpp, features/SpecFeatures.h,
	  features/StringFeatures.h, features/WDFeatures.cpp,
	  features/WDFeatures.h, guilib/GUIFeatures.cpp,
	  guilib/GUIFeatures.h, guilib/GUIKernel.cpp,
	  interface/SGInterface.cpp: many (valgrind) fixes all over the
	  place, Specfeatures work reliably now.

2009-01-18  Soeren Sonnenburg <sonne@debian.org>

	* features/CombinedDotFeatures.cpp, features/CombinedDotFeatures.h,
	  features/Features.cpp, features/Features.h, guilib/GUICommands.h,
	  guilib/GUIFeatures.cpp, guilib/GUIFeatures.h,
	  interface/SGInterface.cpp, interface/SGInterface.h: combined dot
	  features work correctly now.

2009-01-17  Soeren Sonnenburg <sonne@debian.org>

	* features/DotFeatures.cpp, features/DotFeatures.h,
	  features/SimpleFeatures.h, features/SparseFeatures.h: implement
	  dense_dot_range and remove the now obsolete function from sparse
	  features - suddenly linear svms work again ;)

2009-01-16  Soeren Sonnenburg <sonne@debian.org>

	* configure: fix typo in configure, for disable glpk
	* classifier/svm/SVM_light.cpp: compile fix
	* classifier/svm/SVM_light.cpp, classifier/svm/WDSVMOcas.h,
	  interface/OctaveInterface.cpp: remove some cruft, fix a warning
	* classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h,
	  lib/Mathematics.h: write out which solver is taken when (for
	  debugging) and use logsum to stabilize alex's qnorm mkl (doesn't
	  seem to help...)
	* interface/MatlabInterface.cpp: workaround bug in matlab logicals
	  handling
	* interface/OctaveInterface.cpp: obtain boolean value for floats
	  for octave too
	* classifier/svm/SVM_light.cpp: improve logic when which solver is
	  used, compute obj in glpk based on new betas
	* NEWS: fix examples and update NEWS
	* regression/svr/SVR_light.cpp: fix compilation w/ cplex
	* classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h: GLPK
	  support for 1-norm MKL based on code from Chen Guohua
	* classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h,
	  regression/svr/SVR_light.cpp: further remove code duplication
	* classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h,
	  regression/svr/SVR_light.cpp: factor out mkl into separate
	  functions (to avoid code duplication) and use these functions for
	  linadd and vanilla kernels

2009-01-15  Soeren Sonnenburg <sonne@debian.org>

	* classifier/Classifier.cpp, classifier/Classifier.h,
	  classifier/svm/SVM_light.cpp, guilib/GUIClassifier.cpp,
	  guilib/GUIClassifier.h, guilib/GUICommands.h,
	  interface/SGInterface.cpp, interface/SGInterface.h: this adds an
	  option to select the solver type on the fly
	  (cplex/glpk/internal/auto)

2009-01-15  Alexander Zien <Alexander.Zien@tuebingen.mpg.de>

	* classifier/svm/SVM_light.cpp: compiles and works again in
	  slightly more modularized version
	* classifier/svm/SVM_light.cpp:

2009-01-15  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h:
	  potentially integrate alex's q-norm mkl solver
	* classifier/svm/SVM_light.cpp: magic reordering potentially fixes
	  convergence

2009-01-15  Alexander Zien <Alexander.Zien@tuebingen.mpg.de>

	* classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h:

2009-01-15  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM_light.cpp: with debug code
	* features/Features.h, features/SpecFeatures.cpp,
	  features/SpecFeatures.h, features/WDFeatures.cpp,
	  features/WDFeatures.h, guilib/GUIFeatures.cpp,
	  guilib/GUIFeatures.h, interface/SGInterface.cpp: minor fix
	* interface/OctaveInterface.cpp, lib/octave_typemaps.i: fix
	  copy&paste input corruption bug in octave static and modular
	  interfaces
	  occurring only with int32/int16 matrices/vectors (used in
	  functions such as
	  from_position_list!)

2009-01-14  Soeren Sonnenburg <sonne@debian.org>

	* configure: minor formatting change
	* features/SpecFeatures.cpp, features/SpecFeatures.h,
	  features/WDFeatures.cpp, features/WDFeatures.h: potentially
	  complete implementation of WD/SpecFeatures

2009-01-13  Soeren Sonnenburg <sonne@debian.org>

	* features/DotFeatures.h, features/DotFeatures.i,
	  features/Features.i, features/SpecFeatures.i,
	  features/WDFeatures.cpp, features/WDFeatures.i,
	  guilib/GUIClassifier.cpp: continue on WDFeatures
	* distance/Distance.cpp, features/Features.cpp,
	  features/Features.h, features/SimpleFeatures.h,
	  features/SpecFeatures.cpp, features/SpecFeatures.h,
	  features/WDFeatures.cpp, features/WDFeatures.h, kernel/Kernel.h,
	  lib/common.h: Implement spec features. also as dot features are
	  not really a feature class,
	  but more features with a dot property, start implementing feature
	  properties (similar to kernel properties).

2009-01-12  Sebastian Henschel <shogun@kodeaffe.de>

	* NEWS: - Updated NEWS.

2009-01-12  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h: - fix
	  compilation when cplex is not available
	  - use Math_init_random(as.integer(1.0)) in test r-modular test
	  suite (required for swig 1.3.37)
	* NEWS: update NEWS
	* classifier/svm/SVM_light.cpp, lib/Mathematics.h: q-norm mkl for
	  linadd based kernels
	* classifier/svm/SVM_light.cpp: fix convergence criterion, add
	  constraint removal
	* classifier/svm/SVM_light.cpp: remove debug code
	* classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h,
	  lib/Mathematics.h: add q-norm mkl

2009-01-09  Soeren Sonnenburg <sonne@debian.org>

	* features/SpecFeatures.cpp, features/SpecFeatures.h: uint8 should
	  be uint16
	* features/SpecFeatures.cpp, features/SpecFeatures.h,
	  features/WDFeatures.cpp: work in progress checkin for
	  wdfeatures/specfeatures
	* guilib/GUIFeatures.h: try to be clever when converting DNA to
	  binary formats and select RAWDNA as target type
	* guilib/GUIFeatures.h, interface/SGInterface.cpp: add support for
	  sg('convert', 'TRAIN', 'STRING', 'CHAR', 'STRING', 'BYTE') and
	  remove some cruft from GUIFeatures
	* classifier/svm/SVM.h, guilib/GUIClassifier.cpp,
	  guilib/GUIClassifier.h: enable general norm support - interface
	  side only
	* guilib/GUIKernel.cpp: fix crasher with comm* kernel
	* guilib/GUIClassifier.cpp: fix type check, test suite for
	  octave/python-modular runs through, commword kernel fix requires
	  re-generation of test
	* classifier/LinearClassifier.i: merge SparseLinearClassifier.i
	  into LinearClassifier.i
	* NEWS, classifier/Classifier.i, classifier/LDA.cpp,
	  classifier/LDA.h, classifier/LPBoost.cpp, classifier/LPBoost.h,
	  classifier/LPM.cpp, classifier/LPM.h,
	  classifier/LinearClassifier.cpp, classifier/LinearClassifier.h,
	  classifier/Perceptron.cpp, classifier/Perceptron.h,
	  classifier/SparseLinearClassifier.cpp,
	  classifier/SparseLinearClassifier.h,
	  classifier/SparseLinearClassifier.i,
	  classifier/SubGradientLPM.cpp, classifier/SubGradientLPM.h,
	  classifier/svm/LibLinear.cpp, classifier/svm/LibLinear.h,
	  classifier/svm/SVMLin.cpp, classifier/svm/SVMLin.h,
	  classifier/svm/SVMOcas.cpp, classifier/svm/SVMOcas.h,
	  classifier/svm/SVMSGD.cpp, classifier/svm/SVMSGD.h,
	  classifier/svm/SVM_linear.cpp, classifier/svm/SVM_linear.h,
	  classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h, classifier/svm/ssl.cpp,
	  classifier/svm/ssl.h, configure, distributions/hmm/HMM.h,
	  features/CombinedDotFeatures.cpp, features/CombinedDotFeatures.h,
	  features/CombinedDotFeatures.i, features/DotFeatures.h,
	  features/SimpleFeatures.h, features/SparseFeatures.h,
	  features/WDFeatures.cpp, features/WDFeatures.h,
	  guilib/GUIClassifier.cpp, guilib/GUIClassifier.h,
	  interface/SGInterface.cpp, lib/List.h: Integrate new DotFeatures
	  into existing linear classifiers

2009-01-08  Soeren Sonnenburg <sonne@debian.org>

	* features/CombinedDotFeatures.cpp, features/CombinedDotFeatures.h,
	  features/StringFeatures.h, features/WDFeatures.cpp,
	  features/WDFeatures.h, features/WDFeatures.i: started work on
	  WDFeatures + several bugfixes in combineddotfeatures
	* features/CombinedDotFeatures.cpp, features/CombinedDotFeatures.h,
	  features/CombinedDotFeatures.i, features/DotFeatures.cpp,
	  features/DotFeatures.h, features/DotFeatures.i,
	  features/Features.h, features/Features.i,
	  features/RealFeatures.cpp, features/SimpleFeatures.h,
	  features/SparseFeatures.h, lib/Mathematics.h: Implement combined
	  dot features and dot features for simple and sparse features.
	  
	  This required a hierarchy change: simple and sparse features are
	  now derived
	  from dot features (which in turn derive form features). combined
	  dot features
	  use copy & paste code from combined features to avoid multiple
	  inheritance (bad
	  bad diamonds, and dynamic_cast<CRealFeatures>(feat) is
	  #$*Y#$%(%Y&!!!)
	  
	  None of this is tested yet. Still TODO:
	  
	  - integrate into linear classfiers/kernels
	  - implement wd/spec features
	  
	  Not compile tested under any except the cmdline interface.

2009-01-05  Soeren Sonnenburg <sonne@debian.org>

	* features/CombinedDotFeatures.h, features/DotFeatures.h,
	  features/Features.h: prototyping of new dotfeatures and
	  combineddotfeatures

2008-12-30  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIClassifier.cpp: check for SVR before setting tube
	  epsilon
	* structure/DynProg.cpp: don't create the array on the stack
	* configure: sign also cmds
	* Makefile, configure: add iphone detection in configure / and sign
	  binary

2008-12-30  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* base/SGObject.h, base/Version.h:
	* lib/Mathematics.h: minor change for Mac OS and iPhone OS

2008-12-27  Soeren Sonnenburg <sonne@debian.org>

	* kernel/OligoKernel.cpp, kernel/OligoKernel.h: remove unused
	  includes, fixes a crasher occurring with long obsolete matlab
	  versions

2008-12-13  Soeren Sonnenburg <sonne@debian.org>

	* Makefile: build static libshogun.a for libshogun target

2008-12-11  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* structure/DynProg.cpp, structure/DynProg.h: -- changes of
	  structure branche merged back into trunk
	  -- function best_path_call restored

2008-12-09  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUIKernel.cpp: interface:
	  - Fixed compiling issue on normalization of CommString kernels.

2008-12-08  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIKernel.cpp: fix regression for COMM* kernels:
	  normalization argument was ignored

2008-12-05  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM.cpp, classifier/svm/libocas_common.h,
	  clustering/KMeans.cpp, distributions/histogram/Histogram.cpp,
	  guilib/GUIKernel.cpp, interface/SGInterface.cpp,
	  kernel/CombinedKernel.cpp, kernel/Kernel.cpp,
	  kernel/PolyMatchStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.cpp,
	  regression/svr/SVR_light.cpp, structure/DynProg.cpp: hopefully
	  removed all occurences of variable length arrays and log/pow
	  calls

2008-12-04  Soeren Sonnenburg <sonne@debian.org>

	* kernel/PolyMatchWordStringKernel.h: add missing bracket in front
	  of sum
	* classifier/svm/SVM_light.cpp: don't use variable length arrays in
	  svmlight
	* lib/io.h: use C99 variadic macros

2008-11-28  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreePositionStringKernel.i: add an option to set
	  wds kernel position weights

2008-11-26  Soeren Sonnenburg <sonne@debian.org>

	* configure: better description for wordsize detection
	* configure: detect integer word size

2008-11-25  Sebastian Henschel <shogun@kodeaffe.de>

	* ChangeLog: updated changelog
	* ChangeLog, Makefile: - Improved handling of ChangeLog creation a
	  little bit.
	* Makefile: updated changelog
	* Makefile: updated changelog
	* NEWS: - removed immature NEWS items.
	* NEWS: - updated NEWS in preparation for release 0.6.7.

2008-11-24  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM_light.cpp: compile fix introduced by an
	  accidentally inserted 'u'

2008-11-14  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* kernel/WeightedDegreePositionStringKernel.cpp: removed stderr
	  debug outputs

2008-11-07  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/svm/MultiClassSVM.h, guilib/GUIClassifier.cpp,
	  guilib/GUIClassifier.h, guilib/GUICommands.h,
	  interface/SGInterface.cpp, interface/SGInterface.h: static
	  interface:
	  - Added command GET_NUM_SVMS for usage by MultiClassSVMs.
	  - Extended command GET_SVM by optional index parameter to
	  determine which SVM
	  to get out of MultiClassSVM.
	  classifier:
	  - Fixed a segfault opportunity in MultiClassSVM.

2008-11-05  Sebastian Henschel <shogun@kodeaffe.de>

	* features/StringFeatures.i, lib/python_typemaps.i: - Made
	  StringBytesFeatures more useable for python-modular.
	* classifier/svm/WDSVMOcas.cpp, classifier/svm/WDSVMOcas.h: - Fixed
	  improper assignment of labels in constructor of WDSVMOcas leading
	  to
	  segfaults on destruction in (python) modular interface.
	  - Made Little documentation improvement and commented unnecessary
	  printing of
	  weight vector.

2008-11-03  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/svm/WDSVMOcas.h: - Added a default value (of NULL) to
	  argument of WDSVMOcas::classify().
	  - Added a debug print to WDSVMOcas::classify_example().

2008-11-02  Soeren Sonnenburg <sonne@debian.org>

	* interface/PythonInterface.cpp, lib/memory.cpp: really fix
	  contiguous arrays and also a warning in lib/memory.cpp snprintf
	  %lld requires a long long int argument
	* interface/PythonInterface.cpp: potentially better fix, that does
	  not require contiguous vectors

2008-11-01  Soeren Sonnenburg <sonne@debian.org>

	* interface/PythonInterface.cpp: test if array/vector is contigous

2008-10-31  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/LDA.cpp, classifier/svm/SVM_light.cpp,
	  classifier/svm/Tron.cpp, classifier/svm/Tron.h,
	  kernel/SigmoidKernel.cpp, preproc/PCACut.cpp, regression/KRR.cpp,
	  regression/svr/SVR_light.cpp: - BIG replacement XIX: polished a
	  few calls to external libraries.
	* kernel/WeightedDegreeStringKernel.h: kernel:
	  - Removed unused method declaration from
	  WeightedDegreeStringKernel.

2008-10-29  Sebastian Henschel <shogun@kodeaffe.de>

	* kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.cpp: - BIG replacement XVIII:
	  Fixed an earlier introduced bug and documented the
	  line of code accordingly.
	* .generate_link_dependencies.py, lib/common.i: - BIG replacement
	  XVII: our swig setup needs a bit assistance to recognise
	  the new types.
	* kernel/OligoKernel.cpp: - BIG replacement XVI: fixed bug
	  introduced into OligoKernel.
	* lib/common.h: - BIG replacement XV: sorry, need to concentrate
	  more.
	* lib/common.h: - BIG replacement XIV: added int8_t ifdef SUNOS

2008-10-28  Sebastian Henschel <shogun@kodeaffe.de>

	* kernel/OligoKernel.h,
	  kernel/WeightedDegreePositionStringKernel.cpp: kernel:
	  - Fixed compiler warning about missing doc in OligoKernel.
	  - Compile fix to previous change.
	* kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.cpp: kernel:
	  - Eliminated unnecessary variable shortcut in WD kernels.
	* classifier/LDA.cpp, classifier/LinearClassifier.h,
	  classifier/Perceptron.cpp, classifier/SubGradientLPM.cpp,
	  classifier/svm/GMNPSVM.cpp, classifier/svm/GNPPSVM.cpp,
	  classifier/svm/GPBTSVM.cpp, classifier/svm/LibSVM.cpp,
	  classifier/svm/LibSVMMultiClass.cpp,
	  classifier/svm/LibSVMOneClass.cpp,
	  classifier/svm/MultiClassSVM.cpp, classifier/svm/Optimizer.cpp,
	  classifier/svm/Optimizer.h, classifier/svm/SVM.cpp,
	  classifier/svm/SVM.h, classifier/svm/SVMLin.cpp,
	  classifier/svm/SVMOcas.cpp, classifier/svm/SVMOcas.h,
	  classifier/svm/SVMSGD.cpp, classifier/svm/SVM_libsvm.cpp,
	  classifier/svm/SVM_libsvm.h, classifier/svm/SVM_light.cpp,
	  classifier/svm/SVM_light.h, classifier/svm/SVM_linear.cpp,
	  classifier/svm/SVM_linear.h, classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/Tron.cpp, classifier/svm/Tron.h,
	  classifier/svm/WDSVMOcas.cpp, classifier/svm/WDSVMOcas.h,
	  classifier/svm/gmnplib.cpp, classifier/svm/gmnplib.h,
	  classifier/svm/gnpplib.cpp, classifier/svm/gnpplib.h,
	  classifier/svm/gpdt.cpp, classifier/svm/gpdt.h,
	  classifier/svm/gpdtsolve.cpp, classifier/svm/gpdtsolve.h,
	  classifier/svm/gpm.cpp, classifier/svm/gpm.h,
	  classifier/svm/libocas.cpp, classifier/svm/libocas.h,
	  classifier/svm/pr_loqo.cpp, classifier/svm/pr_loqo.h,
	  classifier/svm/qpbsvmlib.cpp, classifier/svm/qpssvmlib.cpp,
	  classifier/svm/qpssvmlib.h, classifier/svm/ssl.cpp,
	  classifier/svm/ssl.h, clustering/KMeans.cpp, clustering/KMeans.h,
	  distance/BrayCurtisDistance.cpp, distance/CanberraMetric.cpp,
	  distance/ChebyshewMetric.cpp, distance/ChiSquareDistance.cpp,
	  distance/CosineDistance.cpp, distance/Distance.cpp,
	  distance/EuclidianDistance.h, distance/GeodesicMetric.cpp,
	  distance/JensenMetric.cpp, distance/ManhattanMetric.cpp,
	  distance/MinkowskiMetric.cpp, distance/SparseEuclidianDistance.h,
	  distance/TanimotoDistance.cpp, distributions/hmm/HMM.cpp,
	  distributions/hmm/HMM.h, features/Alphabet.cpp,
	  features/FKFeatures.cpp, features/FKFeatures.h,
	  features/MindyGramFeatures.cpp, features/MindyGramFeatures.h,
	  features/SimpleFeatures.h, features/TOPFeatures.cpp,
	  features/WordFeatures.cpp, guilib/GUIClassifier.h,
	  guilib/GUIHMM.h, guilib/GUIMath.cpp,
	  kernel/AvgDiagKernelNormalizer.h, kernel/Chi2Kernel.cpp,
	  kernel/GaussianShiftKernel.cpp, kernel/GaussianShiftKernel.h,
	  kernel/Kernel.cpp, kernel/Kernel.h, kernel/LinearByteKernel.cpp,
	  kernel/LinearByteKernel.h, kernel/LinearKernel.cpp,
	  kernel/LinearKernel.h, kernel/LinearStringKernel.cpp,
	  kernel/LinearStringKernel.h, kernel/LinearWordKernel.cpp,
	  kernel/LinearWordKernel.h, kernel/MindyGramKernel.h,
	  kernel/OligoKernel.cpp, kernel/OligoKernel.h,
	  kernel/PolyKernel.cpp, kernel/SigmoidKernel.cpp,
	  kernel/SigmoidKernel.h,
	  kernel/SimpleLocalityImprovedStringKernel.cpp,
	  kernel/SparseGaussianKernel.cpp, kernel/SparseGaussianKernel.h,
	  kernel/SparseLinearKernel.h,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.cpp, lib/Cplex.cpp,
	  lib/Mathematics.cpp, lib/Mathematics.h, lib/Time.cpp, lib/Time.h,
	  lib/Trie.h, lib/octave_typemaps.i, lib/python_typemaps.i,
	  lib/r_typemaps.i, preproc/NormDerivativeLem3.cpp,
	  preproc/PCACut.cpp, preproc/PCACut.h,
	  preproc/PruneVarSubMean.cpp, regression/svr/LibSVR.cpp,
	  regression/svr/SVR_light.cpp, regression/svr/SVR_light.h,
	  structure/DynProg.cpp: - BIG replacement XIII: double ->
	  float64_t (where (hopefully) appropriate)
	* .scrub_docstrings.py, README.developer, classifier/Classifier.h,
	  classifier/KNN.cpp, classifier/KNN.h,
	  classifier/KernelPerceptron.cpp, classifier/KernelPerceptron.h,
	  classifier/LDA.cpp, classifier/LDA.h, classifier/LPBoost.cpp,
	  classifier/LPBoost.h, classifier/LPM.cpp, classifier/LPM.h,
	  classifier/LinearClassifier.h, classifier/LinearClassifier.i,
	  classifier/Perceptron.cpp, classifier/Perceptron.h,
	  classifier/PluginEstimate.cpp, classifier/PluginEstimate.h,
	  classifier/SparseLinearClassifier.h,
	  classifier/SparseLinearClassifier.i,
	  classifier/SubGradientLPM.cpp, classifier/SubGradientLPM.h,
	  classifier/svm/CPLEXSVM.cpp, classifier/svm/GMNPSVM.cpp,
	  classifier/svm/GMNPSVM.h, classifier/svm/GNPPSVM.cpp,
	  classifier/svm/GNPPSVM.h, classifier/svm/GPBTSVM.cpp,
	  classifier/svm/GPBTSVM.h, classifier/svm/LibLinear.cpp,
	  classifier/svm/LibLinear.h, classifier/svm/LibSVM.cpp,
	  classifier/svm/LibSVM.h, classifier/svm/LibSVMMultiClass.cpp,
	  classifier/svm/LibSVMMultiClass.h,
	  classifier/svm/LibSVMOneClass.cpp,
	  classifier/svm/LibSVMOneClass.h, classifier/svm/MPDSVM.cpp,
	  classifier/svm/MPDSVM.h, classifier/svm/MultiClassSVM.cpp,
	  classifier/svm/MultiClassSVM.h, classifier/svm/SVM.cpp,
	  classifier/svm/SVM.h, classifier/svm/SVM.i,
	  classifier/svm/SVMLin.cpp, classifier/svm/SVMLin.h,
	  classifier/svm/SVMOcas.cpp, classifier/svm/SVMOcas.h,
	  classifier/svm/SVMSGD.cpp, classifier/svm/SVMSGD.h,
	  classifier/svm/SVM_libsvm.cpp, classifier/svm/SVM_light.cpp,
	  classifier/svm/SVM_light.h, classifier/svm/SVM_linear.h,
	  classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h, classifier/svm/WDSVMOcas.cpp,
	  classifier/svm/WDSVMOcas.h, classifier/svm/gmnplib.cpp,
	  classifier/svm/gmnplib.h, classifier/svm/gnpplib.cpp,
	  classifier/svm/gnpplib.h, classifier/svm/qpbsvmlib.cpp,
	  classifier/svm/qpbsvmlib.h, classifier/svm/ssl.cpp,
	  classifier/svm/ssl.h, clustering/Hierarchical.cpp,
	  clustering/Hierarchical.h, clustering/Hierarchical.i,
	  clustering/KMeans.cpp, clustering/KMeans.h, clustering/KMeans.i,
	  distance/BrayCurtisDistance.cpp, distance/BrayCurtisDistance.h,
	  distance/CanberraMetric.cpp, distance/CanberraMetric.h,
	  distance/CanberraWordDistance.cpp,
	  distance/CanberraWordDistance.h, distance/ChebyshewMetric.cpp,
	  distance/ChebyshewMetric.h, distance/ChiSquareDistance.cpp,
	  distance/ChiSquareDistance.h, distance/CosineDistance.cpp,
	  distance/CosineDistance.h, distance/Distance.cpp,
	  distance/Distance.h, distance/Distance.i,
	  distance/EuclidianDistance.cpp, distance/EuclidianDistance.h,
	  distance/GeodesicMetric.cpp, distance/GeodesicMetric.h,
	  distance/HammingWordDistance.cpp, distance/HammingWordDistance.h,
	  distance/JensenMetric.cpp, distance/JensenMetric.h,
	  distance/ManhattanMetric.cpp, distance/ManhattanMetric.h,
	  distance/ManhattanWordDistance.cpp,
	  distance/ManhattanWordDistance.h, distance/MinkowskiMetric.cpp,
	  distance/MinkowskiMetric.h, distance/RealDistance.h,
	  distance/SimpleDistance.h, distance/SimpleDistance.i,
	  distance/SparseDistance.h, distance/SparseDistance.i,
	  distance/SparseEuclidianDistance.cpp,
	  distance/SparseEuclidianDistance.h, distance/StringDistance.h,
	  distance/StringDistance.i, distance/TanimotoDistance.cpp,
	  distance/TanimotoDistance.h, distributions/Distribution.cpp,
	  distributions/Distribution.h, distributions/Distribution.i,
	  distributions/histogram/Histogram.cpp,
	  distributions/histogram/Histogram.h,
	  distributions/histogram/Histogram.i, distributions/hmm/GHMM.cpp,
	  distributions/hmm/GHMM.h, distributions/hmm/HMM.cpp,
	  distributions/hmm/HMM.h, distributions/hmm/LinearHMM.cpp,
	  distributions/hmm/LinearHMM.h, distributions/hmm/LinearHMM.i,
	  evaluation/PerformanceMeasures.cpp,
	  evaluation/PerformanceMeasures.h,
	  evaluation/PerformanceMeasures.i, features/FKFeatures.cpp,
	  features/FKFeatures.h, features/Features.h, features/Labels.cpp,
	  features/Labels.h, features/Labels.i, features/RealFeatures.cpp,
	  features/RealFeatures.h, features/RealFeatures.i,
	  features/RealFileFeatures.cpp, features/RealFileFeatures.h,
	  features/SimpleFeatures.h, features/SimpleFeatures.i,
	  features/SparseFeatures.h, features/SparseFeatures.i,
	  features/StringFeatures.h, features/TOPFeatures.cpp,
	  features/TOPFeatures.h, guilib/GUIClassifier.cpp,
	  guilib/GUIClassifier.h, guilib/GUIDistance.cpp,
	  guilib/GUIDistance.h, guilib/GUIFeatures.cpp,
	  guilib/GUIFeatures.h, guilib/GUIHMM.cpp, guilib/GUIHMM.h,
	  guilib/GUIKernel.cpp, guilib/GUIKernel.h, guilib/GUIMath.cpp,
	  guilib/GUIMath.h, guilib/GUIPluginEstimate.cpp,
	  guilib/GUIPluginEstimate.h, guilib/GUIPreProc.cpp,
	  guilib/GUIPreProc.h, guilib/GUIStructure.cpp,
	  guilib/GUIStructure.h, interface/CmdLineInterface.cpp,
	  interface/CmdLineInterface.h, interface/MatlabInterface.cpp,
	  interface/MatlabInterface.h, interface/OctaveInterface.cpp,
	  interface/OctaveInterface.h, interface/PythonInterface.cpp,
	  interface/PythonInterface.h, interface/RInterface.cpp,
	  interface/RInterface.h, interface/SGInterface.cpp,
	  interface/SGInterface.h, kernel/AUCKernel.cpp,
	  kernel/AUCKernel.h, kernel/AvgDiagKernelNormalizer.h,
	  kernel/Chi2Kernel.cpp, kernel/Chi2Kernel.h,
	  kernel/CombinedKernel.cpp, kernel/CombinedKernel.h,
	  kernel/CommUlongStringKernel.cpp, kernel/CommUlongStringKernel.h,
	  kernel/CommWordStringKernel.cpp, kernel/CommWordStringKernel.h,
	  kernel/ConstKernel.cpp, kernel/ConstKernel.h,
	  kernel/CustomKernel.cpp, kernel/CustomKernel.h,
	  kernel/CustomKernel.i, kernel/DiagKernel.cpp,
	  kernel/DiagKernel.h, kernel/DiceKernelNormalizer.h,
	  kernel/DistanceKernel.cpp, kernel/DistanceKernel.h,
	  kernel/FirstElementKernelNormalizer.h,
	  kernel/FixedDegreeStringKernel.cpp,
	  kernel/FixedDegreeStringKernel.h, kernel/GaussianKernel.cpp,
	  kernel/GaussianKernel.h, kernel/GaussianShiftKernel.cpp,
	  kernel/GaussianShiftKernel.h, kernel/GaussianShortRealKernel.cpp,
	  kernel/GaussianShortRealKernel.h,
	  kernel/HistogramWordStringKernel.cpp,
	  kernel/HistogramWordStringKernel.h,
	  kernel/IdentityKernelNormalizer.h, kernel/Kernel.cpp,
	  kernel/Kernel.h, kernel/Kernel.i, kernel/KernelNormalizer.h,
	  kernel/LinearByteKernel.cpp, kernel/LinearByteKernel.h,
	  kernel/LinearKernel.cpp, kernel/LinearKernel.h,
	  kernel/LinearKernel.i, kernel/LinearStringKernel.cpp,
	  kernel/LinearStringKernel.h, kernel/LinearWordKernel.cpp,
	  kernel/LinearWordKernel.h, kernel/LocalAlignmentStringKernel.cpp,
	  kernel/LocalAlignmentStringKernel.h,
	  kernel/LocalityImprovedStringKernel.cpp,
	  kernel/LocalityImprovedStringKernel.h,
	  kernel/MatchWordStringKernel.cpp, kernel/MatchWordStringKernel.h,
	  kernel/MindyGramKernel.cpp, kernel/MindyGramKernel.h,
	  kernel/OligoKernel.cpp, kernel/OligoKernel.h,
	  kernel/PolyKernel.cpp, kernel/PolyKernel.h,
	  kernel/PolyMatchStringKernel.cpp, kernel/PolyMatchStringKernel.h,
	  kernel/PolyMatchWordStringKernel.cpp,
	  kernel/PolyMatchWordStringKernel.h, kernel/PyramidChi2.cpp,
	  kernel/PyramidChi2.h, kernel/SalzbergWordStringKernel.cpp,
	  kernel/SalzbergWordStringKernel.h, kernel/SigmoidKernel.cpp,
	  kernel/SigmoidKernel.h, kernel/SimpleKernel.h,
	  kernel/SimpleKernel.i,
	  kernel/SimpleLocalityImprovedStringKernel.cpp,
	  kernel/SimpleLocalityImprovedStringKernel.h,
	  kernel/SparseGaussianKernel.cpp, kernel/SparseGaussianKernel.h,
	  kernel/SparseKernel.h, kernel/SparseKernel.i,
	  kernel/SparseLinearKernel.cpp, kernel/SparseLinearKernel.h,
	  kernel/SparsePolyKernel.cpp, kernel/SparsePolyKernel.h,
	  kernel/SqrtDiagKernelNormalizer.h, kernel/StringKernel.h,
	  kernel/StringKernel.i, kernel/TanimotoKernelNormalizer.h,
	  kernel/WeightedCommWordStringKernel.cpp,
	  kernel/WeightedCommWordStringKernel.h,
	  kernel/WeightedCommWordStringKernel.i,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreePositionStringKernel.i,
	  kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.h,
	  kernel/WeightedDegreeStringKernel.i, lib/Array.i, lib/Array2.i,
	  lib/Array3.i, lib/Cplex.cpp, lib/Cplex.h, lib/DynamicArray.i,
	  lib/File.cpp, lib/File.h, lib/Mathematics.cpp, lib/Mathematics.h,
	  lib/Trie.cpp, lib/Trie.h, lib/common.h, lib/io.cpp, lib/io.h,
	  lib/octave_typemaps.i, lib/python_typemaps.i, lib/r_typemaps.i,
	  preproc/LogPlusOne.cpp, preproc/LogPlusOne.h,
	  preproc/NormDerivativeLem3.cpp, preproc/NormDerivativeLem3.h,
	  preproc/NormOne.cpp, preproc/NormOne.h, preproc/PCACut.cpp,
	  preproc/PCACut.h, preproc/PruneVarSubMean.cpp,
	  preproc/PruneVarSubMean.h, preproc/SimplePreProc.h,
	  preproc/SimplePreProc.i, regression/KRR.cpp, regression/KRR.h,
	  regression/svr/LibSVR.cpp, regression/svr/LibSVR.h,
	  regression/svr/SVR_light.cpp, regression/svr/SVR_light.h,
	  structure/DynProg.cpp, structure/DynProg.h, structure/DynProg.i,
	  structure/Plif.cpp, structure/Plif.h, structure/Plif.i,
	  structure/PlifArray.cpp, structure/PlifArray.h,
	  structure/PlifBase.h: - BIG replacement XII: DREAL -> float64_t

2008-10-27  Sebastian Henschel <shogun@kodeaffe.de>

	* .scrub_docstrings.py, README.developer,
	  features/SparseFeatures.h, features/SparseFeatures.i,
	  features/StringFeatures.h, lib/Mathematics.h, lib/common.h,
	  lib/python_typemaps.i: - BIG replacement XI: LONGREAL/long double
	  -> float128_t
	* .scrub_docstrings.py, README.developer,
	  classifier/svm/WDSVMOcas.cpp, classifier/svm/WDSVMOcas.h,
	  classifier/svm/gpdt.cpp, classifier/svm/gpdt.h,
	  classifier/svm/gpdtsolve.cpp, classifier/svm/gpm.cpp,
	  classifier/svm/gpm.h, distance/Distance.cpp, distance/Distance.h,
	  distributions/hmm/HMM.cpp, features/ShortRealFeatures.cpp,
	  features/ShortRealFeatures.h, features/ShortRealFeatures.i,
	  features/SimpleFeatures.h, features/SimpleFeatures.i,
	  features/SparseFeatures.h, features/SparseFeatures.i,
	  interface/CmdLineInterface.cpp, interface/CmdLineInterface.h,
	  interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/OctaveInterface.cpp, interface/OctaveInterface.h,
	  interface/PythonInterface.cpp, interface/PythonInterface.h,
	  interface/RInterface.cpp, interface/RInterface.h,
	  interface/SGInterface.cpp, interface/SGInterface.h,
	  kernel/CustomKernel.cpp, kernel/CustomKernel.h,
	  kernel/GaussianShortRealKernel.cpp,
	  kernel/GaussianShortRealKernel.h, kernel/Kernel.cpp,
	  kernel/Kernel.h, kernel/LocalAlignmentStringKernel.cpp,
	  kernel/LocalAlignmentStringKernel.h, kernel/SimpleKernel.h,
	  kernel/SimpleKernel.i,
	  kernel/WeightedDegreePositionStringKernel.cpp, lib/Array.h,
	  lib/Array.i, lib/Array2.h, lib/Array2.i, lib/Array3.h,
	  lib/Array3.i, lib/DynamicArray.i, lib/File.cpp, lib/File.h,
	  lib/Mathematics.cpp, lib/Mathematics.h, lib/Trie.h, lib/common.h,
	  lib/io.cpp, lib/octave_typemaps.i, lib/python_typemaps.i,
	  lib/r_typemaps.i: - BIG replacement X: SHORTREAL/float ->
	  float32_t

2008-10-26  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/svm/MPDSVM.cpp, classifier/svm/SVM_libsvm.cpp,
	  classifier/svm/gnpplib.cpp, classifier/svm/gnpplib.h,
	  classifier/svm/gpdt.cpp, features/StringFeatures.h,
	  lib/Mathematics.h, structure/DynProg.cpp, structure/DynProg.h: -
	  BIG replacement IX: short int -> int16_t, long int -> int32_t,
	  unsigned short
	  -> uint16_t, unsigned long -> uint32_t
	* .scrub_docstrings.py, distance/SimpleDistance.h,
	  distance/SparseDistance.h, distance/StringDistance.h,
	  features/Alphabet.cpp, features/Alphabet.h, features/Features.h,
	  features/ShortFeatures.cpp, features/ShortFeatures.h,
	  features/ShortFeatures.i, features/SimpleFeatures.h,
	  features/SimpleFeatures.i, features/SparseFeatures.h,
	  features/SparseFeatures.i, features/StringFeatures.h,
	  features/StringFeatures.i, guilib/GUIFeatures.cpp,
	  interface/CmdLineInterface.cpp, interface/CmdLineInterface.h,
	  interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/OctaveInterface.cpp, interface/OctaveInterface.h,
	  interface/PythonInterface.cpp, interface/PythonInterface.h,
	  interface/RInterface.cpp, interface/RInterface.h,
	  interface/SGInterface.cpp, interface/SGInterface.h,
	  kernel/SimpleKernel.h, kernel/SimpleKernel.i,
	  kernel/SparseKernel.h, kernel/StringKernel.h,
	  kernel/StringKernel.i, lib/Array.i, lib/Array2.i, lib/Array3.i,
	  lib/DynamicArray.i, lib/File.cpp, lib/File.h, lib/common.h,
	  lib/octave_typemaps.i, lib/python_typemaps.i, lib/r_typemaps.i,
	  preproc/SimplePreProc.h, preproc/SimplePreProc.i,
	  structure/DynProg.h: - BIG replacement VIII: SHORT -> int16_t
	* .scrub_docstrings.py, README.developer, base/Version.h,
	  classifier/svm/gmnplib.cpp, classifier/svm/gmnplib.h,
	  classifier/svm/gnpplib.cpp, classifier/svm/gnpplib.h,
	  distance/Distance.cpp, distributions/hmm/HMM.cpp,
	  features/Alphabet.cpp, features/Alphabet.h, features/Alphabet.i,
	  features/ByteFeatures.cpp, features/CharFeatures.cpp,
	  features/IntFeatures.cpp, features/Labels.cpp,
	  features/MindyGramFeatures.cpp, features/RealFeatures.cpp,
	  features/RealFileFeatures.h, features/ShortRealFeatures.cpp,
	  features/SimpleFeatures.h, features/SparseFeatures.h,
	  features/SparseFeatures.i, features/StringFeatures.h,
	  features/StringFeatures.i, guilib/GUIHMM.cpp,
	  interface/CmdLineInterface.cpp, interface/CmdLineInterface.h,
	  interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/OctaveInterface.cpp, interface/OctaveInterface.h,
	  interface/PythonInterface.cpp, interface/PythonInterface.h,
	  interface/RInterface.cpp, interface/RInterface.h,
	  interface/SGInterface.cpp, interface/SGInterface.h,
	  kernel/CommWordStringKernel.cpp,
	  kernel/FixedDegreeStringKernel.cpp, kernel/Kernel.cpp,
	  kernel/SalzbergWordStringKernel.h, lib/Array.i, lib/Array2.i,
	  lib/Array3.i, lib/Cache.h, lib/Cplex.cpp, lib/DynamicArray.i,
	  lib/File.cpp, lib/File.h, lib/Mathematics.cpp, lib/Mathematics.h,
	  lib/SimpleFile.h, lib/Time.cpp, lib/Time.h, lib/common.h,
	  lib/io.cpp, lib/io.h, lib/python_typemaps.i: - BIG replacement
	  VII: LONG -> int64_t
	* .scrub_docstrings.py, classifier/svm/WDSVMOcas.cpp,
	  distance/SimpleDistance.h, distance/SparseDistance.h,
	  distance/StringDistance.h, distance/StringDistance.i,
	  features/Alphabet.cpp, features/Alphabet.h,
	  features/MindyGramFeatures.cpp, features/MindyGramFeatures.h,
	  features/SimpleFeatures.h, features/SparseFeatures.h,
	  features/SparseFeatures.i, features/StringFeatures.h,
	  features/StringFeatures.i, guilib/GUIFeatures.cpp,
	  guilib/GUIFeatures.h, guilib/GUIPreProc.cpp,
	  interface/SGInterface.cpp, kernel/CommUlongStringKernel.cpp,
	  kernel/CommUlongStringKernel.h, kernel/Kernel.cpp,
	  kernel/Kernel.h, kernel/SimpleKernel.h, kernel/SimpleKernel.i,
	  kernel/SparseKernel.h, kernel/StringKernel.h,
	  kernel/StringKernel.i,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.cpp, lib/Array.i, lib/Array2.i,
	  lib/Array3.i, lib/DynamicArray.i, lib/SimpleFile.h, lib/Trie.h,
	  lib/common.h, lib/memory.cpp, lib/python_typemaps.i,
	  preproc/SimplePreProc.h, preproc/SimplePreProc.i,
	  preproc/SortUlongString.cpp, preproc/SortUlongString.h,
	  preproc/StringPreProc.h, preproc/StringPreProc.i: - BIG
	  replacement VI: ULONG -> uint64_t; unsigned long long int ->
	  uintmax_t
	* .scrub_docstrings.py, README.developer, base/Parallel.h,
	  base/SGObject.h, base/Version.cpp, base/Version.h,
	  classifier/Classifier.cpp, classifier/Classifier.h,
	  classifier/KNN.cpp, classifier/KNN.h,
	  classifier/KernelPerceptron.cpp, classifier/KernelPerceptron.h,
	  classifier/LDA.cpp, classifier/LPBoost.cpp, classifier/LPBoost.h,
	  classifier/LPM.cpp, classifier/LinearClassifier.cpp,
	  classifier/LinearClassifier.h, classifier/LinearClassifier.i,
	  classifier/Perceptron.cpp, classifier/Perceptron.h,
	  classifier/PluginEstimate.cpp, classifier/PluginEstimate.h,
	  classifier/SparseLinearClassifier.cpp,
	  classifier/SparseLinearClassifier.h,
	  classifier/SparseLinearClassifier.i,
	  classifier/SubGradientLPM.cpp, classifier/SubGradientLPM.h,
	  classifier/svm/CPLEXSVM.cpp, classifier/svm/GMNPSVM.cpp,
	  classifier/svm/GNPPSVM.cpp, classifier/svm/GPBTSVM.cpp,
	  classifier/svm/LibLinear.cpp, classifier/svm/LibSVM.cpp,
	  classifier/svm/LibSVMMultiClass.cpp,
	  classifier/svm/LibSVMOneClass.cpp, classifier/svm/MPDSVM.cpp,
	  classifier/svm/MPDSVM.h, classifier/svm/MultiClassSVM.cpp,
	  classifier/svm/MultiClassSVM.h, classifier/svm/Optimizer.cpp,
	  classifier/svm/Optimizer.h, classifier/svm/SVM.cpp,
	  classifier/svm/SVM.h, classifier/svm/SVM.i,
	  classifier/svm/SVMLin.cpp, classifier/svm/SVMOcas.cpp,
	  classifier/svm/SVMOcas.h, classifier/svm/SVMSGD.cpp,
	  classifier/svm/SVMSGD.h, classifier/svm/SVM_libsvm.cpp,
	  classifier/svm/SVM_libsvm.h, classifier/svm/SVM_light.cpp,
	  classifier/svm/SVM_light.h, classifier/svm/SVM_linear.cpp,
	  classifier/svm/SVM_linear.h, classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h, classifier/svm/Tron.cpp,
	  classifier/svm/Tron.h, classifier/svm/WDSVMOcas.cpp,
	  classifier/svm/WDSVMOcas.h, classifier/svm/gmnplib.cpp,
	  classifier/svm/gmnplib.h, classifier/svm/gnpplib.cpp,
	  classifier/svm/gnpplib.h, classifier/svm/gpdt.cpp,
	  classifier/svm/gpdt.h, classifier/svm/gpdtsolve.cpp,
	  classifier/svm/gpdtsolve.h, classifier/svm/gpm.cpp,
	  classifier/svm/gpm.h, classifier/svm/libocas.cpp,
	  classifier/svm/pr_loqo.cpp, classifier/svm/pr_loqo.h,
	  classifier/svm/qpbsvmlib.cpp, classifier/svm/qpbsvmlib.h,
	  classifier/svm/qpssvmlib.cpp, classifier/svm/qpssvmlib.h,
	  classifier/svm/ssl.cpp, classifier/svm/ssl.h,
	  clustering/Hierarchical.cpp, clustering/Hierarchical.h,
	  clustering/Hierarchical.i, clustering/KMeans.cpp,
	  clustering/KMeans.h, clustering/KMeans.i,
	  distance/BrayCurtisDistance.cpp, distance/BrayCurtisDistance.h,
	  distance/CanberraMetric.cpp, distance/CanberraMetric.h,
	  distance/CanberraWordDistance.cpp,
	  distance/CanberraWordDistance.h, distance/ChebyshewMetric.cpp,
	  distance/ChebyshewMetric.h, distance/ChiSquareDistance.cpp,
	  distance/ChiSquareDistance.h, distance/CosineDistance.cpp,
	  distance/CosineDistance.h, distance/Distance.cpp,
	  distance/Distance.h, distance/Distance.i,
	  distance/EuclidianDistance.cpp, distance/EuclidianDistance.h,
	  distance/GeodesicMetric.cpp, distance/GeodesicMetric.h,
	  distance/HammingWordDistance.cpp, distance/HammingWordDistance.h,
	  distance/JensenMetric.cpp, distance/JensenMetric.h,
	  distance/ManhattanMetric.cpp, distance/ManhattanMetric.h,
	  distance/ManhattanWordDistance.cpp,
	  distance/ManhattanWordDistance.h, distance/MinkowskiMetric.cpp,
	  distance/MinkowskiMetric.h, distance/SimpleDistance.h,
	  distance/SimpleDistance.i, distance/SparseDistance.h,
	  distance/SparseDistance.i, distance/SparseEuclidianDistance.cpp,
	  distance/SparseEuclidianDistance.h, distance/StringDistance.h,
	  distance/StringDistance.i, distance/TanimotoDistance.cpp,
	  distance/TanimotoDistance.h, distributions/Distribution.cpp,
	  distributions/Distribution.h, distributions/Distribution.i,
	  distributions/histogram/Histogram.cpp,
	  distributions/histogram/Histogram.h,
	  distributions/histogram/Histogram.i, distributions/hmm/GHMM.cpp,
	  distributions/hmm/GHMM.h, distributions/hmm/HMM.cpp,
	  distributions/hmm/HMM.h, distributions/hmm/LinearHMM.cpp,
	  distributions/hmm/LinearHMM.h, distributions/hmm/LinearHMM.i,
	  evaluation/PerformanceMeasures.cpp,
	  evaluation/PerformanceMeasures.h,
	  evaluation/PerformanceMeasures.i, features/Alphabet.cpp,
	  features/Alphabet.h, features/Alphabet.i,
	  features/ByteFeatures.cpp, features/ByteFeatures.h,
	  features/ByteFeatures.i, features/CharFeatures.cpp,
	  features/CharFeatures.h, features/CharFeatures.i,
	  features/CombinedFeatures.h, features/DummyFeatures.h,
	  features/FKFeatures.cpp, features/FKFeatures.h,
	  features/Features.cpp, features/Features.h,
	  features/IntFeatures.cpp, features/IntFeatures.h,
	  features/IntFeatures.i, features/Labels.cpp, features/Labels.h,
	  features/Labels.i, features/MindyGramFeatures.cpp,
	  features/MindyGramFeatures.h, features/RealFeatures.cpp,
	  features/RealFeatures.h, features/RealFeatures.i,
	  features/RealFileFeatures.cpp, features/RealFileFeatures.h,
	  features/ShortFeatures.cpp, features/ShortFeatures.h,
	  features/ShortFeatures.i, features/ShortRealFeatures.cpp,
	  features/ShortRealFeatures.h, features/ShortRealFeatures.i,
	  features/SimpleFeatures.h, features/SimpleFeatures.i,
	  features/SparseFeatures.h, features/SparseFeatures.i,
	  features/StringFeatures.h, features/StringFeatures.i,
	  features/TOPFeatures.cpp, features/TOPFeatures.h,
	  features/WordFeatures.cpp, features/WordFeatures.h,
	  features/WordFeatures.i, guilib/GUIClassifier.cpp,
	  guilib/GUIClassifier.h, guilib/GUIFeatures.cpp,
	  guilib/GUIFeatures.h, guilib/GUIHMM.cpp, guilib/GUIHMM.h,
	  guilib/GUIKernel.cpp, guilib/GUIKernel.h, guilib/GUIMath.cpp,
	  guilib/GUIMath.h, guilib/GUIPluginEstimate.cpp,
	  guilib/GUIPluginEstimate.h, guilib/GUIPreProc.cpp,
	  guilib/GUIPreProc.h, guilib/GUIStructure.cpp,
	  guilib/GUIStructure.h, interface/CmdLineInterface.cpp,
	  interface/CmdLineInterface.h, interface/MatlabInterface.cpp,
	  interface/MatlabInterface.h, interface/OctaveInterface.cpp,
	  interface/OctaveInterface.h, interface/PythonInterface.cpp,
	  interface/PythonInterface.h, interface/RInterface.cpp,
	  interface/RInterface.h, interface/SGInterface.cpp,
	  interface/SGInterface.h, kernel/AUCKernel.cpp,
	  kernel/AUCKernel.h, kernel/AvgDiagKernelNormalizer.h,
	  kernel/Chi2Kernel.cpp, kernel/Chi2Kernel.h,
	  kernel/CombinedKernel.cpp, kernel/CombinedKernel.h,
	  kernel/CommUlongStringKernel.cpp, kernel/CommUlongStringKernel.h,
	  kernel/CommWordStringKernel.cpp, kernel/CommWordStringKernel.h,
	  kernel/ConstKernel.h, kernel/CustomKernel.cpp,
	  kernel/CustomKernel.h, kernel/CustomKernel.i,
	  kernel/DiagKernel.cpp, kernel/DiagKernel.h,
	  kernel/DiceKernelNormalizer.h, kernel/DistanceKernel.cpp,
	  kernel/DistanceKernel.h, kernel/FirstElementKernelNormalizer.h,
	  kernel/FixedDegreeStringKernel.cpp,
	  kernel/FixedDegreeStringKernel.h, kernel/GaussianKernel.cpp,
	  kernel/GaussianKernel.h, kernel/GaussianShiftKernel.cpp,
	  kernel/GaussianShiftKernel.h, kernel/GaussianShortRealKernel.cpp,
	  kernel/GaussianShortRealKernel.h,
	  kernel/HistogramWordStringKernel.cpp,
	  kernel/HistogramWordStringKernel.h,
	  kernel/IdentityKernelNormalizer.h, kernel/Kernel.cpp,
	  kernel/Kernel.h, kernel/Kernel.i, kernel/KernelMachine.cpp,
	  kernel/KernelNormalizer.h, kernel/LinearByteKernel.cpp,
	  kernel/LinearByteKernel.h, kernel/LinearKernel.cpp,
	  kernel/LinearKernel.h, kernel/LinearKernel.i,
	  kernel/LinearStringKernel.cpp, kernel/LinearStringKernel.h,
	  kernel/LinearWordKernel.cpp, kernel/LinearWordKernel.h,
	  kernel/LocalAlignmentStringKernel.cpp,
	  kernel/LocalAlignmentStringKernel.h,
	  kernel/LocalityImprovedStringKernel.cpp,
	  kernel/LocalityImprovedStringKernel.h,
	  kernel/MatchWordStringKernel.cpp, kernel/MatchWordStringKernel.h,
	  kernel/MindyGramKernel.cpp, kernel/MindyGramKernel.h,
	  kernel/OligoKernel.cpp, kernel/OligoKernel.h,
	  kernel/PolyKernel.cpp, kernel/PolyKernel.h,
	  kernel/PolyMatchStringKernel.cpp, kernel/PolyMatchStringKernel.h,
	  kernel/PolyMatchWordStringKernel.cpp,
	  kernel/PolyMatchWordStringKernel.h, kernel/PyramidChi2.cpp,
	  kernel/PyramidChi2.h, kernel/SalzbergWordStringKernel.cpp,
	  kernel/SalzbergWordStringKernel.h, kernel/SigmoidKernel.cpp,
	  kernel/SigmoidKernel.h, kernel/SimpleKernel.h,
	  kernel/SimpleKernel.i,
	  kernel/SimpleLocalityImprovedStringKernel.cpp,
	  kernel/SimpleLocalityImprovedStringKernel.h,
	  kernel/SparseGaussianKernel.cpp, kernel/SparseGaussianKernel.h,
	  kernel/SparseKernel.h, kernel/SparseLinearKernel.cpp,
	  kernel/SparseLinearKernel.h, kernel/SparsePolyKernel.cpp,
	  kernel/SparsePolyKernel.h, kernel/SqrtDiagKernelNormalizer.h,
	  kernel/StringKernel.h, kernel/StringKernel.i,
	  kernel/TanimotoKernelNormalizer.h,
	  kernel/WeightedCommWordStringKernel.cpp,
	  kernel/WeightedCommWordStringKernel.h,
	  kernel/WeightedCommWordStringKernel.i,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreePositionStringKernel.i,
	  kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.h,
	  kernel/WeightedDegreeStringKernel.i, lib/Array.h, lib/Array.i,
	  lib/Array2.h, lib/Array2.i, lib/Array3.h, lib/Array3.i,
	  lib/Cplex.cpp, lib/Cplex.h, lib/DynamicArray.h,
	  lib/DynamicArray.i, lib/File.cpp, lib/File.h, lib/List.h,
	  lib/Mathematics.cpp, lib/Mathematics.h, lib/Signal.cpp,
	  lib/Signal.h, lib/Trie.cpp, lib/Trie.h, lib/common.h, lib/io.cpp,
	  lib/io.h, lib/matlab.h, lib/octave_typemaps.i,
	  lib/python_typemaps.i, lib/r_typemaps.i, preproc/LogPlusOne.cpp,
	  preproc/LogPlusOne.h, preproc/NormDerivativeLem3.cpp,
	  preproc/NormDerivativeLem3.h, preproc/NormOne.cpp,
	  preproc/NormOne.h, preproc/PCACut.cpp, preproc/PCACut.h,
	  preproc/PruneVarSubMean.cpp, preproc/PruneVarSubMean.h,
	  preproc/SimplePreProc.h, preproc/SortUlongString.cpp,
	  preproc/SortUlongString.h, preproc/SortWordString.cpp,
	  preproc/SortWordString.h, preproc/SparsePreProc.h,
	  preproc/StringPreProc.h, regression/KRR.cpp, regression/KRR.h,
	  regression/svr/LibSVR.cpp, regression/svr/SVR_light.cpp,
	  regression/svr/SVR_light.h, structure/DynProg.cpp,
	  structure/DynProg.h, structure/DynProg.i, structure/Plif.cpp,
	  structure/Plif.h, structure/Plif.i, structure/PlifArray.cpp,
	  structure/PlifArray.h, structure/PlifBase.h: - BIG replacement V:
	  INT/int -> int32_t/int

2008-10-25  Soeren Sonnenburg <sonne@debian.org>

	* features/DummyFeatures.i, features/Features.i: add Nicolas
	  Pinto's swig extension to dummyfeatures

2008-10-25  Sebastian Henschel <shogun@kodeaffe.de>

	* .scrub_docstrings.py, README.developer,
	  classifier/svm/WDSVMOcas.cpp, features/Alphabet.cpp,
	  features/Alphabet.h, features/RealFileFeatures.cpp,
	  features/RealFileFeatures.h, features/SparseFeatures.h,
	  features/SparseFeatures.i, features/StringFeatures.h,
	  features/StringFeatures.i, guilib/GUIMath.cpp, guilib/GUIMath.h,
	  interface/SGInterface.cpp, kernel/CommWordStringKernel.cpp,
	  kernel/WeightedCommWordStringKernel.cpp, lib/Array.i,
	  lib/Array2.i, lib/Array3.i, lib/DynamicArray.i, lib/File.cpp,
	  lib/Mathematics.cpp, lib/Mathematics.h, lib/common.h,
	  lib/python_typemaps.i, preproc/PCACut.cpp,
	  preproc/PruneVarSubMean.cpp: - BIG replacement IV: UINT ->
	  uint32_t
	* .scrub_docstrings.py, README.developer,
	  classifier/PluginEstimate.cpp, classifier/PluginEstimate.h,
	  classifier/svm/SVM_light.cpp, distance/CanberraWordDistance.cpp,
	  distance/CanberraWordDistance.h,
	  distance/HammingWordDistance.cpp, distance/HammingWordDistance.h,
	  distance/ManhattanWordDistance.cpp,
	  distance/ManhattanWordDistance.h, distance/SimpleDistance.h,
	  distance/SimpleDistance.i, distance/SparseDistance.h,
	  distance/SparseDistance.i, distance/StringDistance.h,
	  distance/StringDistance.i, distributions/histogram/Histogram.cpp,
	  distributions/histogram/Histogram.h, distributions/hmm/HMM.cpp,
	  distributions/hmm/HMM.h, distributions/hmm/LinearHMM.cpp,
	  distributions/hmm/LinearHMM.h, features/Alphabet.cpp,
	  features/Alphabet.h, features/FKFeatures.cpp,
	  features/SimpleFeatures.h, features/SimpleFeatures.i,
	  features/SparseFeatures.h, features/SparseFeatures.i,
	  features/StringFeatures.h, features/StringFeatures.i,
	  features/WordFeatures.cpp, features/WordFeatures.h,
	  features/WordFeatures.i, guilib/GUIFeatures.cpp,
	  guilib/GUIFeatures.h, guilib/GUIHMM.cpp,
	  guilib/GUIPluginEstimate.cpp, guilib/GUIPreProc.cpp,
	  interface/CmdLineInterface.cpp, interface/CmdLineInterface.h,
	  interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/OctaveInterface.cpp, interface/OctaveInterface.h,
	  interface/PythonInterface.cpp, interface/PythonInterface.h,
	  interface/RInterface.cpp, interface/RInterface.h,
	  interface/SGInterface.cpp, interface/SGInterface.h,
	  kernel/AUCKernel.cpp, kernel/AUCKernel.h,
	  kernel/CommWordStringKernel.cpp, kernel/CommWordStringKernel.h,
	  kernel/HistogramWordStringKernel.cpp,
	  kernel/HistogramWordStringKernel.h, kernel/LinearWordKernel.cpp,
	  kernel/LinearWordKernel.h, kernel/MatchWordStringKernel.cpp,
	  kernel/MatchWordStringKernel.h,
	  kernel/PolyMatchWordStringKernel.cpp,
	  kernel/PolyMatchWordStringKernel.h,
	  kernel/SalzbergWordStringKernel.cpp,
	  kernel/SalzbergWordStringKernel.h, kernel/SimpleKernel.h,
	  kernel/SimpleKernel.i, kernel/SparseKernel.h,
	  kernel/SparseKernel.i, kernel/StringKernel.h,
	  kernel/StringKernel.i, kernel/WeightedCommWordStringKernel.cpp,
	  kernel/WeightedCommWordStringKernel.h, lib/Array.i, lib/Array2.i,
	  lib/Array3.i, lib/DynamicArray.i, lib/File.cpp, lib/File.h,
	  lib/Mathematics.h, lib/common.h, lib/octave_typemaps.i,
	  lib/python_typemaps.i, lib/r_typemaps.i, preproc/SimplePreProc.h,
	  preproc/SimplePreProc.i, preproc/SortWordString.cpp,
	  preproc/SortWordString.h, preproc/StringPreProc.h,
	  preproc/StringPreProc.i, structure/DynProg.cpp,
	  structure/DynProg.h: - BIG replacement III: WORD -> uint16_t
	* lib/common.h: - Fixed wrongly defined uint8_t for SUN OS.

2008-10-24  Sebastian Henschel <shogun@kodeaffe.de>

	* .scrub_docstrings.py, README.developer,
	  classifier/SubGradientLPM.cpp, classifier/SubGradientLPM.h,
	  classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h, classifier/svm/WDSVMOcas.cpp,
	  classifier/svm/WDSVMOcas.h, distance/SimpleDistance.h,
	  distance/SparseDistance.h, distance/StringDistance.h,
	  distributions/hmm/HMM.cpp, distributions/hmm/HMM.h,
	  distributions/hmm/LinearHMM.cpp, features/Alphabet.cpp,
	  features/Alphabet.h, features/ByteFeatures.cpp,
	  features/ByteFeatures.h, features/ByteFeatures.i,
	  features/MindyGramFeatures.h, features/MindyGramFeatures.i,
	  features/RealFileFeatures.cpp, features/RealFileFeatures.h,
	  features/SimpleFeatures.h, features/SimpleFeatures.i,
	  features/SparseFeatures.h, features/SparseFeatures.i,
	  features/StringFeatures.h, features/StringFeatures.i,
	  features/WordFeatures.cpp, features/WordFeatures.h,
	  guilib/GUIClassifier.cpp, guilib/GUIFeatures.cpp,
	  interface/CmdLineInterface.cpp, interface/CmdLineInterface.h,
	  interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/OctaveInterface.cpp, interface/OctaveInterface.h,
	  interface/PythonInterface.cpp, interface/PythonInterface.h,
	  interface/RInterface.cpp, interface/RInterface.h,
	  interface/SGInterface.cpp, interface/SGInterface.h,
	  kernel/CommWordStringKernel.cpp, kernel/Kernel.cpp,
	  kernel/Kernel.h, kernel/LinearByteKernel.cpp,
	  kernel/LinearByteKernel.h, kernel/SimpleKernel.h,
	  kernel/SimpleKernel.i, kernel/SparseKernel.h,
	  kernel/StringKernel.h, kernel/StringKernel.i,
	  kernel/WeightedCommWordStringKernel.cpp, lib/Array.i,
	  lib/Array2.i, lib/Array3.i, lib/DynamicArray.i, lib/File.cpp,
	  lib/File.h, lib/Mathematics.cpp, lib/Mathematics.h, lib/Trie.h,
	  lib/common.h, lib/octave_typemaps.i, lib/python_typemaps.i,
	  lib/r_typemaps.i, preproc/SimplePreProc.h,
	  preproc/SimplePreProc.i, preproc/StringPreProc.h,
	  preproc/StringPreProc.i, structure/DynProg.h: - BIG replacement
	  II: BYTE -> uint8_t
	* .scrub_docstrings.py, README.developer, base/Version.cpp,
	  base/Version.h, classifier/svm/MultiClassSVM.cpp,
	  classifier/svm/SVM.cpp, classifier/svm/pr_loqo.cpp,
	  distance/BrayCurtisDistance.h, distance/CanberraMetric.h,
	  distance/CanberraWordDistance.h, distance/ChebyshewMetric.h,
	  distance/ChiSquareDistance.h, distance/CosineDistance.h,
	  distance/Distance.cpp, distance/Distance.h,
	  distance/EuclidianDistance.h, distance/GeodesicMetric.h,
	  distance/HammingWordDistance.h, distance/JensenMetric.h,
	  distance/ManhattanMetric.h, distance/ManhattanWordDistance.h,
	  distance/MinkowskiMetric.h, distance/SimpleDistance.h,
	  distance/SimpleDistance.i, distance/SparseDistance.h,
	  distance/SparseDistance.i, distance/SparseEuclidianDistance.h,
	  distance/StringDistance.h, distance/StringDistance.i,
	  distance/TanimotoDistance.h, distributions/hmm/HMM.cpp,
	  distributions/hmm/HMM.h, features/Alphabet.cpp,
	  features/Alphabet.h, features/ByteFeatures.cpp,
	  features/ByteFeatures.h, features/CharFeatures.cpp,
	  features/CharFeatures.h, features/CharFeatures.i,
	  features/Features.cpp, features/Features.h,
	  features/IntFeatures.cpp, features/IntFeatures.h,
	  features/Labels.cpp, features/Labels.h,
	  features/MindyGramFeatures.cpp, features/MindyGramFeatures.h,
	  features/MindyGramFeatures.i, features/RealFeatures.cpp,
	  features/RealFeatures.h, features/RealFileFeatures.cpp,
	  features/RealFileFeatures.h, features/ShortFeatures.cpp,
	  features/ShortFeatures.h, features/ShortRealFeatures.cpp,
	  features/ShortRealFeatures.h, features/SimpleFeatures.h,
	  features/SimpleFeatures.i, features/SparseFeatures.h,
	  features/SparseFeatures.i, features/StringFeatures.h,
	  features/StringFeatures.i, features/WordFeatures.cpp,
	  features/WordFeatures.h, guilib/GUIClassifier.cpp,
	  guilib/GUIClassifier.h, guilib/GUIDistance.cpp,
	  guilib/GUIDistance.h, guilib/GUIFeatures.cpp,
	  guilib/GUIFeatures.h, guilib/GUIHMM.cpp, guilib/GUIHMM.h,
	  guilib/GUIKernel.cpp, guilib/GUIKernel.h, guilib/GUILabels.cpp,
	  guilib/GUILabels.h, guilib/GUIPluginEstimate.cpp,
	  guilib/GUIPluginEstimate.h, guilib/GUIPreProc.cpp,
	  guilib/GUIPreProc.h, guilib/GUIStructure.cpp,
	  guilib/GUIStructure.h, interface/CmdLineInterface.cpp,
	  interface/CmdLineInterface.h, interface/MatlabInterface.cpp,
	  interface/MatlabInterface.h, interface/OctaveInterface.cpp,
	  interface/OctaveInterface.h, interface/PythonInterface.cpp,
	  interface/PythonInterface.h, interface/RInterface.cpp,
	  interface/RInterface.h, interface/SGInterface.cpp,
	  interface/SGInterface.h, kernel/AUCKernel.h, kernel/Chi2Kernel.h,
	  kernel/CombinedKernel.h, kernel/CommUlongStringKernel.h,
	  kernel/CommWordStringKernel.cpp, kernel/CommWordStringKernel.h,
	  kernel/ConstKernel.h, kernel/CustomKernel.h, kernel/DiagKernel.h,
	  kernel/DistanceKernel.h, kernel/FixedDegreeStringKernel.cpp,
	  kernel/FixedDegreeStringKernel.h, kernel/GaussianKernel.h,
	  kernel/GaussianShiftKernel.h, kernel/GaussianShortRealKernel.h,
	  kernel/HistogramWordStringKernel.h, kernel/Kernel.cpp,
	  kernel/Kernel.h, kernel/LinearByteKernel.h,
	  kernel/LinearKernel.h, kernel/LinearStringKernel.cpp,
	  kernel/LinearStringKernel.h, kernel/LinearWordKernel.h,
	  kernel/LocalAlignmentStringKernel.cpp,
	  kernel/LocalAlignmentStringKernel.h,
	  kernel/LocalityImprovedStringKernel.cpp,
	  kernel/LocalityImprovedStringKernel.h,
	  kernel/MatchWordStringKernel.h, kernel/MindyGramKernel.cpp,
	  kernel/MindyGramKernel.h, kernel/OligoKernel.cpp,
	  kernel/OligoKernel.h, kernel/PolyKernel.h,
	  kernel/PolyMatchStringKernel.cpp, kernel/PolyMatchStringKernel.h,
	  kernel/PolyMatchWordStringKernel.h, kernel/PyramidChi2.h,
	  kernel/SalzbergWordStringKernel.h, kernel/SigmoidKernel.h,
	  kernel/SimpleKernel.h, kernel/SimpleKernel.i,
	  kernel/SimpleLocalityImprovedStringKernel.cpp,
	  kernel/SimpleLocalityImprovedStringKernel.h,
	  kernel/SparseGaussianKernel.h, kernel/SparseKernel.h,
	  kernel/SparseLinearKernel.h, kernel/SparsePolyKernel.h,
	  kernel/StringKernel.h, kernel/StringKernel.i,
	  kernel/WeightedCommWordStringKernel.h,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.h, lib/Array.i, lib/Array2.i,
	  lib/Array3.i, lib/DynamicArray.i, lib/File.cpp, lib/File.h,
	  lib/Mathematics.cpp, lib/Mathematics.h, lib/SimpleFile.h,
	  lib/common.h, lib/io.cpp, lib/io.h, lib/octave_typemaps.i,
	  lib/python_typemaps.i, lib/r_typemaps.i, preproc/PreProc.cpp,
	  preproc/PreProc.h, preproc/SimplePreProc.h,
	  preproc/SimplePreProc.i, preproc/SparsePreProc.h,
	  preproc/StringPreProc.h, preproc/StringPreProc.i,
	  structure/DynProg.cpp, structure/DynProg.h, structure/DynProg.i:
	  - BIG replacement I: CHAR -> char
	* lib/common.h: library:
	  - Removed unnecessary P_* typedefs.

2008-10-24  Soeren Sonnenburg <sonne@debian.org>

	* configure: Integrate Chen Guohua's glpk,lpsolve detection

2008-10-21  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/pr_loqo.cpp: lower loglevel for Choldc failed,
	  matrix not pd message, as we are cleanly dealing with that case
	  anyways

2008-10-20  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/GMNPSVM.cpp: potential fix for vojtechs multiclass
	  svm as reported by alexander binder

2008-10-15  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* structure/DynProg.cpp: compiles again, but I cannot test it

2008-10-15  Soeren Sonnenburg <sonne@debian.org>

	* structure/DynProg.cpp: function best_path_call is broken and
	  needs adjustments to new best_path_trans API

2008-10-14  Soeren Sonnenburg <sonne@debian.org>

	* .r-install.sh: fix malformed R description

2008-10-11  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, distance/BrayCurtisDistance.cpp,
	  distance/BrayCurtisDistance.h, distance/CanberraMetric.cpp,
	  distance/CanberraMetric.h, distance/ChebyshewMetric.cpp,
	  distance/ChebyshewMetric.h, distance/ChiSquareDistance.cpp,
	  distance/ChiSquareDistance.h, distance/CosineDistance.cpp,
	  distance/CosineDistance.h, distance/Distance.cpp,
	  distance/Distance.h, distance/DistanceMachine.cpp,
	  distance/DistanceMachine.h, distance/GeodesicMetric.cpp,
	  distance/GeodesicMetric.h, distance/JensenMetric.cpp,
	  distance/JensenMetric.h, distance/ManhattanMetric.cpp,
	  distance/ManhattanMetric.h, distance/MinkowskiMetric.cpp,
	  distance/MinkowskiMetric.h, distance/RealDistance.h,
	  distance/SimpleDistance.h, distance/StringDistance.h,
	  distance/TanimotoDistance.cpp, distance/TanimotoDistance.h: fix
	  documentation and dos2unix files in distance
	* ChangeLog: updated changelog
	* ChangeLog: updated reference documentation
	* NEWS: update news

2008-10-11  Sebastian Henschel <shogun@kodeaffe.de>

	* regression/Regression.h: - Oopsie, forgot to add
	  regression/Regression.h

2008-10-10  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, configure: update news

2008-10-08  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/Classifier.h, distance/Distance.h,
	  features/Alphabet.cpp, features/Alphabet.h,
	  features/ByteFeatures.cpp, features/ByteFeatures.h,
	  features/CharFeatures.cpp, features/CharFeatures.h,
	  features/Features.h, features/StringFeatures.h, kernel/Kernel.h,
	  kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreeStringKernel.h, lib/File.h, lib/common.h,
	  lib/io.h, preproc/PreProc.h, regression/KRR.h,
	  regression/Regression.i, regression/svr/LibSVR.h,
	  regression/svr/SVR_light.h: common:
	  - Moved various enums from lib/common.h into more specific header
	  files.
	  - Renamed E_ALPHABET to EAlphabet.
	  - Hence closing issue #65.

2008-10-04  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/SGInterface.cpp: interface:
	  - Reverted erroneous change to static interface to
	  (POLY)MATCH(WORDSTRING).
	* NEWS: news:
	  - Updated news about the 4 new distances.
	* distance/ChiSquareDistance.i, distance/Distance.i: distance:
	  - Fixed integration of the 4 new distances into the modular
	  interfaces.
	* kernel/OligoKernel.h: documentation:
	  - Fixed compiler warning.

2008-10-02  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUIKernel.cpp, interface/SGInterface.cpp: interface:
	  - Forgot to include changes for Salzberg/HistogramWordString in
	  interface/guilib.
	* kernel/HistogramWordStringKernel.cpp,
	  kernel/HistogramWordStringKernel.h,
	  kernel/SalzbergWordStringKernel.cpp,
	  kernel/SalzbergWordStringKernel.h: kernel:
	  - Fixed forgotten renaming of actual class of HistogramWordString
	  and
	  SalzbergWordString.

2008-09-29  Sebastian Henschel <shogun@kodeaffe.de>

	* features/DummyFeatures.h, kernel/CombinedKernel.h,
	  kernel/DiceKernelNormalizer.h, kernel/OligoKernel.h,
	  kernel/SqrtDiagKernelNormalizer.h,
	  kernel/TanimotoKernelNormalizer.h: documentation:
	  - Added a few docstrings to silence compilation.
	* guilib/GUIKernel.cpp: interface:
	  - Added missing call to set_normalizer when normalizer == false
	  for
	  PolyMatchWordStringKernel in static interface.
	* guilib/GUIKernel.cpp, guilib/GUIKernel.h,
	  interface/SGInterface.cpp: interface:
	  - Extended changes in static interface to Match(Word)String
	  kernels

2008-09-19  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIKernel.cpp, guilib/GUIPreProc.cpp,
	  interface/SGInterface.cpp, kernel/HistogramWordKernel.cpp,
	  kernel/HistogramWordKernel.h, kernel/HistogramWordKernel.i,
	  kernel/HistogramWordStringKernel.cpp,
	  kernel/HistogramWordStringKernel.h,
	  kernel/HistogramWordStringKernel.i, kernel/Kernel.i,
	  kernel/MatchWordStringKernel.cpp, kernel/MatchWordStringKernel.h,
	  kernel/MatchWordStringKernel.i, kernel/PolyMatchWordKernel.cpp,
	  kernel/PolyMatchWordKernel.h, kernel/PolyMatchWordKernel.i,
	  kernel/PolyMatchWordStringKernel.cpp,
	  kernel/PolyMatchWordStringKernel.h,
	  kernel/PolyMatchWordStringKernel.i,
	  kernel/SalzbergWordKernel.cpp, kernel/SalzbergWordKernel.h,
	  kernel/SalzbergWordKernel.i, kernel/SalzbergWordStringKernel.cpp,
	  kernel/SalzbergWordStringKernel.h,
	  kernel/SalzbergWordStringKernel.i, kernel/WordMatchKernel.cpp,
	  kernel/WordMatchKernel.h, kernel/WordMatchKernel.i, lib/common.h,
	  preproc/PreProc.i, preproc/SortWord.cpp, preproc/SortWord.h,
	  preproc/SortWord.i: remove SortWord preproc and rename other
	  string kernels to have WordString suffix

2008-09-19  Sebastian Henschel <shogun@kodeaffe.de>

	* features/WordFeatures.h, features/WordFeatures.i: features:
	  - Implemented get_fm() for WordFeatures.

2008-09-19  Christian Gehl <Christian.Gehl@first.fraunhofer.de>

	* distance/BrayCurtisDistance.cpp, distance/BrayCurtisDistance.h,
	  distance/BrayCurtisDistance.i, distance/CanberraMetric.h,
	  distance/ChebyshewMetric.h, distance/ChiSquareDistance.cpp,
	  distance/ChiSquareDistance.h, distance/ChiSquareDistance.i,
	  distance/CosineDistance.cpp, distance/CosineDistance.h,
	  distance/CosineDistance.i, distance/EuclidianDistance.h,
	  distance/GeodesicMetric.h, distance/JensenMetric.h,
	  distance/ManhattanMetric.h, distance/MinkowskiMetric.h,
	  distance/TanimotoDistance.cpp, distance/TanimotoDistance.h,
	  distance/TanimotoDistance.i, guilib/GUIDistance.cpp,
	  interface/SGInterface.cpp, lib/common.h: added distances:
	  Bray-Curtis, Chi-Square, Cosine, Tanimoto

2008-09-16  Soeren Sonnenburg <sonne@debian.org>

	* kernel/DiceKernelNormalizer.h, kernel/DiceKernelNormalizer.i,
	  kernel/TanimotoKernelNormalizer.h,
	  kernel/TanimotoKernelNormalizer.i: add further kernel
	  normalizers, after reading PyML tutorial

2008-09-05  Soeren Sonnenburg <sonne@debian.org>

	* kernel/OligoKernel.i: add missing file

2008-09-01  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, guilib/GUICommands.h, guilib/GUIKernel.cpp,
	  guilib/GUIKernel.h, interface/SGInterface.cpp,
	  interface/SGInterface.h, kernel/CombinedKernel.cpp,
	  kernel/CombinedKernel.h, kernel/OligoKernel.cpp,
	  kernel/OligoKernel.h: implement precompute_subkernels

2008-08-28  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/MultiClassSVM.cpp, classifier/svm/MultiClassSVM.h,
	  classifier/svm/SVM.h, distributions/Distribution.h,
	  distributions/histogram/Histogram.h, distributions/hmm/GHMM.h,
	  distributions/hmm/HMM.h, distributions/hmm/LinearHMM.h:
	  Documentation updates for distributions. Implement multiclass svm
	  model saving and loading.

2008-08-26  Soeren Sonnenburg <sonne@debian.org>

	* kernel/FirstElementKernelNormalizer.h: add missing file
	* NEWS, clustering/Hierarchical.cpp, guilib/GUIKernel.cpp,
	  guilib/GUIKernel.h, interface/SGInterface.cpp, kernel/Kernel.i,
	  kernel/OligoKernel.cpp, kernel/OligoKernel.h,
	  kernel/WeightedDegreeStringKernel.h, lib/Mathematics.h,
	  lib/common.h: Possibly correctly integrate oligo kernel, however
	  I had to fix an array out of bounds read (thanks valgrind) and as
	  the kernel was very diagonally dominant I added SqrtDiag
	  normalization; wrote examples for all interfaces from cmdline to
	  r-modular :)

2008-08-24  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, classifier/svm/SVM.cpp, classifier/svm/SVM.h,
	  classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h,
	  features/DummyFeatures.h, guilib/GUIClassifier.cpp,
	  guilib/GUICommands.h, guilib/GUIKernel.cpp, guilib/GUIKernel.h,
	  interface/SGInterface.cpp, interface/SGInterface.h,
	  kernel/AUCKernel.cpp, kernel/AvgDiagKernelNormalizer.h,
	  kernel/AvgDiagKernelNormalizer.i, kernel/Chi2Kernel.cpp,
	  kernel/CombinedKernel.cpp, kernel/CombinedKernel.h,
	  kernel/CommUlongStringKernel.cpp, kernel/CommUlongStringKernel.h,
	  kernel/CommWordStringKernel.cpp, kernel/CommWordStringKernel.h,
	  kernel/ConstKernel.cpp, kernel/CustomKernel.cpp,
	  kernel/CustomKernel.h, kernel/DistanceKernel.cpp,
	  kernel/FixedDegreeStringKernel.cpp,
	  kernel/FixedDegreeStringKernel.h, kernel/GaussianKernel.cpp,
	  kernel/GaussianShortRealKernel.cpp,
	  kernel/HistogramWordKernel.cpp,
	  kernel/IdentityKernelNormalizer.h,
	  kernel/IdentityKernelNormalizer.i, kernel/Kernel.cpp,
	  kernel/Kernel.h, kernel/Kernel.i, kernel/KernelNormalizer.h,
	  kernel/KernelNormalizer.i, kernel/LinearByteKernel.cpp,
	  kernel/LinearByteKernel.h, kernel/LinearKernel.cpp,
	  kernel/LinearKernel.h, kernel/LinearStringKernel.cpp,
	  kernel/LinearStringKernel.h, kernel/LinearWordKernel.cpp,
	  kernel/LinearWordKernel.h, kernel/LocalAlignmentStringKernel.cpp,
	  kernel/LocalityImprovedStringKernel.cpp,
	  kernel/MindyGramKernel.cpp, kernel/MindyGramKernel.h,
	  kernel/PolyKernel.cpp, kernel/PolyKernel.h,
	  kernel/PolyMatchStringKernel.cpp, kernel/PolyMatchStringKernel.h,
	  kernel/PolyMatchWordKernel.cpp, kernel/PolyMatchWordKernel.h,
	  kernel/PyramidChi2.cpp, kernel/SalzbergWordKernel.cpp,
	  kernel/SigmoidKernel.cpp,
	  kernel/SimpleLocalityImprovedStringKernel.cpp,
	  kernel/SparseGaussianKernel.cpp, kernel/SparseLinearKernel.cpp,
	  kernel/SparseLinearKernel.h, kernel/SparsePolyKernel.cpp,
	  kernel/SparsePolyKernel.h, kernel/SqrtDiagKernelNormalizer.h,
	  kernel/SqrtDiagKernelNormalizer.i,
	  kernel/WeightedCommWordStringKernel.cpp,
	  kernel/WeightedCommWordStringKernel.h,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.h, kernel/WordMatchKernel.cpp,
	  kernel/WordMatchKernel.h, lib/Mathematics.h, lib/common.h,
	  regression/svr/SVR_light.cpp, regression/svr/SVR_light.h: -
	  implement proper kernel normalisation
	  - remove requirement to set features to custom kernel
	  - fix buggy normalization in wds kernel

2008-08-18  Soeren Sonnenburg <sonne@debian.org>

	* configure: potentially fix mkl detection

2008-08-17  Soeren Sonnenburg <sonne@debian.org>

	* lib/File.cpp, lib/Mathematics.h: fix transpose

2008-08-16  Soeren Sonnenburg <sonne@debian.org>

	* Makefile: adjust makefile
	* guilib/GUIClassifier.cpp: - compile fix when lapack/atlas is not
	  available
	  - don't check .config for interface when running tests but use
	  argument

2008-08-15  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog: updated changelog
	* ChangeLog: updated changelog
	* clustering/Hierarchical.h, clustering/KMeans.h,
	  distributions/Distribution.h, features/Alphabet.h,
	  features/ByteFeatures.h, features/CharFeatures.h,
	  features/CombinedFeatures.h, features/FKFeatures.h,
	  features/Features.h, features/IntFeatures.h, features/Labels.h,
	  features/RealFeatures.h, features/RealFileFeatures.h,
	  features/ShortFeatures.h, features/ShortRealFeatures.h,
	  features/SimpleFeatures.h, features/SparseFeatures.h,
	  features/StringFeatures.h, features/TOPFeatures.h,
	  features/WordFeatures.h, kernel/CombinedKernel.h,
	  kernel/PolyMatchWordKernel.h, kernel/SigmoidKernel.h,
	  regression/svr/LibSVR.h, regression/svr/SVR_light.h: Document
	  everything in features/ and clustering/, fixes for
	  regression/kernel.
	  
	  To be really useful we still need documentation for everything in
	  
	  • classifier/*
	  • distances/*
	  • distributions/*
	  
	  and of course we need some first steps tutorial for the modular
	  interfaces.

2008-08-15  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* kernel/GaussianShiftKernel.h: minor correction
	* kernel/GaussianShiftKernel.h: added some documentation of the
	  GaussianShift kernel

2008-08-14  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, kernel/CommWordStringKernel.h, kernel/CustomKernel.h,
	  kernel/GaussianKernel.h, kernel/GaussianShiftKernel.h,
	  kernel/GaussianShortRealKernel.h, kernel/HistogramWordKernel.h,
	  kernel/Kernel.h, kernel/LinearByteKernel.h,
	  kernel/LinearKernel.h, kernel/LinearStringKernel.h,
	  kernel/LinearWordKernel.h, kernel/LocalAlignmentStringKernel.h,
	  kernel/LocalityImprovedStringKernel.h, kernel/OligoKernel.h,
	  kernel/PolyKernel.h, kernel/PolyMatchStringKernel.cpp,
	  kernel/PolyMatchStringKernel.h, kernel/PolyMatchWordKernel.cpp,
	  kernel/PolyMatchWordKernel.h, kernel/SalzbergWordKernel.cpp,
	  kernel/SalzbergWordKernel.h, kernel/SigmoidKernel.h,
	  kernel/SimpleKernel.h,
	  kernel/SimpleLocalityImprovedStringKernel.h,
	  kernel/SparseGaussianKernel.h, kernel/SparseKernel.h,
	  kernel/SparsePolyKernel.h, kernel/StringKernel.h,
	  kernel/WeightedCommWordStringKernel.h,
	  kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreeStringKernel.h, kernel/WordMatchKernel.h:
	  document kernels

2008-08-13  Soeren Sonnenburg <sonne@debian.org>

	* kernel/CustomKernel.cpp: kill remaining randomness, testsuite
	  runs through now for octave/python/python-modular

2008-08-12  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUIClassifier.cpp: interface:
	  - Fixed issue because SVM parameter C was not passed on from
	  guilib to
	  classifier in static interface.

2008-08-12  Soeren Sonnenburg <sonne@debian.org>

	* clustering/KMeans.cpp, interface/SGInterface.cpp,
	  lib/Mathematics.cpp, lib/Mathematics.h: fix a long standing bug
	  in seeding the random number generator. now seeding is reliable,
	  however all scripts relying on init_random will have to be
	  adjusted
	* kernel/DistanceKernel.cpp: trap distance == NULL

2008-08-11  Sebastian Henschel <shogun@kodeaffe.de>

	* NEWS: - Updated news.
	* Makefile: weird crashes in modular octave:
	  - Does not seem to concern Soeren, but shogun crashes often when
	  working with
	  classifiers in octave modular. a rearranging of the shogun
	  modules loaded on
	  startup, like alphabetical sorting, seems to remedy this.

2008-08-10  Soeren Sonnenburg <sonne@debian.org>

	* Makefile: add make tests for matlab (works now for all except
	  randomized algos :)

2008-08-09  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreePositionStringKernel.h: fix one liner
	  normalization const function - however this still is not the
	  right way to do it

2008-08-06  Cheng Soon Ong <chengsoon.ong@tuebingen.mpg.de>

	* kernel/WeightedDegreePositionStringKernel.h: Added method to
	  explicitly set the normalization.

2008-07-30  Sebastian Henschel <shogun@kodeaffe.de>

	* kernel/SalzbergWordKernel.h: kernel:
	  - Little documentation fix in constructor.

2008-07-24  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIClassifier.cpp, interface/SGInterface.cpp: fix
	  documentation string and LDA / lapack compile error

2008-07-23  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, classifier/svm/SVM.cpp, guilib/GUICommands.h,
	  interface/SGInterface.cpp, interface/SGInterface.h: add
	  save_classifier command (which will currently only work for SVMs)

2008-07-16  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUIPreProc.cpp: interface:
	  - Fixed segfault issue when attaching preprocs.

2008-07-10  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/OctaveInterface.cpp: interface/examples/testsuite:
	  - Fixed missing ! bug in octave interface for reading boolean
	  values, changed
	  examples/testsuite accordingly.
	* structure/DynProg.cpp: structure:
	  - Compile fix: commented non-existing call to print method.

2008-07-05  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/DynProg.cpp: in semi-markov dynamic programming code:
	  * changed max_look_back default length
	  * new version of code only looks at transitions that are actually
	  allowed
	  * some more outputs about max_look_back

2008-07-03  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUIClassifier.cpp: interface:
	  - Very similar fix to previous KRR, but tube_epsilon wasn't
	  actually set in
	  classifier for LibSVR/SVR_Light.
	* guilib/GUIClassifier.cpp, guilib/GUIClassifier.h: interface:
	  - Fixed bug in KRR regression which did not set tau properly
	  within the
	  initialised 'classifier'.
	* interface/SGInterface.cpp: interface/testsuite:
	  - Changed default value for scale parameter of Linear kernels in
	  static
	  interface, so that testsuite for python static now succeeds.
	* clustering/Hierarchical.h, guilib/GUIClassifier.cpp:
	  testsuite/interface:
	  - static and modular interfaces now do the same in Hierarchical
	  clustering,
	  not sure if it is the correct sameness, though.

2008-07-02  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUIClassifier.cpp: testsuite/interface:
	  - Changed default for nu in static interfaces to the same value
	  as in the
	  SVM class. classifier testsuite for python static should now run
	  through.

2008-07-01  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUIClassifier.cpp, guilib/GUIClassifier.h,
	  interface/SGInterface.cpp: interface:
	  - Added parameter gamma to training of classifier LDA which makes
	  testsuite
	  for python static succeed on it.

2008-06-30  Sebastian Henschel <shogun@kodeaffe.de>

	* kernel/OligoKernel.cpp: kernel:
	  - Fixed compile warnings in OligoKernel.

2008-06-28  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUICommands.h, guilib/GUIKernel.cpp,
	  interface/SGInterface.cpp, interface/SGInterface.h,
	  kernel/SalzbergWordKernel.cpp, kernel/SalzbergWordKernel.h:
	  kernel/interface/testsuite/examples:
	  - SalzbergWordKernel: made set_prior_probs available to static
	  interfaces,
	  added set_prior_probs_from_labels to the kernel, adjusted
	  testgenerator
	  and python static/modular examples and testsuite.

2008-06-24  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/SGInterface.cpp: interface:
	  - Fixed a bug when counting arguments for HammingWordDistance.

2008-06-24  Soeren Sonnenburg <sonne@debian.org>

	* features/ShortRealFeatures.i, features/SimpleFeatures.i: fix
	  rename to ShortRealFeatures

2008-06-24  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/SGInterface.cpp: interface:
	  - Set default value in static interface for max_mismatch in
	  WeightedDegreePositionString from 1 to 0 (as in the class'
	  constructor)

2008-06-23  Soeren Sonnenburg <sonne@debian.org>

	* kernel/GaussianShortRealKernel.cpp, kernel/SimpleKernel.h,
	  kernel/SimpleKernel.i: fix compilation and warnings caused by my
	  previous commit
	* features/Features.i, kernel/GaussianShortRealKernel.cpp,
	  kernel/GaussianShortRealKernel.h,
	  kernel/GaussianShortRealKernel.i, kernel/Kernel.i: add gaussian
	  kernel for shortreal features

2008-06-23  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUICommands.h, guilib/GUIMath.cpp, guilib/GUIMath.h,
	  interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Added command init_random to static interfaces.

2008-06-21  Soeren Sonnenburg <sonne@debian.org>

	* kernel/OligoKernel.cpp, kernel/OligoKernel.h, lib/Signal.cpp,
	  preproc/NormOne.cpp: moving the oligokernel in place - currently
	  only formatting changes.. still way to go before it is working in
	  sg

2008-06-20  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, regression/KRR.h, regression/svr/LibSVR.h,
	  regression/svr/SVR_light.h: - document methods in regression/*
	  - update doxyfile to not show methods from inherited classes (its
	  is becoming messy+confusing) and define USE_SVMLIGHT and
	  HAVE_LAPACK/ATLAS to also see these methods documented

2008-06-19  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, preproc/LogPlusOne.h, preproc/NormDerivativeLem3.h,
	  preproc/NormOne.cpp, preproc/NormOne.h, preproc/PCACut.cpp,
	  preproc/PCACut.h, preproc/PreProc.h, preproc/PruneVarSubMean.h,
	  preproc/SimplePreProc.h, preproc/SortUlongString.h,
	  preproc/SortWord.h, preproc/SortWordString.h,
	  preproc/SparsePreProc.h, preproc/StringPreProc.h: document
	  preprocessors
	* base/Parallel.h, base/SGObject.h, base/Version.h, lib/Signal.h:
	  document items in base/
	* evaluation/PerformanceMeasures.h, lib/Array.h, lib/Array2.h,
	  lib/Array3.h, lib/Cache.h, lib/Cplex.h, lib/DynamicArray.h,
	  lib/File.h, lib/List.h, lib/ShogunException.h, lib/Signal.h,
	  lib/SimpleFile.h, lib/Time.h, lib/Trie.h, lib/io.h: document
	  classes in lib/
	* classifier/svm/SVM_light.cpp: remove accidental unconditional
	  active constraint counter increase

2008-06-18  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM_light.cpp: looks like there is some problem in
	  the heuristic?
	* classifier/svm/SVM.cpp, classifier/svm/SVM_light.cpp,
	  interface/OctaveInterface.cpp, interface/PythonInterface.cpp,
	  interface/RInterface.cpp,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.cpp, lib/ShogunException.cpp,
	  lib/Signal.cpp, lib/Signal.h, lib/io.cpp: hopefully fix signal
	  handling:
	  - SVM* / WDKernel* erranously called CSignal::clear() keeping the
	  signal handler active
	  - if a command returned with an error, the signal handler was
	  still set, fix this by removing the signal handler in shogun
	  exception
	  - only use printf in SG_ERROR etc as we are throwing an exception
	  anyway. note that for modular interfaces we need to call
	  CSignal::set_handler(); for all commands that can be expected to
	  run a bit longer
	* classifier/svm/SVM_light.cpp: also implement two/one norm mkl for
	  linadd

2008-06-17  Soeren Sonnenburg <sonne@debian.org>

	* interface/RInterface.cpp: fix index
	* interface/RInterface.cpp: attempt to fix corruption
	* classifier/svm/SVM_light.cpp: potentially fix 1 norm mkl bug
	* guilib/GUICommands.h, guilib/GUIStructure.cpp,
	  guilib/GUIStructure.h, interface/SGInterface.cpp,
	  interface/SGInterface.h, structure/DynProg.cpp,
	  structure/DynProg.h: merge jonas' changes back to trunk

2008-06-16  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog: updated changelog
	* NEWS: update news

2008-06-15  Soeren Sonnenburg <sonne@debian.org>

	* Makefile: fix path for octave modular if
	* Makefile: we don't have any r-doc/vignette or the like
	* Makefile: don't make examples executable
	* Makefile: - also set paths for make reference.
	  - make prepare-release doesn't require root access anymore but
	  does testing in /tmp/
	* Makefile: to run tests now do
	  make
	  make install DESTDIR=/tmp/
	  make tests DESTDIR=/tmp/
	  
	  (with DESTDIR optional :-)

2008-06-14  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM.cpp, classifier/svm/SVM.h,
	  classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h,
	  guilib/GUIClassifier.cpp, guilib/GUIClassifier.h,
	  interface/SGInterface.cpp: - implement 2-norm MKL for non-linadd
	  kernels and add example of how it works in
	  mkl_classify_christmas_star
	  - instead of creating a symlink set octave path to current src
	  dir. this all needs further thinking, maybe it is a good idea to
	  have a general policy like:
	  
	  1. compile (make)
	  2. install (make install)
	  3. test (make tests)
	  
	  thus the install path has to be set in environment variables as
	  the path to shogun:
	  cmdline -> PATH=...
	  octave -> octave -p ...
	  R -> R_PATH==...
	  matlab -> doesn't support this
	  python -> PYTHONPATH=...
	  
	  ... is $DESTDIR/$PYDIR etc

2008-06-13  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog: updated changelog
	* interface/SGInterface.cpp: R tests don't run yet, fix stupid
	  error for WDS 3 kernel
	* ChangeLog: updated changelog
	* Makefile, distance/GeodesicMetric.cpp: run R tests with R_PATH
	  set and trap division by zero and acos input outside [-1,+1]
	  range
	* ChangeLog: updated changelog

2008-06-13  Sebastian Henschel <shogun@kodeaffe.de>

	* NEWS: Add Ocas changes to News.

2008-06-13  Soeren Sonnenburg <sonne@debian.org>

	* interface/SGInterface.cpp: move structure commands to separate
	  group

2008-06-13  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/svm/libocas.cpp, classifier/svm/qpssvmlib.cpp:
	  classifier:
	  - Transformed SG_SINFO into SG_ABS_PROGRESS in Ocas.

2008-06-13  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, guilib/GUIStructure.h, interface/SGInterface.cpp,
	  structure/DynProg.cpp, structure/DynProg.h, structure/Plif.cpp:
	  merge changes from structure branch

2008-06-12  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/svm/SVMOcas.cpp, classifier/svm/WDSVMOcas.cpp,
	  classifier/svm/libocas.cpp, classifier/svm/libocas.h,
	  classifier/svm/qpssvmlib.cpp, classifier/svm/qpssvmlib.h:
	  classifier:
	  - Made Ocas less verbose, actually modifying the way it prints
	  out error
	  messages.

2008-06-12  Christian Gehl <Christian.Gehl@first.fraunhofer.de>

	* distance/GeodesicMetric.cpp: -changed distance function to arcos(
	  x*y/sqrt( (x*x) * (y*y) ) )
	  -distance can handle data, which has not be normalized

2008-06-12  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, interface/OctaveInterface.cpp, kernel/Kernel.cpp:
	  -refresh+resize kernel cache after we actually erease lhs or rhs
	  -fix a bug+warning in octave interface when setting strings

2008-06-11  Soeren Sonnenburg <sonne@debian.org>

	* kernel/KernelMachine.cpp: minor code cleanup
	* Makefile: include test and doc for cmdline interface

2008-06-11  Sebastian Henschel <shogun@kodeaffe.de>

	* features/StringFeatures.h, kernel/Kernel.h, kernel/PyramidChi2.h,
	  lib/File.h, structure/DynProg.h, structure/Plif.h: documentation:
	  - Fixed some doxygen warnings.
	* ., NEWS, classifier, clustering, distance, distributions,
	  evaluation, features, kernel, lib, preproc, regression,
	  structure: - Slightly modified NEWS
	  - updated svn:ignores in various places.

2008-06-11  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog, Makefile, NEWS, interface/SGInterface.cpp,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.cpp: updated changelog
	* ChangeLog, Makefile, NEWS: updated changelog
	* ChangeLog: updated changelog
	* interface/SGInterface.cpp,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.h, lib/Trie.h: fix a couple of
	  crashers due to uninited tries by making sure tables that are
	  cleaned up on cleanup() are inited on init() - this is yet
	  another side effect of correctly removing lhs/rhs and calling
	  kernel cleanup()
	* interface/SGInterface.cpp, kernel/Kernel.cpp, kernel/Kernel.h: -
	  add a function remove_lhs_and_rhs() which simply calls
	  remove_rhs() and remove_lhs() in the right order (recall that the
	  case lhs==rhs is valid and currently needs extra treatment)
	  - add assertions for WDS kernel 2/3

2008-06-11  Sebastian Henschel <shogun@kodeaffe.de>

	* features/StringFeatures.h, kernel/WeightedDegreeStringKernel.cpp:
	  kernel/features:
	  - Previous method to check for vector lengths was wrong.
	* kernel/Kernel.cpp: kernel:
	  - Possibly fixed an issue with regression and kernel cache.

2008-06-10  Sebastian Henschel <shogun@kodeaffe.de>

	* features/StringFeatures.h, kernel/WeightedDegreeStringKernel.cpp:
	  kernel/features:
	  - Check that all vectors have the same length when new features
	  are set for
	  WeightedDegreeString kernel.

2008-06-10  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIStructure.cpp, interface/CmdLineInterface.cpp,
	  interface/CmdLineInterface.h, interface/OctaveInterface.cpp,
	  interface/OctaveInterface.h, interface/PythonInterface.cpp,
	  interface/PythonInterface.h, interface/RInterface.cpp,
	  interface/RInterface.h, lib/Mathematics.h, structure/Plif.cpp,
	  structure/Plif.h: try to get nd-array support also for python and
	  octave (dummy for cmdline and R) + a couple of compile fixes
	* structure/DynProg.cpp: fix compile warnings, logical and mismatch
	* features/StringFeatures.h, guilib/GUICommands.h,
	  guilib/GUIStructure.cpp, guilib/GUIStructure.h,
	  interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/SGInterface.cpp, interface/SGInterface.h,
	  structure/DynProg.cpp, structure/DynProg.h, structure/Plif.cpp,
	  structure/Plif.h, structure/PlifArray.cpp, structure/PlifArray.h,
	  structure/PlifBase.h, structure/Structure.i:
	* lib/Mathematics.h, structure/DynProg.cpp: fix a couple of gcc-4.3
	  compiler warnings
	* interface/CmdLineInterface.cpp, interface/CmdLineInterface.h,
	  lib/Mathematics.h, lib/Signal.cpp: unset signal handler as soon
	  as we enter handle() to fix an issue when ctrl+c was pressed more
	  than once in a row
	* interface/OctaveInterface.cpp, interface/PythonInterface.cpp,
	  interface/RInterface.cpp: remove double error printing

2008-06-09  Soeren Sonnenburg <sonne@debian.org>

	* interface/SGInterface.cpp: fix error msg when command is mistyped
	* Makefile, configure, guilib/GUICommands.h,
	  interface/CmdLineInterface.cpp, interface/SGInterface.cpp,
	  interface/SGInterface.h, interface/SyntaxHighLight.h, lib/io.cpp:
	  - add a make reference to automagically create
	  pages/Static*Interface.mainpage command references
	  - add option to disable syntax hilighting
	  - attempt to compile when atlas takes over lapack functions
	  completely (suse build problems...)

2008-06-09  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/SGInterface.cpp: documentation:
	  - Added help command 'all' to give a brief listing of all
	  commands.

2008-06-06  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/CmdLineInterface.cpp: examples/interface:
	  - Interface cmdline now can read cube matrices.
	* interface/CmdLineInterface.cpp: examples:
	  - Enabled examples for sparse real features with new data set.
	  Something makes
	  shogun segfault within classifiers, though.

2008-06-05  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUIClassifier.cpp, interface/CmdLineInterface.cpp,
	  interface/CmdLineInterface.h: interface
	  - Cmdline interface now tranposes matrices read from a file.
	* guilib/GUICommands.h, interface/SGInterface.cpp,
	  interface/SGInterface.h: interface:
	  - Added command print to print messages via SG_PRINT.

2008-06-04  Soeren Sonnenburg <sonne@debian.org>

	* configure: support cplex11
	* kernel/Kernel.cpp: at least add an assertion that lhs!=NULL and
	  totdoc>0
	* configure: clarify that MKL in configure denotes Intel MKL

2008-06-03  Sebastian Henschel <shogun@kodeaffe.de>

	* kernel/DistanceKernel.cpp: kernel:
	  - Fixed an issue with unproperly referenced distance.
	* kernel/CustomKernel.cpp, kernel/CustomKernel.h: kernel:
	  - Fixed an issue about missing features (another problem which
	  needs to be
	  addressed on this kernel at some time).

2008-06-02  Sebastian Henschel <shogun@kodeaffe.de>

	* kernel/Kernel.cpp: kernel:
	  - Fixed a segfault issue on kernel cleanup when lhs == rhs.

2008-05-30  Soeren Sonnenburg <sonne@debian.org>

	* kernel/AUCKernel.cpp, kernel/AUCKernel.h, kernel/Chi2Kernel.cpp,
	  kernel/Chi2Kernel.h, kernel/CombinedKernel.cpp,
	  kernel/CommUlongStringKernel.cpp,
	  kernel/CommWordStringKernel.cpp, kernel/ConstKernel.h,
	  kernel/CustomKernel.cpp, kernel/DiagKernel.cpp,
	  kernel/DiagKernel.h, kernel/DistanceKernel.cpp,
	  kernel/DistanceKernel.h, kernel/FixedDegreeStringKernel.cpp,
	  kernel/GaussianKernel.cpp, kernel/GaussianKernel.h,
	  kernel/HistogramWordKernel.cpp, kernel/Kernel.cpp,
	  kernel/Kernel.h, kernel/LinearByteKernel.cpp,
	  kernel/LinearKernel.cpp, kernel/LinearStringKernel.cpp,
	  kernel/LinearWordKernel.cpp,
	  kernel/LocalAlignmentStringKernel.cpp,
	  kernel/LocalityImprovedStringKernel.cpp,
	  kernel/LocalityImprovedStringKernel.h,
	  kernel/MindyGramKernel.cpp, kernel/PolyKernel.cpp,
	  kernel/PolyMatchStringKernel.cpp, kernel/PolyMatchWordKernel.cpp,
	  kernel/PyramidChi2.cpp, kernel/SalzbergWordKernel.cpp,
	  kernel/SimpleLocalityImprovedStringKernel.cpp,
	  kernel/SparseGaussianKernel.cpp, kernel/SparseLinearKernel.cpp,
	  kernel/SparsePolyKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WordMatchKernel.cpp, kernel/WordMatchKernel.h: call
	  remove_rhs() and remove_lhs() in cleanup()
	* interface/SGInterface.cpp: colorify outputs
	* guilib/GUICommands.h, interface/SGInterface.cpp,
	  interface/SGInterface.h: add command to enable progress for
	  static interfaces ( progress ON / progress OFF )
	* NEWS: update news
	* .r-install.sh, Makefile: check in forgotten .r-install.sh file
	  and finish make install for r-modular
	* Makefile: make install for r-modular half working
	* Makefile, configure: get static R interface of shogun to install
	  via make install again

2008-05-29  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/Perceptron.cpp: classifier:
	  - Made Perceptron spit out a warning, instead of info when not
	  converged.

2008-05-29  Soeren Sonnenburg <sonne@debian.org>

	* interface/SGInterface.cpp: fix a memory leak in set_custom_kernel
	* Makefile: on clean also rm .RData files

2008-05-28  Sebastian Henschel <shogun@kodeaffe.de>

	* Makefile: - Big move of testcases/examples.
	* interface/CmdLineInterface.h: interface:
	  - Compile fix for cmdline.

2008-05-28  Soeren Sonnenburg <sonne@debian.org>

	* base/SGObject.h: revert accidental change - r-modular is crashy
	  when we do proper garbage collection so better leak memory for
	  now
	* base/SGObject.h, lib/io.cpp: don't show progress by default

2008-05-28  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/KNN.cpp, classifier/KernelPerceptron.cpp,
	  classifier/LDA.cpp, classifier/LPBoost.cpp, classifier/LPM.cpp,
	  classifier/LinearClassifier.cpp, classifier/Perceptron.cpp,
	  classifier/PluginEstimate.cpp,
	  classifier/SparseLinearClassifier.cpp,
	  classifier/SubGradientLPM.cpp, classifier/svm/CPLEXSVM.cpp,
	  classifier/svm/CPLEXSVM.h, classifier/svm/GMNPSVM.cpp,
	  classifier/svm/GNPPSVM.cpp, classifier/svm/GPBTSVM.cpp,
	  classifier/svm/LibLinear.cpp, classifier/svm/LibSVM.cpp,
	  classifier/svm/LibSVMMultiClass.cpp, classifier/svm/MPDSVM.cpp,
	  classifier/svm/MultiClassSVM.cpp, classifier/svm/SVM.cpp,
	  classifier/svm/SVMLin.cpp, classifier/svm/SVMOcas.cpp,
	  classifier/svm/SVMSGD.cpp, classifier/svm/SVM_light.cpp,
	  classifier/svm/SVM_light.h, classifier/svm/SVM_linear.cpp,
	  classifier/svm/SubGradientSVM.cpp, classifier/svm/Tron.cpp,
	  classifier/svm/WDSVMOcas.cpp, classifier/svm/gmnplib.cpp,
	  classifier/svm/gnpplib.cpp, classifier/svm/gpdt.cpp,
	  classifier/svm/qpbsvmlib.cpp, clustering/Hierarchical.cpp,
	  clustering/KMeans.cpp, distance/CanberraWordDistance.cpp,
	  distance/Distance.cpp, distance/DistanceMachine.cpp,
	  distance/HammingWordDistance.cpp, distance/MinkowskiMetric.cpp,
	  distributions/Distribution.cpp,
	  distributions/histogram/Histogram.cpp,
	  distributions/hmm/GHMM.cpp, distributions/hmm/LinearHMM.cpp,
	  features/Alphabet.cpp, features/ByteFeatures.cpp,
	  features/ByteFeatures.h, features/CharFeatures.cpp,
	  features/CharFeatures.h, features/CombinedFeatures.cpp,
	  features/FKFeatures.cpp, features/Features.cpp,
	  features/Labels.cpp, features/MindyGramFeatures.h,
	  features/RealFeatures.h, features/ShortFeatures.cpp,
	  features/ShortFeatures.h, features/SimpleFeatures.h,
	  features/SparseFeatures.h, features/StringFeatures.h,
	  features/TOPFeatures.cpp, features/TOPFeatures.h,
	  features/WordFeatures.cpp, features/WordFeatures.h,
	  guilib/GUIClassifier.cpp, guilib/GUIDistance.cpp,
	  guilib/GUIFeatures.cpp, guilib/GUIHMM.cpp, guilib/GUIKernel.cpp,
	  guilib/GUIMath.cpp, guilib/GUIPreProc.cpp, guilib/GUITime.cpp,
	  interface/OctaveInterface.h, interface/PythonInterface.cpp,
	  interface/PythonInterface.h, interface/RInterface.cpp,
	  interface/SGInterface.cpp, kernel/AUCKernel.cpp,
	  kernel/Chi2Kernel.cpp, kernel/CombinedKernel.cpp,
	  kernel/CommUlongStringKernel.cpp,
	  kernel/CommWordStringKernel.cpp, kernel/CommWordStringKernel.h,
	  kernel/ConstKernel.cpp, kernel/CustomKernel.cpp,
	  kernel/DiagKernel.cpp, kernel/DistanceKernel.cpp,
	  kernel/FixedDegreeStringKernel.cpp,
	  kernel/HistogramWordKernel.cpp, kernel/Kernel.cpp,
	  kernel/KernelMachine.cpp, kernel/LinearByteKernel.cpp,
	  kernel/LinearKernel.cpp, kernel/LinearStringKernel.cpp,
	  kernel/LinearWordKernel.cpp,
	  kernel/LocalAlignmentStringKernel.cpp,
	  kernel/LocalityImprovedStringKernel.cpp,
	  kernel/MindyGramKernel.cpp, kernel/PolyKernel.cpp,
	  kernel/PolyMatchStringKernel.cpp, kernel/PolyMatchWordKernel.cpp,
	  kernel/PyramidChi2.cpp,
	  kernel/SimpleLocalityImprovedStringKernel.cpp,
	  kernel/SparseGaussianKernel.cpp, kernel/SparseLinearKernel.cpp,
	  kernel/SparsePolyKernel.cpp,
	  kernel/WeightedCommWordStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WordMatchKernel.cpp, lib/Array.h, lib/Array2.h,
	  lib/Array3.h, lib/Cache.h, lib/Cplex.cpp, lib/DynamicArray.h,
	  lib/File.cpp, lib/Mathematics.cpp, lib/Signal.cpp,
	  lib/SimpleFile.h, lib/Time.cpp, lib/Trie.h,
	  preproc/LogPlusOne.cpp, preproc/NormOne.cpp, preproc/PreProc.cpp,
	  preproc/SortUlongString.cpp, preproc/SortWord.cpp,
	  preproc/SortWordString.cpp, preproc/StringPreProc.h,
	  regression/KRR.cpp, regression/svr/LibSVR.cpp,
	  regression/svr/SVR_light.cpp, structure/DynProg.cpp,
	  structure/Plif.cpp, structure/PlifArray.cpp: - All derived
	  classes should now call their parent classes on construction.

2008-05-27  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreeStringKernel.cpp, lib/Trie.h: fix a bug in
	  linadd/batch computation for WD* kernels when degree=1 + minor
	  code cleanup

2008-05-26  Sebastian Henschel <shogun@kodeaffe.de>

	* TODO: - Removed TODO, it is now to be found in trac.

2008-05-25  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/svm/SVM_light.cpp, lib/io.cpp, lib/io.h,
	  preproc/PCACut.cpp, regression/svr/SVR_light.cpp: library:
	  - Modified SG_DONE to only display a message when progress bar is
	  enabled.

2008-05-25  Soeren Sonnenburg <sonne@debian.org>

	* lib/lapack.cpp, lib/lapack.h, lib/python_typemaps.i: fix
	  dysfunctional lapack bug (it was only working OK with atlas or
	  when neither atlas or lapack were available)

2008-05-24  Soeren Sonnenburg <sonne@debian.org>

	* TODO: update TODO
	* classifier/svm/gmnplib.cpp, classifier/svm/gnpplib.cpp: allow
	  cachesize == 2 as lower limit

2008-05-23  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/svm/SVM.cpp, classifier/svm/SVM_light.cpp,
	  distance/Distance.cpp, distributions/hmm/HMM.cpp,
	  features/FKFeatures.cpp, features/RealFileFeatures.cpp,
	  features/TOPFeatures.cpp, kernel/Kernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.cpp, lib/io.h,
	  preproc/PCACut.cpp, regression/svr/SVR_light.cpp: library:
	  - Introduced SG_DONE.
	* TODO, lib/io.cpp, lib/io.h: library:
	  - Fixed issue of not terminating when loglevel is set high
	  enough.
	  - Improved efficiency of message printing.
	* interface/SGInterface.cpp: interface:
	  - Extended static interface to support loglevels NOTICE,
	  CRITICAL, ALERT and
	  EMERGENCY. It is arguable if the last 3 are feasible, because
	  Shogun is
	  currently terminated if these situations occur.

2008-05-23  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIPreProc.cpp: compile fix when lapack is not available
	* TODO: updated TODO
	* guilib/GUIClassifier.cpp: compile fix when LAPACK/ATLAS is not
	  available

2008-05-23  Sebastian Henschel <shogun@kodeaffe.de>

	* TODO: - Introduced new section ALMOST DONE.

2008-05-22  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUICommands.h, guilib/GUIHMM.cpp, guilib/GUIHMM.h,
	  interface/CmdLineInterface.cpp, interface/CmdLineInterface.h,
	  interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - More cleanup for guilib:
	  + Made CGUIHMM::append_model available for SGInterface (to be
	  used by
	  CmdLineInterface)
	  + Removed 'commands' N_COMMENT1 and N_COMMENT2, moving the
	  defines into
	  CmdLineInterface.
	* guilib/GUICommands.h, guilib/GUIDistance.cpp,
	  guilib/GUIDistance.h, guilib/GUIFeatures.cpp,
	  guilib/GUIFeatures.h, guilib/GUIHMM.cpp, guilib/GUIHMM.h,
	  guilib/GUIKNN.cpp, guilib/GUIKNN.h, guilib/GUIKernel.cpp,
	  guilib/GUIKernel.h, interface/SGInterface.cpp,
	  interface/SGInterface.h, lib/memory.cpp: interface:
	  - Cleaned up some stuff in guilib, notably:
	  + Removed KNN-specific stuff.
	  + Removed command N_ALPHABET, N_SET_MAX_DIM.
	  + Removed CGUIDistance::clean_distance.
	  + Added commands baum_welch_viterbi_train_defined,
	  del_last_kernel,
	  del_last_features.
	  + Moved implementation of entropy and relative_entropy into
	  CGUIHMM.
	  
	  library:
	  - Saved a function call in overloaded operator delete.

2008-05-22  Soeren Sonnenburg <sonne@debian.org>

	* TODO: updated todo
	* TODO: updated TODO
	* NEWS, TODO: we no catch out of memory errors, so move remove from
	  TODO and add to NEWS :)

2008-05-21  Sebastian Henschel <shogun@kodeaffe.de>

	* lib/ShogunException.i, lib/memory.cpp: memory handling:
	  - bad_alloc is now caught for modular interfaces.
	  - Cosmetic fixes in overloaded new.

2008-05-21  Soeren Sonnenburg <sonne@debian.org>

	* lib/memory.cpp, lib/memory.h: memory handling exceptions now work
	  for all interfaces

2008-05-21  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/CmdLineInterface.cpp, interface/MatlabInterface.cpp,
	  interface/OctaveInterface.cpp, interface/PythonInterface.cpp,
	  interface/RInterface.cpp, lib/memory.cpp: interface:
	  - Improved exception handling for static interfaces.
	  - Better info string in exception thrown by overloaded operator
	  new.

2008-05-20  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/Classifier.cpp, classifier/KNN.cpp,
	  classifier/LDA.cpp, classifier/LPBoost.cpp, classifier/LPM.cpp,
	  classifier/LinearClassifier.cpp, classifier/Perceptron.cpp,
	  classifier/PluginEstimate.cpp, classifier/PluginEstimate.h,
	  classifier/SparseLinearClassifier.cpp,
	  classifier/SubGradientLPM.cpp, classifier/svm/CPLEXSVM.cpp,
	  classifier/svm/GMNPSVM.cpp, classifier/svm/GNPPSVM.cpp,
	  classifier/svm/GPBTSVM.cpp, classifier/svm/LibLinear.cpp,
	  classifier/svm/LibSVM.cpp, classifier/svm/LibSVMMultiClass.cpp,
	  classifier/svm/LibSVMOneClass.cpp, classifier/svm/MPDSVM.h,
	  classifier/svm/MultiClassSVM.cpp, classifier/svm/SVM.cpp,
	  classifier/svm/SVMLin.cpp, classifier/svm/SVMOcas.cpp,
	  classifier/svm/SVMSGD.cpp, classifier/svm/SVM_light.cpp,
	  classifier/svm/SubGradientSVM.cpp, classifier/svm/WDSVMOcas.cpp,
	  classifier/svm/WDSVMOcas.h, classifier/svm/gmnplib.cpp,
	  classifier/svm/gnpplib.cpp, classifier/svm/qpbsvmlib.cpp,
	  clustering/Hierarchical.cpp, clustering/KMeans.cpp,
	  clustering/KMeans.h, distance/Distance.cpp, distance/Distance.h,
	  distance/SimpleDistance.h, distance/SparseDistance.h,
	  distance/SparseEuclidianDistance.cpp, distance/StringDistance.h,
	  distributions/histogram/Histogram.cpp, distributions/hmm/HMM.cpp,
	  distributions/hmm/LinearHMM.cpp, features/Alphabet.cpp,
	  features/Alphabet.h, features/FKFeatures.cpp,
	  features/Features.cpp, features/Labels.cpp,
	  features/MindyGramFeatures.cpp, features/RealFeatures.cpp,
	  features/RealFileFeatures.cpp, features/ShortFeatures.cpp,
	  features/SimpleFeatures.h, features/SparseFeatures.h,
	  features/StringFeatures.h, features/TOPFeatures.cpp,
	  features/WordFeatures.cpp, guilib/GUIClassifier.cpp,
	  guilib/GUIFeatures.cpp, guilib/GUIHMM.cpp, guilib/GUIKNN.cpp,
	  guilib/GUIKernel.cpp, guilib/GUIPreProc.cpp, guilib/GUITime.cpp,
	  interface/CmdLineInterface.cpp, interface/MatlabInterface.cpp,
	  interface/OctaveInterface.cpp, interface/PythonInterface.cpp,
	  interface/SGInterface.cpp, kernel/Chi2Kernel.cpp,
	  kernel/CombinedKernel.cpp, kernel/CombinedKernel.h,
	  kernel/CommUlongStringKernel.cpp,
	  kernel/CommWordStringKernel.cpp, kernel/CustomKernel.cpp,
	  kernel/CustomKernel.h, kernel/FixedDegreeStringKernel.cpp,
	  kernel/GaussianKernel.cpp, kernel/GaussianShiftKernel.cpp,
	  kernel/HistogramWordKernel.cpp, kernel/Kernel.cpp,
	  kernel/Kernel.h, kernel/KernelMachine.cpp,
	  kernel/LinearByteKernel.cpp, kernel/LinearWordKernel.cpp,
	  kernel/LocalAlignmentStringKernel.cpp,
	  kernel/LocalityImprovedStringKernel.cpp,
	  kernel/MindyGramKernel.cpp, kernel/PolyKernel.cpp,
	  kernel/PolyMatchStringKernel.cpp, kernel/PyramidChi2.cpp,
	  kernel/SalzbergWordKernel.cpp, kernel/SigmoidKernel.cpp,
	  kernel/SimpleKernel.h, kernel/SparseGaussianKernel.cpp,
	  kernel/SparseKernel.h, kernel/SparsePolyKernel.cpp,
	  kernel/StringKernel.h, kernel/WeightedCommWordStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WordMatchKernel.cpp, lib/Array.h, lib/Cache.h,
	  lib/Cplex.cpp, lib/File.cpp, lib/Mathematics.cpp,
	  lib/Mathematics.h, lib/Trie.cpp, lib/lapack.cpp,
	  preproc/LogPlusOne.cpp, preproc/NormDerivativeLem3.cpp,
	  preproc/NormOne.cpp, preproc/PCACut.cpp,
	  preproc/PruneVarSubMean.cpp, preproc/SortUlongString.cpp,
	  preproc/SortWord.cpp, preproc/SortWordString.cpp,
	  regression/KRR.cpp, regression/svr/LibSVR.cpp,
	  regression/svr/SVR_light.cpp, structure/DynProg.cpp,
	  structure/Plif.cpp, structure/PlifArray.cpp: - Big deletion of
	  ASSERT where used unnecessarily in conjuntion with operator
	  new.
	  - Also added a couple of whitespace fixes, although this,
	  together with
	  coding-style fixes should be done for real some time later.

2008-05-20  Soeren Sonnenburg <sonne@debian.org>

	* base/SGObject.cpp, classifier/svm/SVM_libsvm.cpp,
	  interface/OctaveInterface.cpp, interface/OctaveInterface.h,
	  lib/common.h, lib/memory.cpp, lib/memory.h, lib/new.cpp,
	  lib/new.h: rename new memory... and *sigh* use std new
	* base/SGObject.cpp, lib/new.cpp, lib/new.h: custom new (seems to
	  work here)

2008-05-19  Sebastian Henschel <shogun@kodeaffe.de>

	* TODO: TODO:
	  - Marked items to take charge of for next release.

2008-05-18  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/MPDSVM.cpp, lib/Cache.h: fix spelling mistake in
	  cache and add some assertions to MPD

2008-05-17  Soeren Sonnenburg <sonne@debian.org>

	* configure: update configure to also use 'native' as march/mcpu
	  flag
	* .authors:

2008-05-16  Soeren Sonnenburg <sonne@debian.org>

	* TODO: more ideas
	* classifier/svm/pr_loqo.cpp: this should fix yaroslavs latest and
	  greatest memory leak :-)
	* guilib/GUICommands.h, interface/SGInterface.cpp,
	  interface/SGInterface.h, kernel/CombinedKernel.cpp: - add debug
	  code for initing subkernels of combined kernel
	  - add command to enable speedup of commwordstringkernel (useful
	  for whole genome predictions)
	* interface/MatlabInterface.cpp: fall back to the matlab prompt on
	  error instead of ignoring errors (though they were printed)

2008-05-16  Yaroslav Halchenko <yoh@psychology.rutgers.edu>

	* distance/Distance.cpp, features/FKFeatures.cpp,
	  features/TOPFeatures.cpp, kernel/Kernel.cpp,
	  kernel/WeightedDegreeStringKernel.cpp, preproc/PCACut.cpp: BF:
	  some SG_PRINT and printf statements into SG_INFO and SG_DEBUG

2008-05-16  Soeren Sonnenburg <sonne@debian.org>

	* .authors, TODO: add cheng to authors, fix footer and add a
	  comment to remind me to run make ChangeLog before actually doing
	  a release

2008-05-15  Soeren Sonnenburg <sonne@debian.org>

	* TODO: brain storming idea

2008-05-15  Sebastian Henschel <shogun@kodeaffe.de>

	* features/StringFeatures.h: features:
	  - Alphabet un/refing bug squished.

2008-05-15  Soeren Sonnenburg <sonne@debian.org>

	* features/StringFeatures.h: fix delete alphabet/missing SG_REF bug
	* features/Alphabet.cpp: assert that alphabet is not NULL
	* NEWS: update news, fix directory name R -> r
	* lib/File.cpp: transpose bug fix
	* NEWS, interface/CmdLineInterface.cpp: exit with code 1 instead of
	  throwing exception when error occurs on cmdline if
	* features/StringFeatures.h, interface/CmdLineInterface.cpp,
	  lib/File.cpp: -fix yet another overflow bug in string
	  features+cmdline if
	  -fix parsing of commands (with return arguments but no
	  parameters) - occured when executing scripts only
	  -implement reading and writing of vectors
	  -rename test scripts to have .sg suffix
	  -add bigger test dataset
	* interface/SGInterface.cpp, lib/File.cpp: -fix bug for reading
	  sparse features in cmdline if (1st dimension was always not read)
	  -use SG_ERROR if command is not known
	  -add some more examples / datasets:
	  
	  status:
	  - things work from cmdline but lhs args not from file (why??)
	  - string features: reading last line still broken (for strings
	  not of same length)
	* features/StringFeatures.h, lib/File.cpp: fix writing of char
	  features and sparse features
	  fix a bug in reading charstring features (forgotten overflow
	  buffer *ugh*)

2008-05-14  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.cpp: remove now (that the
	  alphabet is a protected member variable) the obsoleted get lhs
	  features (which was used to determine the alphabet only)

2008-05-14  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/CmdLineInterface.cpp, lib/File.cpp, lib/File.h:
	  interface:
	  - Added support for writing STRING CHAR features and SPARSE REAL.
	  Dunno if
	  it works, though. reading STRING CHAR is b0rked atm and not sure
	  about
	  SPARSE REAL.
	* kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.cpp: kernel:
	  - Got rid of two compiler warnings about unused variables.
	* interface/CmdLineInterface.cpp, interface/SGInterface.h:
	  interface:
	  - Added newline to error message in SGInterface.
	  - Removed the necessity of spaces before and after equal sign for
	  lhs/rhs in
	  command-line interface.

2008-05-14  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/WDSVMOcas.cpp, kernel/CommWordStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.h: Finally found the bug:
	  get_alphabet() did a SG_REF for the modular interfaces
	  but not for the static ones. This function was heavily used when
	  converting DNA
	  to 0,1,2,3 in the core loops of the string kernels, thus causing
	  a massive
	  slowdown for them (factor 5-30).
	  
	  Also modfied the WD kernels to work with alphabets != DNA/RNA
	  (but disable
	  linadd/batch comp. in this case + add a couple of assertions to
	  trap misuse)
	* classifier/svm/SVM_light.h: remove typedefs, use plain struct FOO
	  only (otherwise older swig versions don't understand the %ignore
	  FOO)
	* features/StringFeatures.h, interface/CmdLineInterface.cpp,
	  interface/CmdLineInterface.h, kernel/Kernel.h, lib/File.cpp,
	  lib/File.h: -also parse lhs
	  -simple ascii reading for cmdline interface should work for
	  simple/sparse/string features now
	  -simple ascii writing for dense real features

2008-05-14  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/CmdLineInterface.cpp, lib/File.cpp, lib/File.h:
	  interface:
	  - Implemented CFile::read_real_valued_dense() for starters. There
	  might be a
	  more elegent way, though.

2008-05-13  Soeren Sonnenburg <sonne@debian.org>

	* lib/File.cpp, lib/File.h: drafty i/o

2008-05-13  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/CmdLineInterface.cpp: interface:
	  - Little compile warning fix.

2008-05-13  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, interface/CmdLineInterface.cpp, interface/SGInterface.cpp:
	  add readline completion and filetype guessing (based on 1st 1024
	  bytes) if signature is not present

2008-05-13  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/CmdLineInterface.cpp: interface:
	  - Poked at reading features from files...

2008-05-12  Soeren Sonnenburg <sonne@debian.org>

	* interface/CmdLineInterface.cpp, interface/SGInterface.cpp: -
	  remove erraneous readline part from SGInterface
	  - delimit also on '\t\n'
	  - don't exit if shogun exception happens on interactive interface
	  (merely display an error) and only quit on ctrl+D or quit/exit
	* interface/CmdLineInterface.cpp, interface/CmdLineInterface.h,
	  interface/SGInterface.cpp: recover code from GUI/TextGUI to get
	  interactive cmdline and tcp interface to work again
	* interface/CmdLineInterface.cpp,
	  kernel/FixedDegreeStringKernel.cpp,
	  kernel/FixedDegreeStringKernel.h, kernel/LinearKernel.h,
	  kernel/PolyKernel.h, kernel/SparseLinearKernel.h,
	  kernel/SparsePolyKernel.h: more documentation and compile fix for
	  cmdline if

2008-05-10  Soeren Sonnenburg <sonne@debian.org>

	* kernel/Chi2Kernel.h, kernel/CombinedKernel.h,
	  kernel/CommUlongStringKernel.h, kernel/CommWordStringKernel.h,
	  kernel/ConstKernel.h, kernel/CustomKernel.h, kernel/DiagKernel.h,
	  kernel/DistanceKernel.h: add some documentation for these kernels

2008-05-10  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/CmdLineInterface.cpp, interface/CmdLineInterface.h,
	  sg.m: interface:
	  - Command line interface can read scalars now and is a bit more
	  relaxed about
	  the command file's contents wrt comments and newlines.
	  - Added section cmdline and one testing command file in its
	  subsection
	  examples.

2008-05-09  Sebastian Henschel <shogun@kodeaffe.de>

	* lib/io.cpp, lib/io.h: library:
	  - Extended class CIO by method skip_blanks to skip spaces and
	  tabs in strings.
	* interface/SGInterface.cpp: interface:
	  - Improved implementation of command '!' (system) to make it
	  suitable for
	  command line interface and increase flexibility for other
	  interfaces - you
	  can now pass several arguments to the command.
	* interface/SGInterface.cpp: interface:
	  - Fixed little bug in help string for command 'loglevel'.
	* configure, interface/CmdLineInterface.cpp,
	  interface/CmdLineInterface.h, interface/SGInterface.cpp,
	  lib/io.cpp: interface:
	  - Made command-line interface operational, it does not do
	  anything at the
	  moment, though.
	  io:
	  - Added some ifdef WIN32 around CSignal::unset_handler() in
	  io::message().

2008-05-09  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM_light.cpp: remove debug code
	* classifier/svm/SVM_light.cpp: init kernel caches when multiple
	  kernels are in use for svm light
	* Makefile: - create symlinks for octave and matlab and introduce
	  make check-examples to
	  check examples for current interface.
	  - make spec/wd/lik kernel examples run non interactively
	  - don't even try to run examples on matlab (as it doesn't give
	  reasonable return codes!)
	  - speed up modular R by precompiling R files (and loading the
	  ones in the examples)
	  - fix distribution octave-modular example
	  
	  AFAICT all examples for all interface run through.
	* Makefile: add tests to also run examples

2008-05-08  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM_light.cpp: fix crasher when precompute is true

2008-05-08  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUICommands.h, interface/SGInterface.cpp:
	  interface/examples:
	  - Added commands train_clustering, new_clustering, get_clustering
	  and modified
	  examples accordingly.
	* guilib/GUICommands.h, interface/SGInterface.cpp: interface:
	  - Added new commands new_regression and train_regression (alias
	  to
	  new_classifier/train_classifier) and adjusted examples.
	  - Completely enabled KRR in examples.

2008-05-08  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM_libsvm.cpp: add some progress to libsvm

2008-05-08  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUIClassifier.cpp, interface/SGInterface.cpp,
	  regression/KRR.cpp: interface:
	  - Fixed KRR in static interface.

2008-05-07  Yaroslav Halchenko <yoh@psychology.rutgers.edu>

	* classifier/svm/gpm.cpp: printf -> SG_S{WARNING,ERROR} withing
	  svm/gpm.cpp

2008-05-06  Sebastian Henschel <shogun@kodeaffe.de>

	* .scrub_docstrings.py: documentation:
	  - Possibly improved issue with CFeatures in
	  swig-autodoc-generation.
	* interface/SGInterface.cpp: interface:
	  - Fixed order of parameters in Poly kernel.
	  - Extended help string of train_classifier to include optional
	  parameters.
	* interface/MatlabInterface.cpp: interface:
	  - Improved bool handling in Matlab interface.

2008-05-05  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUIKernel.cpp: interface:
	  - Clearer output when kernel is initialised with wrong target.
	* interface/SGInterface.cpp: interface:
	  - Fixed recognition of WEIGHTEDDEGREEPOS2_NONORM.

2008-05-05  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, kernel/WeightedCommWordStringKernel.cpp,
	  kernel/WeightedCommWordStringKernel.h,
	  kernel/WeightedCommWordStringKernel.i: allow setting of custom
	  weights for W.C.W.S.K :-)

2008-05-05  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUIClassifier.cpp, guilib/GUIClassifier.h,
	  guilib/GUICommands.h, interface/SGInterface.cpp,
	  interface/SGInterface.h: interface:
	  - Completed support for KRR. KRR seems broken, though.
	* interface/SGInterface.cpp: interface:
	  - Usage of send_command will spit out a warning now.
	  - Help texts adjusted to not use strings as method arguments.

2008-05-04  Soeren Sonnenburg <sonne@debian.org>

	* base/SGObject.h, kernel/CommWordStringKernel.cpp,
	  kernel/CommWordStringKernel.h: the compute_helper function in
	  commwordstringkernel was not anymore declared
	  virtual. this broke weightedcommwordstringkernel for quite some
	  releases :(
	  
	  extract the diagonal optimization into a separate function
	  compute_diag, this
	  should not be turned on for the weightedcommwordstringkernel

2008-05-03  Cheng Soon Ong <chengsoon.ong@tuebingen.mpg.de>

	* kernel/CommWordStringKernel.cpp: Removed irritating Done prints

2008-05-03  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUIClassifier.cpp, guilib/GUIDistance.cpp,
	  guilib/GUIFeatures.cpp, guilib/GUIHMM.cpp, guilib/GUIKNN.cpp,
	  guilib/GUIKernel.cpp, guilib/GUIPluginEstimate.cpp,
	  guilib/GUIPreProc.cpp, interface/SGInterface.cpp,
	  interface/SGInterface.h: interface:
	  - Made command 'clear' do something useful.
	* guilib/GUIFeatures.cpp, guilib/GUIKernel.cpp,
	  interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - It is unnecessary now to supply the number of chars you want to
	  have
	  matched in strmatch if you want to have an exact match.
	  - Some more little fixes.

2008-05-02  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Improved error handling for vectors and handling of spaces in
	  command
	  strings.
	* interface/SGInterface.cpp: interface:
	  - Fixed a bug in default value for SVM C2.
	* guilib/GUIKernel.cpp, interface/SGInterface.cpp: interface:
	  - Made little changes on how WEIGHTEDDEGREEPOS2/3 are
	  implemented.

2008-05-02  Soeren Sonnenburg <sonne@debian.org>

	* interface/MatlabInterface.cpp: better do explicit casts, mxChar
	  is 16bit, CHAR only 8
	* Makefile: speed up loading shogun modules from R a lot

2008-05-02  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUIClassifier.cpp, guilib/GUIClassifier.h,
	  guilib/GUIHMM.cpp, guilib/GUIKernel.cpp, guilib/GUIPreProc.h,
	  interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Fixed a couple of issues, including
	  WeightedDegreePositionString. There
	  seems be a problem with support vectors somewhere, though.

2008-05-01  Sebastian Henschel <shogun@kodeaffe.de>

	* gui, guilib/GUIClassifier.cpp, guilib/GUIClassifier.h,
	  guilib/GUIDistance.cpp, guilib/GUIDistance.h,
	  guilib/GUIFeatures.cpp, guilib/GUIFeatures.h, guilib/GUIHMM.cpp,
	  guilib/GUIHMM.h, guilib/GUIKNN.cpp, guilib/GUIKNN.h,
	  guilib/GUIKernel.cpp, guilib/GUIKernel.h, guilib/GUILabels.cpp,
	  guilib/GUILabels.h, guilib/GUIMath.cpp, guilib/GUIMath.h,
	  guilib/GUIPluginEstimate.cpp, guilib/GUIPluginEstimate.h,
	  guilib/GUIPreProc.cpp, guilib/GUIPreProc.h, guilib/GUITime.cpp,
	  guilib/GUITime.h, interface/MatlabInterface.cpp,
	  interface/MatlabInterface.h, interface/OctaveInterface.cpp,
	  interface/OctaveInterface.h, interface/PythonInterface.cpp,
	  interface/PythonInterface.h, interface/RInterface.cpp,
	  interface/RInterface.h, interface/SGInterface.cpp,
	  interface/SGInterface.h: interface:
	  - Obliterated gui/.
	  - The previous check-in should have meant that WeightedDegree* is
	  b0rked.
	* gui/TextGUI.cpp, guilib/GUIClassifier.cpp,
	  guilib/GUIClassifier.h, guilib/GUIDistance.cpp,
	  guilib/GUIDistance.h, guilib/GUIFeatures.h, guilib/GUIHMM.cpp,
	  guilib/GUIHMM.h, guilib/GUIKernel.cpp, guilib/GUIKernel.h,
	  guilib/GUILabels.cpp, guilib/GUILabels.h, guilib/GUIMath.cpp,
	  guilib/GUIMath.h, guilib/GUIPluginEstimate.cpp,
	  guilib/GUIPluginEstimate.h, guilib/GUIPreProc.cpp,
	  guilib/GUIPreProc.h, interface/SGInterface.cpp,
	  interface/SGInterface.h: interface:
	  - Implemented all changes necessary to support old and new
	  interface.
	  WeightedDegree* (read: vectors in a string) is apparently,
	  though.

2008-04-30  Soeren Sonnenburg <sonne@debian.org>

	* base/SGObject.i, lib/r.h, lib/r_typemaps.i: - really disable
	  garbage collection in r-modular (crashes if on)
	  - implement r-typemaps for setting strings
	  - classifier and regression examples for R work now (except for
	  string based/enum requiring functions)

2008-04-30  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/Perceptron.cpp: classifier:
	  - Fix: Perceptron::train even returned false when it had
	  converged.
	* lib/common.h: lib:
	  - Introduced EPreProcType.

2008-04-28  Sebastian Henschel <shogun@kodeaffe.de>

	* gui/TextGUI.cpp, guilib/GUIFeatures.cpp, guilib/GUIFeatures.h,
	  interface/SGInterface.cpp: interface:
	  - Interface now supports new and legacy way to handle features.

2008-04-27  Soeren Sonnenburg <sonne@debian.org>

	* NEWS: ported regression examples to r-modular - Rswig seems to
	  work now with my
	  recent fixes - the other examples are still missing though WIP

2008-04-25  Sebastian Henschel <shogun@kodeaffe.de>

	* gui/TextGUI.cpp, guilib/GUIKernel.cpp, guilib/GUIKernel.h,
	  interface/SGInterface.cpp, interface/SGInterface.h: interface
	  - Implemented command set/add_kernel in a legacy-tolerant way.
	  all_* examples
	  in octave run through, so there are only spiteful bugs.

2008-04-25  Soeren Sonnenburg <sonne@debian.org>

	* base/SGObject.h, classifier/svm/SVM_light.i, lib/Mathematics.i,
	  lib/Signal.i, lib/Trie.i, lib/io.i, lib/r_typemaps.i: There was
	  actually no bug in SWIG but in R 2.7 (and still is - long input
	  lines
	  cause it to crash, solution posted to Rd mailinglist). Which
	  means R+swig works
	  in principle. However are definitely a couple of (minor/easily
	  fixable) bugs in
	  the R wrapper that need further fixes before shogun fully works:
	  
	  1) the dispatcher (called when an object is constructed) wrongly
	  calls
	  extends(argtypes[1], 'numeric')) which will never be true for a
	  matrix (some
	  magic is needed here). Workaround for now is to not use
	  RealFeatures(my_matrix), but
	  rf=RealFeatures()
	  rf$copy_feature_matrix(rf, my_matrix)
	  2) arguments that take a double* will all be modified via
	  as.numeric(arg) which
	  converts matrices -> vectors. IMHO it does not make sense to do
	  any conversion
	  at all but for compatibility a workaround for now is to use
	  %{ if (!is.numeric($input)) $input = as.numeric($input) %}
	  in the scoercein typemap
	  3) the R2.7 swig mkCharEnc fix (patch submitted)
	* Makefile, configure: rename R-modular / R to r-modular / r (all
	  lowercase )

2008-04-24  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/OctaveInterface.cpp: interface:
	  - Fixed an erroneous check for boolean scalar in Octave
	  interface.

2008-04-24  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM.cpp, structure/DynProg.cpp: - fix crasher in
	  dynprog (double free)
	  - cosmetic code formatting in svm

2008-04-21  Cheng Soon Ong <chengsoon.ong@tuebingen.mpg.de>

	* classifier/svm/SVM.cpp, lib/io.h: Hack to make sure that static
	  sg_io has same display progress settings as svm.io

2008-04-19  Soeren Sonnenburg <sonne@debian.org>

	* Makefile: install octave files with executable bit set
	* Makefile: fix PYTHONPATH on make test
	* ChangeLog: Preparing for new Release shogun_0.6.1
	* Makefile: let make distclean also remove octave-core files,
	  cplex.log and .swp files
	* NEWS, interface/SGInterface.cpp: categorize help in topics

2008-04-18  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/SGInterface.cpp: interface:
	  - Extended help command to list commands in groups.
	* interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Renamed all 'action' to 'command', incl. relating names
	* interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Added remaining commands to make send_command obsolete.

2008-04-18  Soeren Sonnenburg <sonne@debian.org>

	* NEWS: update news
	* kernel/Kernel.h: type : -> ;
	* kernel/Kernel.h: resize cache fix, thanks Christian Widmer
	* classifier/Classifier.i, clustering/Clustering.i,
	  distance/Distance.i, distributions/Distribution.i,
	  evaluation/Evaluation.i, features/Features.i, kernel/Kernel.i,
	  lib/Library.i, preproc/PreProc.i, regression/Regression.i:
	  Disable director in all swig files. This has big impact on
	  
	  a) speed
	  b) wrapper code size
	  c) inheritance.
	  
	  Good news first, every virtual function should be *much faster*
	  now, as the
	  call is not anymore rerouted via the director wrapper to python
	  and then from
	  there to the correct c++ function. Furthermore the wrapper code
	  size decreases
	  a lot, the inheritance chain is shorter and compile times are
	  reduced.
	  
	  The sad news is that virtual functions that *were overloaded via
	  python code*
	  will not be used from inside the C++ code (not sure if anyone
	  expected this to
	  work - so it might not actually be that bad).
	* NEWS: further preps for the release

2008-04-18  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Added a few more commands to make send_command obsolete in the
	  near future.

2008-04-17  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Added a bunch of commands to make send_command obsolete in the
	  near future.

2008-04-17  Soeren Sonnenburg <sonne@debian.org>

	* Makefile, clustering/Hierarchical.i, lib/octave_typemaps.i,
	  lib/python_typemaps.i, regression/KRR.cpp,
	  regression/svr/SVR_light.h: - fix a memory leak in KRR
	  - add forgotten typemap in Hierarchical
	  - add semicolon on make install for octave-modular
	  - add the same examples we have for python-modular to
	  octave-modular: there
	  seems to be still a bug leading to infinity recursions for
	  virtual functions in
	  the octave swig wrapper ... to be debugged

2008-04-16  Soeren Sonnenburg <sonne@debian.org>

	* features/SparseFeatures.h, kernel/CommWordStringKernel.cpp,
	  kernel/HistogramWordKernel.cpp,
	  kernel/LocalityImprovedStringKernel.cpp,
	  kernel/SalzbergWordKernel.cpp: fix a couple of compile warnings
	  on 64bit arch
	* features/ShortRealFeatures.h, features/WordFeatures.h: - compile
	  fix
	  - fix crasher due to united variable in wordfeatures
	  - adjust python examples/testsuite to match new syntax
	* classifier/svm/SVM.i, features/ByteFeatures.i,
	  features/CharFeatures.i, features/IntFeatures.h,
	  features/IntFeatures.i, features/RealFeatures.h,
	  features/RealFeatures.i, features/ShortFeatures.h,
	  features/ShortFeatures.i, features/ShortRealFeatures.h,
	  features/ShortRealFeatures.i, features/SimpleFeatures.i,
	  features/WordFeatures.h, features/WordFeatures.i: * get rid of
	  most %pythoncode extensions, which brings the following
	  incompatible changes:
	  - Byte/Char features have to be created like stringfeatures, i.e.
	  bf=ByteFeatures(alphabet)
	  bf.copy_feature_matrix(array(...))
	  * only the convenience function for SVM remains (for the python
	  interface), in
	  case we later do some define magic we might do
	  a) magic multi argument typemaps, e.g. ByteFeatures(alphabet,
	  feat)
	  b) functions with multiple numpy arrays... e.g. SVM(svs, alphas,
	  b)
	  with CSVM(INT* svs, INT num_svs, DREAL* alphas, INT num_alpha,
	  DREAL b)
	* features/Labels.i, lib/octave_typemaps.i, lib/python_typemaps.i,
	  lib/r_typemaps.i: - resolved conflict, for multiple same name
	  (but with different type) functions
	  - we won't need the elstupido %pythoncode class derivation stuff
	  :-)

2008-04-15  Soeren Sonnenburg <sonne@debian.org>

	* classifier/LinearClassifier.i,
	  classifier/SparseLinearClassifier.i, classifier/svm/SVM.i,
	  clustering/Clustering.i, clustering/KMeans.i, configure,
	  distance/Distance.i, distributions/Distribution.i,
	  evaluation/Evaluation.i, features/Alphabet.i,
	  features/ByteFeatures.i, features/CharFeatures.i,
	  features/IntFeatures.i, features/Labels.i,
	  features/RealFeatures.i, features/ShortFeatures.i,
	  features/ShortRealFeatures.i, features/SimpleFeatures.i,
	  features/StringFeatures.i, features/WordFeatures.i,
	  interface/RInterface.cpp, kernel/CustomKernel.i, kernel/Kernel.i,
	  kernel/LinearKernel.i,
	  kernel/WeightedDegreePositionStringKernel.i,
	  kernel/WeightedDegreeStringKernel.i, lib/R.h, lib/Signal.cpp,
	  lib/io.cpp, lib/matlab.h, lib/octave.h, lib/python.h, lib/r.h,
	  lib/r_typemaps.i, lib/swig_typemaps.i, structure/Structure.i: -
	  wrap all typemaps in lib/swig_typemaps.i (that include
	  python_typemaps.i etc...)
	  - only ever use include lib/r.h when including R files
	  - R does not need a prefix for .so files, e.g. Kernel.R and
	  Kernel.so is the swig output
	  - add python swig support (including typemaps for i/o of vectors
	  and matrices),
	  while it should fully work it does not, guessing:
	  
	  a) debian's R 2.7-prerelease is too new
	  b) swig R wrapper support is far from mature
	  c) subtleties of the R swig/interface or R even, e.g. the test
	  works via R < ../R-modular/examples/first_shot.R
	  but crashes when pasted in interactive mode. as long as the R
	  swig
	  maintainer does not respond this has 0 chance to improve in the
	  future.
	* Makefile, TODO, interface/SGInterface.cpp: - add make install for
	  octave-modular
	  - fix typo in usage help
	  - update todo list
	* lib/Mathematics.h: fix another compile warning
	* features/Alphabet.cpp, features/WordFeatures.cpp,
	  features/WordFeatures.h, kernel/CommWordStringKernel.cpp,
	  kernel/CommWordStringKernel.h, kernel/KernelMachine.cpp,
	  kernel/KernelMachine.h, kernel/PyramidChi2.h,
	  kernel/WeightedDegreePositionStringKernel.h,
	  lib/octave_typemaps.i, structure/DynProg.cpp,
	  structure/DynProg.h: - fix a large number of gcc4.3 compile
	  warnings
	  - add missing documentation
	  - add copyright header to octave_typemaps.i

2008-04-14  Soeren Sonnenburg <sonne@debian.org>

	* lib/octave_typemaps.i: force variable to be in the outer context
	  for IN1/IN2 octave typemaps. they
	  might have been deallocated (as they were local variables)
	  before.
	* ChangeLog: - bugfix in R package building
	  - add a make update-webpage to simplify the release mechanism
	* base/SGObject.h, base/SGObject.i, clustering/KMeans.i,
	  features/Labels.i, kernel/Kernel.i: - add forgotten includes for
	  python_typemap and variable renaming
	  - use ref counting for octave interface too
	  - ignore all further constructors when creating Labels(lab), this
	  seems to please typemaps (as in they are now applied)

2008-04-13  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, classifier/LinearClassifier.i,
	  classifier/SparseLinearClassifier.i, classifier/svm/SVM.i,
	  clustering/Clustering.i, distance/Distance.i,
	  distributions/Distribution.i, evaluation/Evaluation.i,
	  features/Alphabet.i, features/ByteFeatures.i,
	  features/CharFeatures.i, features/IntFeatures.i,
	  features/Labels.cpp, features/Labels.h, features/Labels.i,
	  features/RealFeatures.i, features/ShortFeatures.i,
	  features/ShortRealFeatures.i, features/SimpleFeatures.i,
	  features/StringFeatures.i, features/WordFeatures.i,
	  kernel/CustomKernel.i, kernel/Kernel.i, kernel/LinearKernel.i,
	  kernel/WeightedDegreePositionStringKernel.i,
	  kernel/WeightedDegreeStringKernel.i, lib/octave_typemaps.i,
	  lib/python.h, lib/python_typemaps.i, structure/Structure.i:
	  increadibly, swig for octave is basically working for everything,
	  vectors,
	  matrices and strings (in and out...)... thanks to the swig team
	  and
	  especially Xavier Delacour for the help... needs swig from svn to
	  work

2008-04-13  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/SGInterface.cpp: interface:
	  - Updated help command to give the user a hint how to invoke help
	  for a single
	  command.

2008-04-13  Soeren Sonnenburg <sonne@debian.org>

	* clustering/KMeans.h, features/SimpleFeatures.h,
	  features/StringFeatures.h, kernel/Kernel.h,
	  kernel/KernelMachine.h: fixed a few doxygen documentation
	  warnings

2008-04-12  Soeren Sonnenburg <sonne@debian.org>

	* COPYRIGHT, LICENSE, LICENSE.SVMlight, NEWS: - lots more of
	  documentation

2008-04-12  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Little bugfix to usage string of set_features and proper
	  delete[] in a_help.
	  - Reshuffling of methods to have them grouped properly.
	  - Added many commands which merely call send_command for the time
	  being.
	* interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Removed superflous command test.
	  - Improved help function.

2008-04-12  Soeren Sonnenburg <sonne@debian.org>

	* kernel/Kernel.i: - remove vignette and include documentation in
	  doxygen
	  - get swig-octave to work for Kernels.
	* .authors: add yaroslav to authors, minimal documentation
	* Makefile, base/Documentation.mainpage, classifier/svm/SVM.h,
	  kernel/KernelMachine.h: - svn put tests into tests/ directory
	  - move/merge documenation form .txt files to doxygen
	  - update README and fix doc generation

2008-04-11  Soeren Sonnenburg <sonne@debian.org>

	* interface/RInterface.cpp, interface/SGInterface.cpp: fix the hmm
	  viterbi path: it returns a WORD not real-vector: using
	  set_word_vector is the fix. as R does not support WORD add some
	  fuzzing (return ints for WORD, DREAL for shortreal etc...)
	* .generate_link_dependencies.py, .scrub_docstrings.py, Makefile,
	  base/SGObject.h, base/SGObject.i, classifier/KNN.h,
	  classifier/LinearClassifier.h, classifier/PluginEstimate.cpp,
	  classifier/PluginEstimate.h, classifier/SparseLinearClassifier.h,
	  configure, kernel/Kernel.cpp, kernel/Kernel.h, lib/Signal.cpp:
	  octave-modular compile support

2008-04-10  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/SGInterface.cpp: interface:
	  - Possibly fixed HMM issue.
	  - Forgot to add R toy examples previously.
	* guilib/GUIKernel.cpp, interface/SGInterface.cpp,
	  interface/SGInterface.h: interface:
	  - Fixed a memory access issue, all interfaces with each all_*
	  example file are
	  valgrind-clear. HMM segfault issue is pending.
	* distributions/hmm/HMM.cpp, interface/SGInterface.cpp:
	  HMM/interface:
	  - Mucked around with a bug in HMM, only did some cosmetic fixes.
	  Maybe
	  CHMM::model_probability_comp must be changed? dunno how.

2008-04-10  Soeren Sonnenburg <sonne@debian.org>

	* configure, lib/lapack.cpp, lib/lapack.h: add jochens fixes to
	  properly detect acml and intel mkl
	* classifier/svm/SVM_light.cpp, distance/CanberraMetric.cpp,
	  distance/ChebyshewMetric.cpp, distance/GeodesicMetric.cpp,
	  distance/JensenMetric.cpp, distance/ManhattanMetric.cpp,
	  distance/MinkowskiMetric.cpp, kernel/DiagKernel.cpp,
	  kernel/SigmoidKernel.cpp, preproc/PCACut.cpp,
	  regression/svr/SVR_light.cpp: -don't ever directly include
	  <cblas.h> but use lib/lapack.h instead
	  -remove <cblas.h> from many files that just don't need it

2008-04-09  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/RInterface.cpp: interface:
	  - Added toy examples for R interface and moved plotting examples
	  into plots/.
	  - Mostly cosmetic fixed to other interfaces.

2008-04-09  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/Tron.cpp, configure: convert tron to use cblas

2008-04-08  Soeren Sonnenburg <sonne@debian.org>

	* configure: fix definition of dpotrf_
	* configure: link with cblas in case of atlas
	* configure: Use --dis/enable-lapack again: the HAVE_LAPACK switch
	  is on if blas and any
	  of ACML, MKL, ATLAS or vanilla LAPACK are found (each of which
	  implement the
	  lapack standard). In configure detect if we have one of the many
	  and as we use
	  clapack in case of atlas fall back to Jochen's wrappers if atlas
	  is not available.
	  
	  Tested with lapack and atlas, still needs testing for MKL and
	  ACML (which I don't have)
	* NEWS: update NEWS
	* classifier/PluginEstimate.cpp, configure: - fix compile warning
	  (NULL vs. 0) mismatch
	  - require octave version 3.0
	* interface/MatlabInterface.cpp, lib/matlab.h: compile fix for
	  matlab 6.5 (logical does not exist there...)
	* classifier/svm/SVM_light.cpp: fix single kernel SVM-light
	* lib/Mathematics.h, lib/lapack.cpp, lib/lapack.h: attempt to fix
	  building w/ atlas
	* classifier/svm/pr_loqo.cpp, configure, lib/Mathematics.cpp,
	  lib/Mathematics.h, lib/lapack.cpp, lib/lapack.h,
	  preproc/PCACut.cpp, regression/KRR.cpp: Add ACML and MKL support
	  based on the patches from Jochen Garcke - thanks!

2008-04-08  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/SGInterface.cpp: interface:
	  - Fix double free corruption in SGInterface::a_get_classifier.
	  - Fix python examples for clustering.

2008-04-07  Soeren Sonnenburg <sonne@debian.org>

	* classifier/LinearClassifier.i, kernel/LinearKernel.h,
	  kernel/LinearKernel.i: add a get_w / set_w to linear kernel

2008-04-07  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUIDistance.cpp, guilib/GUIKernel.cpp,
	  interface/SGInterface.cpp: interface:
	  - Added examples for Python interface.
	  - Fixed typo in GUIDistance.
	  - Made error message in GUIKernel more useful.
	  - Fixed bug in SGInterface.

2008-04-06  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/OctaveInterface.cpp, interface/OctaveInterface.h,
	  interface/PythonInterface.cpp, interface/PythonInterface.h,
	  interface/RInterface.cpp, interface/RInterface.h,
	  interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Implemented set_int/real/bool for all 4 interfaces.

2008-04-06  Soeren Sonnenburg <sonne@debian.org>

	* .scrub_docstrings.py, Makefile, clustering/Hierarchical.h,
	  clustering/KMeans.h, configure, features/Features.i,
	  features/SimpleFeatures.h,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h, lib/DynamicArray.h,
	  lib/DynamicArray.i, sg.m: - fix hmm example
	  - fix several naming conflicts (e.g. result is used by swig for
	  return arguments)
	  - get modular R interface to at least compile

2008-04-06  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Replaced set/get_*_matrix by set/get_*_vector where
	  appropriate.
	  - Fixed octave-incompatible example.

2008-04-06  Soeren Sonnenburg <sonne@debian.org>

	* TODO, gui/GUI.h, gui/Python.h, gui/TextGUI.h,
	  guilib/GUIMatlab.cpp, interface/MatlabInterface.cpp,
	  interface/OctaveInterface.cpp, interface/PythonInterface.cpp,
	  interface/RInterface.cpp, lib/R.h, lib/Signal.cpp, lib/io.cpp: -
	  delete remainders of old interfaces and minor compile and
	  cosmetic fixes
	  - update TODO
	* classifier/svm/SVM_light.cpp, gui/Matlab.cpp, gui/Octave.cpp,
	  gui/Python.cpp, gui/R.cpp, guilib/GUIMatlab.h,
	  guilib/GUIOctave.cpp, guilib/GUIOctave.h, guilib/GUIPython.cpp,
	  guilib/GUIPython.h, guilib/GUIR.cpp, guilib/GUIR.h,
	  interface/MatlabInterface.cpp, interface/OctaveInterface.cpp,
	  interface/RInterface.cpp, lib/R.h, lib/Signal.cpp, lib/octave.h:
	  - add signal handling for octave
	  - attempt to get signal handling for R/python to work - it may
	  not - we should
	  use a different (cleaner) mechanism anyway: set a flag when
	  ctrl-c occured, in
	  long loops check that flag every now and then and then return
	  - put extension includes in lib/{R,octave,python,matlab}.h
	  - remove old (and now obsolete) interface files

2008-04-04  Soeren Sonnenburg <sonne@debian.org>

	* interface/OctaveInterface.cpp, interface/PythonInterface.cpp,
	  interface/PythonInterface.h: mostly fixed static python interface
	  (set/get features etc)
	  fixed examples
	* configure, interface/MatlabInterface.h,
	  interface/OctaveInterface.cpp, interface/RInterface.cpp,
	  interface/RInterface.h, interface/SGInterface.cpp,
	  interface/SGInterface.h: - compile fix for octave
	  - use set_real_vector for HMM in SGInterface
	  - R interface cleanups
	  - use a single directory for octave and matlab as octave 3.0
	  supports all
	  matlab types/functions now

2008-04-03  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/PythonInterface.cpp, interface/PythonInterface.h:
	  interface:
	  - Added some safeguards to PythonInterface.
	  - Broke out set_real_matrix for debugging; it is still not
	  working
	  properly.

2008-04-03  Soeren Sonnenburg <sonne@debian.org>

	* interface/RInterface.cpp, interface/RInterface.h,
	  interface/SGInterface.cpp: fix examples for new R interface. we
	  still need to fix get/set vectors for all
	  interfaces

2008-04-03  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/PythonInterface.cpp, interface/PythonInterface.h:
	  interface:
	  - Fixed compilation and implemented create_return_values() in
	  PythonInterface.

2008-04-03  Soeren Sonnenburg <sonne@debian.org>

	* interface/RInterface.cpp: completed R interface - not many
	  datatypes are supported in R :(
	* configure, interface/MatlabInterface.cpp,
	  interface/MatlabInterface.h, interface/OctaveInterface.cpp,
	  interface/OctaveInterface.h, interface/PythonInterface.cpp,
	  interface/PythonInterface.h, interface/RInterface.cpp,
	  interface/RInterface.h, interface/SGInterface.cpp,
	  interface/SGInterface.h: - argh, we need to link to -llapack too
	  as some functions are not clapack
	  - remove submit_return_values, and modify create_return_values,
	  to return true
	  if successfull. change interfaces accordingly
	* configure: we actually require atlas for compilation, not lapack.
	  (clapack_* functions are
	  required) thus always link with -llapack_atlas

2008-04-02  Yaroslav Halchenko <yoh@psychology.rutgers.edu>

	* features/SparseFeatures.h: fix possible segfault in
	  SparseFeatures.h (thanks to Andrey T)

2008-04-02  Soeren Sonnenburg <sonne@debian.org>

	* configure: test swig version

2008-04-02  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/PythonInterface.cpp: interface:
	  - Fixed initialisation of PythonInterface.
	  - Modified examples to use new interface.

2008-04-02  Soeren Sonnenburg <sonne@debian.org>

	* lib/python_typemaps.i: potentially fix a bug in make contiguous

2008-04-01  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/PythonInterface.cpp: interface:
	  - Implemented methods for PythonInterface - they compile but most
	  likely won't work.

2008-04-01  Soeren Sonnenburg <sonne@debian.org>

	* interface/RInterface.cpp, interface/RInterface.h,
	  interface/SGInterface.cpp: get/set_features for R interface: note
	  that the number of arguments check in
	  interface/SGInterface.cpp was disabled - we need an interface
	  change here

2008-03-31  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/MatlabInterface.cpp: interface:
	  - Fixed a copy&paste bug.
	* interface/MatlabInterface.cpp: interface:
	  - Improved handling of cell arrays in get_argument_type in
	  MatlabInterface.
	* interface/PythonInterface.cpp: interface:
	  - Implemented get_argument_type() in PythonInterface.
	* interface/PythonInterface.cpp, interface/PythonInterface.h,
	  interface/SGInterface.h: interface:
	  - Made Python interface compile again.

2008-03-30  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/OctaveInterface.cpp, interface/SGInterface.cpp:
	  interface:
	  - Fixed an erroneous delete[] (and now unnecessary copying of
	  data) while
	  checking octave interface on matlab examples.

2008-03-29  Soeren Sonnenburg <sonne@debian.org>

	* interface/RInterface.cpp, interface/RInterface.h: get R interface
	  to compile again

2008-03-29  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/MatlabInterface.cpp, interface/OctaveInterface.cpp,
	  interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Got rid of SINGLE_STRING

2008-03-28  Soeren Sonnenburg <sonne@debian.org>

	* features/SparseFeatures.h: free the matrix as long as num_vectors
	  is still correct
	* interface/OctaveInterface.cpp, interface/SGInterface.h: octave
	  interface mostly works now (at least svm_classification,
	  test_wd_kernel,
	  svr_regression ...)
	* configure: don't remove configure.log when --help is called
	* classifier/svm/LibSVM.cpp, classifier/svm/LibSVMOneClass.cpp,
	  classifier/svm/MultiClassSVM.cpp, classifier/svm/SVM.cpp,
	  classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h,
	  clustering/Hierarchical.cpp, clustering/KMeans.cpp,
	  distance/Distance.cpp, distance/Distance.h,
	  interface/SGInterface.cpp, kernel/AUCKernel.cpp,
	  kernel/CombinedKernel.cpp, kernel/CustomKernel.cpp,
	  kernel/Kernel.cpp, kernel/Kernel.h, kernel/KernelMachine.cpp,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.cpp, regression/KRR.cpp: - fix
	  another SG_REF / UNREF mismatch: the kernel get_lhs()/rhs()
	  functions need
	  to increment reference counts when returning a feature object,
	  use rhs/lhs
	  internally and otherwise make sure that SG_UNREF is called for
	  each SG_REF
	  (same for CDistance)
	  - add an assertion for get_features to not crash if no feature
	  object is available
	* guilib/GUIPluginEstimate.cpp: adjust for changes in
	  pluginestimate
	* classifier/LinearClassifier.h, classifier/PluginEstimate.cpp,
	  classifier/PluginEstimate.h, classifier/SparseLinearClassifier.h,
	  classifier/svm/MultiClassSVM.cpp, clustering/Hierarchical.cpp,
	  clustering/KMeans.cpp, clustering/KMeans.h,
	  distance/SparseEuclidianDistance.cpp,
	  kernel/HistogramWordKernel.cpp,
	  kernel/LocalAlignmentStringKernel.cpp,
	  kernel/LocalityImprovedStringKernel.cpp,
	  kernel/LocalityImprovedStringKernel.h,
	  kernel/SimpleLocalityImprovedStringKernel.cpp,
	  kernel/SimpleLocalityImprovedStringKernel.h,
	  kernel/WeightedCommWordStringKernel.cpp,
	  regression/svr/LibSVR.cpp, regression/svr/SVR_light.cpp,
	  regression/svr/SVR_light.h: - fix several further memory leaks
	  - make (Simple)LocalityImproved kernel thread safe
	  - PluginEstimate is now derived from classifier (removed obsolete
	  test
	  function, make classifier framework compatible and adjust test
	  suite/examples)

2008-03-27  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.cpp: one further leak
	  (forgotten to free block weights on object destruction)
	* classifier/LinearClassifier.cpp, classifier/LinearClassifier.h,
	  classifier/LinearClassifier.i,
	  classifier/SparseLinearClassifier.h,
	  classifier/SparseLinearClassifier.i,
	  classifier/svm/LibLinear.cpp,
	  classifier/svm/LibSVMMultiClass.cpp, classifier/svm/MPDSVM.cpp,
	  classifier/svm/MultiClassSVM.i, classifier/svm/SVM.cpp,
	  classifier/svm/SVM.h, classifier/svm/SVM.i,
	  classifier/svm/SVMLin.cpp, classifier/svm/gpdtsolve.cpp,
	  classifier/svm/ssl.cpp, features/Labels.cpp,
	  features/SparseFeatures.h: fix several further memory leaks and a
	  stupid double free
	* classifier/svm/SVM.h, classifier/svm/SVM.i,
	  features/SimpleFeatures.h, features/SparseFeatures.h:
	  get_labels() returns a new object so mark it with %newobject
	* classifier/Classifier.h, classifier/LinearClassifier.h,
	  classifier/SparseLinearClassifier.h, distance/DistanceMachine.h,
	  kernel/Kernel.cpp, kernel/KernelMachine.h: in all set_ routines,
	  UNREF the old objects first before overwriting them, this should
	  fix another set of memory leaks like:
	  
	  gk=GaussianKernel(f1,f2,sigma)
	  ..
	  gk.init(f3,f4)
	  ..
	  gk.init(f5,f6)
	* classifier/KNN.cpp, classifier/LDA.cpp, classifier/LPBoost.cpp,
	  classifier/LPM.cpp, classifier/Perceptron.cpp,
	  classifier/SubGradientLPM.cpp, clustering/Hierarchical.cpp,
	  clustering/KMeans.cpp: this should fix another couple of leaks
	  for linear/sparselinear classifiers and
	  distancemachines
	* classifier/svm/SVMSGD.cpp: fix double free
	* classifier/LDA.cpp, classifier/LinearClassifier.cpp,
	  classifier/LinearClassifier.h, classifier/Perceptron.cpp,
	  classifier/SparseLinearClassifier.cpp,
	  classifier/SparseLinearClassifier.h,
	  classifier/svm/LibLinear.cpp, classifier/svm/SVMLin.cpp,
	  classifier/svm/SVMOcas.cpp, classifier/svm/SVMSGD.cpp,
	  classifier/svm/SubGradientSVM.cpp, distance/DistanceMachine.cpp,
	  distance/DistanceMachine.h, interface/OctaveInterface.cpp: fix
	  missing SG_REF/UNREFs on many places: whenever possible use the
	  set_features/set_labels/set_kernel functions as they will take
	  care of
	  SG_REFfing things. UNREFfing is done in the baseclasses, like
	  DistanceMachine,KernelMachine,Classifier,
	  Linear/SparseLinearClassifier
	* configure, interface/MatlabInterface.cpp,
	  interface/OctaveInterface.cpp: - link octave w/ -lcruft (for
	  exception handling)
	  - get/set features at least for double matrices works

2008-03-27  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/MatlabInterface.cpp, interface/SGInterface.cpp,
	  interface/SGInterface.h: interface:
	  - Went through all matlab examples, except those requiring CPLEX
	  and aborted
	  those taking longer than 5 minutes. Fixed some of the examples
	  and fixed the
	  new interface in the process.

2008-03-27  Soeren Sonnenburg <sonne@debian.org>

	* interface/OctaveInterface.cpp, interface/OctaveInterface.h: get
	  octave interface to at least compile again
	* classifier/svm/GMNPSVM.cpp, classifier/svm/GNPPSVM.cpp,
	  classifier/svm/GPBTSVM.cpp, classifier/svm/LibSVM.cpp,
	  classifier/svm/LibSVMMultiClass.cpp,
	  classifier/svm/LibSVMOneClass.cpp,
	  classifier/svm/MultiClassSVM.cpp, classifier/svm/SVM.cpp,
	  classifier/svm/SVM.h, classifier/svm/SVM_light.cpp,
	  classifier/svm/SVM_light.h, regression/KRR.cpp,
	  regression/svr/LibSVR.cpp, regression/svr/SVR_light.cpp,
	  regression/svr/SVR_light.h: use kernel instead of get_kernel()
	  for all classes derived from CKernelMachine
	  to fix the 'get_kernel()' memory leak
	* features/ByteFeatures.cpp, features/CharFeatures.cpp,
	  features/FKFeatures.cpp, features/IntFeatures.cpp,
	  features/RealFeatures.cpp, features/RealFileFeatures.cpp,
	  features/ShortFeatures.cpp, features/ShortRealFeatures.cpp,
	  features/SimpleFeatures.h, features/SparseFeatures.h: based on
	  yaroslavs patch fix the memoryleaks occuring on load and
	  set_(sparse)_feature_matrix
	* classifier/KNN.cpp, classifier/KernelPerceptron.cpp,
	  classifier/LDA.cpp, classifier/LPBoost.cpp, classifier/LPM.cpp,
	  classifier/Perceptron.cpp, classifier/SubGradientLPM.cpp,
	  classifier/svm/CPLEXSVM.cpp, classifier/svm/GMNPSVM.cpp,
	  classifier/svm/GNPPSVM.cpp, classifier/svm/GPBTSVM.cpp,
	  classifier/svm/LibLinear.cpp, classifier/svm/LibSVM.cpp,
	  classifier/svm/LibSVMMultiClass.cpp, classifier/svm/MPDSVM.cpp,
	  classifier/svm/MPDSVM.h, classifier/svm/MultiClassSVM.cpp,
	  classifier/svm/SVM.cpp, classifier/svm/SVMLin.cpp,
	  classifier/svm/SVMOcas.cpp, classifier/svm/SVMSGD.cpp,
	  classifier/svm/SVM_light.cpp, classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/WDSVMOcas.cpp, regression/KRR.cpp,
	  regression/svr/LibSVR.cpp, regression/svr/SVR_light.cpp: attempt
	  to fix the memory leaks for get_labels():
	  now we don't use get_labels in the classes derived from
	  CClassifier, but
	  just the protected member variable 'labels' directly

2008-03-26  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/MatlabInterface.cpp, interface/SGInterface.cpp:
	  interface:
	  - Fixes, fixes, fixes!

2008-03-26  Soeren Sonnenburg <sonne@debian.org>

	* interface/MatlabInterface.cpp: use mxGetPr instead of mxGetData
	  for sparse matrix

2008-03-26  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Getting closer...

2008-03-26  Soeren Sonnenburg <sonne@debian.org>

	* interface/MatlabInterface.cpp, interface/MatlabInterface.h: use
	  nnz for SET_SPARSe

2008-03-26  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/MatlabInterface.cpp, interface/SGInterface.cpp,
	  interface/SGInterface.h, lib/io.h: interface:
	  - Even more fixes, still not quite working
	  lib/io:
	  - Added macro NOTIMPLEMENTED

2008-03-26  Soeren Sonnenburg <sonne@debian.org>

	* interface/MatlabInterface.cpp: another attempt to fix stringf
	* interface/MatlabInterface.cpp: bug fix in SET_STRINGLIST
	* features/StringFeatures.h: add get_featurs functions to string
	  features
	* features/IntFeatures.cpp, features/IntFeatures.i,
	  features/ShortRealFeatures.cpp, features/ShortRealFeatures.h,
	  features/ShortRealFeatures.i, features/SimpleFeatures.h,
	  features/SimpleFeatures.i, features/SparseFeatures.h,
	  lib/File.cpp, lib/File.h, lib/common.h: fix shortreal/int
	  features

2008-03-26  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/MatlabInterface.cpp, interface/SGInterface.cpp:
	  interface:
	  - Some more tidbits

2008-03-26  Soeren Sonnenburg <sonne@debian.org>

	* features/IntFeatures.cpp, features/IntFeatures.h,
	  features/ShortRealFeatures.cpp, features/ShortRealFeatures.h,
	  kernel/GaussianKernel.cpp: add short/int features

2008-03-26  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - First stab at getting set_features to work.

2008-03-25  Soeren Sonnenburg <sonne@debian.org>

	* interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/SGInterface.h: use macros for everthing in matlab
	  interface

2008-03-25  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/SGInterface.h, interface/SGInterfaceDataType.h,
	  interface/SGInterfaceMatrix.h, interface/SGInterfaceStringList.h,
	  interface/SGInterfaceVector.h: interface:
	  - Removed interface helper classes
	* interface/SGInterface.cpp: interface:
	  - Switch from InterfaceVector/Matrix/StringList back to old (but
	  improved)
	  functions get/set_<type>_vector/matrix/string_list

2008-03-25  Soeren Sonnenburg <sonne@debian.org>

	* interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/SGInterface.h: use macros for interface
	* configure: fall back magic to -lutil and -ldl

2008-03-20  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/LibSVMOneClass.cpp: add missing model=NULL
	* classifier/svm/LibSVMMultiClass.cpp,
	  classifier/svm/LibSVMOneClass.cpp: fix leak also for
	  libsvmone/multi class

2008-03-20  Sebastian Henschel <shogun@kodeaffe.de>

	* kernel/WeightedDegreeStringKernel.cpp: kernel:
	  - Added patch from 2706+raetsch: fixed a bug in clean_kernel for
	  the WD kernel

2008-03-20  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* classifier/svm/LibSVM.cpp: included Alexander binders bugfix.

2008-03-20  Soeren Sonnenburg <sonne@debian.org>

	* configure, lib/Mathematics.h: fix compilation if sqrtl is not
	  available (fall back to sqrt)

2008-03-19  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* classifier/svm/MultiClassSVM.cpp: included Alexander Binders
	  bugfix.

2008-03-17  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/SGInterface.cpp, interface/SGInterfaceMatrix.h,
	  interface/SGInterfaceStringList.h, interface/SGInterfaceVector.h:
	  interface:
	  - Removed most const stuff, as it seemed too much hassle
	  - Converted interface methods to use new
	  InterfaceVector/Matrix/StringList

2008-03-14  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/SGInterface.cpp, interface/SGInterface.h,
	  interface/SGInterfaceDataType.h, interface/SGInterfaceMatrix.h,
	  interface/SGInterfaceStringList.h, interface/SGInterfaceVector.h:
	  interface:
	  - Hopefully this approach sucks less in regard to code
	  duplication, templates
	  and polymorphism.

2008-03-10  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* lib/io.cpp: fixed a minor issue in progress reporting.

2008-03-10  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/OctaveInterface.cpp, interface/PythonInterface.h,
	  interface/RInterface.h: interface:
	  - Fixed a couple of compilation issues
	* interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/OctaveInterface.cpp, interface/OctaveInterface.h,
	  interface/PythonInterface.cpp, interface/PythonInterface.h,
	  interface/RInterface.cpp, interface/RInterface.h,
	  interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - A bit of cleanup, made sure that basic input/output still works

2008-03-10  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* classifier/svm/SVM.cpp, classifier/svm/SVM_light.cpp,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.cpp: clear the
	  cancel_computation flag before starting a new computation.
	  Otherwise, they are all canceled.

2008-03-07  Sebastian Henschel <shogun@kodeaffe.de>

	* features/StringFeatures.h, interface/SGInterface.cpp,
	  interface/SGInterface.h: features:
	  - Fixed typo in docstring
	  interface:
	  - Added remaining methods. set_features and the methods with
	  zillions of
	  parameters need discussion and coding, though. And naturally
	  nothing is
	  bound to work yet. :)

2008-03-06  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Even more methods
	* interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Added more methods (best path)

2008-03-05  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/OctaveInterface.cpp, interface/OctaveInterface.h,
	  interface/PythonInterface.cpp, interface/PythonInterface.h,
	  interface/RInterface.cpp, interface/RInterface.h,
	  interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Added a few more methods
	  - Included previously forgotten implementation for F_WORD in
	  C_STRING in
	  get_features
	* interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/OctaveInterface.cpp, interface/OctaveInterface.h,
	  interface/PythonInterface.cpp, interface/PythonInterface.h,
	  interface/RInterface.cpp, interface/RInterface.h,
	  interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Scrapped template stuff, seems to be too hard at the moment
	  - Added get/set functions for SHORT/WORD sparse/dense
	  vectors/matrices
	* interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Added some more functions and made some preparations for
	  templating stuff

2008-03-05  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* kernel/CommWordStringKernel.cpp: removed debug output
	* kernel/CommWordStringKernel.cpp, kernel/CommWordStringKernel.h:
	  implemented a speedup for the kernel normalization.
	  This helps when you have many, long sequences with a relatively
	  low degree (<8).
	* kernel/Kernel.cpp, kernel/Kernel.h: added a function for allowing
	  the direct use of kernel_optimization from python

2008-03-04  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* features/StringFeatures.h: removed debug output
	* features/StringFeatures.h: *** empty log message ***
	* features/StringFeatures.h: fixed a logical bug, which appears
	  when having more than one
	  preprocessor.

2008-03-03  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/OctaveInterface.cpp, interface/OctaveInterface.h,
	  interface/PythonInterface.cpp, interface/PythonInterface.h,
	  interface/RInterface.cpp, interface/RInterface.h,
	  interface/SGInterface.cpp, interface/SGInterface.h: interfaces:
	  - Added methods to get/set char vectors/matrices as need by
	  CSGInterface::a_get_WD_consensus
	* kernel/WeightedDegreePositionStringKernel.cpp: kernel:
	  - Compile fix for WeightedDegreePositionString kernel
	* interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Added some more interface methods.

2008-02-29  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* kernel/WeightedDegreePositionStringKernel.i: One typemap still
	  has a problem (get_POIM2).
	* kernel/WeightedDegreePositionStringKernel.cpp:
	* kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h: initial version of a
	  swiggable POIM interface.

2008-02-29  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreePositionStringKernel.i: draft: split up poim
	  computation
	* kernel/Kernel.h: add set cache size option

2008-02-29  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/OctaveInterface.cpp, interface/OctaveInterface.h,
	  interface/PythonInterface.cpp, interface/PythonInterface.h,
	  interface/RInterface.cpp, interface/RInterface.h,
	  interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Added about 1/3 of interface methods in gui/Matlab.cpp to
	  interface/SGInterface.cpp
	  - Introduced a second counter for arguments (now: in and out)
	  - Made set functions to take a const as first argument

2008-02-29  Soeren Sonnenburg <sonne@debian.org>

	* configure: assume the python libraries are in the standard
	  library paths (should fix a
	  compile failure on opensuse) - not clear if it breaks compilation
	  on OSX etc

2008-02-28  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM_light.cpp, features/Labels.cpp,
	  kernel/Kernel.cpp, kernel/Kernel.h, kernel/KernelMachine.cpp:
	  this should fix a few more memoryleaks reported by Yaroslav
	  including the one for svmlight (kernel cache not being cleaned
	  up)

2008-02-28  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/MatlabInterface.cpp, interface/SGInterface.cpp:
	  interface:
	  - All get/set functions should now be implemented and working in
	  MatlabInterface

2008-02-27  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/MatlabInterface.cpp, interface/SGInterface.cpp:
	  interface:
	  - Implemented most set functions for Matlab (sparse not working
	  correctly,
	  though)

2008-02-27  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/GNPPSVM.cpp: fix leak, by deleting history...

2008-02-27  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/OctaveInterface.cpp, interface/OctaveInterface.h,
	  interface/PythonInterface.cpp, interface/PythonInterface.h,
	  interface/RInterface.cpp, interface/RInterface.h,
	  interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - Replaced get_current_argument by get_arg_increment and
	  implemented
	  set_arg_increment for the interfaces
	  - Added usage of jump list for accessing Shogun methods in a loop
	  instead of
	  endless case switches.

2008-02-26  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/GPBTSVM.cpp, classifier/svm/LibSVM.cpp: fix
	  another delete / free mismatch and another leak (in libsvm)
	* features/SimpleFeatures.h, lib/python_typemaps.i: as we own the
	  features we should erase them whenever they are set, and of
	  course also on exit
	* features/SimpleFeatures.h, lib/python_typemaps.i: fix delete[] /
	  free mismatch
	* interface/MatlabInterface.h, interface/SGInterface.cpp,
	  interface/SGInterface.h: fix compile error with python-modular
	  interface
	* classifier/svm/GPBTSVM.cpp: this should fix the kernel cache
	  memeory leak with gpdtsvm

2008-02-26  Sebastian Henschel <shogun@kodeaffe.de>

	* interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/OctaveInterface.cpp, interface/PythonInterface.cpp,
	  interface/RInterface.cpp, interface/SGInterface.cpp,
	  interface/SGInterface.h: interface:
	  - Implemented a first set function in MatlabInterface and a test
	  function for
	  it in SGInterface
	* interface/MatlabInterface.cpp, interface/MatlabInterface.h,
	  interface/OctaveInterface.cpp, interface/OctaveInterface.h,
	  interface/PythonInterface.cpp, interface/PythonInterface.h,
	  interface/RInterface.cpp, interface/RInterface.h,
	  interface/SGInterface.cpp, interface/SGInterface.h: interface:
	  - switched get functions to call by reference
	  - implemented get functions in MatlabInterface (dunno if it
	  works, though)

2008-02-26  Soeren Sonnenburg <sonne@debian.org>

	* gui/Python.cpp, interface/OctaveInterface.cpp,
	  interface/PythonInterface.cpp, interface/PythonInterface.h,
	  interface/RInterface.cpp, lib/io.cpp: - Implement python
	  interface
	  - Now always throw shogun exceptions on SG_ERROR. These
	  exceptions are catched if
	  thrown by the global interface handle(), catch for octave and R,
	  python for
	  now. We might want to do the same with matlab etc.
	* gui/R.cpp, interface/RInterface.cpp, interface/RInterface.h,
	  interface/SGInterface.cpp: add basic R interface functionality
	  (currently breaks everything except send_command), switch R
	  interface to use .External method
	  
	  to test, use:
	  
	  ./configure --interface=R
	  make
	  
	  R
	  
	  dyn.load('sg.so')
	  sg <- function(...) .External("sg", ...)
	  sg('send_command','help')
	* gui/Octave.cpp, interface/MatlabInterface.cpp,
	  interface/MatlabInterface.h, interface/OctaveInterface.cpp,
	  interface/OctaveInterface.h, interface/SGInterface.cpp,
	  interface/SGInterface.h: - remove get_int_from_string from all
	  interfaces and do this directly in SGInterface (using get_string)
	  - increment arg_counter on retrieval of values in matlab
	  interface
	  - add octave interface functions:
	  NOTE THAT THIS FOR NOW BREAKS THE WHOLE OCTAVE INTERFACE

2008-02-25  Soeren Sonnenburg <sonne@debian.org>

	* interface/MatlabInterface.cpp: more interface functions to deal
	  with int/float/ etc
	* gui/Matlab.cpp, interface/MatlabInterface.cpp,
	  interface/MatlabInterface.h, interface/SGInterface.cpp,
	  interface/SGInterface.h: - generic interface extended
	  - minimal matlab interface based on generic interface, with fall
	  back on old guiinterface
	* interface, interface/SGInterface.h: general interface
	* features/SparseFeatures.h: allow to increase number of dimensions
	  in sparse features

2008-02-21  Sebastian Henschel <shogun@kodeaffe.de>

	* evaluation/PerformanceMeasures.cpp: evaluation:
	  - Fixed balanced error in PerformanceMeasures

2008-02-20  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVMOcas.cpp, features/SparseFeatures.h: - fix
	  stupid bug in sparse features & svmlight file loading
	  - fix memory leak in ocas

2008-02-20  Sebastian Henschel <shogun@kodeaffe.de>

	* evaluation/PerformanceMeasures.cpp,
	  evaluation/PerformanceMeasures.h,
	  evaluation/PerformanceMeasures.i: evaluation:
	  - PerformanceMeasures improved: no alignment to ROC/PRC of
	  accuracy/F-measure,
	  2 dimensional arrays with sorted outputs + measure instead (see
	  get_all_*);
	  code-efficient usage of compute_confusion_matrix; no exception
	  handling hack in
	  constructor

2008-02-20  Soeren Sonnenburg <sonne@debian.org>

	* features/SparseFeatures.h: add example on how to read svm light
	  format
	  fix crasher when writing and labels are None

2008-02-19  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIMatlab.cpp, structure/DynProg.h: really fix building...
	* guilib/GUIMatlab.cpp, structure/DynProg.h: compile & style fixes
	  for dynprog & matlab
	* structure/DynProg.cpp, structure/DynProg.h: reorder definition
	  and add m prefix to member variable
	* AUTHORS, Makefile, NEWS, kernel/PyramidChi2.cpp,
	  kernel/PyramidChi2.h: - remove svmlight tests when svmlight is
	  disabled
	  - prepare for 0.5.1
	  - replace ShogunException by SG_ERROR
	  - include sebastian in AUTHORS

2008-02-19  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* guilib/GUIMatlab.cpp, structure/DynProg.cpp, structure/DynProg.h:
	  precompute content svm values; preliminary modifications; not
	  functionalmake -j 5!

2008-02-19  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/pr_loqo.cpp, configure,
	  evaluation/PerformanceMeasures.cpp,
	  evaluation/PerformanceMeasures.h: - fix warning in pr_loqo
	  - make configure work with newer atlas/blas/lapack
	  - several performance measure fixes

2008-02-18  Sebastian Henschel <shogun@kodeaffe.de>

	* evaluation/Evaluation.i, evaluation/PerformanceMeasures.i:
	  evaluation:
	  - Updated swig-related documation
	* evaluation/PerformanceMeasures.cpp,
	  evaluation/PerformanceMeasures.h: evaluation:
	  - Added get_error0() to PerformanceMeasures
	  - Added a few more explicit typecasts to DREAL for various
	  calculations
	* .doxy2swig.py: documentation:
	  - Improved doxy2swig when handling documented exceptions
	* evaluation/PerformanceMeasures.cpp,
	  evaluation/PerformanceMeasures.h: evaluation:
	  - Various cleanups and docstring updates in PerformanceMeasures

2008-02-17  Soeren Sonnenburg <sonne@debian.org>

	* features/SparseFeatures.h: fix documentation when writing
	  features in svm light format..
	* evaluation/PerformanceMeasures.cpp, features/SparseFeatures.h:
	  implement efficient (and hacky) reading of svm light format (>
	  twice as fast as
	  svmperf2.5) and fix minor warning in perfmeasures

2008-02-16  Sebastian Henschel <shogun@kodeaffe.de>

	* evaluation/PerformanceMeasures.cpp,
	  evaluation/PerformanceMeasures.h: evaluation:
	  - Added DET to PerformanceMeasures

2008-02-15  Soeren Sonnenburg <sonne@debian.org>

	* kernel/PyramidChi2.cpp, kernel/PyramidChi2.h: cleanups

2008-02-15  Sebastian Henschel <shogun@kodeaffe.de>

	* evaluation/PerformanceMeasures.cpp,
	  evaluation/PerformanceMeasures.h: evaluation:
	  - Added CC, WRacc and balance to PerformanceMeasures
	* evaluation/PerformanceMeasures.cpp,
	  evaluation/PerformanceMeasures.h: evaluation:
	  - Added PRC + F-measure to PerformanceMeasures

2008-02-15  Soeren Sonnenburg <sonne@debian.org>

	* Makefile: ignore error when trying to version Doxyfile

2008-02-13  Sebastian Henschel <shogun@kodeaffe.de>

	* evaluation/PerformanceMeasures.cpp,
	  evaluation/PerformanceMeasures.h,
	  evaluation/PerformanceMeasures.i: evaluation:
	  - Added auROC, aoROC and accuracy + error aligned to ROC to
	  PerformanceMeasures
	  - Updated example accordingly

2008-02-12  Alexander Binder <alexander.binder@first.fraunhofer.de>

	* kernel/PyramidChi2.cpp, kernel/PyramidChi2.h,
	  kernel/PyramidChi2.i, lib/common.h: 1)added EKernel_Type
	  K_PYRAMIDCHI2 in common.h
	  2) added PyramidChi2.{h,cpp} as a pyramid kernel over Chi2
	  Kernels in a version which is adapted to shogun

2008-02-08  Soeren Sonnenburg <sonne@debian.org>

	* configure: enable building when doxygen is not installed

2008-02-08  Sebastian Henschel <shogun@kodeaffe.de>

	* evaluation/PerformanceMeasures.cpp,
	  evaluation/PerformanceMeasures.h: evaluation:
	  - Added example for peformance measures ROC, including plotting.
	  Does not work
	  nicely, though.

2008-02-06  Sebastian Henschel <shogun@kodeaffe.de>

	* evaluation/Evaluation.i, evaluation/PerformanceMeasures.cpp,
	  evaluation/PerformanceMeasures.h,
	  evaluation/PerformanceMeasures.i: evaluation:
	  - PerformanceMeasures: first stab at ROC
	* lib/Mathematics.h: lib/Mathematics:
	  - CMath::sign is properly templated now.

2008-02-05  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/MultiClassSVM.h: fix the > 0 thanks yaroslav

2008-02-05  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/svm/SVMSGD.h, evaluation/PerformanceMeasures.h,
	  lib/Mathematics.h: documentation:
	  - Added 2 docstrings
	  lib/Mathematics:
	  - Fixed a compiler warning about 'comparison always true' when
	  template type
	  is something unsigned.
	* .doxy2swig.py, Makefile: documentation:
	  - Added an option --quiet to doxy2swig and applied the option to
	  the Makefile
	  to quieten doxy2swig's output during compilation when everything
	  is ok.
	* lib/Array.h, lib/Array2.h, lib/Array3.h, lib/Cache.h,
	  lib/DynamicArray.h, lib/Library.doxy, lib/List.h,
	  lib/Mathematics.h, lib/ShogunException.h, lib/Signal.h,
	  lib/SimpleFile.h, lib/Time.h, lib/Trie.h, lib/io.h, lib/lapack.h:
	  documentation:
	  - Added docstrings to items in lib/ which got somehow forgotten
	  before the
	  release.
	  lib/Trie:
	  - Renamed one method mistakenly named set_weights_in_tree() to
	  get_weights_in_tree()
	* .generate_link_dependencies.py, evaluation,
	  evaluation/Evaluation.doxy, evaluation/Evaluation.i,
	  evaluation/PerformanceMeasures.cpp,
	  evaluation/PerformanceMeasures.h,
	  evaluation/PerformanceMeasures.i: evaluation:
	  - Added new section 'evaluation' which includes a stub for its
	  first member:
	  PerformanceMeasures

2008-02-04  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVMOcas.h, classifier/svm/SVMSGD.h,
	  guilib/GUIClassifier.cpp, lib/common.h: also allow for bias being
	  disabled in ocas/sgd; add matlab test code, seems to
	  work, sgd and ocas deliver very similar objectives when run for
	  many
	  iterations/low epsilon.
	* classifier/SparseLinearClassifier.i, classifier/svm/SVMSGD.cpp,
	  classifier/svm/SVMSGD.h, guilib/GUIClassifier.cpp,
	  lib/Mathematics.h: add tests and examples for SGD

2008-02-03  Soeren Sonnenburg <sonne@debian.org>

	* CONTRIBUTIONS: add leon
	* classifier/svm/SVMSGD.cpp, classifier/svm/SVMSGD.h,
	  classifier/svm/SVMSGD.i, classifier/svm/WDSVMOcas.cpp,
	  features/SparseFeatures.h, lib/Mathematics.h: add SGD and extend
	  mathmatics/sparse features with a number of helpers
	* Makefile: set PYTHONPATH and PYTHON on make tests, for this
	  test_all.sh was modified to
	  execute $PYTHON

2008-02-02  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog: Preparing for new Release shogun_0.5.0
	* lib/io.cpp, lib/io.h: Apply patch from Yaroslav Halchenko to
	  inherit show_progress
	* distributions/hmm/HMM.cpp, features/SimpleFeatures.h: fix crasher
	  when feature ``matrix'' is not existent, copy HMM model
	  parameters in CHMM(CHMM* h)
	* gui/Octave.cpp: built shogun for all interfaces, fixed minor
	  warning for octave

2008-02-01  Soeren Sonnenburg <sonne@debian.org>

	* features/FKFeatures.cpp, features/TOPFeatures.cpp,
	  lib/DynamicArray.h, lib/Mathematics.h: - INCREF HMM models when
	  inserted into TOP/FK Features.
	  - limit linesearch for prior to 1e-6 ... 1-1e-6
	  - Fix warning in dynamic array
	  - random initialization of random number generator
	* Makefile, distributions/hmm/HMM.cpp, distributions/hmm/HMM.h,
	  lib/Mathematics.h: hopefully fix HMM derivative enumeration and
	  automagically fill in version number in Doxyfile

2008-02-01  Sebastian Henschel <shogun@kodeaffe.de>

	* distributions/hmm/HMM.cpp: distribution:
	  - Previous SG_UNREFing was too aggressive...
	* distributions/hmm/HMM.cpp: distribution:
	  - Hopefully fixed some issues with refcounting

2008-02-01  Soeren Sonnenburg <sonne@debian.org>

	* features/FKFeatures.cpp, features/TOPFeatures.h: add assertions
	  in FKFeatures too and minor docu fix for TOP Features
	* base/Documentation.mainpage: use some more fancy verbatim
	  formatting
	* CONTRIBUTIONS, base/Documentation.mainpage: update contributions,
	  and add some user documentation
	* Makefile: add a make doc target

2008-01-31  Soeren Sonnenburg <sonne@debian.org>

	* features/TOPFeatures.cpp, kernel/PolyKernel.cpp,
	  kernel/PolyMatchStringKernel.cpp, kernel/PolyMatchWordKernel.cpp,
	  kernel/SparsePolyKernel.cpp: argh, really fix warnings (and fix
	  cleverly introduced build errors)

2008-01-31  Sebastian Henschel <shogun@kodeaffe.de>

	* features/TOPFeatures.h: testsuite:
	  - Added testcase generation for TOP/FKFeatures in kernel Linear.
	  This reverts
	  the previous assumption that each kernel can only work on one
	  specific
	  feature type and hence the testsuite has to be reworked in that
	  regard.

2008-01-31  Soeren Sonnenburg <sonne@debian.org>

	* features/TOPFeatures.cpp, kernel/LinearKernel.cpp,
	  kernel/PolyKernel.cpp, kernel/PolyMatchStringKernel.cpp,
	  kernel/PolyMatchWordKernel.cpp, kernel/SparseLinearKernel.cpp,
	  kernel/SparseLinearKernel.h, kernel/SparsePolyKernel.cpp,
	  kernel/WeightedDegreeStringKernel.cpp: fix many warnings and add
	  assertions for TOP features
	* .authors, NEWS, classifier/svm/SVM_linear.cpp,
	  classifier/svm/Tron.cpp, features/TOPFeatures.h: update NEWS,
	  authors, liblinear to 1.22
	* kernel/SalzbergWordKernel.cpp: remove ;

2008-01-30  Sebastian Henschel <shogun@kodeaffe.de>

	* kernel/AUCKernel.h, kernel/Chi2Kernel.h, kernel/CombinedKernel.h,
	  kernel/CommUlongStringKernel.h, kernel/CommWordStringKernel.h,
	  kernel/ConstKernel.h, kernel/CustomKernel.h, kernel/DiagKernel.h,
	  kernel/DistanceKernel.h, kernel/FixedDegreeStringKernel.h,
	  kernel/GaussianKernel.h, kernel/GaussianShiftKernel.h,
	  kernel/HistogramWordKernel.h, kernel/Kernel.doxy,
	  kernel/Kernel.h, kernel/KernelMachine.h,
	  kernel/LinearByteKernel.h, kernel/LinearKernel.h,
	  kernel/LinearStringKernel.h, kernel/LinearWordKernel.h,
	  kernel/LocalAlignmentStringKernel.h,
	  kernel/LocalityImprovedStringKernel.h, kernel/PolyKernel.h,
	  kernel/PolyMatchStringKernel.h, kernel/PolyMatchWordKernel.h,
	  kernel/SalzbergWordKernel.h, kernel/SigmoidKernel.h,
	  kernel/SimpleKernel.h,
	  kernel/SimpleLocalityImprovedStringKernel.h,
	  kernel/SparseGaussianKernel.h, kernel/SparseKernel.h,
	  kernel/SparseLinearKernel.h, kernel/SparsePolyKernel.h,
	  kernel/StringKernel.h, kernel/WeightedCommWordStringKernel.h,
	  kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreeStringKernel.h, kernel/WordMatchKernel.h:
	  documentation:
	  - Added docstrings to anything touched by doxygen in kernel/

2008-01-30  Alexander Binder <alexander.binder@first.fraunhofer.de>

	* kernel/Chi2Kernel.cpp: in Chi2Kernel::compute() checking for d!=0
	  before dividing by d, note: the case d==0 is common for using
	  this kernel with sparse histograms

2008-01-29  Sebastian Henschel <shogun@kodeaffe.de>

	* preproc/LogPlusOne.h, preproc/NormDerivativeLem3.h,
	  preproc/NormOne.h, preproc/PCACut.h, preproc/PreProc.doxy,
	  preproc/PreProc.h, preproc/PruneVarSubMean.h,
	  preproc/SimplePreProc.h, preproc/SortUlongString.h,
	  preproc/SortWord.h, preproc/SortWordString.h,
	  preproc/SparsePreProc.h, preproc/StringPreProc.h: documentation:
	  - Added docstrings to anything touched by doxygen in preproc/

2008-01-28  Sebastian Henschel <shogun@kodeaffe.de>

	* regression/KRR.h, regression/Regression.doxy,
	  regression/svr/LibSVR.h, regression/svr/SVR_light.h:
	  documentation:
	  - Added docstrings to anything touched by doxygen in regression/
	* structure/DynProg.h, structure/Plif.h, structure/PlifArray.h,
	  structure/PlifBase.h, structure/Structure.doxy: documentation:
	  - Added docstrings to anything touched by doxygen in structure/
	* features/Alphabet.h, features/ByteFeatures.h,
	  features/CharFeatures.h, features/CombinedFeatures.h,
	  features/FKFeatures.h, features/Features.doxy,
	  features/Features.h, features/Labels.h, features/RealFeatures.h,
	  features/RealFileFeatures.h, features/ShortFeatures.h,
	  features/SimpleFeatures.h, features/SparseFeatures.h,
	  features/StringFeatures.h, features/TOPFeatures.h,
	  features/WordFeatures.h: documentation:
	  - Added docstrings to anything touched by doxygen in features/

2008-01-27  Sebastian Henschel <shogun@kodeaffe.de>

	* distributions/Distribution.doxy, distributions/Distribution.h,
	  distributions/histogram/Histogram.h, distributions/hmm/GHMM.h,
	  distributions/hmm/HMM.h, distributions/hmm/LinearHMM.h:
	  documentation:
	  - Added docstrings to anything touched by doxygen in
	  distribution/
	* distance/CanberraMetric.h, distance/CanberraWordDistance.h,
	  distance/ChebyshewMetric.h, distance/Distance.doxy,
	  distance/Distance.h, distance/DistanceMachine.h,
	  distance/EuclidianDistance.h, distance/GeodesicMetric.h,
	  distance/HammingWordDistance.h, distance/JensenMetric.h,
	  distance/ManhattanMetric.h, distance/ManhattanWordDistance.h,
	  distance/MinkowskiMetric.h, distance/RealDistance.h,
	  distance/SimpleDistance.h, distance/SparseDistance.h,
	  distance/SparseEuclidianDistance.h, distance/StringDistance.h:
	  documentation:
	  - Added docstrings to anything touched by doxygen in distance/
	* clustering/Clustering.doxy, clustering/Hierarchical.h,
	  clustering/KMeans.h: documentation:
	  Added docstrings to anything touched by doxygen in clustering/

2008-01-25  Sebastian Henschel <shogun@kodeaffe.de>

	* .doxy2swig.py: documentation
	  - Fix for doxy2swig's handling of the tag parametername when it
	  has got a
	  child tag
	* classifier/Classifier.doxy, classifier/Classifier.h,
	  classifier/KNN.h, classifier/KernelPerceptron.h,
	  classifier/LDA.h, classifier/LinearClassifier.h,
	  classifier/Perceptron.h, classifier/PluginEstimate.h,
	  classifier/SparseLinearClassifier.h, classifier/svm/GMNPSVM.h,
	  classifier/svm/GNPPSVM.h, classifier/svm/GPBTSVM.h,
	  classifier/svm/LibLinear.h, classifier/svm/LibSVM.h,
	  classifier/svm/LibSVMMultiClass.h,
	  classifier/svm/LibSVMOneClass.h, classifier/svm/MPDSVM.h,
	  classifier/svm/MultiClassSVM.h, classifier/svm/Optimizer.h,
	  classifier/svm/SVM.h, classifier/svm/SVMLin.h,
	  classifier/svm/SVMOcas.h, classifier/svm/SVM_libsvm.h,
	  classifier/svm/SVM_light.h, classifier/svm/SVM_linear.h,
	  classifier/svm/SubGradientSVM.h, classifier/svm/Tron.h,
	  classifier/svm/WDSVMOcas.h, classifier/svm/gmnplib.h,
	  classifier/svm/gnpplib.h, classifier/svm/gpdt.h,
	  classifier/svm/gpdtsolve.h, classifier/svm/libocas.h,
	  classifier/svm/qpbsvmlib.h, classifier/svm/ssl.h: documentation
	  - Added docstrings to anything touched by doxygen in classifer/

2008-01-24  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/svm/SVM.h, distributions/hmm/HMM.h,
	  features/SimpleFeatures.h, features/SparseFeatures.h,
	  features/StringFeatures.h, kernel/CombinedKernel.h,
	  kernel/Kernel.h, lib/File.h, lib/List.h, structure/DynProg.h:
	  documentation:
	  - Added many docstrings to quieten doxygen, more to come.

2008-01-23  Sebastian Henschel <shogun@kodeaffe.de>

	* lib/io.h: lib:
	  - Enabled proper handling of {en,dis}able_progress from within
	  static
	  functions (hopefully)

2008-01-23  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* base/Version.h: fixed typo.

2008-01-23  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/KNN.cpp: classifier:
	  - KNN now uses SG_PROGESS instead of SG_PRINT
	* LICENSE, NEWS, README, base/Parallel.cpp, base/Parallel.h,
	  base/SGObject.h, base/Version.cpp, base/Version.h,
	  classifier/Classifier.cpp, classifier/Classifier.h,
	  classifier/KNN.cpp, classifier/KNN.h,
	  classifier/KernelPerceptron.cpp, classifier/KernelPerceptron.h,
	  classifier/LDA.cpp, classifier/LDA.h, classifier/LPBoost.cpp,
	  classifier/LPBoost.h, classifier/LPM.cpp, classifier/LPM.h,
	  classifier/LinearClassifier.cpp, classifier/LinearClassifier.h,
	  classifier/Perceptron.cpp, classifier/Perceptron.h,
	  classifier/PluginEstimate.cpp, classifier/PluginEstimate.h,
	  classifier/SparseLinearClassifier.cpp,
	  classifier/SparseLinearClassifier.h,
	  classifier/SubGradientLPM.cpp, classifier/SubGradientLPM.h,
	  classifier/svm/CPLEXSVM.cpp, classifier/svm/CPLEXSVM.h,
	  classifier/svm/GMNPSVM.cpp, classifier/svm/GMNPSVM.h,
	  classifier/svm/GNPPSVM.cpp, classifier/svm/GNPPSVM.h,
	  classifier/svm/GPBTSVM.cpp, classifier/svm/GPBTSVM.h,
	  classifier/svm/LibLinear.cpp, classifier/svm/LibLinear.h,
	  classifier/svm/LibSVM.cpp, classifier/svm/LibSVM.h,
	  classifier/svm/LibSVMMultiClass.cpp,
	  classifier/svm/LibSVMMultiClass.h,
	  classifier/svm/LibSVMOneClass.cpp,
	  classifier/svm/LibSVMOneClass.h, classifier/svm/MPDSVM.cpp,
	  classifier/svm/MPDSVM.h, classifier/svm/MultiClassSVM.cpp,
	  classifier/svm/MultiClassSVM.h, classifier/svm/SVM.cpp,
	  classifier/svm/SVM.h, classifier/svm/SVMLin.cpp,
	  classifier/svm/SVMLin.h, classifier/svm/SVMOcas.cpp,
	  classifier/svm/SVMOcas.h, classifier/svm/SVM_libsvm.cpp,
	  classifier/svm/SVM_libsvm.h, classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h, classifier/svm/WDSVMOcas.cpp,
	  classifier/svm/WDSVMOcas.h, classifier/svm/gmnplib.cpp,
	  classifier/svm/gmnplib.h, classifier/svm/gnpplib.cpp,
	  classifier/svm/gnpplib.h, classifier/svm/gpdt.cpp,
	  classifier/svm/gpdt.h, classifier/svm/gpdtsolve.cpp,
	  classifier/svm/gpdtsolve.h, classifier/svm/gpm.cpp,
	  classifier/svm/gpm.h, classifier/svm/libocas.cpp,
	  classifier/svm/libocas.h, classifier/svm/pr_loqo.cpp,
	  classifier/svm/pr_loqo.h, classifier/svm/qpbsvmlib.cpp,
	  classifier/svm/qpbsvmlib.h, classifier/svm/qpssvmlib.cpp,
	  classifier/svm/qpssvmlib.h, clustering/Hierarchical.cpp,
	  clustering/Hierarchical.h, clustering/KMeans.cpp,
	  clustering/KMeans.h, configure, distance/CanberraMetric.cpp,
	  distance/CanberraMetric.h, distance/CanberraWordDistance.cpp,
	  distance/CanberraWordDistance.h, distance/ChebyshewMetric.cpp,
	  distance/ChebyshewMetric.h, distance/Distance.cpp,
	  distance/Distance.h, distance/DistanceMachine.cpp,
	  distance/DistanceMachine.h, distance/EuclidianDistance.cpp,
	  distance/EuclidianDistance.h, distance/GeodesicMetric.cpp,
	  distance/GeodesicMetric.h, distance/HammingWordDistance.cpp,
	  distance/HammingWordDistance.h, distance/JensenMetric.cpp,
	  distance/JensenMetric.h, distance/ManhattanMetric.cpp,
	  distance/ManhattanMetric.h, distance/ManhattanWordDistance.cpp,
	  distance/ManhattanWordDistance.h, distance/MinkowskiMetric.cpp,
	  distance/MinkowskiMetric.h, distance/RealDistance.h,
	  distance/SimpleDistance.h, distance/SparseDistance.h,
	  distance/SparseEuclidianDistance.cpp,
	  distance/SparseEuclidianDistance.h, distance/StringDistance.h,
	  distributions/Distribution.cpp, distributions/Distribution.h,
	  distributions/histogram/Histogram.cpp,
	  distributions/histogram/Histogram.h, distributions/hmm/GHMM.cpp,
	  distributions/hmm/GHMM.h, distributions/hmm/HMM.cpp,
	  distributions/hmm/HMM.h, distributions/hmm/LinearHMM.cpp,
	  distributions/hmm/LinearHMM.h, features/Alphabet.cpp,
	  features/Alphabet.h, features/ByteFeatures.cpp,
	  features/ByteFeatures.h, features/CharFeatures.cpp,
	  features/CharFeatures.h, features/CombinedFeatures.cpp,
	  features/CombinedFeatures.h, features/FKFeatures.cpp,
	  features/FKFeatures.h, features/Features.cpp,
	  features/Features.h, features/Labels.cpp, features/Labels.h,
	  features/MindyGramFeatures.cpp, features/MindyGramFeatures.h,
	  features/RealFeatures.cpp, features/RealFeatures.h,
	  features/RealFileFeatures.cpp, features/RealFileFeatures.h,
	  features/ShortFeatures.cpp, features/ShortFeatures.h,
	  features/SimpleFeatures.h, features/SparseFeatures.h,
	  features/StringFeatures.cpp, features/StringFeatures.h,
	  features/TOPFeatures.cpp, features/TOPFeatures.h,
	  features/WordFeatures.cpp, features/WordFeatures.h, gui/GUI.cpp,
	  gui/GUI.h, gui/Matlab.cpp, gui/Octave.cpp, gui/Python.cpp,
	  gui/Python.h, gui/R.cpp, gui/TextGUI.cpp, gui/TextGUI.h,
	  guilib/GUIClassifier.cpp, guilib/GUIClassifier.h,
	  guilib/GUICommands.h, guilib/GUIDistance.cpp,
	  guilib/GUIDistance.h, guilib/GUIFeatures.cpp,
	  guilib/GUIFeatures.h, guilib/GUIHMM.cpp, guilib/GUIHMM.h,
	  guilib/GUIKNN.cpp, guilib/GUIKNN.h, guilib/GUIKernel.cpp,
	  guilib/GUIKernel.h, guilib/GUILabels.cpp, guilib/GUILabels.h,
	  guilib/GUIMath.cpp, guilib/GUIMath.h, guilib/GUIMatlab.cpp,
	  guilib/GUIMatlab.h, guilib/GUIOctave.cpp, guilib/GUIOctave.h,
	  guilib/GUIPluginEstimate.cpp, guilib/GUIPluginEstimate.h,
	  guilib/GUIPreProc.cpp, guilib/GUIPreProc.h, guilib/GUIPython.cpp,
	  guilib/GUIPython.h, guilib/GUIR.cpp, guilib/GUIR.h,
	  guilib/GUITime.cpp, guilib/GUITime.h, kernel/AUCKernel.cpp,
	  kernel/AUCKernel.h, kernel/Chi2Kernel.cpp, kernel/Chi2Kernel.h,
	  kernel/CombinedKernel.cpp, kernel/CombinedKernel.h,
	  kernel/CommUlongStringKernel.cpp, kernel/CommUlongStringKernel.h,
	  kernel/CommWordStringKernel.cpp, kernel/CommWordStringKernel.h,
	  kernel/ConstKernel.cpp, kernel/ConstKernel.h,
	  kernel/CustomKernel.cpp, kernel/CustomKernel.h,
	  kernel/DiagKernel.cpp, kernel/DiagKernel.h,
	  kernel/DistanceKernel.cpp, kernel/DistanceKernel.h,
	  kernel/FixedDegreeStringKernel.cpp,
	  kernel/FixedDegreeStringKernel.h, kernel/GaussianKernel.cpp,
	  kernel/GaussianKernel.h, kernel/GaussianShiftKernel.cpp,
	  kernel/GaussianShiftKernel.h, kernel/HistogramWordKernel.cpp,
	  kernel/HistogramWordKernel.h, kernel/Kernel.cpp, kernel/Kernel.h,
	  kernel/KernelMachine.cpp, kernel/KernelMachine.h,
	  kernel/LinearByteKernel.cpp, kernel/LinearByteKernel.h,
	  kernel/LinearKernel.cpp, kernel/LinearKernel.h,
	  kernel/LinearStringKernel.cpp, kernel/LinearStringKernel.h,
	  kernel/LinearWordKernel.cpp, kernel/LinearWordKernel.h,
	  kernel/LocalAlignmentStringKernel.cpp,
	  kernel/LocalAlignmentStringKernel.h,
	  kernel/LocalityImprovedStringKernel.cpp,
	  kernel/LocalityImprovedStringKernel.h,
	  kernel/MindyGramKernel.cpp, kernel/MindyGramKernel.h,
	  kernel/PolyKernel.cpp, kernel/PolyKernel.h,
	  kernel/PolyMatchStringKernel.cpp, kernel/PolyMatchStringKernel.h,
	  kernel/PolyMatchWordKernel.cpp, kernel/PolyMatchWordKernel.h,
	  kernel/SalzbergWordKernel.cpp, kernel/SalzbergWordKernel.h,
	  kernel/SigmoidKernel.cpp, kernel/SigmoidKernel.h,
	  kernel/SimpleKernel.h,
	  kernel/SimpleLocalityImprovedStringKernel.cpp,
	  kernel/SimpleLocalityImprovedStringKernel.h,
	  kernel/SparseGaussianKernel.cpp, kernel/SparseGaussianKernel.h,
	  kernel/SparseKernel.h, kernel/SparseLinearKernel.cpp,
	  kernel/SparseLinearKernel.h, kernel/SparsePolyKernel.cpp,
	  kernel/SparsePolyKernel.h, kernel/StringKernel.h,
	  kernel/WeightedCommWordStringKernel.cpp,
	  kernel/WeightedCommWordStringKernel.h,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.h, kernel/WordMatchKernel.cpp,
	  kernel/WordMatchKernel.h, lib/Array.h, lib/Array2.h,
	  lib/Array3.h, lib/Cache.h, lib/Cplex.cpp, lib/Cplex.h,
	  lib/DynamicArray.h, lib/File.cpp, lib/File.h, lib/List.h,
	  lib/Mathematics.cpp, lib/Mathematics.h, lib/Signal.cpp,
	  lib/Signal.h, lib/SimpleFile.h, lib/Time.cpp, lib/Time.h,
	  lib/Trie.h, lib/common.h, lib/io.cpp, lib/io.h, lib/lapack.cpp,
	  lib/lapack.h, preproc/LogPlusOne.cpp, preproc/LogPlusOne.h,
	  preproc/NormDerivativeLem3.cpp, preproc/NormDerivativeLem3.h,
	  preproc/NormOne.cpp, preproc/NormOne.h, preproc/PCACut.cpp,
	  preproc/PCACut.h, preproc/PreProc.cpp, preproc/PreProc.h,
	  preproc/PruneVarSubMean.cpp, preproc/PruneVarSubMean.h,
	  preproc/SimplePreProc.h, preproc/SortUlongString.cpp,
	  preproc/SortUlongString.h, preproc/SortWord.cpp,
	  preproc/SortWord.h, preproc/SortWordString.cpp,
	  preproc/SortWordString.h, preproc/SparsePreProc.h,
	  preproc/StringPreProc.h, regression/KRR.cpp, regression/KRR.h,
	  regression/svr/LibSVR.cpp, regression/svr/LibSVR.h,
	  regression/svr/SVR_light.cpp, regression/svr/SVR_light.h,
	  structure/DynProg.cpp, structure/DynProg.h, structure/Plif.cpp,
	  structure/Plif.h, structure/PlifArray.cpp, structure/PlifArray.h,
	  structure/PlifBase.h: The big license switch to GPL v3 and
	  copyright switch to 2008

2008-01-23  Soeren Sonnenburg <sonne@debian.org>

	* lib/io.cpp, lib/io.h: fix inverted meaning
	* lib/io.cpp, lib/io.h: disable -> show_progress
	* classifier/svm/MultiClassSVM.h, lib/io.cpp, lib/io.h: option to
	  disable progress and to get number of svms for multiclass svm

2008-01-22  Sebastian Henschel <shogun@kodeaffe.de>

	* .scrub_docstrings.py, Makefile: documentation:
	  - Include a script to scrub the autogenerated python
	  documentation, i.e.
	  replacing DREAL by float, in the make process

2008-01-21  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/Classifier.i, classifier/LinearClassifier.i,
	  classifier/SparseLinearClassifier.i, classifier/svm/SVM.i,
	  clustering/Clustering.i, clustering/Hierarchical.i,
	  clustering/KMeans.i, distance/Distance.i,
	  distributions/Distribution.i,
	  distributions/histogram/Histogram.i,
	  distributions/hmm/LinearHMM.i, features/Alphabet.i,
	  features/Features.i, features/Labels.i, features/RealFeatures.i,
	  features/ShortFeatures.i, features/StringFeatures.i,
	  features/WordFeatures.i, kernel/Kernel.i, lib/Library.i,
	  preproc/PreProc.i, regression/Regression.i, structure/DynProg.i:
	  documentation:
	  - Use swig feature "autodoc" "0" to prevent occurrence of types
	  in function
	  arguments
	  - Use swig feature "autodoc" "docstring" to have correct doc for
	  typemapped
	  functions
	* Makefile: documentation:
	  - Adjusted Makefile to use doxy2swig with option
	  --no-function-definition
	* .doxy2swig.py: documentation:
	  - Bugfix for new option include_function_definition
	* .doxy2swig.py: documentation:
	  - Updated doxy2swig.py from
	  http://www.aero.iitb.ac.in/~prabhu/software/code/python/

2008-01-17  Sebastian Henschel <shogun@kodeaffe.de>

	* distributions/hmm/HMM.cpp, distributions/hmm/HMM.h:
	  distribution/HMM:
	  - Added some (commented) print statements for debugging
	  - Got rid of compiler warning due to call of parent class'
	  constructor at the
	  wrong place

2008-01-15  Soeren Sonnenburg <sonne@debian.org>

	* distributions/hmm/HMM.cpp: call constructor

2008-01-13  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* guilib/GUIMatlab.cpp, structure/DynProg.cpp, structure/DynProg.h:
	  changes for alt_splice mSplicer

2008-01-12  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* guilib/GUIMatlab.cpp: minor changes in argument processing

2008-01-12  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM.h, distance/Distance.cpp, kernel/Kernel.cpp:
	  fix valgrind delete[] delete free mismatches triggered by
	  python-modular testsuite

2008-01-11  Sebastian Henschel <shogun@kodeaffe.de>

	* kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.h: kernel:
	  - Converted tries of WeightedDegreeStringKernel to use dynamic
	  memory
	  allocation
	  - WeighteddegreeStringKernel::set_max_mismatch() calls ::init()
	  when
	  appropriate
	* distributions/hmm/HMM.cpp: distribution/testsuite:
	  - Some more tweaking of HMM, still unfinished

2008-01-10  Sebastian Henschel <shogun@kodeaffe.de>

	* kernel/Kernel.cpp: kernel:
	  - Fixed a little issue with memory created with new (now malloc)
	  when being
	  free'd (from the outside)
	* kernel/HistogramWordKernel.cpp, kernel/SalzbergWordKernel.cpp:
	  kernel:
	  - Fixed memory/NaN issue with in test matrices in
	  {Salzberg,Histogram}WordKernel

2008-01-09  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/libocas.cpp, lib/Mathematics.cpp,
	  lib/Mathematics.h: * fix crasher on clear sg :
	  
	  for some reason matlab newer shogun version reliably crashed on
	  <do things with sg> ; clear sg ; sg ... fix the potentially stack
	  overflow by
	  dynamically allocating memory for the random number generator.
	  
	  * fix warning in ocas

2008-01-09  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/PluginEstimate.h, features/StringFeatures.h,
	  kernel/HistogramWordKernel.cpp, kernel/HistogramWordKernel.h,
	  kernel/SalzbergWordKernel.cpp, kernel/SalzbergWordKernel.h:
	  classifier/kernel:
	  - Modified {Salzberg, Histogram}Word to use StringFeatures<WORD>
	  and bugfixed
	  them a little, so that Shogun does not crash anymore.
	  - Constructor of PluginEstimate now uses default values for
	  pseudos (as taken
	  from Distribution's constructor)
	  - Both kernels spit out nans and wierd test kernel matrices.
	  Apparently, they
	  need more fixing
	  testsuite/examples:
	  - Integrated {Salzberg, Histogram}Word

2008-01-08  Sebastian Henschel <shogun@kodeaffe.de>

	* distributions/hmm/HMM.cpp, distributions/hmm/HMM.h,
	  guilib/GUIHMM.cpp, guilib/GUIHMM.h: distribution:
	  - Some more bits for a better HMM, unfortunately still incomplete
	  due to yet
	  another road block (see mailing-list).

2008-01-08  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/WDSVMOcas.cpp, guilib/GUIMatlab.cpp: - fix crash
	  in figuring out alphabet
	  - allow order 8 for wdocas
	* classifier/svm/WDSVMOcas.cpp: fix compile error in python-modular
	  interface
	* classifier/svm/libocas.cpp: update of libocas, fixes bug in
	  linesearch

2008-01-05  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/WDSVMOcas.cpp, classifier/svm/WDSVMOcas.h,
	  classifier/svm/libocas.cpp: parallelize WDOcas
	* classifier/svm/libocas.cpp: fix rarely occuring bug in libocas
	  (vf)

2008-01-05  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/svm/SubGradientSVM.cpp: classifier:
	  - Silenced SubGradientSVM

2008-01-05  Soeren Sonnenburg <sonne@debian.org>

	* Makefile: hopefully fix dependency building with gcc -MM -MT ...

2008-01-05  Sebastian Henschel <shogun@kodeaffe.de>

	* distributions/Distribution.cpp, distributions/Distribution.h,
	  distributions/Distribution.i: distribution/examples:
	  - Modified Distribution::get_log_likelihood to be wrappable by
	  swig
	  - Added this method to the examples for Distribution

2008-01-05  Soeren Sonnenburg <sonne@debian.org>

	* distributions/hmm/LinearHMM.cpp, features/StringFeatures.h: * fix
	  warning in linear hmm (cast num_symbols to int)
	  * fix loading of strings when lines are longer than 1MB
	  * add progress bar for linecounting and loading

2008-01-04  Soeren Sonnenburg <sonne@debian.org>

	* Makefile, classifier/svm/WDSVMOcas.cpp, configure,
	  features/Alphabet.cpp, features/StringFeatures.h,
	  guilib/GUIMatlab.cpp, lib/Mathematics.cpp, lib/common.h: add
	  read_dna_file function to directly read in strings without having
	  to transfer them from matlab or so
	  
	  example:
	  sg('set_features', 'TRAIN', 'dat.fa', 'DNABINFILE');

2008-01-04  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/PluginEstimate.h,
	  distributions/histogram/Histogram.cpp,
	  distributions/histogram/Histogram.h,
	  distributions/hmm/LinearHMM.cpp, distributions/hmm/LinearHMM.h,
	  distributions/hmm/LinearHMM.i: distribution:
	  - LinearHMM: Renamed hist to transition_probs
	  - Histogram: Moved get/set_histogram into .cpp
	  
	  classifier/testsuite/examples:
	  - Adjusted to changes above
	* clustering/Hierarchical.h: testsuite:
	  - Jury-rigged random initialisation in clustering to produce
	  constant values,
	  helped by yesterday's new init_random() in Mathematics
	  clustering:
	  - Fixed Hierarchical::get_merge_distance() and ::get_pairs()
	  wrapped for swig
	  similarly to yesterday's fix of KMeans::get_radi() and
	  ::get_centers()

2008-01-03  Soeren Sonnenburg <sonne@debian.org>

	* clustering/KMeans.h, distributions/Distribution.cpp,
	  distributions/histogram/Histogram.h,
	  distributions/hmm/LinearHMM.cpp, lib/Cache.h,
	  lib/Mathematics.cpp, lib/Mathematics.h: several fixes and
	  enhancements caused by todays kodeaffe-questioning

2008-01-02  Sebastian Henschel <shogun@kodeaffe.de>

	* features/RealFileFeatures.cpp, preproc/LogPlusOne.cpp,
	  preproc/LogPlusOne.h, preproc/NormDerivativeLem3.cpp,
	  preproc/NormDerivativeLem3.h, preproc/NormOne.cpp,
	  preproc/NormOne.h, preproc/PCACut.cpp, preproc/PCACut.h,
	  preproc/PreProc.i, preproc/PruneVarSubMean.cpp,
	  preproc/PruneVarSubMean.h, preproc/RealPreProc.h,
	  preproc/RealPreProc.i, preproc/ShortPreProc.cpp,
	  preproc/ShortPreProc.h, preproc/ShortPreProc.i,
	  preproc/SimplePreProc.h, preproc/SortUlongString.h,
	  preproc/SortWord.cpp, preproc/SortWord.h,
	  preproc/SortWordString.h, preproc/StringPreProc.h,
	  preproc/WordPreProc.cpp, preproc/WordPreProc.h,
	  preproc/WordPreProc.i: preproc:
	  - Obliterated {Real,Short,Word}PreProc

2007-12-30  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreePositionStringKernel.h: fix error in header
	  file (gcc 4.3 reports this as error multiple parameters named
	  'posweights_lhs')

2007-12-29  Sebastian Henschel <shogun@kodeaffe.de>

	* kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.h: kernel:
	  - Made a few little improvements in WeightedDegreeStringKernel
	  wrt
	  set_max_mismatch()

2007-12-27  Sebastian Henschel <shogun@kodeaffe.de>

	* distributions/hmm/HMM.cpp, distributions/hmm/HMM.h: distribution:
	  - kind of integrated HMM into testsuite; a few things unclear
	  yet, hence no
	  updated examples.

2007-12-22  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVMOcas.cpp, classifier/svm/WDSVMOcas.cpp: bugfix
	* classifier/svm/WDSVMOcas.cpp, classifier/svm/WDSVMOcas.h,
	  lib/Mathematics.cpp, lib/Mathematics.h: traverse data dimension
	  wise, to reduce cache hits. speeds up output
	  computation by factor 3. however it requires data to be
	  transposed(!!!)
	  
	  ...debugging
	* classifier/svm/WDSVMOcas.cpp, lib/Mathematics.h: dyn alloc things
	* classifier/svm/WDSVMOcas.cpp: adding code to figure out why
	  computing output to wd ocas is slow (95% is spend
	  in computing output) - as expected the random access to w is the
	  cause. we need
	  to use the batch computation idea to minimize cache misses. still
	  this
	  implementation is 2 times faster than svm light w/ linadd

2007-12-21  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUIKernel.cpp, kernel/WeightedDegreeStringKernel.h:
	  kernel:
	  - Added some get/set functions to WeightedDegreeStringKernel to
	  reestablish
	  functionality lost through changes in the constructors a few
	  commits before

2007-12-21  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/WDSVMOcas.cpp, classifier/svm/libocas.cpp: fix
	  timing, minor tuning
	* classifier/svm/SVMOcas.cpp, classifier/svm/WDSVMOcas.cpp,
	  classifier/svm/WDSVMOcas.h: output timing statistics
	* classifier/svm/libocas.cpp, classifier/svm/libocas.h: updated to
	  new ocas

2007-12-20  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/WDSVMOcas.cpp, classifier/svm/WDSVMOcas.h: seems
	  to work now - the meaning of epsilon is really completely
	  different so
	  don't expect a solution even close to svmlight...
	* classifier/svm/WDSVMOcas.cpp, classifier/svm/WDSVMOcas.h,
	  guilib/GUIKernel.cpp, kernel/CustomKernel.cpp,
	  kernel/WeightedDegreeStringKernel.h: - fix parts of WD kernel
	  (broken since ABI change)
	  - debugging WDSVMOcas

2007-12-20  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUIPluginEstimate.cpp: guilib:
	  - Forgot to adapt PluginEstimate in guilib
	* classifier/PluginEstimate.cpp, classifier/PluginEstimate.h,
	  distributions/Distribution.h,
	  distributions/histogram/Histogram.cpp,
	  distributions/histogram/Histogram.h,
	  distributions/hmm/LinearHMM.cpp, distributions/hmm/LinearHMM.h:
	  distribution:
	  - Converted LinearHMM from WordFeatures to StringFeatures<WORD>
	  - Swapped arguments in Histogram::get_log_derivative to match the
	  order in
	  LinearHMM and Distribution
	  - Renamed param_num to num_param in Distribution
	  classifier:
	  - Adapted PluginEstimate accordingly to changes in LinearHMM
	  testsuite/examples:
	  - Adapted accordingly to changes in LinearHMM/Histogram

2007-12-20  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/WDSVMOcas.cpp, classifier/svm/WDSVMOcas.h:
	  introduce WD kernel normalization const
	* classifier/svm/WDSVMOcas.cpp, classifier/svm/WDSVMOcas.h,
	  features/Alphabet.cpp, features/Alphabet.h,
	  guilib/GUIClassifier.cpp, guilib/GUIClassifier.h, lib/common.h:
	  finally a working WDOCAS

2007-12-19  Sebastian Henschel <shogun@kodeaffe.de>

	* clustering/Clustering.i, distributions/Distribution.cpp,
	  distributions/Distribution.h, distributions/Distribution.i,
	  distributions/histogram/Histogram.cpp,
	  distributions/histogram/Histogram.h,
	  distributions/histogram/Histogram.i: distribution:
	  - Extended Histogram to get/set histogram from outside
	  - Converted Histogram from WordFeatures to StringFeatures<WORD>
	  - Misc little fixed in Histogram
	  - Renamed get_log_likelihood_all_examples to get_log_likelihood
	  in
	  Distribution
	  testsuite/examples:
	  - Changed test for Histogram accordingly
	  clustering:
	  - Fixed typo in doc-string of Clustering.i

2007-12-19  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/WDSVMOcas.cpp, guilib/GUIClassifier.cpp,
	  guilib/GUIClassifier.h: wdocas needs bytefeatures, adjust
	  interfaces
	* classifier/svm/SVMOcas.cpp, classifier/svm/WDSVMOcas.cpp,
	  classifier/svm/WDSVMOcas.h: tuned WDSVM based on OCAS

2007-12-18  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUIKernel.cpp: kernel:
	  - Fix instantiation of WeightedDegreeString in guilib

2007-12-17  Sebastian Henschel <shogun@kodeaffe.de>

	* clustering/Hierarchical.h, clustering/Hierarchical.i: clustering:
	  - Implemented overload functions for get_merge_distance and
	  get_pairs in
	  Hierarchical, so it can be picked up bei swig.
	  testsuite:
	  - Modified testing for clustering entities accordingly.

2007-12-16  Sebastian Henschel <shogun@kodeaffe.de>

	* kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.h: kernel:
	  - Cleanup in constructors of WeightedDegreeStringKernel
	  testsuite/examples:
	  - Adjusted to aforementioned changes
	* classifier/Classifier.i, classifier/svm/LibSVMMultiClass.cpp,
	  classifier/svm/LibSVMMultiClass.h,
	  classifier/svm/LibSVMMultiClass.i,
	  classifier/svm/LibSVMOneClass.cpp,
	  classifier/svm/LibSVMOneClass.h, classifier/svm/LibSVMOneClass.i,
	  classifier/svm/LibSVM_multiclass.cpp,
	  classifier/svm/LibSVM_multiclass.h,
	  classifier/svm/LibSVM_multiclass.i,
	  classifier/svm/LibSVM_oneclass.cpp,
	  classifier/svm/LibSVM_oneclass.h,
	  classifier/svm/LibSVM_oneclass.i, classifier/svm/MPD.cpp,
	  classifier/svm/MPD.h, classifier/svm/MPD.i,
	  classifier/svm/MPDSVM.cpp, classifier/svm/MPDSVM.h,
	  classifier/svm/MPDSVM.i, classifier/svm/MultiClassSVM.i,
	  guilib/GUIClassifier.cpp: classifier:
	  - Renamed MPD.*, LibSVM_* to file names corresponding to their
	  class name
	  - Adjusted a few accuracies for testing
	* distance/EuclidianDistance.cpp, distance/EuclidianDistance.h:
	  distance:
	  - Added switch to disable sqrt in EuclidianDistance
	  - Added example for NormSquared accordingly
	  - Also added different lengths of feature vectors for some
	  distances in
	  examples
	* distance/CanberraMetric.cpp, distance/ChebyshewMetric.cpp,
	  distance/JensenMetric.cpp, distance/ManhattanMetric.cpp,
	  distance/MinkowskiMetric.cpp, kernel/GaussianKernel.cpp,
	  kernel/GaussianShiftKernel.cpp, kernel/PolyMatchWordKernel.cpp,
	  kernel/SigmoidKernel.cpp: kernel/distance:
	  - Removed unnecessary variable ialen
	* distance/HammingWordDistance.cpp: distance:
	  - Removed unnecessary assertion if vectors of lhs and rhs have
	  same length
	  testsuite:
	  - Adapted DNA features to have different lengths in train and
	  test

2007-12-14  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/WDSVMOcas.cpp, classifier/svm/WDSVMOcas.h,
	  classifier/svm/WDSVMOcas.i, guilib/GUIClassifier.cpp: start OCAS
	  variant tuned to training low order WD kernel SVMs
	* classifier/KNN.cpp, classifier/KNN.h, classifier/Perceptron.cpp,
	  classifier/svm/MultiClassSVM.h,
	  classifier/svm/SubGradientSVM.cpp, clustering/Hierarchical.cpp,
	  clustering/Hierarchical.h, clustering/KMeans.cpp,
	  clustering/KMeans.h, clustering/KMeans.i,
	  distance/CanberraWordDistance.cpp, distance/GeodesicMetric.cpp,
	  distance/ManhattanWordDistance.cpp, distributions/hmm/HMM.h,
	  features/Labels.cpp, kernel/WeightedDegreeStringKernel.h: various
	  fixes based on sebastians many questions
	* ., .authors, .doxy2swig.py, .generate_link_dependencies.py,
	  .version.sh, AUTHORS, CONTRIBUTIONS, ChangeLog, INSTALL, LICENSE,
	  LICENSE.SVMlight, Makefile, NEWS, README, README.developer, TODO,
	  base, base/Parallel.cpp, base/Parallel.h, base/Parallel.i,
	  base/SGObject.cpp, base/SGObject.h, base/SGObject.i,
	  base/Version.cpp, base/Version.h, base/Version.i, classifier,
	  classifier/Classifier.cpp, classifier/Classifier.doxy,
	  classifier/Classifier.h, classifier/Classifier.i,
	  classifier/KNN.cpp, classifier/KNN.h, classifier/KNN.i,
	  classifier/KernelPerceptron.cpp, classifier/KernelPerceptron.h,
	  classifier/KernelPerceptron.i, classifier/LDA.cpp,
	  classifier/LDA.h, classifier/LDA.i, classifier/LPBoost.cpp,
	  classifier/LPBoost.h, classifier/LPBoost.i, classifier/LPM.cpp,
	  classifier/LPM.h, classifier/LPM.i,
	  classifier/LinearClassifier.cpp, classifier/LinearClassifier.h,
	  classifier/LinearClassifier.i, classifier/Perceptron.cpp,
	  classifier/Perceptron.h, classifier/Perceptron.i,
	  classifier/PluginEstimate.cpp, classifier/PluginEstimate.h,
	  classifier/PluginEstimate.i,
	  classifier/SparseLinearClassifier.cpp,
	  classifier/SparseLinearClassifier.h,
	  classifier/SparseLinearClassifier.i,
	  classifier/SubGradientLPM.cpp, classifier/SubGradientLPM.h,
	  classifier/SubGradientLPM.i, classifier/__init__.py,
	  classifier/svm, classifier/svm/CPLEXSVM.cpp,
	  classifier/svm/CPLEXSVM.h, classifier/svm/GMNPSVM.cpp,
	  classifier/svm/GMNPSVM.h, classifier/svm/GMNPSVM.i,
	  classifier/svm/GNPPSVM.cpp, classifier/svm/GNPPSVM.h,
	  classifier/svm/GNPPSVM.i, classifier/svm/GPBTSVM.cpp,
	  classifier/svm/GPBTSVM.h, classifier/svm/GPBTSVM.i,
	  classifier/svm/LibLinear.cpp, classifier/svm/LibLinear.h,
	  classifier/svm/LibLinear.i, classifier/svm/LibSVM.cpp,
	  classifier/svm/LibSVM.h, classifier/svm/LibSVM.i,
	  classifier/svm/LibSVM_multiclass.cpp,
	  classifier/svm/LibSVM_multiclass.h,
	  classifier/svm/LibSVM_multiclass.i,
	  classifier/svm/LibSVM_oneclass.cpp,
	  classifier/svm/LibSVM_oneclass.h,
	  classifier/svm/LibSVM_oneclass.i, classifier/svm/MPD.cpp,
	  classifier/svm/MPD.h, classifier/svm/MPD.i,
	  classifier/svm/MultiClassSVM.cpp, classifier/svm/MultiClassSVM.h,
	  classifier/svm/MultiClassSVM.i, classifier/svm/Optimizer.cpp,
	  classifier/svm/Optimizer.h, classifier/svm/SVM.cpp,
	  classifier/svm/SVM.h, classifier/svm/SVM.i,
	  classifier/svm/SVMLin.cpp, classifier/svm/SVMLin.h,
	  classifier/svm/SVMLin.i, classifier/svm/SVMOcas.cpp,
	  classifier/svm/SVMOcas.h, classifier/svm/SVMOcas.i,
	  classifier/svm/SVM_libsvm.cpp, classifier/svm/SVM_libsvm.h,
	  classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h,
	  classifier/svm/SVM_light.i, classifier/svm/SVM_linear.cpp,
	  classifier/svm/SVM_linear.h, classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h, classifier/svm/SubGradientSVM.i,
	  classifier/svm/Tron.cpp, classifier/svm/Tron.h,
	  classifier/svm/WDSVMOcas.i, classifier/svm/__init__.py,
	  classifier/svm/gmnplib.cpp, classifier/svm/gmnplib.h,
	  classifier/svm/gnpplib.cpp, classifier/svm/gnpplib.h,
	  classifier/svm/gpdt.cpp, classifier/svm/gpdt.h,
	  classifier/svm/gpdtsolve.cpp, classifier/svm/gpdtsolve.h,
	  classifier/svm/gpm.cpp, classifier/svm/gpm.h,
	  classifier/svm/libocas.cpp, classifier/svm/libocas.h,
	  classifier/svm/libocas_common.h, classifier/svm/pr_loqo.cpp,
	  classifier/svm/pr_loqo.h, classifier/svm/qpbsvmlib.cpp,
	  classifier/svm/qpbsvmlib.h, classifier/svm/qpssvmlib.cpp,
	  classifier/svm/qpssvmlib.h, classifier/svm/ssl.cpp,
	  classifier/svm/ssl.h, clustering, clustering/Clustering.doxy,
	  clustering/Clustering.i, clustering/Hierarchical.cpp,
	  clustering/Hierarchical.h, clustering/Hierarchical.i,
	  clustering/KMeans.cpp, clustering/KMeans.h, clustering/KMeans.i,
	  configure, distance, distance/CanberraMetric.cpp,
	  distance/CanberraMetric.h, distance/CanberraMetric.i,
	  distance/CanberraWordDistance.cpp,
	  distance/CanberraWordDistance.h, distance/CanberraWordDistance.i,
	  distance/ChebyshewMetric.cpp, distance/ChebyshewMetric.h,
	  distance/ChebyshewMetric.i, distance/Distance.cpp,
	  distance/Distance.doxy, distance/Distance.h, distance/Distance.i,
	  distance/DistanceMachine.cpp, distance/DistanceMachine.h,
	  distance/DistanceMachine.i, distance/EuclidianDistance.cpp,
	  distance/EuclidianDistance.h, distance/EuclidianDistance.i,
	  distance/GeodesicMetric.cpp, distance/GeodesicMetric.h,
	  distance/GeodesicMetric.i, distance/HammingWordDistance.cpp,
	  distance/HammingWordDistance.h, distance/HammingWordDistance.i,
	  distance/JensenMetric.cpp, distance/JensenMetric.h,
	  distance/JensenMetric.i, distance/ManhattanMetric.cpp,
	  distance/ManhattanMetric.h, distance/ManhattanMetric.i,
	  distance/ManhattanWordDistance.cpp,
	  distance/ManhattanWordDistance.h,
	  distance/ManhattanWordDistance.i, distance/MinkowskiMetric.cpp,
	  distance/MinkowskiMetric.h, distance/MinkowskiMetric.i,
	  distance/RealDistance.h, distance/RealDistance.i,
	  distance/SimpleDistance.h, distance/SimpleDistance.i,
	  distance/SparseDistance.h, distance/SparseDistance.i,
	  distance/SparseEuclidianDistance.cpp,
	  distance/SparseEuclidianDistance.h,
	  distance/SparseEuclidianDistance.i, distance/StringDistance.h,
	  distance/StringDistance.i, distributions,
	  distributions/Distribution.cpp, distributions/Distribution.doxy,
	  distributions/Distribution.h, distributions/Distribution.i,
	  distributions/histogram, distributions/histogram/Histogram.cpp,
	  distributions/histogram/Histogram.h,
	  distributions/histogram/Histogram.i, distributions/hmm,
	  distributions/hmm/GHMM.cpp, distributions/hmm/GHMM.h,
	  distributions/hmm/GHMM.i, distributions/hmm/HMM.cpp,
	  distributions/hmm/HMM.h, distributions/hmm/HMM.i,
	  distributions/hmm/LinearHMM.cpp, distributions/hmm/LinearHMM.h,
	  distributions/hmm/LinearHMM.i, features, features/Alphabet.cpp,
	  features/Alphabet.h, features/Alphabet.i,
	  features/ByteFeatures.cpp, features/ByteFeatures.h,
	  features/ByteFeatures.i, features/CharFeatures.cpp,
	  features/CharFeatures.h, features/CharFeatures.i,
	  features/CombinedFeatures.cpp, features/CombinedFeatures.h,
	  features/CombinedFeatures.i, features/FKFeatures.cpp,
	  features/FKFeatures.h, features/FKFeatures.i,
	  features/Features.cpp, features/Features.doxy,
	  features/Features.h, features/Features.i, features/Labels.cpp,
	  features/Labels.h, features/Labels.i,
	  features/MindyGramFeatures.cpp, features/MindyGramFeatures.h,
	  features/MindyGramFeatures.i, features/RealFeatures.cpp,
	  features/RealFeatures.h, features/RealFeatures.i,
	  features/RealFileFeatures.cpp, features/RealFileFeatures.h,
	  features/RealFileFeatures.i, features/ShortFeatures.cpp,
	  features/ShortFeatures.h, features/ShortFeatures.i,
	  features/SimpleFeatures.h, features/SimpleFeatures.i,
	  features/SparseFeatures.h, features/SparseFeatures.i,
	  features/StringFeatures.cpp, features/StringFeatures.h,
	  features/StringFeatures.i, features/TOPFeatures.cpp,
	  features/TOPFeatures.h, features/TOPFeatures.i,
	  features/WordFeatures.cpp, features/WordFeatures.h,
	  features/WordFeatures.i, features/__init__.py, gui, gui/GUI.cpp,
	  gui/GUI.h, gui/Matlab.cpp, gui/Octave.cpp, gui/Python.cpp,
	  gui/Python.h, gui/R.cpp, gui/TextGUI.cpp, gui/TextGUI.h, guilib,
	  guilib/GUIClassifier.cpp, guilib/GUIClassifier.h,
	  guilib/GUICommands.h, guilib/GUIDistance.cpp,
	  guilib/GUIDistance.h, guilib/GUIFeatures.cpp,
	  guilib/GUIFeatures.h, guilib/GUIHMM.cpp, guilib/GUIHMM.h,
	  guilib/GUIKNN.cpp, guilib/GUIKNN.h, guilib/GUIKernel.cpp,
	  guilib/GUIKernel.h, guilib/GUILabels.cpp, guilib/GUILabels.h,
	  guilib/GUIMath.cpp, guilib/GUIMath.h, guilib/GUIMatlab.cpp,
	  guilib/GUIMatlab.h, guilib/GUIOctave.cpp, guilib/GUIOctave.h,
	  guilib/GUIPluginEstimate.cpp, guilib/GUIPluginEstimate.h,
	  guilib/GUIPreProc.cpp, guilib/GUIPreProc.h, guilib/GUIPython.cpp,
	  guilib/GUIPython.h, guilib/GUIR.cpp, guilib/GUIR.h,
	  guilib/GUITime.cpp, guilib/GUITime.h, kernel,
	  kernel/AUCKernel.cpp, kernel/AUCKernel.h, kernel/AUCKernel.i,
	  kernel/Chi2Kernel.cpp, kernel/Chi2Kernel.h, kernel/Chi2Kernel.i,
	  kernel/CombinedKernel.cpp, kernel/CombinedKernel.h,
	  kernel/CombinedKernel.i, kernel/CommUlongStringKernel.cpp,
	  kernel/CommUlongStringKernel.h, kernel/CommUlongStringKernel.i,
	  kernel/CommWordStringKernel.cpp, kernel/CommWordStringKernel.h,
	  kernel/CommWordStringKernel.i, kernel/ConstKernel.cpp,
	  kernel/ConstKernel.h, kernel/ConstKernel.i,
	  kernel/CustomKernel.cpp, kernel/CustomKernel.h,
	  kernel/CustomKernel.i, kernel/DiagKernel.cpp,
	  kernel/DiagKernel.h, kernel/DiagKernel.i,
	  kernel/DistanceKernel.cpp, kernel/DistanceKernel.h,
	  kernel/DistanceKernel.i, kernel/FixedDegreeStringKernel.cpp,
	  kernel/FixedDegreeStringKernel.h,
	  kernel/FixedDegreeStringKernel.i, kernel/GaussianKernel.cpp,
	  kernel/GaussianKernel.h, kernel/GaussianKernel.i,
	  kernel/GaussianShiftKernel.cpp, kernel/GaussianShiftKernel.h,
	  kernel/GaussianShiftKernel.i, kernel/HistogramWordKernel.cpp,
	  kernel/HistogramWordKernel.h, kernel/HistogramWordKernel.i,
	  kernel/Kernel.cpp, kernel/Kernel.doxy, kernel/Kernel.h,
	  kernel/Kernel.i, kernel/KernelMachine.cpp,
	  kernel/KernelMachine.h, kernel/KernelMachine.i,
	  kernel/LinearByteKernel.cpp, kernel/LinearByteKernel.h,
	  kernel/LinearByteKernel.i, kernel/LinearKernel.cpp,
	  kernel/LinearKernel.h, kernel/LinearKernel.i,
	  kernel/LinearStringKernel.cpp, kernel/LinearStringKernel.h,
	  kernel/LinearStringKernel.i, kernel/LinearWordKernel.cpp,
	  kernel/LinearWordKernel.h, kernel/LinearWordKernel.i,
	  kernel/LocalAlignmentStringKernel.cpp,
	  kernel/LocalAlignmentStringKernel.h,
	  kernel/LocalAlignmentStringKernel.i,
	  kernel/LocalityImprovedStringKernel.cpp,
	  kernel/LocalityImprovedStringKernel.h,
	  kernel/LocalityImprovedStringKernel.i,
	  kernel/MindyGramKernel.cpp, kernel/MindyGramKernel.h,
	  kernel/MindyGramKernel.i, kernel/PolyKernel.cpp,
	  kernel/PolyKernel.h, kernel/PolyKernel.i,
	  kernel/PolyMatchStringKernel.cpp, kernel/PolyMatchStringKernel.h,
	  kernel/PolyMatchStringKernel.i, kernel/PolyMatchWordKernel.cpp,
	  kernel/PolyMatchWordKernel.h, kernel/PolyMatchWordKernel.i,
	  kernel/SalzbergWordKernel.cpp, kernel/SalzbergWordKernel.h,
	  kernel/SalzbergWordKernel.i, kernel/SigmoidKernel.cpp,
	  kernel/SigmoidKernel.h, kernel/SigmoidKernel.i,
	  kernel/SimpleKernel.h, kernel/SimpleKernel.i,
	  kernel/SimpleLocalityImprovedStringKernel.cpp,
	  kernel/SimpleLocalityImprovedStringKernel.h,
	  kernel/SimpleLocalityImprovedStringKernel.i,
	  kernel/SparseGaussianKernel.cpp, kernel/SparseGaussianKernel.h,
	  kernel/SparseGaussianKernel.i, kernel/SparseKernel.h,
	  kernel/SparseKernel.i, kernel/SparseLinearKernel.cpp,
	  kernel/SparseLinearKernel.h, kernel/SparseLinearKernel.i,
	  kernel/SparsePolyKernel.cpp, kernel/SparsePolyKernel.h,
	  kernel/SparsePolyKernel.i, kernel/StringKernel.h,
	  kernel/StringKernel.i, kernel/WeightedCommWordStringKernel.cpp,
	  kernel/WeightedCommWordStringKernel.h,
	  kernel/WeightedCommWordStringKernel.i,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreePositionStringKernel.i,
	  kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.h,
	  kernel/WeightedDegreeStringKernel.i, kernel/WordMatchKernel.cpp,
	  kernel/WordMatchKernel.h, kernel/WordMatchKernel.i,
	  kernel/__init__.py, lib, lib/Array.h, lib/Array.i, lib/Array2.h,
	  lib/Array2.i, lib/Array3.h, lib/Array3.i, lib/Cache.h,
	  lib/Cache.i, lib/Cplex.cpp, lib/Cplex.h, lib/DynamicArray.h,
	  lib/DynamicArray.i, lib/File.cpp, lib/File.h, lib/File.i,
	  lib/Library.doxy, lib/Library.i, lib/List.h, lib/List.i,
	  lib/Mathematics.cpp, lib/Mathematics.h, lib/Mathematics.i,
	  lib/ShogunException.cpp, lib/ShogunException.h,
	  lib/ShogunException.i, lib/Signal.cpp, lib/Signal.h,
	  lib/Signal.i, lib/SimpleFile.h, lib/SimpleFile.i, lib/Time.cpp,
	  lib/Time.h, lib/Time.i, lib/Trie.cpp, lib/Trie.h, lib/Trie.i,
	  lib/__init__.py, lib/common.h, lib/common.i, lib/io.cpp,
	  lib/io.h, lib/io.i, lib/lapack.cpp, lib/lapack.h, lib/lapack.i,
	  lib/matlab.h, lib/python.h, lib/python_typemaps.i, preproc,
	  preproc/LogPlusOne.cpp, preproc/LogPlusOne.h,
	  preproc/LogPlusOne.i, preproc/NormDerivativeLem3.cpp,
	  preproc/NormDerivativeLem3.h, preproc/NormDerivativeLem3.i,
	  preproc/NormOne.cpp, preproc/NormOne.h, preproc/NormOne.i,
	  preproc/PCACut.cpp, preproc/PCACut.h, preproc/PCACut.i,
	  preproc/PreProc.cpp, preproc/PreProc.doxy, preproc/PreProc.h,
	  preproc/PreProc.i, preproc/PruneVarSubMean.cpp,
	  preproc/PruneVarSubMean.h, preproc/PruneVarSubMean.i,
	  preproc/RealPreProc.h, preproc/RealPreProc.i,
	  preproc/ShortPreProc.cpp, preproc/ShortPreProc.h,
	  preproc/ShortPreProc.i, preproc/SimplePreProc.h,
	  preproc/SimplePreProc.i, preproc/SortUlongString.cpp,
	  preproc/SortUlongString.h, preproc/SortUlongString.i,
	  preproc/SortWord.cpp, preproc/SortWord.h, preproc/SortWord.i,
	  preproc/SortWordString.cpp, preproc/SortWordString.h,
	  preproc/SortWordString.i, preproc/SparsePreProc.h,
	  preproc/SparsePreProc.i, preproc/StringPreProc.h,
	  preproc/StringPreProc.i, preproc/WordPreProc.cpp,
	  preproc/WordPreProc.h, preproc/WordPreProc.i, regression,
	  regression/KRR.cpp, regression/KRR.h, regression/KRR.i,
	  regression/Regression.doxy, regression/Regression.i,
	  regression/svr, regression/svr/LibSVR.cpp,
	  regression/svr/LibSVR.h, regression/svr/LibSVR.i,
	  regression/svr/SVR_light.cpp, regression/svr/SVR_light.h,
	  regression/svr/SVR_light.i, sg.m, structure,
	  structure/DynProg.cpp, structure/DynProg.h, structure/DynProg.i,
	  structure/Plif.cpp, structure/Plif.h, structure/Plif.i,
	  structure/PlifArray.cpp, structure/PlifArray.h,
	  structure/PlifArray.i, structure/PlifBase.h,
	  structure/PlifBase.i, structure/Structure.doxy,
	  structure/Structure.i: now the *final* nice correctly set props
	* ., .authors, .doxy2swig.py, .generate_link_dependencies.py,
	  .version.sh, AUTHORS, CONTRIBUTIONS, ChangeLog, INSTALL, LICENSE,
	  LICENSE.SVMlight, Makefile, NEWS, README, README.developer, TODO,
	  base, base/Parallel.cpp, base/Parallel.h, base/Parallel.i,
	  base/SGObject.cpp, base/SGObject.h, base/SGObject.i,
	  base/Version.cpp, base/Version.h, base/Version.i, classifier,
	  classifier/Classifier.cpp, classifier/Classifier.doxy,
	  classifier/Classifier.h, classifier/Classifier.i,
	  classifier/KNN.cpp, classifier/KNN.h, classifier/KNN.i,
	  classifier/KernelPerceptron.cpp, classifier/KernelPerceptron.h,
	  classifier/KernelPerceptron.i, classifier/LDA.cpp,
	  classifier/LDA.h, classifier/LDA.i, classifier/LPBoost.cpp,
	  classifier/LPBoost.h, classifier/LPBoost.i, classifier/LPM.cpp,
	  classifier/LPM.h, classifier/LPM.i,
	  classifier/LinearClassifier.cpp, classifier/LinearClassifier.h,
	  classifier/LinearClassifier.i, classifier/Perceptron.cpp,
	  classifier/Perceptron.h, classifier/Perceptron.i,
	  classifier/PluginEstimate.cpp, classifier/PluginEstimate.h,
	  classifier/PluginEstimate.i,
	  classifier/SparseLinearClassifier.cpp,
	  classifier/SparseLinearClassifier.h,
	  classifier/SparseLinearClassifier.i,
	  classifier/SubGradientLPM.cpp, classifier/SubGradientLPM.h,
	  classifier/SubGradientLPM.i, classifier/__init__.py,
	  classifier/svm, classifier/svm/CPLEXSVM.cpp,
	  classifier/svm/CPLEXSVM.h, classifier/svm/GMNPSVM.cpp,
	  classifier/svm/GMNPSVM.h, classifier/svm/GMNPSVM.i,
	  classifier/svm/GNPPSVM.cpp, classifier/svm/GNPPSVM.h,
	  classifier/svm/GNPPSVM.i, classifier/svm/GPBTSVM.cpp,
	  classifier/svm/GPBTSVM.h, classifier/svm/GPBTSVM.i,
	  classifier/svm/LibLinear.cpp, classifier/svm/LibLinear.h,
	  classifier/svm/LibLinear.i, classifier/svm/LibSVM.cpp,
	  classifier/svm/LibSVM.h, classifier/svm/LibSVM.i,
	  classifier/svm/LibSVM_multiclass.cpp,
	  classifier/svm/LibSVM_multiclass.h,
	  classifier/svm/LibSVM_multiclass.i,
	  classifier/svm/LibSVM_oneclass.cpp,
	  classifier/svm/LibSVM_oneclass.h,
	  classifier/svm/LibSVM_oneclass.i, classifier/svm/MPD.cpp,
	  classifier/svm/MPD.h, classifier/svm/MPD.i,
	  classifier/svm/MultiClassSVM.cpp, classifier/svm/MultiClassSVM.h,
	  classifier/svm/MultiClassSVM.i, classifier/svm/Optimizer.cpp,
	  classifier/svm/Optimizer.h, classifier/svm/SVM.cpp,
	  classifier/svm/SVM.h, classifier/svm/SVM.i,
	  classifier/svm/SVMLin.cpp, classifier/svm/SVMLin.h,
	  classifier/svm/SVMLin.i, classifier/svm/SVMOcas.cpp,
	  classifier/svm/SVMOcas.h, classifier/svm/SVMOcas.i,
	  classifier/svm/SVM_libsvm.cpp, classifier/svm/SVM_libsvm.h,
	  classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h,
	  classifier/svm/SVM_light.i, classifier/svm/SVM_linear.cpp,
	  classifier/svm/SVM_linear.h, classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h, classifier/svm/SubGradientSVM.i,
	  classifier/svm/Tron.cpp, classifier/svm/Tron.h,
	  classifier/svm/WDSVMOcas.cpp, classifier/svm/WDSVMOcas.h,
	  classifier/svm/WDSVMOcas.i, classifier/svm/__init__.py,
	  classifier/svm/gmnplib.cpp, classifier/svm/gmnplib.h,
	  classifier/svm/gnpplib.cpp, classifier/svm/gnpplib.h,
	  classifier/svm/gpdt.cpp, classifier/svm/gpdt.h,
	  classifier/svm/gpdtsolve.cpp, classifier/svm/gpdtsolve.h,
	  classifier/svm/gpm.cpp, classifier/svm/gpm.h,
	  classifier/svm/libocas.cpp, classifier/svm/libocas.h,
	  classifier/svm/libocas_common.h, classifier/svm/pr_loqo.cpp,
	  classifier/svm/pr_loqo.h, classifier/svm/qpbsvmlib.cpp,
	  classifier/svm/qpbsvmlib.h, classifier/svm/qpssvmlib.cpp,
	  classifier/svm/qpssvmlib.h, classifier/svm/ssl.cpp,
	  classifier/svm/ssl.h, clustering, clustering/Clustering.doxy,
	  clustering/Clustering.i, clustering/Hierarchical.cpp,
	  clustering/Hierarchical.h, clustering/Hierarchical.i,
	  clustering/KMeans.cpp, clustering/KMeans.h, clustering/KMeans.i,
	  configure, distance, distance/CanberraMetric.cpp,
	  distance/CanberraMetric.h, distance/CanberraMetric.i,
	  distance/CanberraWordDistance.cpp,
	  distance/CanberraWordDistance.h, distance/CanberraWordDistance.i,
	  distance/ChebyshewMetric.cpp, distance/ChebyshewMetric.h,
	  distance/ChebyshewMetric.i, distance/Distance.cpp,
	  distance/Distance.doxy, distance/Distance.h, distance/Distance.i,
	  distance/DistanceMachine.cpp, distance/DistanceMachine.h,
	  distance/DistanceMachine.i, distance/EuclidianDistance.cpp,
	  distance/EuclidianDistance.h, distance/EuclidianDistance.i,
	  distance/GeodesicMetric.cpp, distance/GeodesicMetric.h,
	  distance/GeodesicMetric.i, distance/HammingWordDistance.cpp,
	  distance/HammingWordDistance.h, distance/HammingWordDistance.i,
	  distance/JensenMetric.cpp, distance/JensenMetric.h,
	  distance/JensenMetric.i, distance/ManhattanMetric.cpp,
	  distance/ManhattanMetric.h, distance/ManhattanMetric.i,
	  distance/ManhattanWordDistance.cpp,
	  distance/ManhattanWordDistance.h,
	  distance/ManhattanWordDistance.i, distance/MinkowskiMetric.cpp,
	  distance/MinkowskiMetric.h, distance/MinkowskiMetric.i,
	  distance/RealDistance.h, distance/RealDistance.i,
	  distance/SimpleDistance.h, distance/SimpleDistance.i,
	  distance/SparseDistance.h, distance/SparseDistance.i,
	  distance/SparseEuclidianDistance.cpp,
	  distance/SparseEuclidianDistance.h,
	  distance/SparseEuclidianDistance.i, distance/StringDistance.h,
	  distance/StringDistance.i, distributions,
	  distributions/Distribution.cpp, distributions/Distribution.doxy,
	  distributions/Distribution.h, distributions/Distribution.i,
	  distributions/histogram, distributions/histogram/Histogram.cpp,
	  distributions/histogram/Histogram.h,
	  distributions/histogram/Histogram.i, distributions/hmm,
	  distributions/hmm/GHMM.cpp, distributions/hmm/GHMM.h,
	  distributions/hmm/GHMM.i, distributions/hmm/HMM.cpp,
	  distributions/hmm/HMM.h, distributions/hmm/HMM.i,
	  distributions/hmm/LinearHMM.cpp, distributions/hmm/LinearHMM.h,
	  distributions/hmm/LinearHMM.i, features, features/Alphabet.cpp,
	  features/Alphabet.h, features/Alphabet.i,
	  features/ByteFeatures.cpp, features/ByteFeatures.h,
	  features/ByteFeatures.i, features/CharFeatures.cpp,
	  features/CharFeatures.h, features/CharFeatures.i,
	  features/CombinedFeatures.cpp, features/CombinedFeatures.h,
	  features/CombinedFeatures.i, features/FKFeatures.cpp,
	  features/FKFeatures.h, features/FKFeatures.i,
	  features/Features.cpp, features/Features.doxy,
	  features/Features.h, features/Features.i, features/Labels.cpp,
	  features/Labels.h, features/Labels.i,
	  features/MindyGramFeatures.cpp, features/MindyGramFeatures.h,
	  features/MindyGramFeatures.i, features/RealFeatures.cpp,
	  features/RealFeatures.h, features/RealFeatures.i,
	  features/RealFileFeatures.cpp, features/RealFileFeatures.h,
	  features/RealFileFeatures.i, features/ShortFeatures.cpp,
	  features/ShortFeatures.h, features/ShortFeatures.i,
	  features/SimpleFeatures.h, features/SimpleFeatures.i,
	  features/SparseFeatures.h, features/SparseFeatures.i,
	  features/StringFeatures.cpp, features/StringFeatures.h,
	  features/StringFeatures.i, features/TOPFeatures.cpp,
	  features/TOPFeatures.h, features/TOPFeatures.i,
	  features/WordFeatures.cpp, features/WordFeatures.h,
	  features/WordFeatures.i, features/__init__.py, gui, gui/GUI.cpp,
	  gui/GUI.h, gui/Matlab.cpp, gui/Octave.cpp, gui/Python.cpp,
	  gui/Python.h, gui/R.cpp, gui/TextGUI.cpp, gui/TextGUI.h, guilib,
	  guilib/GUIClassifier.cpp, guilib/GUIClassifier.h,
	  guilib/GUICommands.h, guilib/GUIDistance.cpp,
	  guilib/GUIDistance.h, guilib/GUIFeatures.cpp,
	  guilib/GUIFeatures.h, guilib/GUIHMM.cpp, guilib/GUIHMM.h,
	  guilib/GUIKNN.cpp, guilib/GUIKNN.h, guilib/GUIKernel.cpp,
	  guilib/GUIKernel.h, guilib/GUILabels.cpp, guilib/GUILabels.h,
	  guilib/GUIMath.cpp, guilib/GUIMath.h, guilib/GUIMatlab.cpp,
	  guilib/GUIMatlab.h, guilib/GUIOctave.cpp, guilib/GUIOctave.h,
	  guilib/GUIPluginEstimate.cpp, guilib/GUIPluginEstimate.h,
	  guilib/GUIPreProc.cpp, guilib/GUIPreProc.h, guilib/GUIPython.cpp,
	  guilib/GUIPython.h, guilib/GUIR.cpp, guilib/GUIR.h,
	  guilib/GUITime.cpp, guilib/GUITime.h, kernel,
	  kernel/AUCKernel.cpp, kernel/AUCKernel.h, kernel/AUCKernel.i,
	  kernel/Chi2Kernel.cpp, kernel/Chi2Kernel.h, kernel/Chi2Kernel.i,
	  kernel/CombinedKernel.cpp, kernel/CombinedKernel.h,
	  kernel/CombinedKernel.i, kernel/CommUlongStringKernel.cpp,
	  kernel/CommUlongStringKernel.h, kernel/CommUlongStringKernel.i,
	  kernel/CommWordStringKernel.cpp, kernel/CommWordStringKernel.h,
	  kernel/CommWordStringKernel.i, kernel/ConstKernel.cpp,
	  kernel/ConstKernel.h, kernel/ConstKernel.i,
	  kernel/CustomKernel.cpp, kernel/CustomKernel.h,
	  kernel/CustomKernel.i, kernel/DiagKernel.cpp,
	  kernel/DiagKernel.h, kernel/DiagKernel.i,
	  kernel/DistanceKernel.cpp, kernel/DistanceKernel.h,
	  kernel/DistanceKernel.i, kernel/FixedDegreeStringKernel.cpp,
	  kernel/FixedDegreeStringKernel.h,
	  kernel/FixedDegreeStringKernel.i, kernel/GaussianKernel.cpp,
	  kernel/GaussianKernel.h, kernel/GaussianKernel.i,
	  kernel/GaussianShiftKernel.cpp, kernel/GaussianShiftKernel.h,
	  kernel/GaussianShiftKernel.i, kernel/HistogramWordKernel.cpp,
	  kernel/HistogramWordKernel.h, kernel/HistogramWordKernel.i,
	  kernel/Kernel.cpp, kernel/Kernel.doxy, kernel/Kernel.h,
	  kernel/Kernel.i, kernel/KernelMachine.cpp,
	  kernel/KernelMachine.h, kernel/KernelMachine.i,
	  kernel/LinearByteKernel.cpp, kernel/LinearByteKernel.h,
	  kernel/LinearByteKernel.i, kernel/LinearKernel.cpp,
	  kernel/LinearKernel.h, kernel/LinearKernel.i,
	  kernel/LinearStringKernel.cpp, kernel/LinearStringKernel.h,
	  kernel/LinearStringKernel.i, kernel/LinearWordKernel.cpp,
	  kernel/LinearWordKernel.h, kernel/LinearWordKernel.i,
	  kernel/LocalAlignmentStringKernel.cpp,
	  kernel/LocalAlignmentStringKernel.h,
	  kernel/LocalAlignmentStringKernel.i,
	  kernel/LocalityImprovedStringKernel.cpp,
	  kernel/LocalityImprovedStringKernel.h,
	  kernel/LocalityImprovedStringKernel.i,
	  kernel/MindyGramKernel.cpp, kernel/MindyGramKernel.h,
	  kernel/MindyGramKernel.i, kernel/PolyKernel.cpp,
	  kernel/PolyKernel.h, kernel/PolyKernel.i,
	  kernel/PolyMatchStringKernel.cpp, kernel/PolyMatchStringKernel.h,
	  kernel/PolyMatchStringKernel.i, kernel/PolyMatchWordKernel.cpp,
	  kernel/PolyMatchWordKernel.h, kernel/PolyMatchWordKernel.i,
	  kernel/SalzbergWordKernel.cpp, kernel/SalzbergWordKernel.h,
	  kernel/SalzbergWordKernel.i, kernel/SigmoidKernel.cpp,
	  kernel/SigmoidKernel.h, kernel/SigmoidKernel.i,
	  kernel/SimpleKernel.h, kernel/SimpleKernel.i,
	  kernel/SimpleLocalityImprovedStringKernel.cpp,
	  kernel/SimpleLocalityImprovedStringKernel.h,
	  kernel/SimpleLocalityImprovedStringKernel.i,
	  kernel/SparseGaussianKernel.cpp, kernel/SparseGaussianKernel.h,
	  kernel/SparseGaussianKernel.i, kernel/SparseKernel.h,
	  kernel/SparseKernel.i, kernel/SparseLinearKernel.cpp,
	  kernel/SparseLinearKernel.h, kernel/SparseLinearKernel.i,
	  kernel/SparsePolyKernel.cpp, kernel/SparsePolyKernel.h,
	  kernel/SparsePolyKernel.i, kernel/StringKernel.h,
	  kernel/StringKernel.i, kernel/WeightedCommWordStringKernel.cpp,
	  kernel/WeightedCommWordStringKernel.h,
	  kernel/WeightedCommWordStringKernel.i,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreePositionStringKernel.i,
	  kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.h,
	  kernel/WeightedDegreeStringKernel.i, kernel/WordMatchKernel.cpp,
	  kernel/WordMatchKernel.h, kernel/WordMatchKernel.i,
	  kernel/__init__.py, lib, lib/Array.h, lib/Array.i, lib/Array2.h,
	  lib/Array2.i, lib/Array3.h, lib/Array3.i, lib/Cache.h,
	  lib/Cache.i, lib/Cplex.cpp, lib/Cplex.h, lib/DynamicArray.h,
	  lib/DynamicArray.i, lib/File.cpp, lib/File.h, lib/File.i,
	  lib/Library.doxy, lib/Library.i, lib/List.h, lib/List.i,
	  lib/Mathematics.cpp, lib/Mathematics.h, lib/Mathematics.i,
	  lib/ShogunException.cpp, lib/ShogunException.h,
	  lib/ShogunException.i, lib/Signal.cpp, lib/Signal.h,
	  lib/Signal.i, lib/SimpleFile.h, lib/SimpleFile.i, lib/Time.cpp,
	  lib/Time.h, lib/Time.i, lib/Trie.cpp, lib/Trie.h, lib/Trie.i,
	  lib/__init__.py, lib/common.h, lib/common.i, lib/io.cpp,
	  lib/io.h, lib/io.i, lib/lapack.cpp, lib/lapack.h, lib/lapack.i,
	  lib/matlab.h, lib/python.h, lib/python_typemaps.i, preproc,
	  preproc/LogPlusOne.cpp, preproc/LogPlusOne.h,
	  preproc/LogPlusOne.i, preproc/NormDerivativeLem3.cpp,
	  preproc/NormDerivativeLem3.h, preproc/NormDerivativeLem3.i,
	  preproc/NormOne.cpp, preproc/NormOne.h, preproc/NormOne.i,
	  preproc/PCACut.cpp, preproc/PCACut.h, preproc/PCACut.i,
	  preproc/PreProc.cpp, preproc/PreProc.doxy, preproc/PreProc.h,
	  preproc/PreProc.i, preproc/PruneVarSubMean.cpp,
	  preproc/PruneVarSubMean.h, preproc/PruneVarSubMean.i,
	  preproc/RealPreProc.h, preproc/RealPreProc.i,
	  preproc/ShortPreProc.cpp, preproc/ShortPreProc.h,
	  preproc/ShortPreProc.i, preproc/SimplePreProc.h,
	  preproc/SimplePreProc.i, preproc/SortUlongString.cpp,
	  preproc/SortUlongString.h, preproc/SortUlongString.i,
	  preproc/SortWord.cpp, preproc/SortWord.h, preproc/SortWord.i,
	  preproc/SortWordString.cpp, preproc/SortWordString.h,
	  preproc/SortWordString.i, preproc/SparsePreProc.h,
	  preproc/SparsePreProc.i, preproc/StringPreProc.h,
	  preproc/StringPreProc.i, preproc/WordPreProc.cpp,
	  preproc/WordPreProc.h, preproc/WordPreProc.i, regression,
	  regression/KRR.cpp, regression/KRR.h, regression/KRR.i,
	  regression/Regression.doxy, regression/Regression.i,
	  regression/svr, regression/svr/LibSVR.cpp,
	  regression/svr/LibSVR.h, regression/svr/LibSVR.i,
	  regression/svr/SVR_light.cpp, regression/svr/SVR_light.h,
	  regression/svr/SVR_light.i, sg.m, structure,
	  structure/DynProg.cpp, structure/DynProg.h, structure/DynProg.i,
	  structure/Plif.cpp, structure/Plif.h, structure/Plif.i,
	  structure/PlifArray.cpp, structure/PlifArray.h,
	  structure/PlifArray.i, structure/PlifBase.h,
	  structure/PlifBase.i, structure/Structure.doxy,
	  structure/Structure.i: ignore '*doxygen_xml' '*_wrap.h'
	  '*_wrap.cxx' '*.so' '*_doxygen.i' '.depend' '.config' 'tags'

2007-12-12  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/svm/LibSVM_oneclass.cpp,
	  classifier/svm/LibSVM_oneclass.h: testsuite/LibSVMOneClass:
	  Extended LibSVMOneClass' constructor and added the
	  SVM to testuite.

2007-12-12  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIMatlab.cpp: fix warning in matlab interface

2007-12-10  Sebastian Henschel <shogun@kodeaffe.de>

	* distributions/histogram/Histogram.cpp,
	  distributions/histogram/Histogram.h, distributions/hmm/HMM.cpp:
	  Added support for distributions in testsuite, but again, dunno
	  yet how to test
	  properly.
	  Fixed erroneous delete statement in HMM's destructor.
	* clustering/Hierarchical.cpp, clustering/Hierarchical.h,
	  clustering/KMeans.cpp, clustering/KMeans.h: Added support for
	  clustering in testsuite. But since classify() returns NULL,
	  dunno yet what to test for.

2007-12-09  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUIMatlab.cpp, guilib/GUIPython.cpp, guilib/GUIR.cpp:
	  Fixed a few compile issues with CustomKernel.

2007-12-08  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/KNN.cpp, classifier/KNN.h, classifier/Perceptron.cpp,
	  classifier/Perceptron.h: What started out to be an addition of
	  classifiers Perceptron and KNN to the
	  testsuite became a slightly bigger change. And since many
	  testdata files have
	  changed, svm was renamed to classifier to have even more changed
	  files.

2007-12-07  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/svm/LibLinear.cpp, classifier/svm/LibLinear.h,
	  kernel/LocalAlignmentStringKernel.cpp: - Added testing support
	  for Linear SVMs SubGradientSVM (defunct), SVMOcas,
	  SVMLin, LibLinear.
	  - Dropped bias from test files' filenames which might result in
	  fewer
	  filename fluctuation.
	  - Fixed a memory problem in LocalAlignmentStringKernel found
	  through valgrind
	  when investigating another issue.

2007-12-05  Sebastian Henschel <shogun@kodeaffe.de>

	* classifier/svm/MultiClassSVM.cpp: Added tests for
	  LibSVM[Multi|One]class and GMNPSVM. Something seems to be
	  wrong, though.
	  Fixed serious error in tester for SVMs.

2007-12-03  Sebastian Henschel <shogun@kodeaffe.de>

	* kernel/WeightedDegreePositionStringKernel.cpp: Added tests for
	  SVM_light/GPBT with kernels Linear/WD/WDS/Comm*.
	  Modified initialisation of shifts in WDS a bit (and hopefully did
	  not
	  break it).
	* classifier/Classifier.i, classifier/svm/MPD.cpp,
	  classifier/svm/MPD.h, classifier/svm/MPD.i: Included swig
	  interface for MPDSVM in build process and added second
	  constructor to class.
	  Added tests for SMVs GPBTSVM, LibSVM, MPDSVM. Some values for
	  biases/alphas/support vectors seem to be a bit or completely out
	  of bounds;
	  needs a fix.

2007-12-02  Sebastian Henschel <shogun@kodeaffe.de>

	* distance/Canberra.cpp, distance/Canberra.h, distance/Canberra.i,
	  distance/CanberraMetric.cpp, distance/CanberraMetric.h,
	  distance/CanberraMetric.i, distance/Chebyshew.cpp,
	  distance/Chebyshew.h, distance/Chebyshew.i,
	  distance/ChebyshewMetric.cpp, distance/ChebyshewMetric.h,
	  distance/ChebyshewMetric.i, distance/Distance.i,
	  distance/Geodesic.cpp, distance/Geodesic.h, distance/Geodesic.i,
	  distance/GeodesicMetric.cpp, distance/GeodesicMetric.h,
	  distance/GeodesicMetric.i, distance/Jensen.cpp,
	  distance/Jensen.h, distance/Jensen.i, distance/JensenMetric.cpp,
	  distance/JensenMetric.h, distance/JensenMetric.i,
	  distance/Manhattan.cpp, distance/Manhattan.h,
	  distance/Manhattan.i, distance/ManhattanMetric.cpp,
	  distance/ManhattanMetric.h, distance/ManhattanMetric.i,
	  distance/Minkowski.cpp, distance/Minkowski.h,
	  distance/Minkowski.i, distance/MinkowskiMetric.cpp,
	  distance/MinkowskiMetric.h, distance/MinkowskiMetric.i,
	  guilib/GUIDistance.cpp: Added suffix 'Metric' to the metric
	  distances, extended their constructors to
	  accept features and added tests for them.
	* distance/SparseEuclidianDistance.cpp,
	  distance/SparseEuclidianDistance.h, features/SparseFeatures.h,
	  kernel/SparseGaussianKernel.cpp, kernel/SparseGaussianKernel.h:
	  Put square optimisation back into SparseGaussianKernel (and added
	  to
	  SparseEuclidianDistance).

2007-11-30  Sebastian Henschel <shogun@kodeaffe.de>

	* distance/SparseEuclidianDistance.cpp, features/SparseFeatures.h,
	  kernel/SparseGaussianKernel.cpp: Presumably fixed issue with NaN
	  values in SparseEuclidianDistance.
	  Unfortunately, lost some speed in SparseGaussianKernel, but will
	  be improved very
	  soon.
	* distance/CanberraWordDistance.cpp,
	  distance/CanberraWordDistance.h,
	  distance/HammingWordDistance.cpp, distance/HammingWordDistance.h,
	  distance/ManhattanWordDistance.cpp,
	  distance/ManhattanWordDistance.h: Added (and adjusted)
	  Canberra/Manhattan/HammingWordDistances to testsuite.
	  Fixed a little bug in cleaning data directories when generator is
	  run.
	* guilib/GUIKernel.cpp, kernel/Kernel.cpp, lib/common.h: Previous
	  purge of Canberra/Hamming/ManhattanWordKernels was incomplete and
	  presumably broke build of other interfaces than python-modular.
	* clustering/KMeans.cpp, distance/Distance.i,
	  distance/EuclidianDistance.cpp, distance/EuclidianDistance.h,
	  distance/EuclidianDistance.i, distance/NormSquaredDistance.cpp,
	  distance/NormSquaredDistance.h, distance/NormSquaredDistance.i,
	  distance/SparseEuclidianDistance.cpp,
	  distance/SparseEuclidianDistance.h,
	  distance/SparseEuclidianDistance.i,
	  distance/SparseNormSquaredDistance.cpp,
	  distance/SparseNormSquaredDistance.h,
	  distance/SparseNormSquaredDistance.i, guilib/GUIDistance.cpp,
	  lib/common.h: Renamed SquaredNorm to Euclidian (with compute()
	  modified to return the
	  result's sqrt).
	* distance/Distance.cpp, distance/Distance.i,
	  distance/NormSquaredDistance.cpp, distance/NormSquaredDistance.h:
	  Established infrastructure to test Distances (including an update
	  to
	  NormSquaredDistance).

2007-11-29  Sebastian Henschel <shogun@kodeaffe.de>

	* kernel/CanberraWordKernel.cpp, kernel/CanberraWordKernel.h,
	  kernel/CanberraWordKernel.i, kernel/HammingWordKernel.cpp,
	  kernel/HammingWordKernel.h, kernel/HammingWordKernel.i,
	  kernel/Kernel.i, kernel/ManhattanWordKernel.cpp,
	  kernel/ManhattanWordKernel.h, kernel/ManhattanWordKernel.i:
	  Purged kernels Manhattan/Canberra/HammingWord.
	* distance/CanberraWordDistance.cpp,
	  distance/CanberraWordDistance.h, distance/CanberraWordDistance.i,
	  distance/Distance.cpp, distance/Distance.h,
	  distance/HammingWordDistance.cpp, distance/HammingWordDistance.h,
	  distance/HammingWordDistance.i,
	  distance/ManhattanWordDistance.cpp,
	  distance/ManhattanWordDistance.h,
	  distance/ManhattanWordDistance.i, kernel/CanberraWordKernel.cpp,
	  kernel/CanberraWordKernel.h, kernel/DistanceKernel.cpp,
	  kernel/DistanceKernel.h, kernel/HammingWordKernel.cpp,
	  kernel/HammingWordKernel.h, kernel/Kernel.cpp, kernel/Kernel.h,
	  kernel/ManhattanWordKernel.cpp, kernel/ManhattanWordKernel.h:
	  Converted Manhattan/Hamming/CanberraWordKernel/Distance to
	  String<WORD>.
	  As can be seen in the output generated by the testsuite, the
	  aforementioned
	  kernels and distances yield the same results, so the kernels will
	  be removed
	  with the next commit.

2007-11-27  Soeren Sonnenburg <sonne@debian.org>

	* base/Version.cpp, base/Version.h, classifier/Classifier.doxy,
	  classifier/Classifier.i, classifier/KNN.cpp,
	  classifier/svm/SVM.h, clustering/Clustering.i,
	  distance/DistanceMachine.i,
	  distributions/histogram/Histogram.cpp: - some cleanups while
	  showing sebastian the code
	  - some more docu for SVM.h

2007-11-26  Soeren Sonnenburg <sonne@debian.org>

	* classifier/Classifier.doxy, clustering/Clustering.doxy,
	  distance/Distance.doxy, distributions/Distribution.doxy,
	  features/Features.doxy, kernel/Kernel.doxy, lib/Library.doxy,
	  preproc/PreProc.doxy, regression/Regression.doxy,
	  structure/Structure.doxy: let doxygen only scan .h files, ignore
	  *_wrap.h files, speeds things up tremendously
	* .generate_link_dependencies.py: add void deps to
	  clustering/CLustering_doxygen.i

2007-11-25  Soeren Sonnenburg <sonne@debian.org>

	* Makefile, clustering/Clustering.i: clustering should include
	  clustering stuff not classifiers... argh
	  cleanup Makefile
	* Makefile, configure: allow to disable doxygen python-modular doc
	  generation
	* Makefile: adjust make clean
	* classifier/Classifier.i, clustering/Clustering.i,
	  distance/Distance.i, distributions/Distribution.i,
	  features/Features.i, lib/Library.i, preproc/PreProc.i,
	  regression/Regression.i, structure/Structure.i: USE -> HAVE
	* .doxy2swig.py, .generate_link_dependencies.py, Makefile,
	  classifier/Classifier.doxy, classifier/Classifier.i,
	  clustering/Clustering.doxy, clustering/Clustering.i, configure,
	  distance/Distance.doxy, distance/Distance.i,
	  distributions/Distribution.doxy, distributions/Distribution.i,
	  features/Features.doxy, features/Features.i, kernel/Kernel.doxy,
	  kernel/Kernel.i, lib/Library.doxy, lib/Library.i,
	  preproc/PreProc.doxy, preproc/PreProc.i,
	  regression/Regression.doxy, regression/Regression.i,
	  structure/Structure.doxy, structure/Structure.i: add build logic
	  for shogun w/ doxyfile
	* configure: argh, fix typo
	* .doxy2swig.py, Makefile, NEWS, configure: OK, the roadmap to
	  0.5.0 is clear, we aim for a complete test suite for
	  python-modular and doxygen online help in python (from cmdline),
	  doxygen
	  documentation and examples
	  
	  - first steps to autodetect makefile/build depency integreation
	  for doxygen
	* kernel/CustomKernel.cpp, kernel/CustomKernel.h,
	  kernel/CustomKernel.i, lib/Mathematics.h: fixes for custom
	  kernel, potentially needs adjustments in other interfaces

2007-11-24  Sebastian Henschel <shogun@kodeaffe.de>

	* kernel/CustomKernel.cpp, kernel/CustomKernel.h: Added testing for
	  Custom kernel, while bugfixing and cleaning it. The testdata
	  looks weird, though, and has to be investigated further.

2007-11-24  Soeren Sonnenburg <sonne@debian.org>

	* features/StringFeatures.h: fix a compile warning

2007-11-23  Sebastian Henschel <shogun@kodeaffe.de>

	* features/StringFeatures.i: Added CommUlongStringKernel for
	  testing.
	* distance/Canberra.i: Added a first testcase for Distance kernel
	  with one Distance and broke
	  out some stuff into more modules in the test generator.
	  (unsorted Python dicts are annoying in file names, hence the long
	  list of
	  changed data files)

2007-11-23  Soeren Sonnenburg <sonne@debian.org>

	* .authors: add Christoph Lampert to authors
	* NEWS, clustering/Hierarchical.cpp, clustering/Hierarchical.h,
	  clustering/KMeans.h: fix dates
	* classifier/svm/libocas.cpp, classifier/svm/libocas.h,
	  classifier/svm/qpssvmlib.cpp, classifier/svm/qpssvmlib.h: fill in
	  copyright information

2007-11-23  Sebastian Henschel <shogun@kodeaffe.de>

	* guilib/GUIDistance.cpp: More Manhatten->Manhattan changes.

2007-11-23  Soeren Sonnenburg <sonne@debian.org>

	* kernel/ManhattanWordKernel.i: include should not be needed

2007-11-23  Sebastian Henschel <shogun@kodeaffe.de>

	* base/SGObject.h, base/SGObject.i, features/Features.cpp,
	  kernel/CombinedKernel.cpp, kernel/Kernel.cpp: Added/changed debug
	  stuff which seemed helpful in finding fix mentioned in
	  previous check-in.

2007-11-23  Soeren Sonnenburg <sonne@debian.org>

	* lib/List.h: don't call delete but SG_UNREF for swig interface in
	  list, should fix double free w/ combined kernel

2007-11-21  Sebastian Henschel <shogun@kodeaffe.de>

	* features/StringFeatures.h: While unsuccesfully finding a way to
	  handle typemaps and templates properly in
	  features/StringFeatures.i, found and fixed a segfault in
	  features/StringFeatures.h:get_string.

2007-11-21  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, guilib/GUIPython.cpp: fix building of python interface
	  update NEWS for new release

2007-11-20  Sebastian Henschel <shogun@kodeaffe.de>

	* kernel/AUCKernel.cpp, kernel/Kernel.h: Added ASSERTs to prevent
	  AUC kernel from segfaulting when subkernel is not
	  properly initialised; also added similar ASSERTs to
	  kernel/Kernel.h:kernel().

2007-11-20  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/LibSVM.cpp: fix memory leak in libsvm wrapper as
	  reported by alexander binder

2007-11-19  Soeren Sonnenburg <sonne@debian.org>

	* distance/Distance.i, distance/RealDistance.i,
	  distance/SparseDistance.i, kernel/CombinedKernel.cpp,
	  kernel/CombinedKernel.h: - don't forget to SG_UNREF kernels in
	  CombinedKernel on deletion
	  - add sparse distance
	  - add debug code to analyse double free in combined kernel
	* features/RealFeatures.cpp, features/RealFeatures.h,
	  guilib/GUIKernel.cpp, kernel/Kernel.cpp, kernel/Kernel.i,
	  kernel/ManhattanWordKernel.cpp, kernel/ManhattanWordKernel.h,
	  kernel/ManhattanWordKernel.i, kernel/ManhattenWordKernel.cpp,
	  kernel/ManhattenWordKernel.h, kernel/ManhattenWordKernel.i,
	  lib/Mathematics.cpp, lib/Mathematics.h, lib/common.h: manhattEn
	  -> manhattAn
	  move align function from realfeatures to mathematics

2007-11-18  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* guilib/GUIMatlab.cpp, structure/DynProg.cpp: reenabled a feature
	  that was disabled for optimization (but its still fast).
	* structure/DynProg.cpp: fix uninitialized memory reads.
	* structure/DynProg.cpp: two fixes of some previous
	  optimizations... :-|

2007-11-17  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* guilib/GUIMatlab.cpp, structure/DynProg.cpp, structure/DynProg.h:
	  Speedups for the Viterbi-algorithm.
	  Runs now about twice as fast and still gives the same results for
	  nbest=1.
	  Untestet for nbest>1.

2007-11-15  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* guilib/GUIMatlab.cpp, structure/DynProg.cpp, structure/DynProg.h,
	  structure/Plif.cpp: testing...

2007-11-15  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIMatlab.cpp, lib/Array.h, lib/Array2.h, lib/Array3.h,
	  structure/DynProg.cpp: argh! this is the
	  whydidntanyonenoticethisearlier-bug which must have been around
	  for almost a year...
	  
	  ASSERT was undefined in matlab interface... so THERE WAS NO ERROR
	  CHECKING

2007-11-14  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.h: now destroy tree then
	  recreate an empty one
	* classifier/svm/SVMOcas.h,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.cpp: really destroy the tree
	  after doing a full batch computation run, this should
	  especially help the wd* kernels when many of them are chained via
	  the combined
	  kernel to reduce memory usage

2007-11-13  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/DynProg.cpp: revert
	* kernel/CombinedKernel.cpp, structure/DynProg.cpp: fixed typo

2007-11-13  Soeren Sonnenburg <sonne@debian.org>

	* kernel/CombinedKernel.cpp: fix serious bug in output computation
	  which could occur only when a kernel
	  supporting batch computation was used in conjunction with a
	  kernel neither
	  capable of batch computation and linadd AND the number of threads
	  was > 1
	  
	  note that this may have lead to wrong svm - models on TRAINING if
	  svm lightwas
	  used and could also lead to random corruptions when computing
	  output via
	  classify

2007-11-13  Christoph Lampert <christoph.lampert@tuebingen.mpg.de>

	* guilib/GUIPython.cpp: fixed naming and type differences between
	  get_svm and set_svm

2007-11-12  Sebastian Henschel <shogun@kodeaffe.de>

	* features/StringFeatures.i, kernel/AUCKernel.cpp,
	  kernel/AUCKernel.h, kernel/CanberraWordKernel.cpp,
	  kernel/CanberraWordKernel.h, kernel/Chi2Kernel.cpp,
	  kernel/Chi2Kernel.h, kernel/Chi2Kernel.i,
	  kernel/CombinedKernel.cpp, kernel/CombinedKernel.h,
	  kernel/CommUlongStringKernel.cpp, kernel/CommUlongStringKernel.h,
	  kernel/CommWordStringKernel.cpp, kernel/CommWordStringKernel.h,
	  kernel/ConstKernel.cpp, kernel/ConstKernel.h,
	  kernel/CustomKernel.cpp, kernel/CustomKernel.h,
	  kernel/DiagKernel.cpp, kernel/DiagKernel.h,
	  kernel/DistanceKernel.cpp, kernel/DistanceKernel.h,
	  kernel/FixedDegreeStringKernel.cpp,
	  kernel/FixedDegreeStringKernel.h, kernel/GaussianKernel.cpp,
	  kernel/GaussianKernel.h, kernel/GaussianShiftKernel.cpp,
	  kernel/GaussianShiftKernel.h, kernel/HammingWordKernel.cpp,
	  kernel/HammingWordKernel.h, kernel/HistogramWordKernel.cpp,
	  kernel/HistogramWordKernel.h, kernel/Kernel.cpp, kernel/Kernel.h,
	  kernel/Kernel.i, kernel/KernelMachine.cpp,
	  kernel/KernelMachine.h, kernel/LinearByteKernel.cpp,
	  kernel/LinearByteKernel.h, kernel/LinearByteKernel.i,
	  kernel/LinearKernel.cpp, kernel/LinearKernel.h,
	  kernel/LinearKernel.i, kernel/LinearStringKernel.cpp,
	  kernel/LinearStringKernel.h, kernel/LinearWordKernel.cpp,
	  kernel/LinearWordKernel.h, kernel/LocalAlignmentStringKernel.cpp,
	  kernel/LocalAlignmentStringKernel.h,
	  kernel/LocalityImprovedStringKernel.cpp,
	  kernel/LocalityImprovedStringKernel.h,
	  kernel/ManhattenWordKernel.cpp, kernel/ManhattenWordKernel.h,
	  kernel/MindyGramKernel.cpp, kernel/MindyGramKernel.h,
	  kernel/PolyKernel.cpp, kernel/PolyKernel.h,
	  kernel/PolyMatchStringKernel.cpp, kernel/PolyMatchStringKernel.h,
	  kernel/PolyMatchWordKernel.cpp, kernel/PolyMatchWordKernel.h,
	  kernel/SalzbergWordKernel.cpp, kernel/SalzbergWordKernel.h,
	  kernel/SigmoidKernel.cpp, kernel/SigmoidKernel.h,
	  kernel/SimpleKernel.h, kernel/SimpleKernel.i,
	  kernel/SimpleLocalityImprovedStringKernel.cpp,
	  kernel/SimpleLocalityImprovedStringKernel.h,
	  kernel/SparseGaussianKernel.cpp, kernel/SparseGaussianKernel.h,
	  kernel/SparseKernel.h, kernel/SparseLinearKernel.cpp,
	  kernel/SparseLinearKernel.h, kernel/SparsePolyKernel.cpp,
	  kernel/SparsePolyKernel.h, kernel/StringKernel.h,
	  kernel/StringKernel.i, kernel/WeightedCommWordStringKernel.cpp,
	  kernel/WeightedCommWordStringKernel.h,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreePositionStringKernel.i,
	  kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.h,
	  kernel/WeightedDegreeStringKernel.i, kernel/WordMatchKernel.cpp,
	  kernel/WordMatchKernel.h: Primarily added constructor with
	  Features to each kernel.
	  Testing system has been vastly expanded by this, adding new
	  kernels and
	  their features.
	  Also cleaned up kernels' .h files and a bit .cpp files.

2007-11-12  Soeren Sonnenburg <sonne@debian.org>

	* features/Features.cpp, features/RealFeatures.cpp,
	  features/SimpleFeatures.h, kernel/Kernel.cpp: more %ld -> %p
	  pointer printing fixes
	* guilib/GUIKernel.cpp: use %p to print pointers

2007-11-11  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* guilib/GUIKernel.cpp: fix
	* guilib/GUIKernel.cpp: Implemented matlab interface for
	  GaussianShift kernel.
	  (untested)

2007-11-09  Soeren Sonnenburg <sonne@debian.org>

	* features/Labels.cpp, guilib/GUIKernel.cpp, kernel/Chi2Kernel.cpp,
	  kernel/Chi2Kernel.h, kernel/GaussianKernel.cpp,
	  kernel/GaussianKernel.h: fix Chi2 kernel / 2class label test bug
	  reported by Christoph Lampert
	* classifier/svm/GPBTSVM.cpp, classifier/svm/LibLinear.cpp,
	  classifier/svm/LibSVM.cpp, classifier/svm/SVMOcas.cpp,
	  classifier/svm/SVM_light.cpp, features/Labels.cpp,
	  features/Labels.h, kernel/Kernel.cpp, lib/common.h: - make all
	  svms check that they indeed get a +1/-1 labeling bug reported by
	  Sebastian Hensche - thanks!
	  - update kernel name printing / fix duplicate id, reported by
	  Christoph Lampert

2007-11-03  Soeren Sonnenburg <sonne@debian.org>

	* Makefile: argh, fix C C++ mixup on make depend / fixes
	  python-modular build
	* Makefile, configure, guilib/GUIClassifier.cpp,
	  kernel/KernelMachine.cpp: Use gcc -MM now to generate
	  dependencies (and fall back to makedepend if gcc
	  is not available). This has the big advantage that we generate
	  dependencies
	  only for non-system header files and that gcc knows all the
	  preprocessor
	  macros and we don't need makedepend anymore :)
	  
	  Finally enable batch computation/linadd in kernelmachines by
	  default

2007-11-02  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM_light.cpp, classifier/svm/ssl.cpp, configure,
	  lib/Mathematics.h, lib/Signal.cpp, regression/svr/SVR_light.cpp:
	  - check for existance of log2 in a more principled way + add fall
	  back
	  - add support for Interix based on patches provided by S V N
	  Vishwanathan

2007-10-30  Sebastian Henschel <shogun@kodeaffe.de>

	* features/Alphabet.h: as it turned out, failed testing of a
	  CommonWordString kernel with
	  matlab was _NOT_ due to an error in guilib/ or features/, the
	  error was
	  in the matlab code which tried to convert the training features
	  twice,
	  instead of using the test features. *sigh*
	* features/Alphabet.h: blob of things in the regression tests; sort
	  of first getting in touch
	  with it and finding bugs.
	  mainly moved generator and generated mfiles into testsuite/ and
	  added/implemented some tests for matlab. some tests still do not
	  run
	  through, though.
	* lib/Mathematics.cpp: added display_vector for long long int

2007-10-29  Soeren Sonnenburg <sonne@debian.org>

	* kernel/CanberraWordKernel.cpp, kernel/CanberraWordKernel.h,
	  kernel/Chi2Kernel.cpp, kernel/Chi2Kernel.h,
	  kernel/CommWordStringKernel.cpp, kernel/CommWordStringKernel.h,
	  kernel/DiagKernel.cpp, kernel/DiagKernel.h,
	  kernel/DistanceKernel.cpp, kernel/DistanceKernel.h,
	  kernel/FixedDegreeStringKernel.cpp,
	  kernel/FixedDegreeStringKernel.h, kernel/HammingWordKernel.cpp,
	  kernel/HammingWordKernel.h, kernel/HistogramWordKernel.cpp,
	  kernel/HistogramWordKernel.h, kernel/LinearByteKernel.cpp,
	  kernel/LinearByteKernel.h, kernel/LinearWordKernel.cpp,
	  kernel/LinearWordKernel.h,
	  kernel/LocalityImprovedStringKernel.cpp,
	  kernel/LocalityImprovedStringKernel.h,
	  kernel/ManhattenWordKernel.cpp, kernel/ManhattenWordKernel.h,
	  kernel/PolyMatchWordKernel.cpp, kernel/PolyMatchWordKernel.h,
	  kernel/SalzbergWordKernel.cpp, kernel/SalzbergWordKernel.h,
	  kernel/SigmoidKernel.cpp, kernel/SigmoidKernel.h,
	  kernel/WeightedCommWordStringKernel.cpp,
	  kernel/WeightedCommWordStringKernel.h,
	  kernel/WordMatchKernel.cpp, kernel/WordMatchKernel.h: megabytes
	  -> INT
	* configure, kernel/Kernel.h, kernel/PolyKernel.cpp,
	  kernel/PolyKernel.h: make size the last argument with default=10

2007-10-27  Sebastian Henschel <shogun@kodeaffe.de>

	* configure: needed to add include of GCC header files on Debian
	  (pre)lenny amd64 to make it compile
	* configure: little bugfix: extra includes should be appended by
	  '-I', not '-L'

2007-10-26  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVMOcas.cpp: avoid a couple of (useless) memory
	  init's / copies

2007-10-25  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVMOcas.cpp, classifier/svm/SVMOcas.h,
	  classifier/svm/libocas.cpp, gui/TextGUI.cpp,
	  guilib/GUIClassifier.cpp, guilib/GUIClassifier.h,
	  guilib/GUICommands.h: finally - ocas works

2007-10-25  Vojtech Franc <fravoj@first.fraunhofer.de>

	* classifier/svm/SVMOcas.cpp, classifier/svm/libocas.cpp: addgin
	  debug code

2007-10-25  Soeren Sonnenburg <sonne@debian.org>

	* .authors, base/SGObject.h, classifier/LDA.h,
	  classifier/LinearClassifier.h, lib/Mathematics.h,
	  preproc/NormOne.cpp: add mr. kodeaffe to list of authors + minor
	  code edits we spotted while talking about the source

2007-10-24  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVMOcas.cpp, classifier/svm/SVMOcas.h: one bug
	  less...

2007-10-24  Vojtech Franc <fravoj@first.fraunhofer.de>

	* classifier/svm/SVMOcas.cpp, features/SparseFeatures.h: fixed some
	  of the bugs

2007-10-24  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVMOcas.cpp, classifier/svm/SVMOcas.h,
	  classifier/svm/libocas.cpp, classifier/svm/libocas.h,
	  classifier/svm/libocas_common.h, classifier/svm/qpssvmlib.cpp,
	  classifier/svm/qpssvmlib.h, features/SparseFeatures.h, lib/io.h:
	  debugging ocas

2007-10-24  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* lib/common.h:
	* lib/common.h, structure/DynProg.cpp, structure/DynProg.h: some
	  timing routines and speedups for DynProg.

2007-10-23  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVMOcas.cpp, classifier/svm/SVMOcas.h,
	  classifier/svm/libocas.cpp, classifier/svm/libocas.h,
	  classifier/svm/libocas_common.h, classifier/svm/qpssvmlib.cpp,
	  classifier/svm/qpssvmlib.h, guilib/GUIClassifier.cpp,
	  lib/Mathematics.h: start integration of libocas
	  (avoiding code duplication/resyncs between ocas/shogun)

2007-10-22  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVMOcas.cpp, lib/Mathematics.h, lib/common.h:
	  compile fix:
	  static classes cannot access dynamic class members,
	  thus make number of threads an argument to paraaaallel qsort

2007-10-22  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* kernel/GaussianShiftKernel.cpp, kernel/GaussianShiftKernel.h,
	  kernel/GaussianShiftKernel.i, kernel/Kernel.i: added the
	  GaussianShiftKernel. Could not test it.
	  Hope it works.

2007-10-21  Soeren Sonnenburg <sonne@debian.org>

	* classifier/SparseLinearClassifier.i, classifier/svm/SVMOcas.cpp,
	  classifier/svm/SVMOcas.h, classifier/svm/SVMOcas.i,
	  classifier/svm/SVMPerf.cpp, classifier/svm/SVMPerf.h,
	  classifier/svm/SVMPerf.i, classifier/svm/qpssvmlib.cpp,
	  classifier/svm/qpssvmlib.h, features/SparseFeatures.h,
	  guilib/GUIClassifier.cpp, lib/Mathematics.cpp, lib/Mathematics.h,
	  lib/common.h: dysfunctional inital merge-try of SVMOcas

2007-10-18  Konrad Rieck <Konrad.Rieck@first.fraunhofer.de>

	* features/MindyGramFeatures.cpp, features/MindyGramFeatures.h,
	  guilib/GUIFeatures.h, kernel/MindyGramKernel.cpp: added support
	  for faster gram addition

2007-10-18  Soeren Sonnenburg <sonne@debian.org>

	* lib/python_typemaps.i: fix a major memory leak (occured for all
	  functions returning arrays to python)
	  we still need some interface polishing here, i.e.
	  
	  1. the array is malloc'd in the python typemaps
	  2. the C++ functions fill in content
	  
	  or
	  
	  1. the C++ functions just return pointers to objects
	  2. in the python typemaps the array is malloc'd and content is
	  copied from
	  the C++ functions

2007-10-17  Soeren Sonnenburg <sonne@debian.org>

	* Makefile, configure: add example for shogun's new library
	  interface - libshogun

2007-10-14  Soeren Sonnenburg <sonne@debian.org>

	* features/Features.cpp, features/StringFeatures.h,
	  kernel/CommWordStringKernel.cpp, kernel/Kernel.cpp: - fix a
	  memory leak in python modular interface (occurring with any
	  kernel)
	  - remove some debug code

2007-10-10  Soeren Sonnenburg <sonne@debian.org>

	* NEWS: prepare for release 0.4.3

2007-10-09  Soeren Sonnenburg <sonne@debian.org>

	* lib/Mathematics.h: add insertion sort

2007-10-04  Soeren Sonnenburg <sonne@debian.org>

	* lib/Trie.cpp: code cleanup in obtaining w - no function change

2007-09-28  Soeren Sonnenburg <sonne@debian.org>

	* features/Alphabet.cpp: fix warnings
	* configure, features/Alphabet.cpp, features/Alphabet.h,
	  features/StringFeatures.h, features/StringFeatures.i,
	  guilib/GUIMatlab.cpp, kernel/CommWordStringKernel.h,
	  kernel/WeightedCommWordStringKernel.cpp,
	  kernel/WeightedCommWordStringKernel.h: * allow building with
	  custom cc settings and add option to disable cpu detection
	  * adjust R build system
	  * fix weighted commword kernel (normalization was wrong due to
	  change in
	  commword kernel) and add support for sliding window init

2007-09-25  Soeren Sonnenburg <sonne@debian.org>

	* classifier/SubGradientLPM.cpp, lib/Trie.cpp: - this should fix a
	  boundary bug in poim computation
	  - compile fix when cplex is available

2007-09-19  Soeren Sonnenburg <sonne@debian.org>

	* gui/R.cpp, guilib/GUIR.cpp, kernel/Kernel.cpp, lib/Mathematics.h,
	  lib/io.cpp: compile fixes for R/python-modular/python
	* ChangeLog: Preparing for new Release shogun_0.4.2
	* NEWS, clustering/Hierarchical.cpp, clustering/KMeans.cpp,
	  lib/common.h: - make svn-tag-release now does a whole release
	  (just make sure src/NEWS is updated)
	  - minor clustering fixes

2007-09-13  Soeren Sonnenburg <sonne@debian.org>

	* classifier/KNN.cpp, classifier/svm/SubGradientSVM.cpp,
	  clustering/Hierarchical.cpp, clustering/Hierarchical.h,
	  distance/Chebyshew.cpp, distance/Distance.h, gui/Matlab.cpp,
	  guilib/GUIClassifier.cpp, guilib/GUICommands.h,
	  guilib/GUIMatlab.cpp, guilib/GUIMatlab.h, lib/Mathematics.h,
	  structure/DynProg.cpp: hierarchical clustering works now

2007-09-12  Soeren Sonnenburg <sonne@debian.org>

	* clustering/Hierarchical.cpp, clustering/Hierarchical.h,
	  distance/NormSquaredDistance.cpp, guilib/GUIClassifier.cpp,
	  lib/Mathematics.h: still debugging hierarchical clustering
	* clustering/Clustering.i, clustering/Hierarchical.cpp,
	  clustering/Hierarchical.h, clustering/Hierarchical.i,
	  clustering/KMeans.h, guilib/GUIClassifier.cpp, lib/Mathematics.h,
	  lib/common.h: add aggregative single linkage hierarchical
	  clustering (to be debugged)

2007-09-11  Soeren Sonnenburg <sonne@debian.org>

	* classifier/KNN.h, clustering/KMeans.cpp, clustering/KMeans.h,
	  distributions/hmm/HMM.cpp, guilib/GUIClassifier.cpp,
	  lib/Mathematics.h: fix clustering and random number generation
	  for INT/DREAL
	* NEWS, clustering/KMeans.cpp, clustering/KMeans.h,
	  guilib/GUIClassifier.cpp, guilib/GUIClassifier.h,
	  guilib/GUIMatlab.cpp: add get_classifier support for KMeans and
	  radius estimate fixes
	* classifier/KNN.h, clustering, clustering/Clustering.i,
	  clustering/KMeans.cpp, clustering/KMeans.h, clustering/KMeans.i,
	  distance/Distance.i, distance/NormSquaredDistance.cpp,
	  distance/NormSquaredDistance.h, distance/NormSquaredDistance.i,
	  distance/SparseDistance.h,
	  distance/SparseNormSquaredDistance.cpp,
	  distance/SparseNormSquaredDistance.h,
	  distance/SparseNormSquaredDistance.i, guilib/GUIClassifier.cpp,
	  guilib/GUIClassifier.h, guilib/GUIDistance.cpp,
	  guilib/GUIDistance.h, guilib/GUIKernel.cpp, kernel/Kernel.i,
	  kernel/SparseNormSquaredKernel.cpp,
	  kernel/SparseNormSquaredKernel.h,
	  kernel/SparseNormSquaredKernel.i, lib/common.h: add clustering
	  methods support

2007-09-05  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIMatlab.cpp,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.h, lib/Trie.cpp, lib/Trie.h:
	  convert Trie to template and add DNATrie, POIMTrie as examples;
	  this is to not require the WDS kernel to use 24 extra bytes per
	  node
	* base/Version.cpp, base/Version.h, gui/Python.cpp,
	  guilib/GUIPython.cpp, kernel/LocalAlignmentStringKernel.cpp,
	  lib/Trie.cpp, lib/Trie.h: use INT idx in Trie
	  fix compile warnings (gcc4.2 warns about const char*)
	* kernel/WeightedDegreePositionStringKernel.cpp, lib/Trie.cpp,
	  lib/Trie.h: POIMs work...!

2007-09-03  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/LibLinear.cpp, classifier/svm/LibLinear.h,
	  classifier/svm/SVM_linear.cpp, classifier/svm/SVM_linear.h,
	  classifier/svm/Tron.cpp, classifier/svm/Tron.h,
	  guilib/GUIClassifier.cpp: fix compilation with --disable-lapack

2007-08-31  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog: release 0.4.1
	* CONTRIBUTIONS, NEWS, guilib/GUIMatlab.cpp, kernel/AUCKernel.cpp,
	  kernel/GaussianKernel.i, kernel/KernelMachine.i,
	  kernel/LinearByteKernel.h, kernel/SimpleKernel.i, lib/Trie.h:
	  cleanups, prepare for release 0.4.1
	* classifier/SubGradientLPM.i: subgradlpm interface file
	* classifier/LPBoost.i, classifier/SparseLinearClassifier.i,
	  classifier/svm/LibLinear.i, classifier/svm/MPD.i,
	  kernel/CanberraWordKernel.i, kernel/HammingWordKernel.i,
	  kernel/ManhattenWordKernel.i: add missing interface files

2007-08-30  Alexander Zien <Alexander.Zien@tuebingen.mpg.de>

	* guilib/GUIMatlab.cpp,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h, lib/Trie.cpp,
	  lib/Trie.h: POIMS: Enabled to output partial scores, to aid
	  debugging.

2007-08-29  Soeren Sonnenburg <sonne@debian.org>

	* gui/Matlab.cpp, guilib/GUIMatlab.cpp, guilib/GUIMatlab.h,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h: add support for
	  POIMs and custom distributions
	* distributions/histogram/Histogram.cpp, gui/Matlab.cpp,
	  gui/Octave.cpp, gui/Python.cpp, gui/R.cpp, gui/TextGUI.cpp,
	  guilib/GUICommands.h: move all the commands into a common header
	  file GUICommands.h

2007-08-29  Alexander Zien <Alexander.Zien@tuebingen.mpg.de>

	* kernel/WeightedDegreePositionStringKernel.cpp, lib/Trie.cpp,
	  lib/Trie.h:

2007-08-28  Soeren Sonnenburg <sonne@debian.org>

	* gui/Matlab.cpp, guilib/GUIMatlab.cpp, guilib/GUIMatlab.h: get
	  normal support

2007-08-28  Alexander Zien <Alexander.Zien@tuebingen.mpg.de>

	* kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h:

2007-08-24  Alexander Zien <Alexander.Zien@tuebingen.mpg.de>

	* kernel/WeightedDegreePositionStringKernel.cpp:
	* kernel/WeightedDegreePositionStringKernel.cpp, lib/Trie.cpp:

2007-08-24  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIKernel.cpp: add POS2_NONORM kernel
	* classifier/svm/LibLinear.cpp, classifier/svm/SVM_linear.cpp,
	  classifier/svm/SVM_linear.h: avoid copying and directly use
	  SparseFeatures<DREAL> in liblinear

2007-08-23  Alexander Zien <Alexander.Zien@tuebingen.mpg.de>

	* kernel/WeightedDegreePositionStringKernel.cpp, lib/Trie.cpp,
	  lib/Trie.h:

2007-08-23  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVMLin.cpp, classifier/svm/Tron.cpp: finally fix
	  SVMLin+liblinear
	* kernel/WeightedDegreePositionStringKernel.cpp: build whole
	  tree...

2007-08-22  Soeren Sonnenburg <sonne@debian.org>

	* regression/KRR.cpp: test whether kernel is inited on train()
	* gui/Matlab.cpp, guilib/GUIMatlab.cpp, guilib/GUIMatlab.h,
	  kernel/WeightedDegreePositionStringKernel.cpp, lib/Trie.h: add
	  compute_poim_wd test script/matlab interface access function

2007-08-22  Alexander Zien <Alexander.Zien@tuebingen.mpg.de>

	* lib/Trie.cpp:
	* kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h, lib/Trie.cpp,
	  lib/Trie.h:

2007-08-22  Soeren Sonnenburg <sonne@debian.org>

	* classifier/LinearClassifier.i,
	  classifier/SparseLinearClassifier.i,
	  classifier/svm/LibLinear.cpp, classifier/svm/SVMLin.cpp,
	  classifier/svm/SVMLin.h, classifier/svm/SVM_linear.cpp,
	  classifier/svm/Tron.cpp, classifier/svm/Tron.h,
	  classifier/svm/ssl.cpp, kernel/CustomKernel.cpp,
	  kernel/CustomKernel.h, kernel/CustomKernel.i: - add
	  python-modular support for the custom kernel
	  - lots of fixes for SVMLin / Liblinear

2007-08-21  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVMLin.cpp, classifier/svm/SVMLin.h,
	  classifier/svm/ssl.cpp, classifier/svm/ssl.h, configure,
	  guilib/GUIClassifier.cpp: fix typo in configure
	  add option to disable bias in svmlin bias

2007-08-21  Alexander Zien <Alexander.Zien@tuebingen.mpg.de>

	* kernel/WeightedDegreePositionStringKernel.POIM.cpp,
	  lib/Trie.POIM.cpp, lib/Trie.POIM.h, lib/Trie.cpp, lib/Trie.h:

2007-08-21  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIClassifier.cpp, lib/io.cpp: fix the python
	  examples/python io

2007-08-20  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/LibLinear.cpp, classifier/svm/LibLinear.h,
	  classifier/svm/SVM_linear.cpp, classifier/svm/SVM_linear.h,
	  classifier/svm/Tron.cpp, features/SparseFeatures.h,
	  guilib/GUIClassifier.cpp, guilib/GUIMatlab.cpp: add liblinear L2
	  / LR support including example. currently data is internally
	  copied, more intrusive changes to liblinear are required to fix
	  this:
	  
	  ( liblinear uses 1-based indices and terminates sparse vectors
	  with -1,
	  additionally a 'bias feature' may need to be added )

2007-08-17  Soeren Sonnenburg <sonne@debian.org>

	* features/StringFeatures.h, gui/Matlab.cpp,
	  guilib/GUIFeatures.cpp, guilib/GUIMatlab.cpp: add support for
	  sliding window 'skip' option, which skips the first
	  n characters of the generated string (same thing as when using
	  convert
	  to do higher oder conversions)
	  
	  e.g. if you use:
	  sg('send_command', sprintf('convert TEST STRING CHAR STRING WORD
	  %i %i', order, order-1));
	  
	  then for a window len of 50 the order-1 chars should be skipped:
	  sg('send_command', sprintf('slide_window TEST 50 1 %d',
	  order-1));
	  
	  sg('from_position_list','TEST', 50,
	  0:(total_test_len-len-order+1), order-1);
	* guilib/GUIFeatures.cpp, guilib/GUIMatlab.cpp,
	  kernel/CommWordStringKernel.cpp, kernel/CommWordStringKernel.h,
	  kernel/WeightedCommWordStringKernel.cpp,
	  kernel/WeightedCommWordStringKernel.h: - add matlab support for
	  get features of type string/word
	  - make POIMs work with weighted spec kernel
	  - fix further issues with sliding window/spec (works for order=1
	  now)

2007-08-17  Alexander Zien <Alexander.Zien@tuebingen.mpg.de>

	* kernel/WeightedDegreePositionStringKernel.POIM.cpp,
	  lib/Trie.POIM.cpp, lib/Trie.POIM.h:

2007-08-17  Soeren Sonnenburg <sonne@debian.org>

	* features/StringFeatures.h, kernel/CommWordStringKernel.cpp,
	  kernel/CommWordStringKernel.h,
	  kernel/WeightedCommWordStringKernel.cpp,
	  kernel/WeightedCommWordStringKernel.h, lib/Mathematics.cpp,
	  lib/Mathematics.h, preproc/SortUlongString.cpp,
	  preproc/SortWord.cpp, preproc/SortWordString.cpp: add radix sort
	  and make it the new default for spec* kernels, furthermore
	  add checks for spec kernel compute (whether all preprocs attached
	  to features
	  are actually applied). then also sort the the features when doing
	  init
	  (potentially resolving the problem with sliding window/spec
	  kernel)

2007-08-16  Soeren Sonnenburg <sonne@debian.org>

	* kernel/CommWordStringKernel.cpp: remove debug code
	* kernel/CommWordStringKernel.cpp: POIM for spec bugfixes

2007-08-16  Konrad Rieck <Konrad.Rieck@first.fraunhofer.de>

	* features/MindyGramFeatures.h, kernel/MindyGramKernel.cpp,
	  kernel/MindyGramKernel.h: removed several minor but fatal bugs in
	  Mindy distance to kernel mapping. In essence either use RBF
	  conversion or check that the distance is a negative CPD kernel.

2007-08-15  Soeren Sonnenburg <sonne@debian.org>

	* lib/Trie.h: new trie fields
	* classifier/svm/SubGradientSVM.cpp: rename A0 -> A_zero , B0 ->
	  B_zero as there seems to be some
	  naming collision with numpy
	* kernel/CommWordStringKernel.cpp: fix R svm example/enhance matlab
	  veriant
	  debugging spec poims

2007-08-13  Konrad Rieck <Konrad.Rieck@first.fraunhofer.de>

	* features/MindyGramFeatures.cpp, features/MindyGramFeatures.h,
	  kernel/MindyGramKernel.h: added support for latest Mindy library

2007-08-08  Soeren Sonnenburg <sonne@debian.org>

	* kernel/CommWordStringKernel.cpp: removed debug code/make toy
	  example more convincing

2007-08-07  Soeren Sonnenburg <sonne@debian.org>

	* kernel/CommWordStringKernel.cpp: spectrum poim seems to work...
	* features/Alphabet.cpp, kernel/LocalAlignmentStringKernel.cpp,
	  kernel/LocalAlignmentStringKernel.h: - protein alphabet is now
	  (as all the others) only UPPERCASE
	  - add example for LA kernel
	* guilib/GUIKernel.cpp, kernel/CommWordStringKernel.cpp,
	  kernel/Kernel.i, kernel/LocalAlignmentStringKernel.cpp,
	  kernel/LocalAlignmentStringKernel.h,
	  kernel/LocalAlignmentStringKernel.i, lib/common.h: add support
	  for JP's local alignment kernel
	* classifier/svm/Tron.cpp, gui/Matlab.cpp, guilib/GUIMatlab.cpp,
	  guilib/GUIMatlab.h, kernel/CommWordStringKernel.cpp,
	  kernel/CommWordStringKernel.h,
	  kernel/WeightedDegreePositionStringKernel.cpp, lib/Mathematics.h:
	  add function to compute POIM from spectrum kernel

2007-08-06  Soeren Sonnenburg <sonne@debian.org>

	* CONTRIBUTIONS, classifier/svm/LibLinear.cpp,
	  classifier/svm/LibLinear.h, classifier/svm/SVM_linear.cpp,
	  classifier/svm/SVM_linear.h, classifier/svm/Tron.cpp,
	  classifier/svm/Tron.h, guilib/GUIClassifier.cpp, lib/common.h:
	  add Xiang-Rui Wang and Chih-Jen Lin's
	  liblinear (for LS-logistic regression / L2 svm)

2007-08-03  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIFeatures.cpp, guilib/GUIMatlab.cpp: add support for
	  BYTE/WORD/ULONG based stringfeatures for sliding
	  window/position list

2007-08-02  Soeren Sonnenburg <sonne@debian.org>

	* features/StringFeatures.h: potentially fix the erraneous delete[]
	  happening after calling from_window_list

2007-07-31  Soeren Sonnenburg <sonne@debian.org>

	* kernel/Kernel.h: fix compilation with --disable-svm-light

2007-07-30  Soeren Sonnenburg <sonne@debian.org>

	* configure, lib/Cplex.h: cplex 10 compat fixes as suggested by
	  Gorden Jemwa
	* Makefile: merge changes from 0.4.0
	* ChangeLog, Makefile: release 0.4.0
	* ChangeLog: update changelog
	* configure: set default gcc first
	* configure: forgotten break in pthread detection
	* configure: some cygwin/solaris configure fixes
	  
	  (though it still won't compile using solaris' compiler as it does
	  not support
	  dynamic argument macros)

2007-07-29  Soeren Sonnenburg <sonne@debian.org>

	* configure: remove undefined suppress from configure
	* base/Version.cpp, base/Version.h, classifier/svm/LibSVM.cpp,
	  classifier/svm/SVM_light.cpp: fix the remaining python-modular
	  interface examples

2007-07-28  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIOctave.cpp: fix get_svm for octave
	* kernel/CommWordStringKernel.cpp, kernel/CommWordStringKernel.h,
	  kernel/WeightedCommWordStringKernel.cpp: * argh, fix bug in spec
	  kernels: normalize functions needs lhs on add_to_normal
	  and rhs on compute optimized
	* classifier/Classifier.h, guilib/GUIClassifier.cpp: fix oneclass
	  svm bug

2007-07-27  Soeren Sonnenburg <sonne@debian.org>

	* classifier/KNN.h, classifier/Perceptron.h,
	  classifier/SubGradientLPM.h, classifier/svm/CPLEXSVM.h,
	  classifier/svm/GMNPSVM.h, classifier/svm/GNPPSVM.h,
	  classifier/svm/GPBTSVM.h, classifier/svm/LibSVM.h,
	  classifier/svm/LibSVM_multiclass.h,
	  classifier/svm/LibSVM_oneclass.h, classifier/svm/MPD.h,
	  classifier/svm/SVMLin.h, classifier/svm/SVMPerf.h,
	  classifier/svm/SVM_light.h, classifier/svm/SubGradientSVM.h,
	  guilib/GUIClassifier.cpp, guilib/GUIKernel.cpp,
	  guilib/GUIOctave.cpp, lib/Trie.cpp, lib/common.h,
	  regression/svr/LibSVR.h, regression/svr/SVR_light.h: * fix many
	  of the script errors for matlab/octave,
	  currently crashing: test_one_class_svm.m test_complex_scenario.m
	* guilib/GUIPython.cpp, kernel/Kernel.i: * fix compilation error in
	  old python interfacew
	  * fix warning in new python interface
	* NEWS, kernel/FixedDegreeStringKernel.i,
	  kernel/LocalityImprovedStringKernel.i: * update NEWS
	  * fix remaining CharKernel occurances

2007-07-23  Soeren Sonnenburg <sonne@debian.org>

	* features/StringFeatures.h, kernel/CommWordStringKernel.cpp,
	  kernel/CommWordStringKernel.h,
	  kernel/WeightedCommWordStringKernel.cpp,
	  kernel/WeightedCommWordStringKernel.h: + add linadd functionality
	  + svm test case/example

2007-07-22  Soeren Sonnenburg <sonne@debian.org>

	* features/StringFeatures.h, guilib/GUIFeatures.h,
	  kernel/WeightedCommWordStringKernel.cpp: an example on how to use
	  the weighted spectrum kernel

2007-07-21  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedCommWordStringKernel.cpp,
	  kernel/WeightedCommWordStringKernel.h: - update octave example
	  - approaching the WDCWS kernel :-)
	* features/StringFeatures.h, guilib/GUIKernel.cpp,
	  guilib/GUIMatlab.cpp, kernel/CommWordKernel.cpp,
	  kernel/CommWordKernel.h, kernel/CommWordKernel.i,
	  kernel/Kernel.cpp, kernel/Kernel.i, kernel/SpectrumKernel.cpp,
	  kernel/SpectrumKernel.h, kernel/SpectrumKernel.i,
	  kernel/WeightedCommWordStringKernel.cpp,
	  kernel/WeightedCommWordStringKernel.h,
	  kernel/WeightedCommWordStringKernel.i, lib/common.h,
	  lib/suffixarray, preproc/SortWordString.cpp: - remove Spectrum
	  Kernel / suffix arrays due to licensing conflict (MPL vs. GPL)
	  - remove CommWord kernel
	  - add WeightedCommWordString Kernel

2007-07-12  Soeren Sonnenburg <sonne@debian.org>

	* base/SGObject.h: fix warning in base/SGObject

2007-07-11  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* lib/Mathematics.cpp: fixed minor compilation problem

2007-07-09  Soeren Sonnenburg <sonne@debian.org>

	* configure, guilib/GUIKernel.cpp, kernel/CommWordKernel.h,
	  kernel/LinearKernel.cpp, kernel/LinearKernel.h,
	  kernel/PolyKernel.cpp, kernel/PolyKernel.h,
	  kernel/SparseLinearKernel.cpp, kernel/SparseLinearKernel.h,
	  kernel/SparsePolyKernel.cpp, kernel/SparsePolyKernel.h: code
	  cleanup for sparse/linear kernels

2007-07-08  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* kernel/Kernel.cpp: added a missing case switch.

2007-06-18  Soeren Sonnenburg <sonne@debian.org>

	* configure: fix syntax error in configure
	* features/StringFeatures.h: split asserts and don't fail if string
	  is already a sling window
	  string and shorter than window len

2007-06-16  Soeren Sonnenburg <sonne@debian.org>

	* NEWS, base/Version.cpp, base/Version.h,
	  classifier/Classifier.cpp, configure, distributions/hmm/HMM.h,
	  gui/Matlab.cpp, guilib/GUIFeatures.cpp, guilib/GUIHMM.cpp,
	  kernel/WeightedDegreePositionStringKernel.cpp: gcc-4.2 warning
	  fixes

2007-06-07  Soeren Sonnenburg <sonne@debian.org>

	* classifier/SubGradientLPM.cpp, classifier/svm/SubGradientSVM.cpp:
	  implement time limit also for subgradientsvm/lpm
	* classifier/Classifier.cpp, classifier/Classifier.h,
	  classifier/LPBoost.cpp, classifier/LPM.cpp,
	  classifier/svm/SVM.cpp, classifier/svm/SVM.h,
	  guilib/GUIClassifier.cpp, lib/Cplex.cpp, lib/Cplex.h: allow
	  setting training time limit for LPM/LPBoost
	* classifier/SubGradientLPM.cpp, classifier/svm/SubGradientSVM.cpp:
	  use abs(alpha*norm(w)^2) ... note that with floats abs may be
	  negative
	  for values very close to zero
	* classifier/SubGradientLPM.cpp, classifier/svm/SubGradientSVM.cpp:
	  remove <1e-6
	* classifier/SubGradientLPM.cpp, classifier/svm/SubGradientSVM.cpp:
	  argh, need to use abs(alpha) in convergence crit. of course

2007-06-06  Soeren Sonnenburg <sonne@debian.org>

	* classifier/SubGradientLPM.cpp, classifier/SubGradientLPM.h,
	  classifier/svm/SubGradientSVM.cpp, guilib/GUIClassifier.cpp: use
	  speedups from subgradientsvm
	* classifier/LPBoost.cpp, lib/Cplex.cpp: don't allocate columns on
	  stack (fixes lpboost crash)
	* lib/Cplex.cpp: uncomment debug code
	* classifier/SubGradientLPM.cpp, classifier/svm/SubGradientSVM.cpp,
	  lib/Cplex.cpp, lib/Mathematics.cpp: use cplex result directly

2007-06-05  Soeren Sonnenburg <sonne@debian.org>

	* classifier/SubGradientLPM.cpp, lib/Cplex.cpp: still not 100% the
	  same
	* lib/Cplex.cpp: add further ASSERTS
	* classifier/SubGradientLPM.cpp, guilib/GUIClassifier.cpp,
	  lib/Cplex.cpp: subgradLPM works now on 2d toy data
	* classifier/SubGradientLPM.cpp, classifier/SubGradientLPM.h,
	  lib/Cplex.cpp, lib/Cplex.h: finding minimum subgradient seems to
	  work now... now for the line search
	* classifier/SubGradientLPM.cpp:
	* classifier/LPBoost.cpp, classifier/LPM.cpp,
	  classifier/SubGradientLPM.cpp, classifier/svm/CPLEXSVM.cpp,
	  classifier/svm/qpbsvmlib.cpp, lib/Cplex.cpp, lib/Cplex.h:
	  debuggin...

2007-06-04  Soeren Sonnenburg <sonne@debian.org>

	* classifier/SubGradientLPM.cpp, classifier/SubGradientLPM.h,
	  guilib/GUIClassifier.cpp, lib/Mathematics.h: still not even close
	* classifier/LPBoost.cpp, lib/Cplex.cpp, lib/Cplex.h: - fix lpboost
	  now for the subgradientlpm
	* classifier/LPBoost.cpp, classifier/SubGradientLPM.cpp,
	  classifier/SubGradientLPM.h, guilib/GUIClassifier.cpp,
	  lib/common.h: add stubs for SubGradientLPM
	* classifier/LPBoost.cpp, lib/Cplex.cpp: lpboost still not working
	  correctly...

2007-06-03  Soeren Sonnenburg <sonne@debian.org>

	* classifier/LPBoost.cpp, classifier/LPBoost.h, classifier/LPM.cpp,
	  classifier/LPM.h, classifier/svm/SVM_light.cpp,
	  classifier/svm/qpbsvmlib.cpp, guilib/GUIClassifier.cpp,
	  lib/Cplex.cpp, lib/Cplex.h: add lpboost code, I've yet to
	  understand how to obtain the result...
	* classifier/LPM.cpp, guilib/GUIClassifier.cpp, lib/Cplex.cpp,
	  lib/Mathematics.cpp, lib/Mathematics.h: LPM works now, now for
	  LPBoos
	* classifier/LPBoost.cpp, classifier/LPBoost.h, classifier/LPM.cpp,
	  classifier/LPM.h, features/SparseFeatures.h,
	  guilib/GUIClassifier.cpp, lib/Cplex.cpp, lib/Cplex.h: +
	  get_transpose() in sparse features
	  + wrap LPM
	* classifier/LPBoost.cpp, classifier/LPBoost.h, classifier/LPM.cpp,
	  classifier/LPM.h, guilib/GUIClassifier.cpp, lib/Cplex.cpp,
	  lib/Cplex.h, lib/common.h: +stubs for LPM/LPBoost, doing LPM now

2007-05-31  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h, guilib/GUIClassifier.cpp,
	  lib/Mathematics.h: still playing with convergence criterion
	* classifier/svm/SVM.cpp, classifier/svm/SVM.h,
	  classifier/svm/SVM_light.cpp, classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h, classifier/svm/pr_loqo.cpp,
	  gui/TextGUI.cpp, guilib/GUIClassifier.cpp,
	  guilib/GUIClassifier.h: add svm_use_bias option, and support in
	  svm_light/subgradient svm
	* classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h: option to disable bias

2007-05-30  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SubGradientSVM.cpp: playing with convergence
	  criterion

2007-05-29  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SubGradientSVM.cpp,
	  kernel/WeightedDegreeStringKernel.cpp: - fix early convergence of
	  subgradient svm
	  - fix double free in wd kernel

2007-05-28  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SubGradientSVM.cpp, lib/Cplex.cpp, lib/matlab.h:
	  forgot to check in matlab build fix:
	  
	  #if !defined(MX_API_VER) || MX_API_VER<0x07040000
	  
	  then define mwSize to be INT etc...

2007-05-25  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/GPBTSVM.cpp, classifier/svm/gpdt.h,
	  classifier/svm/gpdtsolve.cpp, classifier/svm/gpdtsolve.h,
	  classifier/svm/gpm.cpp, classifier/svm/gpm.h: -correct copyright
	  -add ctrl+c etc support to GPBTSVM
	* classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h, classifier/svm/qpbsvmlib.cpp,
	  guilib/GUIMatlab.cpp, lib/Cplex.cpp, lib/matlab.h: make sparse
	  matrices work with matlab 7.4
	* classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h, guilib/GUIMatlab.cpp,
	  lib/Mathematics.cpp: - fix & test get/set features for sparse
	  vectors
	  - cleanup get/set features for dense vec's (lets hope no bugs)
	  - subgradsvm: check for overlap between qp's
	* guilib/GUIMatlab.cpp:
	* guilib/GUIMatlab.cpp: add sparse matrix matalb i/o support

2007-05-24  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SubGradientSVM.cpp, classifier/svm/qpbsvmlib.cpp,
	  classifier/svm/qpbsvmlib.h: add gradient descent
	* classifier/svm/SubGradientSVM.cpp: compute only 1/2 of the Q
	  matrix
	* classifier/svm/SubGradientSVM.cpp, classifier/svm/qpbsvmlib.cpp,
	  lib/Mathematics.h: use gauss seidel by default
	* classifier/svm/qpbsvmlib.cpp, classifier/svm/qpbsvmlib.h:
	  implement greedy gauss seidel
	* classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h, gui/TextGUI.cpp,
	  guilib/GUIClassifier.cpp, guilib/GUIClassifier.h, lib/Cplex.cpp:
	  - let cplex timeout after 0.5 seconds
	  - option to set max qpsize in subgradientsvm
	* classifier/svm/gpdt.cpp, classifier/svm/gpdtsolve.cpp: update
	  gpbt svm to version nov 2006 (released in january 2007)

2007-05-23  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SubGradientSVM.cpp: - update subgradient svm
	  example
	  - fix objective comput. for subgradient svm
	  - introduce limit to qpsize. if we cannot solve the problem with
	  500 vectors at bound we choose a random but valid subgradient
	* features/SparseFeatures.h, guilib/GUIMatlab.cpp,
	  kernel/LinearKernel.cpp, kernel/LinearKernel.h,
	  kernel/SparseGaussianKernel.h, kernel/SparseLinearKernel.cpp,
	  kernel/SparseLinearKernel.h, lib/common.h: - assign seperate
	  types for sparselinear and sparsegaussian kernel
	  - support get_kernel_optimization for sparse linear kernel
	  
	  huh ?? gpbtsvm seems quite a bit faster than svmlight !!
	* classifier/svm/GPBTSVM.cpp, classifier/svm/gpdtsolve.cpp,
	  classifier/svm/gpdtsolve.h: linadd fix #1
	* classifier/svm/gpdt.h, classifier/svm/gpdtsolve.cpp: * enable
	  linadd for GPDT svm
	* classifier/svm/SubGradientSVM.h, guilib/GUIClassifier.cpp: make
	  qpsize configurable

2007-05-22  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/qpbsvmlib.cpp, lib/Cplex.cpp, lib/Cplex.h: remove
	  debug output & cleanups
	* classifier/svm/SubGradientSVM.cpp, classifier/svm/qpbsvmlib.cpp,
	  lib/Cplex.cpp: muten subgrad svm
	* classifier/svm/SubGradientSVM.cpp, classifier/svm/qpbsvmlib.cpp,
	  lib/Cplex.cpp: ...debugging...
	* lib/Cplex.cpp: potential cplex fix
	* classifier/svm/SubGradientSVM.cpp, classifier/svm/qpbsvmlib.cpp,
	  lib/Cplex.cpp, lib/Cplex.h, lib/Mathematics.cpp,
	  lib/Mathematics.h: debugging...
	* classifier/svm/SubGradientSVM.cpp, classifier/svm/qpbsvmlib.cpp,
	  lib/Cplex.cpp: cplex dense_to_cplex_sparse fix

2007-05-21  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/CPLEXSVM.cpp, classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h, classifier/svm/qpbsvmlib.cpp,
	  classifier/svm/qpbsvmlib.h, lib/Cplex.cpp, lib/Cplex.h: - add lp
	  and qp wrappers for cplex
	  - add cplex as a method in qpbsvmlib
	* configure: fix cplex autodetection
	* classifier/svm/SubGradientSVM.cpp, classifier/svm/qpbsvmlib.cpp:
	  fix uninitialised variables

2007-05-19  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SubGradientSVM.cpp, classifier/svm/gpdtsolve.cpp,
	  classifier/svm/gpm.cpp, classifier/svm/qpbsvmlib.cpp,
	  classifier/svm/qpbsvmlib.h, structure/Plif.cpp: * fix copyright
	  in grad proj techn. svm
	  * add pr_loqo to qpbsvmlib

2007-05-18  Soeren Sonnenburg <sonne@debian.org>

	* classifier/LinearClassifier.h, classifier/svm/SVM_libsvm.cpp,
	  classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h, classifier/svm/pr_loqo.cpp,
	  gui/Matlab.cpp, guilib/GUIClassifier.cpp, guilib/GUIClassifier.h,
	  guilib/GUIMatlab.cpp, guilib/GUIMatlab.h, lib/Mathematics.h: *
	  fix matlab7.4 warnings (INT casts...)
	  * change argument order of vec1_plus_scalar_times_vec2
	  * turn pr_loqo warnings into debug messages
	  * add generic [bias,weights]=sg('get_classifier') call
	  * autoadjust epsilon for subgradient svm

2007-05-15  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIClassifier.cpp: synonymize SVMLIGHT with LIGHT for
	  compatibility
	* guilib/GUIR.cpp: fix get_matrix stuff
	* Makefile, classifier/svm/SubGradientSVM.cpp: R test update

2007-05-11  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SubGradientSVM.cpp, gui/Octave.cpp, gui/R.cpp,
	  guilib/GUIOctave.h, guilib/GUIR.cpp, guilib/GUIR.h: classifier
	  interface build fixes for R/Octave
	* classifier/svm/SubGradientSVM.cpp: add problematic example
	* classifier/LDA.cpp, classifier/LPM.cpp,
	  classifier/LinearClassifier.cpp, classifier/LinearClassifier.h,
	  classifier/SparseLinearClassifier.cpp,
	  classifier/SparseLinearClassifier.h, classifier/svm/SVM.h,
	  classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h, classifier/svm/qpbsvmlib.cpp,
	  features/SparseFeatures.h, gui/GUI.h, gui/Matlab.cpp, gui/R.cpp,
	  gui/TextGUI.cpp, gui/TextGUI.h, guilib/GUIClassifier.cpp,
	  guilib/GUIClassifier.h, guilib/GUIKernel.cpp,
	  guilib/GUIMatlab.cpp, guilib/GUIMatlab.h, guilib/GUIOctave.cpp,
	  guilib/GUIR.cpp, guilib/GUIR.h, guilib/GUISVM.cpp,
	  guilib/GUISVM.h, kernel/KernelMachine.cpp,
	  kernel/KernelMachine.h, lib/Mathematics.h: -remove guisvm
	  -convert everything to work with guiclassifier
	  -fix subgradientsvm

2007-05-10  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h, gui/Octave.cpp,
	  guilib/GUIOctave.cpp, guilib/GUIOctave.h: - fix valgrind errors
	  - add classifier interface to octave
	* classifier/SparseLinearClassifier.h,
	  classifier/svm/SubGradientSVM.cpp, features/SparseFeatures.h,
	  guilib/GUIClassifier.cpp: ...debugging
	* guilib/GUIClassifier.cpp: remove unused variable
	* classifier/LDA.cpp, guilib/GUIClassifier.cpp: fix a LDA bias sign
	  bug
	* classifier/LDA.cpp, classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h, classifier/svm/qpbsvmlib.h,
	  guilib/GUIClassifier.cpp, guilib/GUIClassifier.h,
	  lib/Mathematics.h, lib/common.h: generic sg('new_classifier FOO')
	  / sg('classify')
	  functionality for lots of FOO

2007-05-09  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SubGradientSVM.cpp, classifier/svm/gmnplib.cpp,
	  classifier/svm/qpbsvmlib.cpp, classifier/svm/qpbsvmlib.h,
	  lib/Mathematics.h: make gbpsvmlib/gmnplib use CMath::max/min/abs
	* classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h, classifier/svm/qpbsvmlib.cpp,
	  classifier/svm/qpbsvmlib.h, lib/Mathematics.cpp,
	  lib/Mathematics.h: add vojtechs QP solver

2007-05-08  Soeren Sonnenburg <sonne@debian.org>

	* classifier/Classifier.h, classifier/svm/SVMPerf.cpp,
	  classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h, features/SparseFeatures.h,
	  kernel/SparseLinearKernel.cpp, kernel/SparsePolyKernel.cpp,
	  lib/Mathematics.h: add helper functions for sparse feature
	  vectors:
	  
	  to compute dot products:
	  sparse x sparse
	  sparse x dense
	  to add sparse vectors to dense ones
	  
	  and let the sparse linear/poly kernel make use of them

2007-05-07  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* gui/Matlab.cpp, guilib/GUIMatlab.cpp, guilib/GUIMatlab.h,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h: Implemented
	  extensions in order to allow position weights per example.
	  Unsolved issues:
	  * normalization -> switch it off
	  * linadd & batch_computation -> switch it off
	  
	  An example script is given in
	  matlab/examples/test_wdshift_position_weights.m.

2007-04-30  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h: - fix threading bugs
	  in WDS kernel (it was never working correctly with > 1
	  thread), due to position_mask and max_shift vec being member
	  variables.
	  
	  solution: make max_shift_vec a local variable and remove (the
	  anyway unused)
	  position_mask completely
	* kernel/WeightedDegreePositionStringKernel.cpp: print
	  normalization_cons
	* classifier/svm/SVM_light.cpp, kernel/CombinedKernel.cpp: forgot
	  adding lin contributions for last thread

2007-04-29  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM_light.cpp: Fixed a stupid (variable name
	  collision, t was used for time and threads in 2
	  nested loops) SVM light training bug which occurred only with
	  
	  threads>=2,
	  linadd=0,
	  batch_computation=0
	  svm -> reactivate_inactive examples
	  
	  (got triggered by the test_wd_wds_parallel.m example). Judging
	  from (previous)
	  comments in the code it looks like Gunnar has seen this at some
	  point but
	  forgot to tell me...
	* classifier/svm/SVM_libsvm.cpp, guilib/GUIFeatures.cpp: * remove
	  obsolete/nonworking examples
	  * adjust examples to work with new stringfeatures
	  * fix one class svm crasher
	* classifier/SparseLinearClassifier.cpp,
	  classifier/SparseLinearClassifier.i, classifier/svm/SVMPerf.cpp,
	  classifier/svm/SVMPerf.h, classifier/svm/SVMPerf.i,
	  classifier/svm/SubGradientSVM.cpp,
	  classifier/svm/SubGradientSVM.h, classifier/svm/SubGradientSVM.i,
	  guilib/GUIKernel.cpp, guilib/GUIMatlab.cpp, kernel/Kernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.h, lib/common.h: * remove PHYL
	  kernel completely
	  * remove nonsense normalisation in WD*kernels (sqrtdiag lhs/rhs
	  etc),
	  the wd/wds kernel really need merging
	  * fix test_wdshift_kernel script
	  * add stubs for vojtechs subgradient svm and svmperf

2007-04-25  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/LibSVM.cpp: fix the 2-class case by introducing
	  sign=model->label[0]
	* classifier/svm/LibSVM_multiclass.cpp: * multiclass libsvm fix for
	  label permutations:
	  libsvm internally relabels all examples and stores that label in
	  model->label.
	  thus the svm pair (i,j) translates to (model->label[i],
	  model->label[j]), so
	  the solution is to compute the svm index for the
	  (model->label[i], model->label[j]) pair
	  * note that if (model->label[i] > model->label[j]), signs have to
	  be flipped, which
	  also occured to us in the 2-class case, as libsvm internally uses
	  +1 for the first
	  occuring class and -1 for the other (which is why have to flip
	  signs if the
	  first label<0) for 2-class problems too.
	  * apapart from that it delivers very similar results to vojtech's
	  L2-multiclass b-svm
	* classifier/Classifier.i, classifier/KernelPerceptron.i,
	  classifier/LDA.i, classifier/LPM.i,
	  classifier/LinearClassifier.i, classifier/Perceptron.i,
	  classifier/SparseLinearClassifier.i, classifier/svm/GMNPSVM.cpp,
	  classifier/svm/GMNPSVM.i, classifier/svm/GNPPSVM.i,
	  classifier/svm/GPBTSVM.i, classifier/svm/LibSVM.i,
	  classifier/svm/LibSVM_multiclass.cpp,
	  classifier/svm/LibSVM_multiclass.h,
	  classifier/svm/LibSVM_multiclass.i,
	  classifier/svm/LibSVM_oneclass.cpp,
	  classifier/svm/LibSVM_oneclass.h,
	  classifier/svm/LibSVM_oneclass.i,
	  classifier/svm/MultiClassSVM.cpp, classifier/svm/MultiClassSVM.h,
	  classifier/svm/MultiClassSVM.i, classifier/svm/SVM.h,
	  classifier/svm/SVM.i, classifier/svm/SVMLin.i,
	  classifier/svm/SVM_libsvm.cpp, classifier/svm/SVM_libsvm.h,
	  classifier/svm/SVM_light.i, classifier/svm/gmnplib.cpp,
	  distance/DistanceMachine.i, guilib/GUISVM.cpp,
	  kernel/KernelMachine.i, lib/common.h, regression/Regression.i,
	  regression/svr/LibSVR.cpp, regression/svr/LibSVR.i,
	  regression/svr/SVR_light.i: * add LibSVM multiclass support +
	  test script
	  * currently labelings maybe shuffled similiar to what we had with
	  2-class libsvm
	  * reshuffle python classifiers/regressors, add the other missing
	  svms to the python interface
	  * apply dos2unix on gmnp svm

2007-04-23  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM_libsvm.cpp, classifier/svm/SVM_libsvm.h,
	  features/StringFeatures.h, gui/Matlab.cpp, guilib/GUIMatlab.cpp,
	  guilib/GUIMatlab.h, kernel/CommWordStringKernel.cpp,
	  kernel/CommWordStringKernel.h: * add shrinking method of libsvm
	  2.84
	  * implement end test 'finding the most likely sequence'
	  for spectrum kernel
	  * add sg('get_SPEC_consensus') command + matlab example,
	  * fix svm_lin/svm .py scripts (axis tight/dynamically adjust
	  interval)

2007-04-20  Soeren Sonnenburg <sonne@debian.org>

	* features/StringFeatures.h,
	  kernel/WeightedDegreePositionStringKernel.cpp, lib/Trie.cpp: fix
	  crashes when calling obtain_by_sliding_window
	  or obtain_from_position_list - TWICE
	* kernel/WeightedDegreePositionStringKernel.cpp, lib/Trie.cpp,
	  lib/Trie.h: get_WD_consensus is finally working correctly.

2007-04-17  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreePositionStringKernel.cpp, lib/Trie.cpp:
	  b0rken: backtracking needs to go over full tree (max. all 4^d
	  strings)

2007-04-16  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreePositionStringKernel.cpp, lib/Mathematics.h,
	  lib/Trie.cpp, lib/Trie.h: display matrix column major + further
	  consensus work
	* gui/Matlab.cpp, guilib/GUIKernel.cpp, guilib/GUIMatlab.cpp,
	  guilib/GUIMatlab.h,
	  kernel/WeightedDegreePositionStringKernel.cpp, lib/Trie.cpp,
	  lib/Trie.h: +fix string/char features, kernels before based on
	  charfeatures should work
	  again in matlab
	  +add code + example for consensus computation for WDS kernel

2007-04-15  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIMatlab.cpp,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h, lib/Trie.cpp,
	  lib/Trie.h: -fix from_position_list for TEST data (strlen(TEST)
	  == 4 !!!)
	  -start impl. of consensus
	  -whitespace cleanups

2007-04-12  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/GMNPSVM.cpp, classifier/svm/GMNPSVM.h,
	  classifier/svm/MultiClassSVM.cpp, classifier/svm/MultiClassSVM.h,
	  classifier/svm/SVM.h, classifier/svm/gmnplib.cpp,
	  classifier/svm/gmnplib.h, guilib/GUIPython.cpp: -add multiclass
	  svm wrapper
	  -add L2-b-svm multiclass matlab example
	  -vojtechs multiclass svm is now working

2007-04-05  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/GMNPSVM.cpp, classifier/svm/GMNPSVM.h,
	  classifier/svm/GMNPSVM.i, classifier/svm/gmnplib.cpp,
	  classifier/svm/gmnplib.h, classifier/svm/gnpplib.h,
	  features/Labels.cpp, features/Labels.h, guilib/GUISVM.cpp,
	  lib/common.h: + add vojtech's multiclass bsvm

2007-04-04  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* guilib/GUIPython.cpp:
	* guilib/GUIPython.cpp: solved transpose-problem of old python
	  interface

2007-04-02  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIOctave.cpp, guilib/GUIPython.cpp, guilib/GUIR.cpp,
	  kernel/LocalityImprovedStringKernel.cpp: R/python/octave
	  interface compile fixes + trivial warning in LIK

2007-04-02  Andre Noll <Andre.Noll@tuebingen.mpg.de>

	* kernel/SimpleLocalityImprovedStringKernel.cpp:
	  CSimpleLocalityImprovedStringKernel: simplify init()
	  
	  This trivial patch gets rid of an identation by immediately
	  returning
	  false in case result==false.
	* kernel/SimpleLocalityImprovedStringKernel.cpp,
	  kernel/SimpleLocalityImprovedStringKernel.h:
	  CSimpleLocalityImprovedStringKernel: change type of size
	  parameter from LONG to INT
	* kernel/SimpleLocalityImprovedStringKernel.cpp,
	  kernel/SimpleLocalityImprovedStringKernel.h:
	  SimpleLocalityImprovedStringKernel: trivial whitespace cleanups
	* guilib/GUIKernel.cpp, kernel/Kernel.i,
	  kernel/SimpleLocalityImprovedCharKernel.cpp,
	  kernel/SimpleLocalityImprovedCharKernel.h,
	  kernel/SimpleLocalityImprovedCharKernel.i,
	  kernel/SimpleLocalityImprovedStringKernel.cpp,
	  kernel/SimpleLocalityImprovedStringKernel.h,
	  kernel/SimpleLocalityImprovedStringKernel.i:
	  SimpleLocalityImprovedCharKernel ->
	  SimpleLocalityImprovedStringKernel conversion
	  
	  This gets rid of the last remaining char kernel.
	* guilib/GUIKernel.cpp, guilib/GUIMatlab.cpp: make the matlab
	  interface work again
	  
	  In the beginning was the plan, and then the specification;
	  And the plan was without form, and the specification was void.
	  
	  [...]
	  
	  And the President looked upon the product, and saw that it was
	  very good.
	* kernel/Kernel.i, kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreeCharKernel.i,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h,
	  kernel/WeightedDegreePositionCharKernel.i: remove
	  WeightedDegreeCharKernel and WeightedDegreePositionCharKernel
	  
	  These have been replaced by the corresponding string kernel.
	* kernel/LinearStringKernel.cpp: LinearStringKernel: simplify
	  compute_optimized()
	* kernel/LinearStringKernel.cpp: LinearStringKernel: Use
	  clear_normal() to initialize the normal vector.
	* kernel/LinearStringKernel.cpp: LinearStringKernel: Kill result
	  variable
	  
	  Also, add a comment to don't open code the dot product but to use
	  the corresponding function from Mathematics.h once this works
	  with
	  templates.
	* kernel/LinearStringKernel.cpp: LinearStringKernel: Simplify
	  clear_normal()
	  
	  Just use memset() to zero-out the array.
	* kernel/LinearStringKernel.cpp: LinearStringKernel: Kill pointless
	  cast
	* kernel/LinearStringKernel.cpp, kernel/LinearStringKernel.h:
	  CLinearStringKernel: Change type of size parameter from LONG to
	  INT
	* kernel/LinearStringKernel.cpp, kernel/LinearStringKernel.h:
	  LinearStringKernel: Trivial whitespace cleanups
	* kernel/Kernel.i, kernel/LinearCharKernel.cpp,
	  kernel/LinearCharKernel.h, kernel/LinearCharKernel.i,
	  kernel/LinearStringKernel.cpp, kernel/LinearStringKernel.h,
	  kernel/LinearStringKernel.i: rename LinearCharKernel to
	  LinearStringKernel
	  
	  and make it compile again.
	* kernel/WeightedDegreeCharKernelPolyA.cpp,
	  kernel/WeightedDegreeCharKernelPolyA.h,
	  kernel/WeightedDegreeCharKernelPolyA.i,
	  kernel/WeightedDegreePositionPhylCharKernel.cpp,
	  kernel/WeightedDegreePositionPhylCharKernel.h: Remove
	  WeightedDegreeCharKernelPolyA and
	  WeightedDegreePositionPhylCharKernel
	  
	  They are unused according to Soeren, so changing them to become a
	  String kernel is a waste of time.
	  
	  deleted: trunk/src/kernel/WeightedDegreeCharKernelPolyA.cpp
	  deleted: trunk/src/kernel/WeightedDegreeCharKernelPolyA.h
	  deleted: trunk/src/kernel/WeightedDegreeCharKernelPolyA.i
	  deleted:
	  trunk/src/kernel/WeightedDegreePositionPhylCharKernel.cpp
	  deleted: trunk/src/kernel/WeightedDegreePositionPhylCharKernel.h
	* kernel/PolyMatchStringKernel.i: PolyMatchStringKernel.i: Fix
	  missing char->string replacement
	* kernel/PolyMatchStringKernel.cpp, kernel/PolyMatchStringKernel.h:
	  PolyMatchStringKernel: Simplify compute()
	  
	  Also, change the "size" parameter of the contructor from LONG to
	  INT
	* kernel/PolyMatchStringKernel.cpp: PolyMatchStringKernel: use
	  init_sqrt_diag()
	* kernel/PolyMatchStringKernel.cpp: PolyMatchStringKernel: Kill
	  pointless initializations with 1
	* kernel/FixedDegreeStringKernel.cpp,
	  kernel/FixedDegreeStringKernel.h, kernel/Kernel.cpp,
	  kernel/Kernel.h: move init_sqrt_diag() from
	  CFixedDegreeStringKernel to CKernel
	  
	  It is needed for other kernels as well, so this will aid in
	  removing duplicated code.
	* kernel/Kernel.i: char -> string conversion for kernel/Kernel.i
	* kernel/PolyMatchStringKernel.cpp: PolyMatchStringKernel: more
	  trivial whitespace cleanups
	* kernel/PolyMatchStringKernel.cpp, kernel/PolyMatchStringKernel.h:
	  PolyMatchStringKernel: Trivial whitespace cleanup
	* guilib/GUIKernel.cpp, kernel/PolyMatchStringKernel.cpp,
	  kernel/PolyMatchStringKernel.h, kernel/PolyMatchStringKernel.i:
	  PolyMatchStringKernel: replace char features by string features
	* guilib/GUIKernel.cpp, kernel/PolyMatchCharKernel.cpp,
	  kernel/PolyMatchCharKernel.h, kernel/PolyMatchCharKernel.i,
	  kernel/PolyMatchStringKernel.cpp, kernel/PolyMatchStringKernel.h,
	  kernel/PolyMatchStringKernel.i: rename PolyMatchCharKernel to
	  PolyMatchStringKernel
	  
	  renamed: trunk/src/kernel/PolyMatchCharKernel.cpp ->
	  trunk/src/kernel/PolyMatchStringKernel.cpp
	  renamed: trunk/src/kernel/PolyMatchCharKernel.h ->
	  trunk/src/kernel/PolyMatchStringKernel.h
	  renamed: trunk/src/kernel/PolyMatchCharKernel.i ->
	  trunk/src/kernel/PolyMatchStringKernel.i
	* kernel/FixedDegreeStringKernel.cpp,
	  kernel/FixedDegreeStringKernel.h: FixedDegreeStringKernel:
	  Introduce init_sqrt_diag()
	  
	  This private method computes the vector containing the square
	  root
	  of the diagonal elements of the kernel. This computation is
	  needed
	  twice in the current code, so it makes sense to move that code
	  into
	  its own helper function.
	* kernel/FixedDegreeStringKernel.cpp: FixedDegreeStringKernel: Kill
	  pointless initialization
	  
	  The entries of sqrtdiag_lhs and sqrtdiag_rhs are all set to one,
	  only
	  to reset them to their proper value a few lines later (without
	  using
	  them in between of course). So kill that pointless
	  initialization.
	* kernel/FixedDegreeStringKernel.cpp: FixedDegreeStringKernel: Fix
	  ASSERT() placement
	  
	  It's pointless to check for memory allocation failure _after_
	  using
	  the return value of new.
	* kernel/FixedDegreeStringKernel.cpp: FixedDegreeStringKernel: Kill
	  pointless NULL assignment
	  
	  A new value is assigned to sqrtdiag_lhs one line below.
	* kernel/FixedDegreeStringKernel.cpp: FixedDegreeStringKernel: Use
	  DREAL instead of double
	  
	  We're returning DREAL, so this makes more sense.
	* kernel/FixedDegreeStringKernel.cpp: FixedDegreeStringKernel:
	  Simplify compute()
	  
	  Only the product of the squareroots of lhs and rhs
	  is used, so compute it in one go.
	* kernel/FixedDegreeStringKernel.cpp,
	  kernel/FixedDegreeStringKernel.h: FixedDegreeStringKernel:
	  Trivial whitespace fixes
	* guilib/GUIKernel.cpp, kernel/FixedDegreeStringKernel.cpp,
	  kernel/FixedDegreeStringKernel.h,
	  kernel/FixedDegreeStringKernel.i: FixedDegreeStringKernel:
	  replace char features by string features
	* guilib/GUIKernel.cpp, kernel/FixedDegreeCharKernel.cpp,
	  kernel/FixedDegreeCharKernel.h, kernel/FixedDegreeCharKernel.i,
	  kernel/FixedDegreeStringKernel.cpp,
	  kernel/FixedDegreeStringKernel.h,
	  kernel/FixedDegreeStringKernel.i: Rename FixedDegreeCharKernel to
	  FixedDegreeStringKernel
	  
	  renamed: trunk/src/kernel/FixedDegreeCharKernel.cpp ->
	  trunk/src/kernel/FixedDegreeStringKernel.cpp
	  renamed: trunk/src/kernel/FixedDegreeCharKernel.h ->
	  trunk/src/kernel/FixedDegreeStringKernel.h
	  renamed: trunk/src/kernel/FixedDegreeCharKernel.i ->
	  trunk/src/kernel/FixedDegreeStringKernel.i
	* kernel/LocalityImprovedStringKernel.cpp:
	  LocalityImprovedStringKernel: Kill another instance of open coded
	  pow()
	* kernel/LocalityImprovedStringKernel.cpp:
	  LocalityImprovedStringKernel: Final whitespace cleanups
	* kernel/LocalityImprovedStringKernel.cpp:
	  LocalityImprovedStringKernel: Don't open code the pow() function.
	* kernel/LocalityImprovedStringKernel.cpp:
	  LocalityImprovedStringKernel: More trivial whitespace cleanups
	  
	  Replace spaces by tabs and add additional spaces according to
	  Coding style.
	* kernel/LocalityImprovedStringKernel.cpp:
	  LocalityImprovedStringKernel: Simplify for loop
	  
	  One line of code is obviously equivalent to the six lines we've
	  had before.
	* kernel/LocalityImprovedStringKernel.cpp:
	  LocalityImprovedStringKernel: Trivial whitespace cleanup
	  
	  Only replace leading spaces by tabs.
	* kernel/LocalityImprovedStringKernel.cpp:
	  LocalityImprovedStringKernel: minor cleanup in init()
	* guilib/GUIKernel.cpp, kernel/LocalityImprovedStringKernel.cpp,
	  kernel/LocalityImprovedStringKernel.h,
	  kernel/LocalityImprovedStringKernel.i:
	  LocalityImprovedStringKernel: replace char features by string
	  features
	* guilib/GUIKernel.cpp, kernel/LocalityImprovedCharKernel.cpp,
	  kernel/LocalityImprovedCharKernel.h,
	  kernel/LocalityImprovedCharKernel.i,
	  kernel/LocalityImprovedStringKernel.cpp,
	  kernel/LocalityImprovedStringKernel.h,
	  kernel/LocalityImprovedStringKernel.i: rename
	  LocalityImprovedCharKernel to LocalityImprovedStringKernel
	  
	  The change to GUIKernel.cpp was neccessary to make it compile
	  again.
	  
	  modified: trunk/src/guilib/GUIKernel.cpp
	  renamed: trunk/src/kernel/LocalityImprovedCharKernel.cpp ->
	  trunk/src/kernel/LocalityImprovedStringKernel.cpp
	  renamed: trunk/src/kernel/LocalityImprovedCharKernel.h ->
	  trunk/src/kernel/LocalityImprovedStringKernel.h
	  renamed: trunk/src/kernel/LocalityImprovedCharKernel.i ->
	  trunk/src/kernel/LocalityImprovedStringKernel.i

2007-03-31  Soeren Sonnenburg <sonne@debian.org>

	* configure: readd the undefined suppress to the configure options
	  whether the rest works only time will tell :-)

2007-03-25  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* Makefile: fixed some problems on intel macs... soeren, please
	  check it.
	  G

2007-03-22  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* configure: fixed some configure issues on imacs. seems to work.

2007-03-14  Soeren Sonnenburg <sonne@debian.org>

	* gui/Matlab.cpp, guilib/GUIKernel.cpp, guilib/GUIMatlab.cpp: WD
	  kernel string support

2007-03-14  Andre Noll <Andre.Noll@tuebingen.mpg.de>

	* lib/Trie.h: Trie.h: Simplify check_treemem()
	  
	  and reduce line length and white space usage according
	  to the shogun coding style.
	* lib/Trie.h: Trie.h: Trivial whitespace cleanups

2007-03-14  Soeren Sonnenburg <sonne@debian.org>

	* gui/Matlab.cpp, guilib/GUIMatlab.cpp: matlab interface compile
	  fix
	* features/StringFeatures.h, features/StringFeatures.i,
	  gui/Matlab.cpp, gui/TextGUI.cpp, guilib/GUIFeatures.cpp,
	  guilib/GUIFeatures.h, guilib/GUIMatlab.cpp, guilib/GUIMatlab.h,
	  guilib/GUIOctave.cpp, kernel/Kernel.i,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreeStringKernel.cpp,
	  kernel/WeightedDegreeStringKernel.h,
	  kernel/WeightedDegreeStringKernel.i, lib/common.h: obtain by
	  sliding window / by position list

2007-03-13  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUISVM.cpp: by default use linadd

2007-03-12  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreePositionStringKernel.cpp: also add missing
	  init to wds -string kernel
	* kernel/WeightedDegreePositionCharKernel.cpp: fix WDS (missing
	  NULL init of shifts)
	* features/StringFeatures.h, kernel/CommUlongStringKernel.h,
	  kernel/CommWordKernel.cpp, kernel/CommWordKernel.h,
	  kernel/WeightedDegreePositionStringKernel.i: * merge changes from
	  0.3.2
	  * add sliding window stringfeatures example
	  * allow features to be None for WDS kernel

2007-03-09  Soeren Sonnenburg <sonne@debian.org>

	* lib/Array.i, lib/Array2.i, lib/Array3.i: filter swig array
	  Overloaded warnings
	* kernel/SimpleLocalityImprovedCharKernel.cpp: add locality
	  improved kernel example
	* features/CharFeatures.cpp, features/CharFeatures.i,
	  features/StringFeatures.h, kernel/DistanceKernel.cpp,
	  kernel/SpectrumKernel.cpp, kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernelPolyA.cpp,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h,
	  kernel/WeightedDegreePositionCharKernel.i,
	  kernel/WeightedDegreePositionPhylCharKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h: * allow the alphabet
	  type in the Stringfeatures constructor
	  * add support for wds CHAR kernel / update example
	  
	  important issue valid for all kernels:
	  in init(lhs, rhs), the first call should be
	  SuperClass::init(lhs,rhs);
	  as this will check for NULL ptr, valid feature class & type
	  
	  this was broken for the WD* kernels and lead to hard to track
	  erros.
	* kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h,
	  kernel/WeightedDegreePositionStringKernel.i: wds STRING kernel
	  now works from inside of python.
	  
	  although it means code duplication, I will merge changes to the
	  wds CHAR kernel

2007-03-08  Soeren Sonnenburg <sonne@debian.org>

	* gui/Matlab.cpp, guilib/GUIMatlab.h, lib/io.cpp, lib/matlab.h,
	  structure/Plif.cpp, structure/Plif.h: introduce lib/matlab.h
	  which encapsulates
	  the compatibilty define (as we already have
	  for python)
	  
	  note that the plif & best_path_trans functions
	  spit out quite some warnings...breakage to be expected
	* guilib/GUIMatlab.h: matlab 7.4 compile/compatibility fix
	* Makefile, base/SGObject.i, distributions/hmm/HMM.cpp,
	  distributions/hmm/LinearHMM.cpp, features/FKFeatures.i,
	  features/Features.i, features/RealFileFeatures.i,
	  features/StringFeatures.h, features/StringFeatures.i,
	  features/TOPFeatures.h, features/TOPFeatures.i,
	  features/WordFeatures.cpp, kernel/CommWordKernel.i,
	  kernel/CustomKernel.i, kernel/DiagKernel.i,
	  kernel/DistanceKernel.i, kernel/FixedDegreeCharKernel.i,
	  kernel/GaussianKernel.i, kernel/HistogramWordKernel.i,
	  kernel/Kernel.i, kernel/LinearByteKernel.i,
	  kernel/LinearCharKernel.i, kernel/LinearKernel.i,
	  kernel/LinearWordKernel.i, kernel/LocalityImprovedCharKernel.i,
	  kernel/PolyKernel.i, kernel/PolyMatchCharKernel.i,
	  kernel/PolyMatchWordKernel.i, kernel/SalzbergWordKernel.i,
	  kernel/SimpleKernel.i, kernel/SimpleLocalityImprovedCharKernel.i,
	  kernel/SparseGaussianKernel.i, kernel/SparseKernel.i,
	  kernel/SparseLinearKernel.i, kernel/SparseNormSquaredKernel.i,
	  kernel/SparsePolyKernel.i,
	  kernel/WeightedDegreeCharKernelPolyA.i, kernel/WordMatchKernel.i,
	  lib/io.i: include markov chain example and add missing
	  features/kernels to
	  the python interface (though I really only wanted to interface
	  the WDS kernel ...)

2007-03-07  Soeren Sonnenburg <sonne@debian.org>

	* kernel/GaussianKernel.cpp: remove debug output
	* ChangeLog, TODO, kernel/WeightedDegreePositionCharKernel.i,
	  kernel/WeightedDegreePositionStringKernel.i: * update to 0.3.2
	  * start wds kernel python interf.

2007-03-06  Soeren Sonnenburg <sonne@debian.org>

	* base/Version.h, distributions/hmm/HMM.cpp, gui/Octave.cpp: merge
	  changes back to trunk
	* NEWS, guilib/GUIHMM.cpp, guilib/GUIOctave.cpp,
	  structure/DynProg.i: release shogun 0.3.2 fixing a number of bugs
	  in the examples
	  and several valgrind hits in octave/hmm adding support for
	  numpy boolean -> for msplicer v0.2

2007-03-05  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* base/Version.h: fixed version string.
	  G

2007-03-04  Soeren Sonnenburg <sonne@debian.org>

	* lib/python_typemaps.i: * much more detailed error outputs when
	  types/dims don't match
	  * workaround a numpy issue when long == int (long and int are
	  different
	  types inside of numpy, but both are 32bit on 32bit machines)
	  if they are 32bit and same size then treat long as int

2007-03-03  Soeren Sonnenburg <sonne@debian.org>

	* README.developer, base/SGObject.h, classifier/Classifier.cpp,
	  classifier/Classifier.h, features/CombinedFeatures.h,
	  features/StringFeatures.h, guilib/GUIKernel.cpp,
	  kernel/CombinedKernel.h, kernel/Kernel.cpp,
	  kernel/KernelMachine.cpp, kernel/KernelMachine.h: make obj->ref()
	  / obj->unref() a macro
	  SG_REF(obj)
	  SG_UNREF(obj)
	  which is empty for the static interfaces
	* base/SGObject.h, guilib/GUIKernel.cpp, kernel/KernelMachine.h,
	  kernel/WeightedDegreePositionCharKernel.i: as we now unref()
	  objects on destruction we have to
	  make sure no one else killed the object before we unref() it
	  this however may happen in all the static guis (matlab,...) so
	  all interfaces except the python-modular one are broken if
	  commands
	  like clean_features/clean_kernels are called in wrong order
	  
	  this fixes just enough to make the test_wd_kernel script run

2007-03-02  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM.cpp, features/StringFeatures.h,
	  features/StringFeatures.i, kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.i,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.i,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h,
	  lib/python_typemaps.i: this adds support for string featuers in
	  python as follows:
	  
	  >>> from shogun.Features import *
	  >>> x=StringCharFeatures(Alphabet(DNA))
	  >>> x.set_string_features(['blafoo','hallo','dummdidumm'])
	  >>> x.select_feature_vector(1)
	  >>> x.get_str()
	  array(['h', 'a', 'l', 'l', 'o'],
	  dtype='|S1')
	  
	  there is a certain overhaul in the WD* kernels necessary -
	  as the shift kernel is not yet really supported (and we are
	  losing
	  control if we go on duplicating the code like this...)

2007-03-02  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/DynProg.cpp: cleaned up a bit. still works.
	* guilib/GUIMatlab.cpp, lib/Array.h, lib/Array2.h, lib/Array3.h,
	  structure/DynProg.cpp: Mainly debug changes... cleanup soon.
	  G

2007-03-01  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog, kernel/WeightedDegreePositionCharKernel.h,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h,
	  lib/python_typemaps.i: get rid of unused function definitions
	  causing compile
	  problems
	* kernel/Kernel.i, kernel/WeightedDegreePositionCharKernel.i,
	  kernel/WeightedDegreePositionStringKernel.i, lib/python.h: add
	  missing files and include WDS kernel in Kernel.i
	* ChangeLog, classifier/LinearClassifier.i,
	  classifier/SparseLinearClassifier.i, classifier/svm/SVM.i,
	  distance/Distance.i, features/Alphabet.i,
	  features/ByteFeatures.i, features/CharFeatures.i,
	  features/Labels.i, features/RealFeatures.i,
	  features/ShortFeatures.i, features/SimpleFeatures.i,
	  features/StringFeatures.h, features/StringFeatures.i,
	  features/WordFeatures.i, guilib/GUIPython.cpp, kernel/Kernel.i,
	  kernel/WeightedDegreeCharKernel.i,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.cpp,
	  kernel/WeightedDegreePositionStringKernel.h, lib/Signal.cpp,
	  lib/Signal.h, lib/io.cpp, lib/numpy.i, lib/python_typemaps.i,
	  regression/svr/SVR_light.cpp, structure/Structure.i: * this adds
	  a obtain_by_sliding_window function to StringFeatures
	  * for that to work we need the WD kernel to work on string
	  features
	  which is what WeightedDegreePositionStringKernel introduces. as
	  this is
	  yet another code duplication we should get rid of (or creat a
	  generic
	  WD kernel object every WD kernel derives from).
	  * numpy.i is renamed to python_typemaps.i (as we need lists of
	  strings to be mapped to string features - not exactly a numeric
	  problem)

2007-02-27  Soeren Sonnenburg <sonne@debian.org>

	* features/StringFeatures.i: replace $self -> self as this seems to
	  be troublesome on
	  older swig versions

2007-02-27  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* lib/Array.h: fixed another wrong free...

2007-02-27  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog, features/Features.i, features/ShortFeatures.h,
	  features/ShortFeatures.i, features/SimpleFeatures.h,
	  features/SimpleFeatures.i, features/StringFeatures.h,
	  features/StringFeatures.i, features/WordFeatures.h,
	  features/WordFeatures.i: workaround some broken swig oddities
	  (which were working using
	  swig 1.3.2x): swig does not apply typemaps to templated classes
	  anymore... use %extend and define wrapper functions to call
	  the real functions...

2007-02-27  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* lib/numpy.i, structure/DynProg.i:

2007-02-27  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog, base/SGObject.h, configure: * this fixes the many
	  pointer related warnings
	  * also fixes configure for atlas/lapack

2007-02-26  Soeren Sonnenburg <sonne@debian.org>

	* README.developer, base/Parallel.cpp, base/Parallel.h,
	  base/SGObject.h, base/SGObject.i, classifier/Classifier.cpp,
	  classifier/Classifier.h, classifier/Classifier.i,
	  classifier/PluginEstimate.cpp, classifier/svm/GNPPSVM.cpp,
	  classifier/svm/GPBTSVM.cpp, classifier/svm/GPBTSVM.h,
	  classifier/svm/LibSVM.cpp, classifier/svm/SVM.cpp,
	  classifier/svm/SVM.h, classifier/svm/SVM_light.cpp,
	  classifier/svm/gnpplib.cpp, distance/Distance.cpp,
	  distributions/Distribution.cpp, features/Alphabet.cpp,
	  features/CombinedFeatures.h, features/Features.cpp,
	  features/Labels.cpp, features/SimpleFeatures.h,
	  features/StringFeatures.h, gui/Matlab.cpp, gui/Octave.cpp,
	  gui/R.cpp, gui/TextGUI.cpp, guilib/GUIClassifier.cpp,
	  guilib/GUIDistance.cpp, guilib/GUIFeatures.cpp,
	  guilib/GUIHMM.cpp, guilib/GUIKernel.cpp, guilib/GUILabels.cpp,
	  guilib/GUIMath.cpp, guilib/GUIMatlab.cpp, guilib/GUIOctave.cpp,
	  guilib/GUIPluginEstimate.cpp, guilib/GUIPreProc.cpp,
	  guilib/GUIPython.cpp, guilib/GUISVM.cpp, guilib/GUITime.cpp,
	  kernel/CombinedKernel.cpp, kernel/CombinedKernel.h,
	  kernel/GaussianKernel.cpp, kernel/GaussianKernel.h,
	  kernel/Kernel.cpp, kernel/KernelMachine.cpp,
	  kernel/KernelMachine.h, lib/Array.h, lib/Cache.h, lib/Cplex.cpp,
	  lib/DynamicArray.h, lib/File.cpp, lib/Mathematics.cpp,
	  lib/Signal.cpp, lib/Signal.h, lib/SimpleFile.h, lib/Time.cpp,
	  lib/Trie.cpp, lib/io.cpp, lib/io.h, preproc/PreProc.cpp,
	  structure/DynProg.cpp: * introduced reference counted objects for
	  automagic swig object deallocation
	  * fixed a crasher bug in Array destructor
	  * updated developer readme
	  * added python signal handling: ctrl+c now raises a keyboard
	  exception if not
	  in a big loop. in big loops it asks whether to immediately
	  stop/prematurely stop
	  * fix crasher bugs (array out of bounds read/write) in
	  translate_from_single_order
	  
	  using the reference counts from above we may now think of taking
	  references
	  to numpy objects instead of copying them :-)

2007-02-23  Andre Noll <Andre.Noll@tuebingen.mpg.de>

	* lib/io.cpp: io.cpp: trivial whitespace cleanup

2007-02-22  Andre Noll <Andre.Noll@tuebingen.mpg.de>

	* .authors: add myself to authors
	* lib/Array.h: further Array.h cleanups
	  
	  - remove unneccessary template
	  - simplify resize_array()
	  - reduce line width
	  - get rid of some duplicate SG_PRINT()s
	  - add myself to authors

2007-02-22  Soeren Sonnenburg <sonne@debian.org>

	* .authors, ChangeLog, lib/Array.h: * added jonas to authors
	  * added andre's array cleanup patches - now it is readable
	  again!!
	  
	  - The whole file was indented by one tab. Why?
	  - This patch replaces the #ifdef ARRAY_STATISTICS mess we've had
	  before
	  by a set of macros which expand to nothing if ARRAY_STATISTICS is
	  not defined.
	* ChangeLog, classifier/SparseLinearClassifier.cpp,
	  classifier/SparseLinearClassifier.h, classifier/svm/SVMLin.cpp,
	  classifier/svm/ssl.cpp, classifier/svm/ssl.h,
	  guilib/GUIKernel.cpp, kernel/LinearKernel.cpp,
	  kernel/LinearKernel.h: +impl. bias in svmlin
	* classifier/SparseLinearClassifier.cpp,
	  classifier/SparseLinearClassifier.h,
	  classifier/SparseLinearClassifier.i, classifier/svm/SVMLin.cpp,
	  classifier/svm/SVMLin.h, classifier/svm/ssl.cpp,
	  classifier/svm/ssl.h: make SVMLin work in practice (works only
	  w/o bias sofa)

2007-02-22  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* Makefile, guilib/GUIKernel.cpp: * removed CharPolyKernel
	  * add make test

2007-02-21  Jonas Behr <Jonas.Behr@tuebingen.mpg.de>

	* kernel/CharPolyKernel.cpp, kernel/CharPolyKernel.h,
	  kernel/CharPolyKernel.i: removed unused CharPolyKernel
	  updated test scripts

2007-02-21  Soeren Sonnenburg <sonne@debian.org>

	* CONTRIBUTIONS, ChangeLog, classifier/Classifier.i,
	  classifier/SparseLinearClassifier.cpp,
	  classifier/SparseLinearClassifier.h,
	  classifier/SparseLinearClassifier.i,
	  classifier/svm/KerthiPrimalSVM.cpp,
	  classifier/svm/KerthiPrimalSVM.h, classifier/svm/SVMLin.cpp,
	  classifier/svm/SVMLin.h, classifier/svm/ssl.cpp,
	  classifier/svm/ssl.h, features/ByteFeatures.h,
	  features/CharFeatures.h, features/FKFeatures.cpp,
	  features/FKFeatures.h, features/Features.i,
	  features/RealFeatures.h, features/RealFileFeatures.cpp,
	  features/RealFileFeatures.h, features/ShortFeatures.h,
	  features/SimpleFeatures.h, features/SparseFeatures.h,
	  features/SparseFeatures.i, features/StringFeatures.i,
	  features/TOPFeatures.cpp, features/TOPFeatures.h,
	  features/WordFeatures.h, lib/Mathematics.h: * further cleanup
	  patches from andre (Mathematics.h):
	  - The code fails badly in case size==1.
	  -Also, clean up the placement of spaces of that function
	  according
	  to README.developers.
	  The code was broken for n<=0: For n==0 it would print only
	  "name=[", and it would segfault for n<0. Fix that up as well.
	  We're compiling with -O, so gcc will unroll the last iteration of
	  the loop, i.e. the new code should not be slower than the old
	  code.
	  - Kill four pointless loops and don't segfault for rows<=0 or
	  cols<=0.
	  * remove broken KerthiPrimalSVM
	  * implement CSparseLinearClassifier
	  * derive CSVMLin from CSparseLinearClassifier
	  * add example on how to use SVMLin from python
	  * update AUTHORS, CONTRIBUTIONS
	  * make all the cache sizes in all the feature objects
	  Constructors
	  INT (as they are in MB anyway)
	  
	  Yes. We now have Sindhwani/Keerthis primal svm in shogun.

2007-02-20  Soeren Sonnenburg <sonne@debian.org>

	* configure: 3.1 merging
	* ChangeLog: releasing
	* base/Parallel.h, classifier/svm/SVMLin.cpp,
	  classifier/svm/SVMLin.h: build fix on osx
	* ChangeLog, base/Parallel.h, configure: * number of processors
	  autodetection for LINUX/DARWIN
	  removed that part from configure
	* NEWS, configure: bugfix release 0.3.1
	* ChangeLog, lib/Mathematics.h: define a binary search helper
	  function as suggested by andre
	* lib/Mathematics.h: (more of andre's cleanups)
	  
	  More or less a trivial cleanup that reduces lines of code quite a
	  bit
	  while improving readability.
	  
	  The only nontrivial change is the skip of the register keyword
	  for
	  the diff variable. Nowadays, register should not be used anymore
	  as
	  it does more harm than good. We're using -O anyway.

2007-02-19  Soeren Sonnenburg <sonne@debian.org>

	* base/Parallel.h, configure, lib/Mathematics.h: * fix configure
	  check for sysconf _SC_NPROCESSORS_ONLN (should work now on macs)
	  * use cxx_check to test for powl()
	  * use random() in randperm()
	* ChangeLog, classifier/svm/SVMLin.cpp, classifier/svm/SVMLin.h,
	  lib/Mathematics.h: * applied andre's cleanup patches
	  * some more SVMLin fixes

2007-02-18  Soeren Sonnenburg <sonne@debian.org>

	* configure, lib/io.h: rework configure to put -D$OS also into
	  DEFINES

2007-02-17  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog, INSTALL, lib/io.cpp, lib/io.h, structure/DynProg.cpp:
	  * update install instructions ( --enable-<interface> ->
	  --interface=<interface> )
	  * select functions seems to require a non const dirent* on DARWIN

2007-02-17  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* lib/io.cpp, lib/io.h, structure/DynProg.cpp: had to fix a few
	  thinks to get it to compile on intel macs.

2007-02-16  Soeren Sonnenburg <sonne@debian.org>

	* distributions/hmm/GHMM.h: make con/destructor public

2007-02-14  Torsten Werner <mail.twerner@googlemail.com>

	* Makefile: Don't count empty lines.

2007-02-14  Soeren Sonnenburg <sonne@debian.org>

	* README.developer: * Release 0.3.0
	  * update developer README
	* ChangeLog, NEWS, lib/io.cpp, lib/io.h: this will be version
	  0.3.0, add io set_target_to_stderr/stdout functions

2007-02-14  Vojtech Franc <fravoj@first.fraunhofer.de>

	* classifier/svm/GNPPSVM.cpp, classifier/svm/GNPPSVM.h,
	  classifier/svm/gnpplib.cpp, classifier/svm/gnpplib.h: Copyright
	  info updated, fixed stopping condition bug.

2007-02-14  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog, NEWS, structure/DynProg.cpp, structure/DynProg.h:
	  remove debug code, prepare for new release 0.3.1

2007-02-13  Soeren Sonnenburg <sonne@debian.org>

	* .authors, ChangeLog, guilib/GUISVM.cpp: add vojtech to authors /
	  finish relabeling to GNPP SVM
	* ChangeLog, classifier/svm/GNPPSVM.cpp,
	  classifier/svm/gnpplib.cpp, kernel/Kernel.cpp: + fixed some (?)
	  npp svm bugs

2007-02-13  Vojtech Franc <fravoj@first.fraunhofer.de>

	* classifier/svm/GNPPSVM.i: swig interface
	* classifier/svm/GNPPSVM.cpp, classifier/svm/GNPPSVM.h,
	  classifier/svm/SVM.i, classifier/svm/gnpplib.cpp,
	  classifier/svm/gnpplib.h, guilib/GUISVM.cpp, lib/common.h: added
	  GNPP (Generalized Nearest Point Problem) SVM

2007-02-13  Soeren Sonnenburg <sonne@debian.org>

	* README.developer: updated sections about macros
	* README.developer:
	* README.developer: + update coding conventions (limit #ifdef
	  usage)
	* .authors, ChangeLog, INSTALL, README.developer,
	  classifier/svm/SVM.cpp, features/CombinedFeatures.cpp: updated
	  authors and coding conventions

2007-02-12  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/Plif.cpp, structure/PlifArray.cpp: works.
	  cleanup.
	* structure/Plif.cpp:
	* structure/Plif.cpp:
	* structure/Plif.cpp, structure/Plif.h:
	* structure/Plif.cpp:
	* structure/Plif.cpp: more debug output...
	  
	  PS: need this many checkins since I'm comparing matlab and python
	  to give same results and need two svn checkouts in sync.

2007-02-12  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog, features/CombinedFeatures.i, features/Features.i,
	  guilib/GUIKernel.cpp, kernel/CombinedKernel.cpp,
	  kernel/CombinedKernel.h, kernel/CombinedKernel.i,
	  kernel/Kernel.i: * add combined kernel / combined features to
	  python interf.

2007-02-12  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/Plif.cpp, structure/PlifArray.cpp:
	* structure/Plif.cpp, structure/PlifArray.cpp: some more fixes...
	* structure/Plif.cpp: *** empty log message ***
	* structure/PlifArray.cpp: more debug stuff ... (sorry for the
	  spam).
	* structure/PlifArray.cpp: *** empty log message ***
	* structure/DynProg.cpp:

2007-02-12  Soeren Sonnenburg <sonne@debian.org>

	* features/Alphabet.i: * put python-modular examples in separate
	  directory
	  * fix get_hist()

2007-02-11  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/DynProg.cpp: minor debug changes.
	  G

2007-02-11  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog, configure, lib/Mathematics.h: * add a configure test
	  for powl(), as the ifdef construct in
	  lib/Mathmatics.h was flawed (damn!). now HAVE_POWL is set if
	  powl() exists
	* lib/Mathematics.h: * add powl function again (actually only the
	  ifdef needed removal)

2007-02-11  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* lib/Mathematics.h, structure/DynProg.cpp: finally... the pow
	  problem is gone.
	  G
	* lib/Mathematics.h: more problems with the pow function
	* lib/Mathematics.h: *** empty log message ***
	* lib/Mathematics.h: somebody did not complete code here ...
	  G

2007-02-10  Konrad Rieck <Konrad.Rieck@first.fraunhofer.de>

	* kernel/MindyGramKernel.cpp, kernel/MindyGramKernel.h: added
	  support for similarity coefficients (which boils down to some
	  strange normalization of the histogram intersection kernel. this
	  is unpublished, btw.)

2007-02-10  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog, lib/Mathematics.h: + fall back to double precision pow
	  if powl is not available

2007-02-09  Konrad Rieck <Konrad.Rieck@first.fraunhofer.de>

	* classifier/svm/SVM.cpp, classifier/svm/SVM.h,
	  classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h,
	  gui/TextGUI.cpp, guilib/GUIFeatures.h, guilib/GUISVM.cpp,
	  guilib/GUISVM.h, kernel/MindyGramKernel.cpp, lib/Time.h: improved
	  mindy features and kernel
	  cur_time fix in time class
	  support for max_train_time in svm light
	* guilib/GUIFeatures.h, guilib/GUIKernel.cpp: fixed incorrect
	  matlab interface to changed Mindy functions

2007-02-09  Soeren Sonnenburg <sonne@debian.org>

	* features/StringFeatures.h: * make empty files (strings) a fatal
	  error

2007-02-09  Konrad Rieck <Konrad.Rieck@first.fraunhofer.de>

	* kernel/MindyGramKernel.cpp: removed annoying goto statement
	* kernel/MindyGramKernel.cpp, kernel/MindyGramKernel.h: more mindy
	  changes

2007-02-09  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog, features/MindyGramFeatures.i,
	  kernel/CommUlongStringKernel.cpp, kernel/MindyGramKernel.i: fix
	  for spectrum kernel (yet another init problem)

2007-02-08  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog, features/Alphabet.h, features/Alphabet.i: * add
	  typemapped get_hist() function

2007-02-08  Konrad Rieck <Konrad.Rieck@first.fraunhofer.de>

	* guilib/GUIFeatures.h: untested patches for matlab gui
	* configure, features/Features.i, features/MindyGramFeatures.cpp,
	  features/MindyGramFeatures.h, features/MindyGramFeatures.i,
	  guilib/GUIFeatures.h, guilib/GUIKernel.cpp, kernel/Kernel.i,
	  kernel/MindyGramKernel.cpp, kernel/MindyGramKernel.h,
	  kernel/MindyGramKernel.i: fixed bugs in mindy and improved swig
	  support

2007-02-07  Torsten Werner <mail.twerner@googlemail.com>

	* Makefile: * don't use grep to count lines

2007-02-05  Konrad Rieck <Konrad.Rieck@first.fraunhofer.de>

	* configure, kernel/MindyGramKernel.cpp, kernel/MindyGramKernel.h:
	  NULL may not be defined.

2007-02-01  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* guilib/GUIMatlab.cpp, structure/DynProg.cpp:

2007-02-01  Soeren Sonnenburg <sonne@debian.org>

	* Makefile, TODO, configure: * updated make linecount ... hmmhh
	  83556 lines

2007-01-31  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog, structure/DynProg.cpp, structure/DynProg.h: * rename
	  best_path_set_seq to best_path_set_seq3d
	  
	  GU -> please NOTE!
	* lib/ShogunException.i: * the forgotten file...
	* classifier/svm/GPBTSVM.cpp, classifier/svm/LibSVM.cpp,
	  classifier/svm/LibSVM_oneclass.cpp, classifier/svm/MPD.cpp,
	  regression/KRR.cpp, regression/svr/LibSVR.cpp,
	  regression/svr/SVR_light.cpp: * also call base constructors here
	* ChangeLog, classifier/svm/SVM.cpp, classifier/svm/SVM.h,
	  classifier/svm/SVM.i, kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.i: * updated wd examples
	  * fix init for wd kernel
	  * call KernelMachine Constructor in SVM constructor

2007-01-29  Soeren Sonnenburg <sonne@debian.org>

	* .generate_link_dependencies.py, ChangeLog,
	  classifier/Classifier.i, distance/Distance.i,
	  distributions/Distribution.i, features/Features.i,
	  kernel/Kernel.i, lib/Library.i, lib/ShogunException.cpp,
	  lib/ShogunException.h, lib/io.cpp, lib/io.h, lib/io.i,
	  preproc/PreProc.i, regression/Regression.i,
	  structure/Structure.i: * swig exception handling
	  * LDA examples
	  * updated krr/svm examples

2007-01-29  Christian Gehl <Christian.Gehl@first.fraunhofer.de>

	* guilib/GUIKernel.cpp: added DistanceKernel creation to
	  create_kernel method
	* guilib/GUIDistance.cpp: added CanberraWordDistance
	* kernel/DistanceKernel.cpp: change init (init call for CKernel)
	  and delete (Distance=NULL)

2007-01-29  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog, Makefile, classifier/Classifier.h, classifier/LDA.cpp,
	  classifier/LDA.h, classifier/LinearClassifier.cpp,
	  classifier/LinearClassifier.h, configure,
	  features/StringFeatures.i, kernel/KernelMachine.cpp,
	  kernel/KernelMachine.h, kernel/SpectrumKernel.cpp, lib/Array2.h,
	  lib/Mathematics.cpp, lib/Mathematics.h, lib/io.cpp, lib/io.h,
	  lib/io.i, lib/lapack.cpp, lib/lapack.h, lib/suffixarray/ESA.cpp,
	  lib/suffixarray/ESA.h, lib/suffixarray/ErrorCode.h: * finally a
	  working pinv and LDA :-)
	  * overload classify() for linear / kernel methods
	  * compile fixes for suffixarray/Spec kernel
	  * trying to get exceptions working

2007-01-28  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* guilib/GUIMatlab.cpp, structure/DynProg.cpp, structure/DynProg.h:
	  changed dimensionality of seq_matrix in best_path_trans.
	  It is three dimensional now and the third dimension has to match
	  with the second dimension of state_signals.
	  untestet
	  
	  @Soeren, when you use it, just drop the second column of
	  state_signals (with all zeros in it).

2007-01-26  Soeren Sonnenburg <sonne@debian.org>

	* lib/Mathematics.cpp, lib/Mathematics.h: * quieten status
	  printouts for modular python interface
	* ChangeLog, distance/RealDistance.h, distance/StringDistance.h:
	  compile fix for distance stuff
	* ChangeLog, base/SGObject.cpp, distance/CanberraWordDistance.cpp,
	  gui/TextGUI.cpp, lib/Mathematics.cpp, lib/Mathematics.h: * move
	  CMath math declaration into base/SGObject.cpp
	  * move version printout into CMath ...

2007-01-25  Christian Gehl <Christian.Gehl@first.fraunhofer.de>

	* distance/Distance.i, distance/SimpleDistance.i: change some
	  lines; add new distance interfaces
	* distance/CanberraWordDistance.i, distance/HammingWordDistance.i,
	  distance/ManhattanWordDistance.i: swig interface files
	* kernel/DistanceKernel.i: swig interface: DistanceKernel
	* kernel/DistanceKernel.cpp, kernel/DistanceKernel.h: new kernel;
	  uses distance objects
	* guilib/GUIDistance.cpp: distance adjustment
	  Diese und die folgenden Zeilen werden ignoriert --
	  
	  M GUIDistance.cpp
	* distance/StringDistance.h: renewed
	* distance/CanberraWordDistance.cpp,
	  distance/CanberraWordDistance.h,
	  distance/HammingWordDistance.cpp, distance/HammingWordDistance.h,
	  distance/ManhattanWordDistance.cpp,
	  distance/ManhattanWordDistance.h: new distances
	* distance/Canberra.cpp, distance/Canberra.h,
	  distance/Chebyshew.cpp, distance/Chebyshew.h,
	  distance/Distance.cpp, distance/Distance.h,
	  distance/Geodesic.cpp, distance/Geodesic.h, distance/Jensen.cpp,
	  distance/Jensen.h, distance/Manhattan.cpp, distance/Manhattan.h,
	  distance/Minkowski.cpp, distance/Minkowski.h,
	  distance/SimpleDistance.h: renewed distance
	* lib/common.h: added K_DISTANCE and D_CANBERRA

2007-01-25  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* lib/Array.h, lib/Array3.h: + added 'const' in overloaded
	  operator=

2007-01-25  Soeren Sonnenburg <sonne@debian.org>

	* Makefile: * quieten svn2cl error (if svn2cl does not exist)
	* ChangeLog, lib/Array.h, lib/Array2.h, structure/DynProg.cpp: *
	  remove some debug output
	  * array display functions use name now

2007-01-24  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/DynProg.cpp, structure/DynProg.h: preparation for
	  changes ... should work as before...
	  G

2007-01-24  Soeren Sonnenburg <sonne@debian.org>

	* README, regression/Regression.i: -updates for the debian package
	  * compile fix for don't use svmlight
	  * updated project URL

2007-01-23  Soeren Sonnenburg <sonne@debian.org>

	* .authors, ChangeLog, base/SGObject.cpp, base/SGObject.h,
	  gui/GUI.cpp, gui/Matlab.cpp, gui/Octave.cpp, gui/R.cpp,
	  lib/io.cpp, lib/io.h, structure/DynProg.cpp, structure/Plif.cpp,
	  structure/Plif.h: + add c.gehl to authors
	  + create a global cio variable for static interfaces that points
	  to the static io variable in CSGObject to get a global loglevel
	  option;
	  for modular interfaces this is tweakably per class (except for
	  static
	  functions/ C-files where a global sg_io variable is used)

2007-01-23  Christian Gehl <Christian.Gehl@first.fraunhofer.de>

	* lib/common.h: new distance types

2007-01-23  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog, base/Version.cpp, base/Version.h,
	  kernel/CommUlongStringKernel.cpp,
	  kernel/CommWordStringKernel.cpp, kernel/CommWordStringKernel.h,
	  lib/io.cpp, lib/io.h, preproc/SortUlongString.cpp,
	  structure/DynProg.cpp, structure/DynProg.h, structure/DynProg.i:
	  +get_loglevel()

2007-01-22  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/DynProg.h: scores & losses should be return
	  arguments...
	  
	  G

2007-01-22  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog, Makefile: - don't regroup changelog
	* guilib/GUIMatlab.cpp: + matlab build fix
	* Makefile, base/SGObject.cpp, base/SGObject.h, base/SGObject.i,
	  base/Version.cpp, base/Version.h, classifier/Classifier.i,
	  classifier/KRR.cpp, classifier/KRR.h, classifier/KRR.i,
	  classifier/KernelPerceptron.i, classifier/svm/SVM.cpp,
	  classifier/svm/SVM.h, classifier/svm/SVM_light.cpp, configure,
	  distance/Canberra.i, distance/Chebyshew.i, distance/Distance.cpp,
	  distance/Distance.i, distance/DistanceMachine.i,
	  distance/Geodesic.i, distance/Jensen.i, distance/Manhattan.i,
	  distance/Minkowski.i, distance/RealDistance.i,
	  distance/SimpleDistance.i, distance/StringDistance.i,
	  distributions/Distribution.i,
	  distributions/histogram/Histogram.i, distributions/hmm/GHMM.cpp,
	  distributions/hmm/GHMM.h, distributions/hmm/GHMM.i,
	  distributions/hmm/HMM.cpp, distributions/hmm/HMM.h,
	  distributions/hmm/HMM.i, distributions/hmm/LinearHMM.h,
	  distributions/hmm/LinearHMM.i, features/Features.i,
	  features/SparseFeatures.h, gui/GUI.cpp, gui/Python.cpp,
	  gui/R.cpp, gui/TextGUI.cpp, guilib/GUIHMM.cpp, guilib/GUIHMM.h,
	  guilib/GUIMatlab.cpp, guilib/GUIOctave.cpp, guilib/GUIR.cpp,
	  kernel/CombinedKernel.cpp, kernel/CommUlongStringKernel.cpp,
	  kernel/CommWordKernel.cpp, kernel/CommWordStringKernel.cpp,
	  kernel/Kernel.cpp, kernel/Kernel.i, kernel/KernelMachine.h,
	  kernel/KernelMachine.i, kernel/MindyGramKernel.cpp,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.i,
	  kernel/WeightedDegreePositionCharKernel.cpp, lib/Library.i,
	  preproc/LogPlusOne.i, preproc/NormDerivativeLem3.i,
	  preproc/NormOne.i, preproc/PCACut.cpp, preproc/PCACut.i,
	  preproc/PreProc.i, preproc/PruneVarSubMean.i,
	  preproc/RealPreProc.i, preproc/ShortPreProc.i,
	  preproc/SimplePreProc.i, preproc/SortWord.i,
	  preproc/SortWordString.i, preproc/SparsePreProc.i,
	  preproc/StringPreProc.i, preproc/WordPreProc.i,
	  regression/KRR.cpp, regression/KRR.h, regression/KRR.i,
	  regression/Regression.i, regression/svr/LibSVR.cpp,
	  regression/svr/LibSVR.h, regression/svr/LibSVR.i,
	  regression/svr/SVR_light.cpp, regression/svr/SVR_light.h,
	  regression/svr/SVR_light.i, structure/DynProg.cpp,
	  structure/Structure.i: - configure now uses ./configure
	  --interface=INTERFACE
	  where INTERFACE is one of cmdline, python-modular, python, R,
	  R-modular octave or matlab
	  - moved Kernel Ridge Regression into regression/
	  - python swig interface now has a fully wrapped Regression,
	  Preprocessor and Distribution module
	  - version class functions are now static
	  - HMM now uses #parallel threads as specified by CParallel
	  - enabled typed autodoc for all modules
	  - update copyright -> 2007
	  - updated swig python examples (new: svr regression, updated: krr
	  regression/svm examples)

2007-01-21  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/DynProg.cpp:
	* structure/DynProg.cpp, structure/DynProg.h: first version ... for
	  what's needed to go on with mSplicer.
	  
	  G

2007-01-20  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIMatlab.cpp, structure/Plif.cpp: - matlab build fix
	* ChangeLog, README.developer, base/SGObject.h, base/Version.cpp,
	  classifier/Classifier.h, classifier/KNN.cpp, classifier/KNN.h,
	  classifier/LDA.cpp, classifier/Perceptron.cpp,
	  classifier/PluginEstimate.cpp, classifier/PluginEstimate.h,
	  classifier/svm/CPLEXSVM.cpp, classifier/svm/GPBTSVM.cpp,
	  classifier/svm/LibSVM.cpp, classifier/svm/LibSVM_oneclass.cpp,
	  classifier/svm/MPD.cpp, classifier/svm/Optimizer.cpp,
	  classifier/svm/SVM.cpp, classifier/svm/SVM.h,
	  classifier/svm/SVM_libsvm.cpp, classifier/svm/SVM_light.cpp,
	  classifier/svm/gpdtsolve.cpp, classifier/svm/gpdtsolve.h,
	  classifier/svm/pr_loqo.cpp, classifier/svm/ssl.cpp,
	  distance/Distance.cpp, distance/SimpleDistance.h,
	  distributions/hmm/HMM.cpp, distributions/hmm/HMM.h, exceptions,
	  features/Alphabet.cpp, features/Alphabet.h,
	  features/ByteFeatures.cpp, features/CharFeatures.cpp,
	  features/CombinedFeatures.cpp, features/FKFeatures.cpp,
	  features/Features.cpp, features/Features.h, features/Labels.cpp,
	  features/Labels.h, features/MindyGramFeatures.cpp,
	  features/MindyGramFeatures.h, features/RealFeatures.cpp,
	  features/RealFileFeatures.cpp, features/SimpleFeatures.h,
	  features/SparseFeatures.h, features/StringFeatures.h,
	  features/TOPFeatures.cpp, features/WordFeatures.cpp, gui/GUI.cpp,
	  gui/GUI.h, gui/Matlab.cpp, gui/Octave.cpp, gui/Python.cpp,
	  gui/R.cpp, gui/TextGUI.cpp, guilib/GUIClassifier.cpp,
	  guilib/GUIClassifier.h, guilib/GUIDistance.cpp,
	  guilib/GUIDistance.h, guilib/GUIFeatures.cpp,
	  guilib/GUIFeatures.h, guilib/GUIHMM.cpp, guilib/GUIHMM.h,
	  guilib/GUIKNN.cpp, guilib/GUIKNN.h, guilib/GUIKernel.cpp,
	  guilib/GUIKernel.h, guilib/GUILabels.cpp, guilib/GUILabels.h,
	  guilib/GUIMath.cpp, guilib/GUIMath.h, guilib/GUIMatlab.cpp,
	  guilib/GUIMatlab.h, guilib/GUIOctave.cpp, guilib/GUIOctave.h,
	  guilib/GUIPluginEstimate.cpp, guilib/GUIPluginEstimate.h,
	  guilib/GUIPreProc.cpp, guilib/GUIPreProc.h, guilib/GUIPython.cpp,
	  guilib/GUIPython.h, guilib/GUIR.cpp, guilib/GUIR.h,
	  guilib/GUISVM.cpp, guilib/GUISVM.h, guilib/GUITime.h,
	  kernel/AUCKernel.cpp, kernel/AUCKernel.h,
	  kernel/CanberraWordKernel.cpp, kernel/CanberraWordKernel.h,
	  kernel/CharPolyKernel.cpp, kernel/CharPolyKernel.h,
	  kernel/Chi2Kernel.cpp, kernel/Chi2Kernel.h,
	  kernel/CombinedKernel.cpp, kernel/CombinedKernel.h,
	  kernel/CommUlongStringKernel.cpp, kernel/CommUlongStringKernel.h,
	  kernel/CommWordKernel.cpp, kernel/CommWordKernel.h,
	  kernel/CommWordStringKernel.cpp, kernel/CommWordStringKernel.h,
	  kernel/ConstKernel.cpp, kernel/ConstKernel.h,
	  kernel/CustomKernel.cpp, kernel/CustomKernel.h,
	  kernel/FixedDegreeCharKernel.cpp, kernel/FixedDegreeCharKernel.h,
	  kernel/GaussianKernel.cpp, kernel/GaussianKernel.h,
	  kernel/HammingWordKernel.cpp, kernel/HammingWordKernel.h,
	  kernel/HistogramWordKernel.cpp, kernel/HistogramWordKernel.h,
	  kernel/Kernel.cpp, kernel/Kernel.h, kernel/LinearByteKernel.cpp,
	  kernel/LinearByteKernel.h, kernel/LinearCharKernel.cpp,
	  kernel/LinearCharKernel.h, kernel/LinearKernel.cpp,
	  kernel/LinearKernel.h, kernel/LinearWordKernel.cpp,
	  kernel/LinearWordKernel.h, kernel/LocalityImprovedCharKernel.cpp,
	  kernel/LocalityImprovedCharKernel.h,
	  kernel/ManhattenWordKernel.cpp, kernel/ManhattenWordKernel.h,
	  kernel/MindyGramKernel.cpp, kernel/PolyKernel.cpp,
	  kernel/PolyKernel.h, kernel/PolyMatchCharKernel.cpp,
	  kernel/PolyMatchCharKernel.h, kernel/PolyMatchWordKernel.cpp,
	  kernel/PolyMatchWordKernel.h, kernel/SalzbergWordKernel.cpp,
	  kernel/SalzbergWordKernel.h, kernel/SigmoidKernel.cpp,
	  kernel/SigmoidKernel.h, kernel/SimpleKernel.h,
	  kernel/SimpleLocalityImprovedCharKernel.cpp,
	  kernel/SimpleLocalityImprovedCharKernel.h,
	  kernel/SparseGaussianKernel.cpp, kernel/SparseGaussianKernel.h,
	  kernel/SparseKernel.h, kernel/SparseLinearKernel.cpp,
	  kernel/SparseLinearKernel.h, kernel/SparseNormSquaredKernel.cpp,
	  kernel/SparseNormSquaredKernel.h, kernel/SparsePolyKernel.cpp,
	  kernel/SparsePolyKernel.h, kernel/StringKernel.h,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreeCharKernelPolyA.cpp,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h,
	  kernel/WeightedDegreePositionPhylCharKernel.cpp,
	  kernel/WordMatchKernel.cpp, kernel/WordMatchKernel.h,
	  lib/Array.h, lib/Array2.h, lib/Array3.h, lib/Cache.h,
	  lib/Cplex.cpp, lib/Mathematics.cpp, lib/Mathematics.h,
	  lib/ShogunException.cpp, lib/ShogunException.h, lib/Signal.cpp,
	  lib/Signal.h, lib/SimpleFile.h, lib/Time.cpp, lib/Time.h,
	  lib/Trie.cpp, lib/Trie.h, lib/common.h, lib/io.cpp, lib/io.h,
	  lib/numpy.i, preproc/PCACut.cpp, preproc/PreProc.cpp,
	  preproc/PreProc.h, preproc/PruneVarSubMean.cpp,
	  preproc/SortUlongString.cpp, preproc/SortUlongString.h,
	  preproc/SortWordString.cpp, preproc/SortWordString.h,
	  preproc/StringPreProc.h, regression/svr/LibSVR.cpp,
	  regression/svr/SVR_light.cpp, structure/DynProg.cpp,
	  structure/Plif.cpp, structure/Plif.h, structure/PlifArray.cpp: -
	  updated coding conventions
	  - new io functions SG_DEBUG, SG_ERROR etc - use only those!
	  this will through exceptions in python
	  - kernel init function takes only lhs + rhs
	  - all objects now derive from CSGObject

2007-01-19  Soeren Sonnenburg <sonne@debian.org>

	* structure/DynProg.cpp, structure/DynProg.h, structure/DynProg.i:
	  +best_path*deriv setup functions
	* preproc/PreProc.i, preproc/SortUlongString.i: + rbf kernel
	  example
	  + preproc + sortulong fix
	* ChangeLog, classifier/Classifier.i, distance/Distance.i,
	  distributions/hmm/HMM.i, features/Features.i,
	  features/StringFeatures.h, kernel/Kernel.i, lib/Library.i,
	  preproc/PreProc.i, structure/Structure.i: +added SGObject to
	  object hierarchy
	  +fixed forward declaration of StringFeatures

2007-01-19  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* kernel/Kernel.i, preproc/PreProc.i, preproc/SortUlongString.i,
	  preproc/StringPreProc.i: + added first preprocessing interfaces

2007-01-19  Soeren Sonnenburg <sonne@debian.org>

	* .authors, ChangeLog, Makefile, NEWS: automagic ChangeLog
	  generation using svn2cl
	  (debian package subversion-tools)
	* base, base/Parallel.cpp, base/Parallel.h, base/Parallel.i,
	  base/SGObject.h, base/SGObject.i, base/Version.cpp,
	  base/Version.h, base/Version.i, classifier/Classifier.h,
	  classifier/svm/SVM.cpp, classifier/svm/SVM_light.cpp,
	  distance/Distance.cpp, distance/Distance.h,
	  distributions/Distribution.h, distributions/hmm/HMM.cpp,
	  features/Features.h, gui/TextGUI.cpp, guilib/GUIMatlab.cpp,
	  guilib/GUIPython.cpp, guilib/GUIR.cpp, kernel/CombinedKernel.cpp,
	  kernel/Kernel.cpp, kernel/Kernel.h,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionPhylCharKernel.cpp, lib/Array.h,
	  lib/Cache.h, lib/Cplex.h, lib/DynamicArray.h, lib/File.h,
	  lib/Library.i, lib/Mathematics.h, lib/Parallel.cpp,
	  lib/Parallel.h, lib/Parallel.i, lib/SGObject.h, lib/SGObject.i,
	  lib/Signal.h, lib/SimpleFile.h, lib/Time.h, lib/Trie.h,
	  lib/Version.cpp, lib/Version.h, lib/Version.i, preproc/PreProc.h,
	  regression/svr/SVR_light.cpp, structure/DynProg.h,
	  structure/PlifBase.h: -move the `base' objects
	  (Parallel/SGObject/Version) into base/
	  -except for the GUI and io everything should be (directly or
	  indirectly)
	  derived from SGObject
	* classifier/Classifier.h, classifier/LDA.cpp, classifier/LDA.h,
	  classifier/LinearClassifier.h, classifier/LinearClassifier.i,
	  distance/Distance.h, distributions/Distribution.h,
	  features/Features.h, kernel/Kernel.h, lib/Array.h, lib/Cache.h,
	  lib/Cplex.h, lib/DynamicArray.h, lib/File.h, lib/Library.i,
	  lib/Mathematics.h, lib/SGObject.h, lib/SGObject.i, lib/Signal.h,
	  lib/SimpleFile.h, lib/Time.h, lib/Trie.h, lib/Version.cpp,
	  lib/Version.h, preproc/PreProc.h, structure/DynProg.h,
	  structure/PlifBase.h: make all objects to be derived from
	  SGObject

2007-01-18  Soeren Sonnenburg <sonne@debian.org>

	* structure/DynProg.cpp, structure/DynProg.i: get path interf.
	* structure/DynProg.cpp, structure/DynProg.h, structure/DynProg.i:
	  +yesterdays msplicer related fixes/debug output

2007-01-17  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* lib/Array.h, lib/Array2.h, lib/Array3.h, structure/DynProg.cpp:
	  some more outputs...
	  G

2007-01-15  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/DynProg.cpp: some fixes and checks for oldtempvv and
	  oldtempii.
	  (taking Soerens valgrind runs into account)

2007-01-11  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* kernel/WeightedDegreeCharKernel.cpp: additional check ...
	* classifier/svm/SVM_light.cpp: *** empty log message ***

2007-01-10  Soeren Sonnenburg <sonne@debian.org>

	* Makefile, configure: + configure/Makefile install path fix
	* .version.sh: + improved debian target / version generation

2007-01-10  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* testfile: removed testfile
	* testfile: added just to see whether the SVNPoller script works

2007-01-08  Soeren Sonnenburg <sonne@debian.org>

	* .version.sh: .version.sh calls svn info again, as $Id is not
	  regularly updated...
	* classifier/Classifier.cpp, classifier/Classifier.h,
	  classifier/KNN.cpp, classifier/KNN.h, classifier/KRR.cpp,
	  classifier/KRR.h, classifier/KernelPerceptron.cpp,
	  classifier/KernelPerceptron.h, classifier/LDA.cpp,
	  classifier/LDA.h, classifier/LPM.cpp, classifier/LPM.h,
	  classifier/LinearClassifier.cpp, classifier/LinearClassifier.h,
	  classifier/Perceptron.cpp, classifier/Perceptron.h,
	  classifier/PluginEstimate.cpp, classifier/PluginEstimate.h,
	  classifier/svm/CPLEXSVM.cpp, classifier/svm/CPLEXSVM.h,
	  classifier/svm/GPBTSVM.cpp, classifier/svm/GPBTSVM.h,
	  classifier/svm/KerthiPrimalSVM.cpp,
	  classifier/svm/KerthiPrimalSVM.h, classifier/svm/LibSVM.cpp,
	  classifier/svm/LibSVM.h, classifier/svm/LibSVM_oneclass.cpp,
	  classifier/svm/LibSVM_oneclass.h, classifier/svm/MPD.cpp,
	  classifier/svm/MPD.h, classifier/svm/SVM.cpp,
	  classifier/svm/SVM.h, classifier/svm/SVM_libsvm.cpp,
	  classifier/svm/SVM_libsvm.h, classifier/svm/gpdt.cpp,
	  classifier/svm/gpdt.h, classifier/svm/gpdtsolve.cpp,
	  classifier/svm/gpm.cpp, classifier/svm/pr_loqo.cpp,
	  classifier/svm/pr_loqo.h, distance/Canberra.h,
	  distance/Chebyshew.h, distance/Distance.cpp,
	  distance/DistanceMachine.cpp, distance/DistanceMachine.h,
	  distance/Jensen.h, distance/Manhattan.h, distance/Minkowski.cpp,
	  distance/Minkowski.h, distance/RealDistance.h,
	  distance/StringDistance.h, distributions/Distribution.cpp,
	  distributions/Distribution.h,
	  distributions/histogram/Histogram.cpp,
	  distributions/histogram/Histogram.h, distributions/hmm/GHMM.cpp,
	  distributions/hmm/GHMM.h, distributions/hmm/HMM.cpp,
	  distributions/hmm/HMM.h, distributions/hmm/LinearHMM.cpp,
	  distributions/hmm/LinearHMM.h, features/ByteFeatures.cpp,
	  features/ByteFeatures.h, features/CharFeatures.cpp,
	  features/CharFeatures.h, features/CombinedFeatures.cpp,
	  features/CombinedFeatures.h, features/FKFeatures.cpp,
	  features/FKFeatures.h, features/Features.cpp,
	  features/Features.h, features/Labels.cpp, features/Labels.h,
	  features/RealFeatures.cpp, features/RealFeatures.h,
	  features/RealFileFeatures.cpp, features/RealFileFeatures.h,
	  features/ShortFeatures.cpp, features/ShortFeatures.h,
	  features/SimpleFeatures.h, features/SparseFeatures.h,
	  features/StringFeatures.cpp, features/StringFeatures.h,
	  features/TOPFeatures.cpp, features/TOPFeatures.h,
	  features/WordFeatures.cpp, features/WordFeatures.h, gui/GUI.cpp,
	  gui/GUI.h, gui/Matlab.cpp, gui/Octave.cpp, gui/Python.cpp,
	  gui/Python.h, gui/TextGUI.cpp, gui/TextGUI.h,
	  guilib/GUIClassifier.cpp, guilib/GUIClassifier.h,
	  guilib/GUIDistance.cpp, guilib/GUIDistance.h,
	  guilib/GUIFeatures.cpp, guilib/GUIFeatures.h, guilib/GUIHMM.cpp,
	  guilib/GUIHMM.h, guilib/GUIKNN.cpp, guilib/GUIKNN.h,
	  guilib/GUIKernel.cpp, guilib/GUIKernel.h, guilib/GUILabels.cpp,
	  guilib/GUILabels.h, guilib/GUIMath.cpp, guilib/GUIMath.h,
	  guilib/GUIMatlab.cpp, guilib/GUIMatlab.h, guilib/GUIOctave.cpp,
	  guilib/GUIOctave.h, guilib/GUIPluginEstimate.cpp,
	  guilib/GUIPluginEstimate.h, guilib/GUIPreProc.cpp,
	  guilib/GUIPreProc.h, guilib/GUIPython.cpp, guilib/GUIPython.h,
	  guilib/GUIR.cpp, guilib/GUIR.h, guilib/GUISVM.cpp,
	  guilib/GUISVM.h, guilib/GUITime.cpp, guilib/GUITime.h,
	  kernel/AUCKernel.cpp, kernel/AUCKernel.h,
	  kernel/CanberraWordKernel.cpp, kernel/CanberraWordKernel.h,
	  kernel/CharPolyKernel.cpp, kernel/CharPolyKernel.h,
	  kernel/Chi2Kernel.cpp, kernel/Chi2Kernel.h,
	  kernel/CombinedKernel.cpp, kernel/CombinedKernel.h,
	  kernel/CommUlongStringKernel.cpp, kernel/CommUlongStringKernel.h,
	  kernel/CommWordKernel.cpp, kernel/CommWordKernel.h,
	  kernel/CommWordStringKernel.cpp, kernel/CommWordStringKernel.h,
	  kernel/ConstKernel.cpp, kernel/ConstKernel.h,
	  kernel/CustomKernel.cpp, kernel/CustomKernel.h,
	  kernel/DiagKernel.cpp, kernel/DiagKernel.h,
	  kernel/FixedDegreeCharKernel.cpp, kernel/FixedDegreeCharKernel.h,
	  kernel/GaussianKernel.cpp, kernel/GaussianKernel.h,
	  kernel/HammingWordKernel.cpp, kernel/HammingWordKernel.h,
	  kernel/HistogramWordKernel.cpp, kernel/HistogramWordKernel.h,
	  kernel/Kernel.cpp, kernel/Kernel.h, kernel/KernelMachine.cpp,
	  kernel/KernelMachine.h, kernel/LinearByteKernel.cpp,
	  kernel/LinearByteKernel.h, kernel/LinearCharKernel.cpp,
	  kernel/LinearCharKernel.h, kernel/LinearKernel.cpp,
	  kernel/LinearKernel.h, kernel/LinearWordKernel.cpp,
	  kernel/LinearWordKernel.h, kernel/LocalityImprovedCharKernel.cpp,
	  kernel/LocalityImprovedCharKernel.h,
	  kernel/ManhattenWordKernel.cpp, kernel/ManhattenWordKernel.h,
	  kernel/MindyGramKernel.cpp, kernel/MindyGramKernel.h,
	  kernel/PolyKernel.cpp, kernel/PolyKernel.h,
	  kernel/PolyMatchCharKernel.cpp, kernel/PolyMatchCharKernel.h,
	  kernel/PolyMatchWordKernel.cpp, kernel/PolyMatchWordKernel.h,
	  kernel/SalzbergWordKernel.cpp, kernel/SalzbergWordKernel.h,
	  kernel/SigmoidKernel.cpp, kernel/SigmoidKernel.h,
	  kernel/SimpleKernel.h,
	  kernel/SimpleLocalityImprovedCharKernel.cpp,
	  kernel/SimpleLocalityImprovedCharKernel.h,
	  kernel/SparseGaussianKernel.cpp, kernel/SparseGaussianKernel.h,
	  kernel/SparseKernel.h, kernel/SparseLinearKernel.cpp,
	  kernel/SparseLinearKernel.h, kernel/SparseNormSquaredKernel.cpp,
	  kernel/SparseNormSquaredKernel.h, kernel/SparsePolyKernel.cpp,
	  kernel/SparsePolyKernel.h, kernel/StringKernel.h,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreeCharKernelPolyA.cpp,
	  kernel/WeightedDegreeCharKernelPolyA.h,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h,
	  kernel/WeightedDegreePositionPhylCharKernel.cpp,
	  kernel/WeightedDegreePositionPhylCharKernel.h,
	  kernel/WordMatchKernel.cpp, kernel/WordMatchKernel.h,
	  lib/Array.h, lib/Array2.h, lib/Array3.h, lib/Cache.h,
	  lib/Cplex.cpp, lib/Cplex.h, lib/DynamicArray.h, lib/File.cpp,
	  lib/File.h, lib/List.h, lib/Mathematics.cpp, lib/Mathematics.h,
	  lib/Parallel.cpp, lib/Parallel.h, lib/Signal.cpp, lib/Signal.h,
	  lib/SimpleFile.h, lib/Time.cpp, lib/Time.h, lib/Trie.h,
	  lib/Version.cpp, lib/Version.h, lib/common.h, lib/io.cpp,
	  lib/io.h, lib/lapack.cpp, lib/lapack.h, preproc/LogPlusOne.cpp,
	  preproc/LogPlusOne.h, preproc/NormDerivativeLem3.cpp,
	  preproc/NormDerivativeLem3.h, preproc/NormOne.cpp,
	  preproc/NormOne.h, preproc/PCACut.cpp, preproc/PCACut.h,
	  preproc/PreProc.cpp, preproc/PreProc.h,
	  preproc/PruneVarSubMean.cpp, preproc/PruneVarSubMean.h,
	  preproc/RealPreProc.h, preproc/ShortPreProc.cpp,
	  preproc/ShortPreProc.h, preproc/SimplePreProc.h,
	  preproc/SortUlongString.cpp, preproc/SortUlongString.h,
	  preproc/SortWord.cpp, preproc/SortWord.h,
	  preproc/SortWordString.cpp, preproc/SortWordString.h,
	  preproc/SparsePreProc.h, preproc/StringPreProc.h,
	  preproc/WordPreProc.cpp, preproc/WordPreProc.h,
	  regression/svr/LibSVR.cpp, regression/svr/LibSVR.h,
	  regression/svr/SVR_light.cpp, regression/svr/SVR_light.h,
	  structure/DynProg.cpp, structure/DynProg.h, structure/Plif.cpp,
	  structure/Plif.h, structure/PlifArray.cpp, structure/PlifArray.h,
	  structure/PlifBase.h: update copyright info
	  1999-2006 -> 1999-2007
	* tests: -remove obsolete tests dir
	* configure, lib/Parallel.h, structure/DynProg.h,
	  structure/DynProg.i: +fix configure/parallel to really detect
	  __SC_NPROCESSORS_ONLN
	  +allow setting of a single genestr

2007-01-08  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/DynProg.cpp:

2007-01-06  Soeren Sonnenburg <sonne@debian.org>

	* lib/Parallel.h: +#ifdef _SC_NPROCESSORS_ONLN

2007-01-05  Soeren Sonnenburg <sonne@debian.org>

	* configure: +remove more of svmlight
	  +compiler tuning now takes place after compiler is detected
	  and only valid options are added
	* classifier/svm/Optimizer.cpp, classifier/svm/SVM.i,
	  gui/TextGUI.cpp, guilib/GUIClassifier.cpp, guilib/GUIKernel.cpp,
	  guilib/GUIKernel.h, guilib/GUISVM.cpp, kernel/Kernel.cpp,
	  kernel/Kernel.h, kernel/WeightedDegreePositionCharKernel.cpp,
	  regression/svr/SVR_light.h: +really remove all copyrighted "all
	  rights reserved" SVMLight files + parts
	  
	  when called with, e.g.:
	  
	  $ make vanilla-package COMPRESS=gzip EXTRAVERSION=+svn20070105
	  SVMLIGHT=no

2007-01-04  Soeren Sonnenburg <sonne@debian.org>

	* features/Alphabet.cpp, features/StringFeatures.h,
	  features/StringFeatures.i, gui/Matlab.cpp, gui/R.cpp,
	  guilib/GUIMatlab.cpp, guilib/GUIMatlab.h, guilib/GUIR.cpp,
	  kernel/CommUlongStringKernel.cpp, kernel/CommUlongStringKernel.h,
	  kernel/CommUlongStringKernel.i, kernel/CommWordStringKernel.i,
	  kernel/Kernel.h, kernel/Kernel.i, kernel/StringKernel.i,
	  lib/common.h: +all the necessary stuff for spam detection works
	  now
	  speed & accuracy are still an isssue

2007-01-03  Soeren Sonnenburg <sonne@debian.org>

	* features/StringFeatures.h, features/StringFeatures.i: +string
	  features can now easily read strings-files from a directory (to
	  classify e.g. spam)

2007-01-03  Mikio Braun <Mikio.Braun@first.fraunhofer.de>

	* classifier/KRR.cpp: added a todo to KRR.cpp
	* classifier/Classifier.i, classifier/KRR.cpp, classifier/KRR.h,
	  classifier/KRR.i: Hello!
	  
	  KRR is working now, together with two examples for python.
	  Yuhu!
	  
	  -M
	* lib/common.h, lib/lapack.cpp, lib/lapack.h: forgot something
	* classifier/KRR.cpp, classifier/KRR.h, classifier/KRR.i:
	  Kernel-ridge-regression

2007-01-03  Soeren Sonnenburg <sonne@debian.org>

	* configure, lib/Array.h, lib/Array2.h, lib/Array3.h: +LINK is now
	  is set from COMP_CPP
	  +Array uses ASSERT again and undefs/defs ASSERT

2006-12-30  Soeren Sonnenburg <sonne@debian.org>

	* features/StringFeatures.h:

2006-12-29  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* guilib/GUIMatlab.cpp, structure/DynProg.cpp: now with
	  conservation.
	* guilib/GUIMatlab.cpp, lib/Array2.h, lib/Array3.h,
	  structure/DynProg.cpp: before I change the conservation stuff...
	  G

2006-12-29  Soeren Sonnenburg <sonne@debian.org>

	* features/StringFeatures.h, lib/Array.h, lib/Array2.h, lib/io.cpp,
	  lib/io.h: +read_dir

2006-12-29  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* guilib/GUIMatlab.cpp, structure/DynProg.cpp,
	  structure/PlifArray.cpp: should work for nGASP cat-1

2006-12-29  Soeren Sonnenburg <sonne@debian.org>

	* lib/lapack.h: missing endif

2006-12-29  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* guilib/GUIMatlab.cpp, kernel/CommWordKernel.h, lib/Array.h,
	  lib/Array2.h, lib/Array3.h, lib/Mathematics.h,
	  structure/DynProg.cpp, structure/DynProg.h: optimized
	  best_path_trans svm computations.

2006-12-28  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* lib/Array.h: fixed ifndef -> ifdef line 118

2006-12-28  Soeren Sonnenburg <sonne@debian.org>

	* lib/io.cpp, lib/io.h: get rid of another bazillion of warnings
	* structure/DynProg.cpp: compile fix

2006-12-28  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* exceptions/ShogunException.cpp, exceptions/ShogunException.h: +
	  sorry, forgot to check-in these files

2006-12-27  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* lib/Array.h: reverted to the old Array.h version including the
	  statistics.
	* structure/DynProg.cpp, structure/DynProg.h:

2006-12-22  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* classifier/svm/SVM.cpp, classifier/svm/SVM_light.cpp,
	  kernel/Kernel.cpp, kernel/WeightedDegreePositionCharKernel.cpp: +
	  removed the rest of the ugly ifdefs
	* classifier/LDA.cpp, classifier/PluginEstimate.cpp,
	  classifier/svm/MPD.cpp, classifier/svm/Optimizer.cpp,
	  exceptions/Exception.h, features/Alphabet.cpp,
	  features/ByteFeatures.cpp, features/CharFeatures.cpp,
	  features/Features.cpp, features/Labels.cpp,
	  features/MindyGramFeatures.cpp, features/RealFeatures.cpp,
	  features/TOPFeatures.cpp, features/WordFeatures.cpp,
	  kernel/CombinedKernel.cpp, kernel/CommUlongStringKernel.cpp,
	  kernel/CommWordKernel.cpp, kernel/CommWordStringKernel.cpp,
	  kernel/CustomKernel.cpp, kernel/HistogramWordKernel.cpp,
	  kernel/LinearByteKernel.cpp, kernel/LinearCharKernel.cpp,
	  kernel/LinearWordKernel.cpp, kernel/MindyGramKernel.cpp,
	  kernel/SalzbergWordKernel.cpp,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreePositionPhylCharKernel.cpp,
	  kernel/WordMatchKernel.cpp, lib/io.cpp, lib/io.h: + added
	  sg_error function so lib/io
	  + removed ugly #ifdef HAVE_PYTHON throw Exception else CIO
	  by sg_error(func_ptr,fmt,...)
	  
	  TODO:
	  + not all exceptions were removed.

2006-12-21  Soeren Sonnenburg <sonne@debian.org>

	* lib/io.h, structure/DynProg.i: +tiny fixes
	* lib/Array.i, lib/Array2.i, lib/Array3.i, lib/DynamicArray.i:
	  +forgotten interface files
	* lib/Array.h, lib/Array2.h, lib/Array3.h, lib/Library.i, lib/io.h,
	  structure/DynProg.cpp, structure/DynProg.h: -remove array
	  profiling stuff (what are profilers for huh ?)
	  +dynprog now uses dynarray...
	  +actually anything that requires a list should use DynamicArray !

2006-12-20  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* guilib/GUIMatlab.cpp, lib/Array.h, lib/Mathematics.h,
	  structure/DynProg.cpp, structure/DynProg.h: a few changes related
	  to path sampling.
	  G
	* structure/DynProg.cpp: implemented some kind of suboptimal path
	  sampling.

2006-12-20  Soeren Sonnenburg <sonne@debian.org>

	* gui/R.cpp:
	* gui/R.cpp: +build fix
	  -remove obsolete @hmm
	* lib/io.cpp: compile fix
	* structure/PlifArray.i:
	* g.R, lib/DynamicArray.h, structure/DynProg.cpp,
	  structure/PlifArray.cpp, structure/Structure.i: +CAUTION:
	  reverted DynamicArray to original dynarray (+some bugfixes)

2006-12-20  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* lib/DynamicArray.h: *** empty log message ***

2006-12-20  Soeren Sonnenburg <sonne@debian.org>

	* lib/Signal.cpp, lib/Signal.h: ifndef -> ifdef HAVE_MATLAB...
	* Makefile, lib/Time.i: also erase .R files on clean

2006-12-20  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* guilib/GUIHMM.cpp: does not compile without this fix.

2006-12-20  Soeren Sonnenburg <sonne@debian.org>

	* Makefile, classifier/Classifier.h, classifier/svm/SVM_light.h,
	  classifier/svm/gpdt.cpp, classifier/svm/gpdt.h,
	  classifier/svm/gpdtsolve.cpp, configure, lib/File.cpp,
	  lib/Library.i, lib/List.i, lib/Mathematics.i, lib/Parallel.i,
	  lib/Signal.i, lib/SimpleFile.i, lib/Time.i, lib/Trie.i,
	  lib/Version.i, lib/config.i, lib/io.cpp, lib/io.i: +make
	  configure append CFLAGS, CXXFLAGS from environment
	  +./configure --cflags= --cxxflags=
	  +COMPFLAGS_SWIG_CPP is generated from COMPFLAGS_CPP but does not
	  give any warnings
	  +fix renaming Classes CTime -> Time
	  +fix several format string errors
	  +make gpdt svm use CIO::message
	  
	  want to know how many CPUs your machine has ? then do:
	  
	  from shogun.Library import Parallel
	  print Parallel.get_num_cpus()
	  
	  (msplicer already uses this :)

2006-12-19  Soeren Sonnenburg <sonne@debian.org>

	* distributions/hmm/HMM.cpp, kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.cpp, lib/Cache.i,
	  lib/File.i, lib/Library.i, lib/List.i, lib/Mathematics.i,
	  lib/Parallel.cpp, lib/Parallel.h, lib/Parallel.i, lib/Signal.i,
	  lib/SimpleFile.i, lib/Time.i, lib/Trie.h, lib/Trie.i,
	  lib/Version.i, lib/common.h, lib/io.i: +export everything under
	  lib as shogun.Library
	  (for that it was necessary to make the local classes in CTrie
	  local)

2006-12-19  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* lib/numpy.i: + changed typecode error message to be part of a
	  standard python 'TypeError' exception

2006-12-19  Soeren Sonnenburg <sonne@debian.org>

	* classifier/Classifier.i, classifier/svm/SVM.i, configure,
	  distance/Distance.i, features/ByteFeatures.i,
	  features/CharFeatures.i, features/Features.i, features/Labels.i,
	  features/RealFeatures.i, features/ShortFeatures.i,
	  features/SimpleFeatures.i, features/WordFeatures.i,
	  kernel/Kernel.i, kernel/WeightedDegreeCharKernel.i, lib/common.h,
	  lib/common.i, lib/numpy.i, structure/DynProg.h,
	  structure/DynProg.i, structure/Plif.i, structure/Structure.i: + R
	  swig support ( --enable-swig-R)
	* guilib/GUIMatlab.cpp, guilib/GUIMatlab.h, guilib/GUIOctave.h,
	  guilib/GUIPython.h, guilib/GUIR.h, lib/io.cpp: at least all
	  interfaces DO compile now
	* classifier/svm/gpdt.cpp, classifier/svm/gpdt.h,
	  guilib/GUIOctave.cpp: gpdt compile fixes
	  octave string/char features fix
	* classifier/svm/SVM_light.cpp, lib/numpy.i,
	  regression/svr/SVR_light.cpp: remove cplex related shadows...
	* classifier/svm/SVM.h, lib/numpy.i: +fix returning matrices
	  #%#!#@? !!fortran order!!
	* gui/GUI.cpp, gui/GUI.h, gui/Matlab.cpp, gui/Octave.cpp,
	  gui/Python.cpp, gui/Python.h, gui/R.cpp, gui/TextGUI.cpp,
	  gui/TextGUI.h, guilib/GUIClassifier.cpp, guilib/GUIClassifier.h,
	  guilib/GUIDistance.cpp, guilib/GUIDistance.h,
	  guilib/GUIFeatures.cpp, guilib/GUIFeatures.h, guilib/GUIHMM.cpp,
	  guilib/GUIHMM.h, guilib/GUIKNN.cpp, guilib/GUIKNN.h,
	  guilib/GUIKernel.cpp, guilib/GUIKernel.h, guilib/GUILabels.cpp,
	  guilib/GUILabels.h, guilib/GUIMath.cpp, guilib/GUIMath.h,
	  guilib/GUIMatlab.cpp, guilib/GUIMatlab.h, guilib/GUIOctave.cpp,
	  guilib/GUIOctave.h, guilib/GUIPluginEstimate.cpp,
	  guilib/GUIPluginEstimate.h, guilib/GUIPreProc.cpp,
	  guilib/GUIPreProc.h, guilib/GUIPython.cpp, guilib/GUIPython.h,
	  guilib/GUIR.cpp, guilib/GUIR.h, guilib/GUISVM.cpp,
	  guilib/GUISVM.h, guilib/GUITime.cpp, guilib/GUITime.h: +don't
	  include any of the gui/* guilib/* classes when building with
	  HAVE_SWIG
	  (#ifndef SWIG ... #endif)
	* lib/numpy.i, structure/Plif.i, structure/PlifBase.h: + do not
	  allow type conversion
	  + print out errors on wrong types
	* classifier/svm/LibSVM.cpp, classifier/svm/LibSVM_oneclass.cpp,
	  classifier/svm/SVM_libsvm.cpp, classifier/svm/SVM_light.cpp,
	  classifier/svm/SVM_light.h, classifier/svm/gpdt.cpp,
	  classifier/svm/gpdtsolve.cpp, classifier/svm/gpdtsolve.h,
	  classifier/svm/gpm.cpp, classifier/svm/ssl.cpp, configure,
	  distributions/hmm/HMM.cpp, distributions/hmm/LinearHMM.cpp,
	  features/ByteFeatures.cpp, features/CharFeatures.cpp,
	  features/FKFeatures.cpp, features/RealFeatures.cpp,
	  kernel/HistogramWordKernel.cpp, kernel/LinearCharKernel.cpp,
	  kernel/SalzbergWordKernel.cpp,
	  kernel/SparseNormSquaredKernel.cpp, kernel/SpectrumKernel.cpp,
	  lib/File.cpp, lib/File.h, lib/SimpleFile.h, lib/Time.cpp,
	  lib/numpy.i, lib/suffixarray/ChildTable.cpp,
	  lib/suffixarray/ChildTable.h, lib/suffixarray/ESA.cpp,
	  preproc/PruneVarSubMean.cpp, regression/svr/LibSVR.cpp,
	  regression/svr/SVR_light.cpp, regression/svr/SVR_light.h,
	  structure/Plif.cpp, structure/PlifBase.i, structure/Structure.i:
	  +configure now enables further warnings: -Wall -Wformat -Wshadow
	  +removed rest of the shadow warnings
	  - !WE NEED A CLEAR POLICY ON NAMING VARIABLES!
	  +introduced new hidden bugs
	  +Plifbase swigify
	  
	  NOTE: swig generates a bazillion of shadowed code, some is due to
	  us
	  (naming in function headers), a lot is not

2006-12-18  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* lib/DynamicArray.h, structure/DynProg.cpp: minor fixes.
	* gui/Matlab.cpp, guilib/GUIMatlab.cpp, lib/Array.h,
	  structure/DynProg.cpp, structure/DynProg.h: extension to
	  codon-based content sensors.
	  few fixes and cleanups.

2006-12-18  Soeren Sonnenburg <sonne@debian.org>

	* lib/numpy.i:
	* classifier/svm/SVM.h:
	* classifier/svm/SVM.h: debugging...

2006-12-18  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/Plif.cpp: cleanup
	* guilib/GUIMatlab.cpp, lib/DynamicArray.h,
	  structure/PlifArray.cpp, structure/PlifArray.h: few more bugfixes
	  in PlifArray and cleanup in GUIMatlab
	* classifier/KNN.cpp, classifier/KNN.h, distance/Distance.cpp,
	  distributions/hmm/HMM.cpp, distributions/hmm/HMM.h,
	  features/Labels.cpp, features/SimpleFeatures.h,
	  features/StringFeatures.h, features/WordFeatures.cpp,
	  gui/Matlab.cpp, gui/TextGUI.cpp, guilib/GUIFeatures.cpp,
	  guilib/GUIHMM.cpp, guilib/GUIKernel.cpp, guilib/GUIMatlab.cpp,
	  guilib/GUIMatlab.h, kernel/CombinedKernel.h,
	  kernel/CommUlongStringKernel.h, kernel/CommWordKernel.h,
	  kernel/CommWordStringKernel.h, kernel/HistogramWordKernel.cpp,
	  kernel/Kernel.cpp, kernel/Kernel.h, kernel/LinearByteKernel.cpp,
	  kernel/LinearWordKernel.cpp, kernel/SpectrumKernel.cpp,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h,
	  kernel/WeightedDegreePositionPhylCharKernel.cpp, lib/Array.h,
	  lib/Array2.h, lib/Array3.h, lib/DynamicArray.h, lib/List.h,
	  lib/Trie.h, preproc/PCACut.cpp, structure/Plif.cpp,
	  structure/Plif.h, structure/PlifArray.cpp, structure/PlifArray.h:
	  Many, many minor changes to avoid shadowing, which can easily
	  lead (and has led) to mistakes.

2006-12-18  Soeren Sonnenburg <sonne@debian.org>

	* lib/Mathematics.h:
	* lib/Mathematics.h: fix floor/ceil/round

2006-12-18  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* lib/Mathematics.h: ceil hangs on amd64 ... do you know a fix?
	  (I avoid using it).
	* structure/PlifArray.cpp: use DynamicArray instead of Array.
	* lib/DynamicArray.h: fixes in append_element() and element().
	* structure/DynProg.cpp: FibHeap cleanup.
	* structure/Plif.cpp, structure/Plif.h: removed uneeded feature.
	* structure/PlifBase.h: missing file.

2006-12-17  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* guilib/GUIMatlab.cpp, structure/PlifArray.h: improved the special
	  case of only one plif for a transition.
	  G
	* gui/Matlab.cpp, guilib/GUIMatlab.cpp, lib/Array.h,
	  structure/DynProg.cpp, structure/DynProg.h, structure/Plif.cpp,
	  structure/Plif.h, structure/PlifArray.cpp, structure/PlifArray.h:
	  Many changes related to Plifs:
	  - removed field next_pen in Plif
	  - created pure virtual parent class PlifBase
	  - created an container class PlifArray that can store several
	  plifs
	  - changed the matlab interface:
	  * plif structure ignores the next_pen field
	  * the penalties matrix can be three dimensional now to support
	  many plifs
	* guilib/GUIKernel.cpp, guilib/GUIMatlab.cpp,
	  kernel/WeightedDegreePositionCharKernel.h,
	  kernel/WeightedDegreePositionPhylCharKernel.cpp,
	  kernel/WeightedDegreePositionPhylCharKernel.h, lib/Trie.h: tested
	  version of the WeightedDegree kernel with shifts that allows to
	  use conservation features.
	  use set_weights to set weights of the size seq_length x
	  num_examples.
	  These weights have to be set for training *and* test examples. If
	  not initialized, then 1 is used.
	* kernel/WeightedDegreePositionCharKernel.cpp: more of the same
	  kind ...
	* kernel/WeightedDegreePositionCharKernel.cpp: *** empty log
	  message ***
	* kernel/WeightedDegreePositionCharKernel.cpp: fixed a bug that
	  affected the correct usage of the position weights in
	  combination with shifts.
	* guilib/GUIKernel.cpp, guilib/GUIMatlab.cpp, kernel/Kernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h,
	  kernel/WeightedDegreePositionPhylCharKernel.h, lib/common.h:
	  integrated phyl kernel in matlab interface.
	  Still untested.

2006-12-16  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h,
	  kernel/WeightedDegreePositionPhylCharKernel.cpp,
	  kernel/WeightedDegreePositionPhylCharKernel.h, lib/Trie.cpp,
	  lib/Trie.h, lib/common.h: experimental code for using
	  conservation weights in the WD shift kernel.
	* kernel/WeightedDegreePositionCharKernel.h: cleanup
	* kernel/WeightedDegreePositionCharKernel.cpp: cleanup

2006-12-15  Soeren Sonnenburg <sonne@debian.org>

	* structure/DynProg.cpp, structure/DynProg.h, structure/DynProg.i:
	  +typemap fix
	  +debugging..
	* structure/DynProg.h: cleanups
	* configure: die on non linux arch / print err msg
	* configure: +put -lcplex also in POSTLINKFLAGS
	* configure: make cplex autodetection work on x86 & x86_64 ... all
	  the others need to specify --includes --libs
	* kernel/WDCharKernel.i: remove obsolete file
	* configure: +cplex autodetection

2006-12-14  Soeren Sonnenburg <sonne@debian.org>

	* configure: +document --destdir option
	* configure, lib/Mathematics.h, structure/DynProg.cpp,
	  structure/Plif.cpp, structure/Plif.h: +configure fixes
	  +ceil,floor
	  +plif limits are now real valued
	* structure/Plif.h: + get_penalty access funcitons

2006-12-13  Soeren Sonnenburg <sonne@debian.org>

	* LICENSE: +debian target for R
	  +add licensing note for Msuffsort

2006-12-12  Soeren Sonnenburg <sonne@debian.org>

	* lib/fibheap.cpp, lib/fibheap.h, structure/DynProg.cpp: remove
	  unused fibheap file (which has unclear license)
	* CONTRIBUTIONS, Makefile, classifier/Classifier.i,
	  classifier/svm/SVMLin.cpp, classifier/svm/SVMLin.h,
	  classifier/svm/SVMLin.i, classifier/svm/ssl.cpp,
	  classifier/svm/ssl.h, configure, lib/common.h: +autodetection for
	  -fPIC/-fpic for R frontend
	  +./configure --enable-swig --enable-python is now ./configure
	  --enable-swig-python
	  (just one configure option per interface for consistency)
	  +top level makefile is removed from distribution
	  +added SVMLin source code

2006-12-06  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* guilib/GUIMatlab.cpp, structure/DynProg.cpp: minor fixes.
	  G
	* guilib/GUIMatlab.cpp, structure/DynProg.cpp: many bug fixes.
	  G
	* structure/DynProg.cpp:
	* guilib/GUIMatlab.cpp, lib/Array.h, structure/DynProg.cpp: many
	  fixes.
	  G
	* guilib/GUIMatlab.cpp: *** empty log message ***
	* gui/Matlab.cpp, guilib/GUIMatlab.cpp, guilib/GUIMatlab.h,
	  structure/DynProg.cpp, structure/DynProg.h: extension for Dynamic
	  programming with loss relative to another segmentation.
	  G

2006-12-05  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/Plif.cpp: minor bug fixed
	  G

2006-12-05  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog:
	* classifier/svm/SVM.i, kernel/SpectrumKernel.i,
	  structure/DynProg.i, structure/Plif.i, structure/Structure.i:
	  preparing release 0.2.1
	* configure, gui/Matlab.cpp: +fix matlab build/compile for macosx
	  (intel and ppc)

2006-12-05  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/Plif.cpp:

2006-12-04  Soeren Sonnenburg <sonne@debian.org>

	* Makefile: fix makefile for make 3.80

2006-12-04  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* exceptions/AlphabetException.cpp.o,
	  exceptions/ClassifierException.cpp.o,
	  exceptions/FeatureException.cpp.o,
	  exceptions/KernelException.cpp.o,
	  exceptions/LabelException.cpp.o,
	  exceptions/PluginException.cpp.o, exceptions/SVMException.cpp.o:
	  removed binary files
	* exceptions/AlphabetException.cpp,
	  exceptions/AlphabetException.cpp.o,
	  exceptions/AlphabetException.h,
	  exceptions/ClassifierException.cpp,
	  exceptions/ClassifierException.cpp.o,
	  exceptions/FeatureException.cpp,
	  exceptions/FeatureException.cpp.o,
	  exceptions/KernelException.cpp, exceptions/KernelException.cpp.o,
	  exceptions/LabelException.cpp, exceptions/LabelException.cpp.o,
	  exceptions/PluginException.cpp, exceptions/PluginException.cpp.o,
	  exceptions/PluginException.h, exceptions/SVMException.cpp,
	  exceptions/SVMException.cpp.o: added forgotten files
	* classifier/KNN.h, classifier/LDA.cpp,
	  classifier/PluginEstimate.cpp, classifier/PluginEstimate.h,
	  classifier/svm/MPD.cpp, classifier/svm/Optimizer.cpp,
	  classifier/svm/SVM.cpp, classifier/svm/SVM_light.cpp,
	  exceptions/ClassifierException.h, exceptions/Exception.h,
	  exceptions/FeatureException.h, exceptions/KernelException.h,
	  exceptions/LabelException.h, exceptions/SVMException.h,
	  features/Alphabet.cpp, features/Alphabet.h,
	  features/ByteFeatures.cpp, features/CharFeatures.cpp,
	  features/Features.cpp, features/Features.h, features/Labels.cpp,
	  features/MindyGramFeatures.cpp, features/MindyGramFeatures.h,
	  features/RealFeatures.cpp, features/SimpleFeatures.h,
	  features/SparseFeatures.h, features/StringFeatures.h,
	  features/TOPFeatures.cpp, features/WordFeatures.cpp,
	  kernel/CombinedKernel.cpp, kernel/CommUlongStringKernel.cpp,
	  kernel/CommWordKernel.cpp, kernel/CommWordStringKernel.cpp,
	  kernel/CustomKernel.cpp, kernel/HistogramWordKernel.cpp,
	  kernel/Kernel.cpp, kernel/LinearByteKernel.cpp,
	  kernel/LinearCharKernel.cpp, kernel/LinearWordKernel.cpp,
	  kernel/MindyGramKernel.cpp, kernel/SalzbergWordKernel.cpp,
	  kernel/SimpleKernel.h,
	  kernel/SimpleLocalityImprovedCharKernel.cpp,
	  kernel/SparseKernel.h, kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h,
	  kernel/WordMatchKernel.cpp, preproc/PreProc.h: + added variable
	  argument support for Exception constructors
	  + Wrapped all CIO(ERROR,.. -> Exception with
	  #ifdef HAVE_PYTHON

2006-12-03  Torsten Werner <mail.twerner@googlemail.com>

	* Makefile: some refactoring
	* .version.sh, classifier/svm/Optimizer.cpp, classifier/svm/SVM.i,
	  configure, guilib/GUIClassifier.cpp, guilib/GUISVM.cpp,
	  regression/svr/SVR_light.h: - make it possible to build the
	  package without SVMlight
	  - .version.sh:
	  - don't call 'svn info' anymore
	  - use 'Id' keyword instead
	  - rationale: it should work in every source tree, not only in svn
	  working dirs

2006-12-02  Torsten Werner <mail.twerner@googlemail.com>

	* LICENSE.SVMlight: fix and beautify R build
	* Makefile, configure: fixed installation of non swig python module
	* Makefile: fix permissions of installed python files
	* Makefile: more refactoring
	* .version.sh, Makefile: - src/.version.sh: make sure we use a sane
	  locale
	  - src/Makefile: simplified
	  - Makefile: bugfix + use svn in release target

2006-12-02  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/Plif.cpp, structure/Plif.h: little extension...
	  G

2006-12-01  Soeren Sonnenburg <sonne@debian.org>

	* Makefile:

2006-11-30  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIR.cpp: fix string features in R

2006-11-30  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* classifier/Classifier.h, classifier/svm/SVM.h, exceptions,
	  exceptions/ClassifierException.h, exceptions/Exception.h,
	  exceptions/FeatureException.h, exceptions/KernelException.h,
	  exceptions/LabelException.h, exceptions/SVMException.h,
	  features/Features.h, features/Labels.h, kernel/Kernel.h: + Moved
	  exceptions to own folder.
	  TODO
	  + implement variable arguments stuff using streams
	* classifier/Classifier.h, classifier/KNN.h, classifier/LDA.cpp,
	  classifier/PluginEstimate.cpp, classifier/PluginEstimate.h,
	  classifier/svm/MPD.cpp, classifier/svm/Optimizer.cpp,
	  classifier/svm/SVM.cpp, classifier/svm/SVM.h,
	  classifier/svm/SVM.i, classifier/svm/SVM_light.cpp: + added
	  PluginException, SVMException and ClassifierException
	  + all python test cases are still running

2006-11-30  Soeren Sonnenburg <sonne@debian.org>

	* Makefile, configure: +updated makefile/confiugre for R

2006-11-30  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* features/Alphabet.cpp, features/Alphabet.h,
	  features/ByteFeatures.cpp, features/CharFeatures.cpp,
	  features/Features.cpp, features/Features.h, features/Labels.cpp,
	  features/Labels.h, features/MindyGramFeatures.cpp,
	  features/MindyGramFeatures.h, features/RealFeatures.cpp,
	  features/SimpleFeatures.h, features/SparseFeatures.h,
	  features/StringFeatures.h, features/TOPFeatures.cpp,
	  features/WordFeatures.cpp: + Added classes LabelException,
	  FeatureException and AlphabetException.
	  + Replaced all CIO::message(ERROR.. by the corresponding
	  Exception.
	* kernel/CombinedKernel.cpp, kernel/CommUlongStringKernel.cpp,
	  kernel/CommWordKernel.cpp, kernel/CommWordStringKernel.cpp,
	  kernel/CustomKernel.cpp, kernel/HistogramWordKernel.cpp,
	  kernel/Kernel.cpp, kernel/Kernel.h, kernel/LinearByteKernel.cpp,
	  kernel/LinearCharKernel.cpp, kernel/LinearWordKernel.cpp,
	  kernel/MindyGramKernel.cpp, kernel/SalzbergWordKernel.cpp,
	  kernel/SimpleKernel.h,
	  kernel/SimpleLocalityImprovedCharKernel.cpp,
	  kernel/SparseKernel.h, kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h,
	  kernel/WordMatchKernel.cpp: + added class KernelException to
	  Kernel.h
	  + modified whole kernel directory to support KernelException
	  instead of using CIO::message(ERROR..
	  all other CIO::messages are untouched.
	  TODO:
	  + generate FeatureException and ClassifierException and modify
	  files according the above rule.

2006-11-29  Soeren Sonnenburg <sonne@debian.org>

	* Makefile, configure: +octave install dir fixes
	* Makefile, classifier/LDA.cpp, configure: +integrated torsten
	  werners rpath/destdir configure patches
	* classifier/LDA.cpp, classifier/LDA.h, lib/Mathematics.cpp,
	  structure/Plif.cpp, structure/Plif.h: +some asserts in Plif
	  +some work on lda
	* configure, structure/Plif.h: fix configure typo for lapack

2006-11-28  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/DynProg.cpp: nicer printing...
	  G
	* structure/DynProg.cpp: bug fixed.
	  G

2006-11-28  Soeren Sonnenburg <sonne@debian.org>

	* structure/Plif.cpp, structure/Plif.h: +plif constructor has now
	  has a len argument

2006-11-28  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* guilib/GUIMatlab.cpp, lib/Array.h, lib/Array2.h, lib/Array3.h,
	  structure/DynProg.cpp, structure/Plif.cpp: fixed a bug in Plif
	  cache initialization.
	  other minor changes.
	  G

2006-11-28  Soeren Sonnenburg <sonne@debian.org>

	* INSTALL, classifier/svm/SVM.cpp, classifier/svm/SVM_light.cpp,
	  configure, distance/Distance.cpp, gui/R.cpp, gui/TextGUI.cpp,
	  kernel/CombinedKernel.cpp, kernel/Kernel.cpp,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.cpp, lib/Mathematics.h,
	  lib/Parallel.h, lib/Signal.cpp, lib/Signal.h, lib/io.cpp,
	  regression/svr/SVR_light.cpp, structure/Plif.h: +compile fixes
	  for win32/cygwin (now matlab/R work at least partially)
	  +update install guide

2006-11-26  Soeren Sonnenburg <sonne@debian.org>

	* Makefile, classifier/Classifier.h, classifier/svm/SVM.cpp,
	  classifier/svm/SVM.h, classifier/svm/SVM.i,
	  classifier/svm/SVM_light.cpp, configure: +many fixes...

2006-11-24  Soeren Sonnenburg <sonne@debian.org>

	* configure: allow configure to be run from a path outside of
	  shogun
	* classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h: make
	  shogun compile without svmlight
	  
	  !!!! NEVER EVER UNCOMMENT THE CHECKS FOR USE_SVMLIGHT !!!
	* classifier/svm/SVM.h, classifier/svm/SVM.i: +add get_alphas
	* classifier/Classifier.i, classifier/svm/SVM.i: SVM should be
	  under Classifier:
	  
	  so: from shogun.Classifier import SVM

2006-11-23  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* guilib/GUIMatlab.cpp, lib/Array.h, structure/DynProg.cpp,
	  structure/DynProg.h, structure/Plif.cpp, structure/Plif.h: a few
	  mem leaks fixed..
	  
	  G

2006-11-23  Soeren Sonnenburg <sonne@debian.org>

	* configure: +cygwin path magic

2006-11-23  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* gui/Matlab.cpp, guilib/GUIMatlab.cpp, structure/DynProg.cpp,
	  structure/DynProg.h, structure/Plif.cpp: minor fixes/extensions
	  in structure stuff.
	  G

2006-11-21  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/DynProg.cpp:
	* gui/Matlab.cpp, guilib/GUIMatlab.cpp, structure/DynProg.cpp,
	  structure/DynProg.h, structure/Plif.cpp, structure/Plif.h: quite
	  a few hacks...
	  G

2006-11-20  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/Optimizer.cpp, classifier/svm/SVM.cpp,
	  classifier/svm/SVM_light.cpp, configure,
	  distributions/hmm/HMM.cpp, gui/GUI.cpp, gui/Matlab.cpp,
	  guilib/GUIHMM.cpp, kernel/SpectrumKernel.cpp,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.cpp, lib/Mathematics.h,
	  lib/Signal.cpp, lib/Signal.h, lib/io.cpp,
	  lib/suffixarray/BoundedRangeWeight.cpp,
	  lib/suffixarray/ChildTable.cpp,
	  lib/suffixarray/ConstantWeight.cpp, lib/suffixarray/ESA.cpp,
	  lib/suffixarray/ExpDecayWeight.cpp,
	  lib/suffixarray/KSpectrumWeight.cpp, lib/suffixarray/LCP.cpp,
	  lib/suffixarray/LCP.h, lib/suffixarray/W_msufsort.cpp: towards
	  cygwin + matlab.

2006-11-20  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* gui/Matlab.cpp, guilib/GUIMatlab.cpp, lib/Array.h, lib/Array3.h,
	  structure/DynProg.cpp, structure/DynProg.h: DynProg derivatives
	  work now in matlab.
	  G

2006-11-18  Soeren Sonnenburg <sonne@debian.org>

	* configure: + use die "error message" when something is missing +
	  some matlab/win32 checks

2006-11-16  Soeren Sonnenburg <sonne@debian.org>

	* INSTALL, Makefile, README, configure, lib/DynamicArray.h: +fix
	  configure for R interface on osx
	  +updated readme/installation instructions, as I now
	  **trommelwirbel**
	  managed to build all the interfaces (well lets ignore matlab) on
	  OSX too.
	  +this *should* make the dynamic array resize function work with
	  zero size again.
	  +configure now checks for lapack-3 first, as this is indeed
	  different
	  from standard lapack (it uses a completely different api - and we
	  need exactly
	  that one) I also enhanced the lapack .c compile test in
	  configure.

2006-11-15  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* guilib/GUIMatlab.cpp: increased to max_order=12.
	  G
	* guilib/GUIMatlab.cpp: extended max_order for visualization from 8
	  to 10.
	  G

2006-11-15  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* classifier/svm/SVM.h, classifier/svm/SVM.i: + addded support for
	  "numpy_matrix = svm.get_alphas()"

2006-11-15  Soeren Sonnenburg <sonne@debian.org>

	* configure, guilib/GUIR.cpp: configure don't use lapack-3

2006-11-14  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIMatlab.cpp: +fix bug in set_features. the feature
	  object should be created *AFTER* the alphabet
	  has a fully initialized histogram

2006-11-14  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* gui/Matlab.cpp, guilib/GUIMatlab.cpp, guilib/GUIMatlab.h,
	  structure/DynProg.cpp, structure/DynProg.h, structure/Plif.h:
	  implemented interface for best_path_trans_deriv.
	  Untested.
	  G

2006-11-12  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM.cpp, classifier/svm/SVM_light.cpp,
	  kernel/CombinedKernel.cpp, kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.cpp: this should make wd
	  / wds kernel work for vanilla+linadd+batch kernel computation
	  
	  a) single threaded in svm training + testing
	  b) multi threaded in svm training + testing (including
	  reactive_inactive_examples)
	  
	  I've found some bugs in combined kernel / batch
	  computation/linadd ...
	  so be cautious with that... though it should work
	  
	  this of course helps all kernels in testing too and speed up
	  other linadd enabled
	  kernels in svm training / testing too
	  
	  yay :-)
	* classifier/svm/SVM.cpp, classifier/svm/SVM.h,
	  classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h,
	  kernel/CombinedKernel.cpp, kernel/CombinedKernel.h,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.cpp: THIS IS ALL UNTESTED
	  AND PROBABLY BROKEN CODE
	  
	  +this should parallelize:
	  
	  SVM evaluation for:
	  batch computation (WD kernel, WDS kernel, combined kernel)
	  linadd / vanilla kernel computation
	  
	  SVM training for
	  batch computation
	  linadd / vanilla kernel computation
	  
	  THIS IS ALL UNTESTED AND PROBABLY BROKEN CODE
	  
	  I probably need help testing it...
	* kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h: experimental:
	  parallelized compute_batch

2006-11-10  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM.cpp, classifier/svm/SVM_light.cpp,
	  kernel/CombinedKernel.cpp, kernel/CombinedKernel.h,
	  kernel/Kernel.cpp, kernel/Kernel.h,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h: + batch computation
	  now needs an index array (enumeration of vectors for which output
	  is to be computed)
	  + fix serious bug (which probably (not yet) never ever occured):
	  batch computation + combined kernel assigned
	  the weight of the combined kernel not the subkernel
	  + stuff is only tested for wds kernel (same result as before +
	  valgrind verified) but I am quite confident
	  this works for wd kernel (trivially) too / combined kernel
	  untested same applies here
	  + fixed a valgrind error in WD_scoring
	* Makefile, classifier/svm/SVM_light.cpp, guilib/GUISVM.cpp: +print
	  out whether batch comput is on / on svm training
	  +fix make clean
	  +fix batch computation on reactivate_inactive_examples (should
	  work,
	  i.e. in testing got same results
	  a) with linadd on, batch off
	  b) linadd off (batch on/off)
	  c) linadd on, batch on

2006-11-10  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* kernel/WeightedDegreeCharKernel.cpp: Fixed a problem with
	  "compute_scoring". It previously produced different results on
	  WDS and WD (actually the implementation was different). I copied
	  the code from WDS... (not so nice). Alex is currently testing it.
	  G

2006-11-10  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM_light.cpp: call batchcomput only if
	  num_suppvec >0 / free temporary arrays afterwards
	* configure: use cut -c 1 instead of head -c 1 (non posix...)
	* .generate_link_dependencies.py, INSTALL, Makefile, configure: +
	  add a lot more build instructions in INSTALL
	  + fix configure etc to make python, octave, python/swig work on
	  windows/cygwin

2006-11-09  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* classifier/svm/SVM_light.cpp: Implemented batch computation in
	  svm_light inactive example reactivation.
	  UNTESTED. Soeren.. please have a look at it and try it.
	  Its still not optimal, as it computes the output for all
	  examples...
	  
	  Gu

2006-11-08  Soeren Sonnenburg <sonne@debian.org>

	* Makefile, configure: +fix == syntax error in configure
	  +ignore configure- files on make
	  +print test error in wd kernel py example

2006-11-07  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* lib/io.h, lib/io.i: + added module for io
	  + setting of loglevels is now possible

2006-11-07  Soeren Sonnenburg <sonne@debian.org>

	* configure: matlab devel check only when matlab is on

2006-11-06  Soeren Sonnenburg <sonne@debian.org>

	* configure: matlab autodetection for cygwin
	* configure: now matlab should be autodetected
	* configure: matlab autodetection
	* configure: configure+matlab autodetection

2006-11-06  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* kernel/Chi2Kernel.cpp, kernel/Chi2Kernel.h, kernel/Chi2Kernel.i,
	  kernel/Kernel.i, kernel/SigmoidKernel.cpp,
	  kernel/SigmoidKernel.h, kernel/SigmoidKernel.i: + added Sigmoid
	  and Chi2 kernel interfaces
	* kernel/Kernel.i, kernel/LinearKernel.cpp, kernel/LinearKernel.h,
	  kernel/LinearKernel.i, kernel/PolyKernel.cpp,
	  kernel/PolyKernel.h, kernel/PolyKernel.i: + added Constructors
	  for RealFeatures
	* kernel/Kernel.i, kernel/LinearKernel.i, kernel/PolyKernel.i: +
	  added framework for testsuite for the kernels
	  + modified interfaces for Poly and Linear Kernel
	  + added doctstring support via the %feature("autodoc", "0")
	  directive
	  TODO
	  + write some test cases for Poly, Gaussian and Linear
	* kernel/AUCKernel.i, kernel/Kernel.i: + added AUCKernel

2006-11-06  Soeren Sonnenburg <sonne@debian.org>

	* configure: try to be smart and convert ~ into $HOME

2006-11-06  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* kernel/WeightedDegreeCharKernel.cpp, structure/Plif.h:

2006-11-06  Soeren Sonnenburg <sonne@debian.org>

	* configure: exclusive or for --enable-matlab --enable-python etc

2006-11-05  Soeren Sonnenburg <sonne@debian.org>

	* distance/Distance.i, distance/DistanceMachine.i: +Distance .i
	  files
	* classifier/svm/SVM.cpp, kernel/WeightedDegreeCharKernel.cpp,
	  lib/Trie.cpp, lib/Trie.h: this fixes linadd/batch computation w/
	  WD kernel
	* kernel/GaussianKernel.cpp, kernel/GaussianKernel.h,
	  kernel/WeightedDegreeCharKernel.i: ok this is what the what the
	  wd kernel python interface now looks like:
	  
	  wdk = WeightedDegreeCharKernel(trainfeat, trainfeat, degree)
	  
	  or:
	  
	  weights =
	  arange(1,degree+1,dtype=double)[::-1]/sum(arange(1,degree+1,dtype=double))
	  wdk = WeightedDegreeCharKernel(trainfeat, trainfeat, degree,
	  weights=weights)
	  
	  
	  see:
	  python/examples/test_wdk.py

2006-11-04  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreeCharKernel.i: w/o batch computation/kernel
	  optimization the py wd kernel
	  is now equiv to the oct/matlab versions

2006-11-03  Soeren Sonnenburg <sonne@debian.org>

	* classifier/Classifier.i, classifier/svm/SVM.i,
	  distributions/hmm/HMM.cpp, distributions/hmm/HMM.h,
	  kernel/KernelMachine.i: make it compile again ...

2006-11-03  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* classifier/Classifier.i, classifier/svm/SVM.i,
	  kernel/KernelMachine.i: fixed some bugs

2006-11-02  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* distributions/hmm/HMM.i: + basic hmm stuff is working under
	  python
	  + need more tests

2006-11-01  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/DynProg.h: compile-error fixed.
	  G

2006-11-01  Soeren Sonnenburg <sonne@debian.org>

	* gui/Octave.cpp, guilib/GUIOctave.cpp,
	  kernel/WeightedDegreeCharKernel.cpp: remove the structure stuff
	  from guioctave to make it compile again -> we need a build bot!!!

2006-11-01  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/DynProg.cpp:
	* structure/DynProg.cpp, structure/DynProg.h:

2006-11-01  Soeren Sonnenburg <sonne@debian.org>

	* classifier/Classifier.i, classifier/KNN.h, classifier/KNN.i,
	  classifier/svm/SVM.i, configure, distance/Distance.cpp,
	  distance/Distance.h, guilib/GUIKernel.cpp,
	  kernel/KernelMachine.i, kernel/WDCharKernel.cpp,
	  kernel/WDCharKernel.h, kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h, lib/fibheap.cpp,
	  structure/DynProg.h, structure/Plif.cpp: trying to fix the wd
	  kernel... / python interf. for struct stuff

2006-11-01  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/Plif.cpp, structure/Plif.h: Implemented support for
	  computing cumulative derivatives of the Plifs.
	  G
	* lib/DynamicArray.h: fixed a few bug that only appeared if
	  ARRAY_ASSERT is used.
	  G

2006-10-31  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* guilib/GUIKernel.cpp, kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.cpp, lib/Trie.cpp,
	  lib/Trie.h: fixed a few bugs in the WD and WDS kernel related to
	  position_weights.
	  G

2006-10-30  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* lib/DynArray.h, lib/DynArray.i, lib/DynArray2.h, lib/DynArray3.h:
	  remove the old files.
	  G
	* kernel/CommUlongStringKernel.h, lib/Array.h, lib/Array2.h,
	  lib/Array3.h, lib/DynamicArray.h, structure/DynProg.cpp,
	  structure/DynProg.h: Created a static array class and added the
	  automatic resize stuff in a derived class CDynamicArray. All
	  higher dimensional arrays are derived from the static array
	  class.
	  
	  G

2006-10-29  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* lib/DynArray2.h, lib/DynArray3.h, structure/DynProg.cpp,
	  structure/DynProg.h: some last changes.
	  Should be all nice and smooth now.
	  G
	* lib/io.h:
	* structure/DynProg.cpp:
	* lib/DynArray.h:
	* lib/DynArray.h, lib/DynArray2.h, lib/DynArray3.h,
	  structure/DynProg.cpp, structure/DynProg.h: speedups and debug.
	  G

2006-10-28  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/DynProg.cpp, structure/DynProg.h:
	* structure/DynProg.cpp:
	* lib/DynArray.h, structure/DynProg.cpp:
	* structure/DynProg.cpp:
	* lib/DynArray.h: *** empty log message ***
	* lib/DynArray.h: minor fix.
	  G
	* lib/DynArray.h, lib/DynArray2.h, lib/DynArray3.h, lib/Trie.h,
	  structure/DynProg.cpp: added some statistics functions for
	  DynArrays.
	  G

2006-10-27  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* lib/DynArray.h, lib/DynArray3.h, lib/io.h, structure/DynProg.cpp:
	  seems to work, but it is slower...
	  G
	* guilib/GUIMatlab.cpp, lib/DynArray.h, lib/DynArray2.h,
	  lib/DynArray3.h, lib/io.h, structure/DynProg.cpp,
	  structure/Plif.cpp: the matlab interface seems to still work
	  after a few minor bug fixes.
	  performing more checks now.
	  
	  G
	* guilib/GUIMatlab.cpp, lib/DynArray.h, lib/DynArray2.h,
	  lib/DynArray3.h, structure/DynProg.cpp, structure/DynProg.h: Code
	  is done.. now it needs some testing.
	  G

2006-10-26  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* lib/DynArray.h, lib/DynArray2.h, lib/DynArray3.h: fixed a few
	  DynArray bugs.
	  G
	* structure/DynProg.cpp: @Soeren: do I have to alloc the return
	  argument as well, or is this done outside? (e.g. in
	  best_path_get_states)
	  G
	* structure/DynProg.cpp: minor fix
	  G
	* structure/DynProg.cpp, structure/DynProg.h: The functions to be
	  swigged are implemented... but not tested yet.
	  Please swig them.
	  
	  Gu
	* lib/DynArray.h, lib/DynArray2.h, lib/DynArray3.h,
	  structure/DynProg.cpp, structure/DynProg.h:
	* lib/DynArray2.h, lib/DynArray3.h: compiles again
	  G
	* lib/DynArray2.h, lib/DynArray3.h, structure/DynProg.cpp:
	* lib/DynArray.h, lib/DynArray2.h, lib/DynArray3.h,
	  structure/DynProg.cpp, structure/DynProg.h: does not compile...
	  G
	* structure/DynProg.h: *** empty log message ***

2006-10-26  Soeren Sonnenburg <sonne@debian.org>

	* TODO:

2006-10-26  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* structure/DynProg.cpp, structure/DynProg.h:
	* lib/DynArray3.h, structure/DynProg.cpp, structure/DynProg.h:
	* gui/Matlab.cpp: removed model_prob_no_b_trans.
	  Hope nobody needs it.
	  G
	* distributions/hmm/HMM.cpp, distributions/hmm/HMM.h,
	  distributions/hmm/HMM_bestpath.cpp,
	  distributions/hmm/HMM_bestpath_2struct.cpp,
	  distributions/hmm/HMM_bestpath_simple.cpp,
	  distributions/hmm/fibheap.cpp, distributions/hmm/fibheap.h,
	  gui/Matlab.cpp, guilib/GUIMatlab.cpp, guilib/GUIMatlab.h,
	  lib/DynArray.h, lib/DynArray2.h, lib/Plif.cpp, lib/Plif.h,
	  lib/fibheap.cpp, lib/fibheap.h, structure, structure/DynProg.cpp,
	  structure/DynProg.h, structure/Plif.cpp, structure/Plif.h: a lot
	  of changes for the Dynamic Programing stuff.
	  It is in a new class now and in a new sub directory "structure".
	  
	  Gu

2006-10-26  Soeren Sonnenburg <sonne@debian.org>

	* distance/Distance.h, lib/Mathematics.h: forgotten fix for
	  <float.h>

2006-10-26  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* classifier/Classifier.i, classifier/KNN.i,
	  classifier/KernelPerceptron.i, classifier/LDA.i,
	  classifier/LPM.i, classifier/LinearClassifier.i,
	  classifier/Perceptron.i, classifier/PluginEstimate.i,
	  distance/Distance.h, kernel/Kernel.i: + added interface for
	  several classifiers (not tested yet)
	  + changed "float.h" to <float.h> in distance/Distance.h
	  TODO
	  + add -lcblas -llapack -latlas to linking flags for swig _wrap
	  files

2006-10-26  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* guilib/GUIMatlab.cpp, lib/Plif.h: new Plifs compile and should
	  also work.
	  Now working on the bestpath stuff.
	  G

2006-10-25  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* distributions/hmm/HMM_bestpath_2struct.cpp:
	* distributions/hmm/HMM_bestpath.cpp, lib/Plif.cpp, lib/Plif.h:
	  almost there...
	* distributions/hmm/penalty_info.cpp,
	  distributions/hmm/penalty_info.h:
	* distributions/hmm/HMM.h, distributions/hmm/HMM_bestpath.cpp,
	  distributions/hmm/penalty_info.cpp,
	  distributions/hmm/penalty_info.h, guilib/GUIMatlab.cpp,
	  lib/Plif.cpp, lib/Plif.h: tmp ci.
	  G

2006-10-25  Soeren Sonnenburg <sonne@debian.org>

	* distance/Distance.h, guilib/GUIDistance.cpp: +fix mathematics /
	  realsparse features include
	* classifier/KNN.cpp, classifier/KNN.h, distance,
	  distance/Canberra.cpp, distance/Canberra.h,
	  distance/Chebyshew.cpp, distance/Chebyshew.h,
	  distance/Distance.cpp, distance/Distance.h,
	  distance/DistanceMachine.cpp, distance/DistanceMachine.h,
	  distance/Geodesic.cpp, distance/Geodesic.h, distance/Jensen.cpp,
	  distance/Jensen.h, distance/Manhattan.cpp, distance/Manhattan.h,
	  distance/Minkowski.cpp, distance/Minkowski.h,
	  distance/RealDistance.h, distance/SimpleDistance.h,
	  distance/StringDistance.h, gui/GUI.h, gui/TextGUI.cpp,
	  gui/TextGUI.h, guilib/GUIClassifier.cpp, guilib/GUIClassifier.h,
	  guilib/GUIDistance.cpp, guilib/GUIDistance.h, guilib/GUIKNN.cpp,
	  lib/common.h: + distances (christians work)

2006-10-25  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* classifier/svm/CPLEXSVM.cpp:

2006-10-24  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* lib/Trie.h:
	* kernel/WeightedDegreeCharKernel.cpp, lib/Trie.cpp, lib/Trie.h:
	  made sure nobody uses compact tries with mismatches (conceptually
	  not really possible).
	  G
	* guilib/GUIKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h,
	  kernel/WeightedDegreePositionCharKernel_new.cpp,
	  kernel/WeightedDegreePositionCharKernel_new.h: I moved the
	  experimental code to WDS kernel class..
	  The function compute_scoring is still in the WDS class, most of
	  the dependent functions are to be found in the class CTrie.
	  G

2006-10-23  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* kernel/WeightedDegreePositionCharKernel_new.cpp,
	  kernel/WeightedDegreePositionCharKernel_new.h, lib/Trie.cpp,
	  lib/Trie.h: transformed the compute_scoring code.
	  G
	* guilib/GUIKernel.cpp, kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h,
	  kernel/WeightedDegreePositionCharKernel_new.cpp,
	  kernel/WeightedDegreePositionCharKernel_new.h, lib/Trie.cpp,
	  lib/Trie.h: WD and WDS_new should be usable now with all
	  combinations of options.
	  I did not test MKL.
	  
	  I will migrate the compute_scoring functions now and then rename
	  the class to WeightedDegreePositionCharKernel (from
	  WeightedDegreePositionCharKernel_new).
	  
	  Gu
	* guilib/GUIKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel_new.cpp, lib/Trie.cpp,
	  lib/Trie.h: Was still working. I cannot find the bug. It has
	  something to do with the terminal nodes, but I cannot figure it
	  out.
	  Have to disable compact nodes for FASTBUTMEMHUNGRY WDS kernel..
	  G

2006-10-22  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* lib/Trie.h: minor change.
	  G
	* kernel/WeightedDegreePositionCharKernel_new.cpp: Introduced
	  SLOWBUTMEMEFFICIENT for batch_computation. Gives the same results
	  as with normal kernels and with init_kernel_optimization.
	  
	  But there are still differences of up to 1e-3 in the outputs when
	  I use FASTBUTMEMHUNGRY.
	  I explain it with numerical difficulties, but I'm not sure...
	  
	  Gu
	* lib/Trie.h: The option SLOWBUTMEMEFFICIENT works, but
	  FASTBUTMEMHUNGRY still deviates (also batch_computation) for WDS
	  kernel.
	  Numerical problems?
	  G
	* kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel_new.cpp, lib/Trie.h:
	  there are still minor differences...
	  Why?
	  Gu

2006-10-21  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel_new.cpp, lib/Trie.h:
	  almost works...
	  G
	* kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel_new.cpp, lib/Trie.cpp,
	  lib/Trie.h: WD kernel works again.
	  The new WDS kernel does not work yet.
	  If you don't use WeightedDegreePositionCharKernel_new, you are
	  not affected.
	  G
	* lib/Trie.h: still working.
	  G
	* lib/Trie.h:
	* lib/Trie.h:
	* guilib/GUIKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel_new.h:
	* kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreePositionCharKernel_new.cpp,
	  kernel/WeightedDegreePositionCharKernel_new.h, lib/Trie.cpp,
	  lib/Trie.h: Experimental... changed quite a few things in the WD
	  and WDs code...
	  Still trying.
	  G

2006-10-21  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM.cpp, features/Alphabet.i, features/Features.i,
	  features/StringFeatures.h, features/StringFeatures.i,
	  kernel/Kernel.i, kernel/SpectrumKernel.cpp,
	  kernel/SpectrumKernel.h, kernel/StringKernel.i,
	  kernel/WeightedDegreePositionCharKernel.cpp, lib/common.h,
	  lib/suffixarray/BWT.h, lib/suffixarray/BoundedRangeWeight.cpp,
	  lib/suffixarray/BoundedRangeWeight.h,
	  lib/suffixarray/ChildTable.cpp, lib/suffixarray/ChildTable.h,
	  lib/suffixarray/ConstantWeight.cpp,
	  lib/suffixarray/ConstantWeight.h, lib/suffixarray/ESA.cpp,
	  lib/suffixarray/ESA.h, lib/suffixarray/ErrorCode.h,
	  lib/suffixarray/ExpDecayWeight.cpp,
	  lib/suffixarray/ExpDecayWeight.h, lib/suffixarray/I_LCPFactory.h,
	  lib/suffixarray/I_SAFactory.h, lib/suffixarray/I_WeightFactory.h,
	  lib/suffixarray/InductionSort.cpp,
	  lib/suffixarray/InductionSort.h,
	  lib/suffixarray/KSpectrumWeight.cpp,
	  lib/suffixarray/KSpectrumWeight.h, lib/suffixarray/LCP.cpp,
	  lib/suffixarray/LCP.h, lib/suffixarray/MSufSort.cpp,
	  lib/suffixarray/MSufSort.h, lib/suffixarray/Stack.h,
	  lib/suffixarray/W_kasai_lcp.cpp, lib/suffixarray/W_kasai_lcp.h,
	  lib/suffixarray/W_msufsort.cpp, lib/suffixarray/W_msufsort.h: +
	  spec kernel w/ sa (not working...)

2006-10-20  Alexander Zien <Alexander.Zien@tuebingen.mpg.de>

	* kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h: massive speedup of
	  compute_scoring

2006-10-20  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM.cpp, classifier/svm/SVM.h:
	  +init_kernel_optimization in svm object
	  +fix numpy_svm exmaple

2006-10-20  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* classifier/svm/SVM.cpp, kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h, lib/Trie.cpp,
	  lib/Trie.h: fixed batch computation bug.
	  G

2006-10-20  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreePositionCharKernel.cpp: +fix wrong mem
	  access
	  +return all degrees at once (reshape necessary...)
	* classifier/svm/SVM.h,
	  kernel/WeightedDegreePositionCharKernel.cpp:

2006-10-20  Alexander Zien <Alexander.Zien@tuebingen.mpg.de>

	* kernel/WeightedDegreePositionCharKernel.cpp: one more wd score
	  computation fix
	* kernel/WeightedDegreePositionCharKernel.cpp:

2006-10-19  Soeren Sonnenburg <sonne@debian.org>

	* configure, kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreeCharKernel.i, lib/io.cpp, lib/numpy.i: + a
	  wd kernel example, random acgt vs. aaaaa ...
	  kernel matrix gives neat results,
	  but svm currently leads to a constant result (whoops ?)

2006-10-19  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* lib/Trie.h:
	* classifier/svm/SVM_light.cpp, lib/Trie.cpp, lib/Trie.h: WD Kernel
	  with compacted leaves works ... finally.
	  In some toy experiments needed about 7 times less memory and is
	  even a bit faster:
	  
	  10k trainings daten, 500k test daten, ohne optimierung
	  8642059 tree elements
	  49.59s svm training
	  0.64s init_kernel_optimization
	  22.24s testing
	  
	  10k trainings daten, 500k test daten, mit optimierung
	  1395742 tree elements
	  45.37s svm training
	  0.37s init_kernel_optimization
	  17.78s testing
	  
	  max(abs(out-out2))=3.3993e-08
	  
	  Cheers, G
	* classifier/svm/SVM.cpp: *** empty log message ***
	* lib/io.cpp: *** empty log message ***
	* lib/Trie.cpp, lib/Trie.h:
	* lib/Trie.cpp, lib/Trie.h:
	* classifier/KNN.cpp, classifier/KernelPerceptron.cpp,
	  classifier/LDA.cpp, classifier/LPM.cpp,
	  classifier/Perceptron.cpp, classifier/svm/KerthiPrimalSVM.cpp,
	  classifier/svm/MPD.cpp, classifier/svm/Optimizer.cpp,
	  classifier/svm/SVM.cpp, classifier/svm/SVM_libsvm.cpp,
	  classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h,
	  classifier/svm/pr_loqo.cpp, distributions/Distribution.cpp,
	  distributions/Distribution.h,
	  distributions/histogram/Histogram.cpp, distributions/hmm/GHMM.h,
	  distributions/hmm/HMM.cpp, distributions/hmm/HMM.h,
	  distributions/hmm/HMM_bestpath.cpp,
	  distributions/hmm/HMM_bestpath_2struct.cpp,
	  distributions/hmm/HMM_bestpath_simple.cpp,
	  distributions/hmm/penalty_info.h, features/SimpleFeatures.h,
	  features/SparseFeatures.h, features/StringFeatures.h,
	  features/TOPFeatures.cpp, guilib/GUIMath.cpp,
	  kernel/AUCKernel.cpp, kernel/CommUlongStringKernel.h,
	  kernel/CommWordStringKernel.h, kernel/ConstKernel.h,
	  kernel/CustomKernel.h, kernel/LinearByteKernel.cpp,
	  kernel/LinearCharKernel.cpp, kernel/LinearWordKernel.cpp,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WordMatchKernel.cpp, lib/Trie.cpp, lib/Trie.h, lib/io.cpp,
	  preproc/LogPlusOne.cpp, preproc/NormOne.cpp, preproc/PCACut.cpp,
	  preproc/PruneVarSubMean.cpp, preproc/SortUlongString.cpp,
	  preproc/SortWord.cpp, preproc/SortWordString.cpp,
	  regression/svr/SVR_light.cpp: renamed Mathmatics into Mathematics
	  Many subsequent changes.
	  G
	* lib/Mathematics.i, lib/Mathmatics.i:
	* lib/Cache.h, lib/DynArray.h, lib/Mathematics.cpp,
	  lib/Mathematics.h, lib/Mathmatics.cpp, lib/Mathmatics.h,
	  lib/Mathmatics.i, lib/Trie.cpp, lib/Trie.h, lib/io.cpp: many
	  changes still working.
	  G

2006-10-19  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreePositionCharKernel.cpp,
	  lib/suffixarray/MSufSort.h: ...looks promising... but needs
	  another check by alex

2006-10-19  Alexander Zien <Alexander.Zien@tuebingen.mpg.de>

	* kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h:

2006-10-19  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h:
	* README.developer:

2006-10-19  Alexander Zien <Alexander.Zien@tuebingen.mpg.de>

	* kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h:

2006-10-19  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h:
	* features/ByteFeatures.h, features/ByteFeatures.i,
	  features/CharFeatures.h, features/CharFeatures.i,
	  features/RealFeatures.i,
	  kernel/WeightedDegreePositionCharKernel.cpp, lib/numpy.i:

2006-10-19  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* features/Alphabet.cpp: fixed bug.
	  G
	* features/Alphabet.cpp, features/Alphabet.h, lib/common.h:
	  Introduced an "RNA" alphabet.
	  G
	* lib/Trie.cpp, lib/Trie.h: still working...
	  G
	* kernel/WeightedDegreeCharKernel.cpp, lib/Trie.cpp, lib/Trie.h:
	  experimental WD kernel with compacted ends...
	  I'm still testing.
	  G

2006-10-18  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreePositionCharKernel.cpp:
	* configure:
	* Makefile, configure: +disable -fexception w/ matlab as pthreads
	  won't compile (syntax errr...
	  +exclude configure-* from linking
	* configure: +some more matlab detection
	* kernel/ConstKernel.i:
	* README.developer, TODO:
	* .generate_link_dependencies.py, Makefile, features/Labels.cpp,
	  features/RealFeatures.h, features/RealFeatures.i,
	  features/SimpleFeatures.h, kernel/Kernel.cpp, kernel/Kernel.h,
	  kernel/Kernel.i, kernel/WeightedDegreePositionCharKernel.cpp,
	  lib/numpy.i: +updated examples (retreat talk)
	  +fix makefile dependency generation
	  +fix swig IN/OUT typemaps to use fortran order

2006-10-15  Soeren Sonnenburg <sonne@debian.org>

	* lib/numpy.i: oopsi, wrong malloc sizes
	* configure: +fix octave support under osx
	* configure: create a .dll (not .so) for R/python under cygwin
	* Makefile, configure, guilib/GUIPython.cpp: +make configure work
	  on osx w/ python
	  try ./configure --enable-python --python=python2.4
	  if python -c "import numpy;" fails
	* .generate_link_dependencies.py, Makefile, configure,
	  features/Alphabet.cpp, features/Alphabet.h,
	  features/ByteFeatures.cpp, features/ByteFeatures.h,
	  features/CharFeatures.cpp, features/CharFeatures.h,
	  features/FKFeatures.cpp, features/FKFeatures.h,
	  features/RealFeatures.cpp, features/RealFeatures.h,
	  features/RealFeatures.i, features/RealFileFeatures.cpp,
	  features/RealFileFeatures.h, features/ShortFeatures.cpp,
	  features/ShortFeatures.h, features/SimpleFeatures.h,
	  features/SimpleFeatures.i, features/TOPFeatures.cpp,
	  features/TOPFeatures.h, features/WordFeatures.cpp,
	  features/WordFeatures.h, gui/Octave.cpp, gui/Python.h, gui/R.cpp,
	  guilib/GUIHMM.cpp, guilib/GUIMatlab.cpp, guilib/GUIOctave.cpp,
	  guilib/GUIPython.cpp, guilib/GUIR.cpp, lib/io.cpp,
	  lib/lapack.cpp, lib/numpy.i, lib/suffixarray/MSufSort.h:
	  +configure now does a lot more checks (tries to build simple
	  R,octave,python,numpy
	  scripts, checks for makedepend,swig etc...)
	  +Makefile should take care of swig dependencies now (incorporated
	  in .generate_link_dep...)
	  +fixed octave,python and R interface to work again :-)
	  +python now uses compatibility layer of numpy -> no more numarray
	  necessary
	  +updated all (oct/py/R) examples to work again

2006-10-13  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog, TODO:
	* Makefile, classifier/svm/LibSVM.cpp, classifier/svm/LibSVM.h,
	  classifier/svm/LibSVM.i, classifier/svm/SVM.i,
	  classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h,
	  classifier/svm/SVM_light.i, features/ByteFeatures.i,
	  features/CharFeatures.i, features/Labels.cpp, features/Labels.h,
	  features/Labels.i, features/RealFeatures.i,
	  features/ShortFeatures.i, features/SimpleFeatures.h,
	  features/SimpleFeatures.i, features/WordFeatures.i,
	  kernel/GaussianKernel.i, kernel/Kernel.i, lib/numpy.i: ...finally
	  working numpy & swig

2006-10-12  Soeren Sonnenburg <sonne@debian.org>

	* features/Alphabet.cpp, features/Alphabet.h,
	  features/ByteFeatures.i, features/CharFeatures.h,
	  features/CharFeatures.i, features/Features.i,
	  features/Labels.cpp, features/Labels.h, features/Labels.i,
	  features/RealFeatures.h, features/RealFeatures.i,
	  features/ShortFeatures.i, features/SimpleFeatures.h,
	  features/SimpleFeatures.i, features/WordFeatures.i, lib/numpy.i:
	  this works now :)
	  
	  import features.Features as f
	  import numpy as N
	  
	  feat1 = f.CharFeatures(N.chararray((10,5),1),f.DNA)
	  feat2 = f.ShortFeatures(N.zeros((10,5),N.short))
	  feat3 = f.WordFeatures(N.zeros((10,5),N.uint16))
	  feat4 = f.RealFeatures(N.zeros((10,5),N.double))
	  feat5 = f.ByteFeatures(N.zeros((10,5),N.uint8),f.DNA)
	  lab = f.Labels(N.array([1,2.,3]))

2006-10-12  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* features/CharFeatures.i, features/Features.i, lib/numpy.i: dadfa

2006-10-12  Soeren Sonnenburg <sonne@debian.org>

	* Makefile, features/CharFeatures.h, features/CharFeatures.i,
	  lib/numpy.i: ...

2006-10-12  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* features/CharFeatures.h, features/CharFeatures.i, lib/numpy.i:
	  trying to get numpy typemapping to work.

2006-10-11  Soeren Sonnenburg <sonne@debian.org>

	* features/CharFeatures.h, features/CharFeatures.i,
	  features/Features.i, lib/numpy.i: it works :-)
	  
	  import numpy as N
	  import features.Features as f
	  a=f.CCharFeatures(f.DNA, 10)
	  print a.doubleSum(N.array([1.,2.,3.,4.,5.]))
	  a.testNumpy2(N.zeros((5,10),'i'))
	  
	  x=N.chararray((3,10),1)
	  for i in xrange(10):
	  x[(0,i)]='a'
	  for i in xrange(10):
	  x[(1,i)]='b'
	  for i in xrange(10):
	  x[(2,i)]='c'
	  
	  a.testNumpy(x)
	  
	  a.doubleSum([1,2,3.14,4])

2006-10-11  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* features/CharFeatures.h, features/CharFeatures.i, lib/numpy.i:
	  added some shit
	* features/Features.i, lib/numpy.i: cleaned up numpy file added
	  numpy.i to Features.
	* lib/numpy.i: added numpy typemaps
	* features/CharFeatures.i, features/Features.i,
	  features/Labels.cpp, features/Labels.h, features/Labels.i,
	  features/SimpleFeatures.h, kernel/Kernel.i,
	  kernel/SimpleKernel.i, kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreeCharKernel.i, lib/common.i: removed LONG
	  from WeightedDegreeCharKernel, fix for the "thisown" problem.

2006-10-11  Soeren Sonnenburg <sonne@debian.org>

	* features/Alphabet.cpp, features/Alphabet.h, guilib/GUIMatlab.cpp:
	  + also check alphabet for uint8 charfeatures (not just
	  string*freatures)
	* features/Alphabet.cpp, lib/common.h: + IUPAC_NUCLEIC_ACID and
	  IUPAC_AMINO_ACID alphabets (16 / 23 symbols)
	* distributions/hmm/HMM.cpp, features/Alphabet.cpp,
	  features/Alphabet.h, features/ShortFeatures.cpp,
	  features/SimpleFeatures.h, features/SparseFeatures.h,
	  features/SparseRealFeatures.cpp, features/SparseRealFeatures.h,
	  features/SparseRealFeatures.i, features/StringFeatures.h,
	  features/WordFeatures.cpp, guilib/GUIFeatures.cpp,
	  guilib/GUIFeatures.h, guilib/GUIKernel.cpp, guilib/GUIKernel.h,
	  guilib/GUIMatlab.cpp, guilib/GUIPreProc.cpp,
	  kernel/SimpleKernel.h, kernel/SparseGaussianKernel.cpp,
	  kernel/SparseGaussianKernel.h, kernel/SparseKernel.h,
	  kernel/SparseLinearKernel.cpp, kernel/SparseLinearKernel.h,
	  kernel/SparseNormSquaredKernel.cpp,
	  kernel/SparseNormSquaredKernel.h, kernel/SparsePolyKernel.cpp,
	  kernel/SparsePolyKernel.h, kernel/StringKernel.h,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.cpp: -removed
	  sparserealfeatures
	  +introduce strict alphabet checking on set features (valid number
	  of symbols
	  and whether each symbol is valid will be checked)
	  - remove B_n B_* etc from DNA alphabet as DNA == ACGT
	* Makefile, TODO, classifier/svm/SVM_light.h:

2006-10-11  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* Makefile, classifier/svm/SVM.i, classifier/svm/SVM_light.cpp,
	  classifier/svm/SVM_light.h, classifier/svm/SVM_light.i,
	  classifier/svm/__init__.py: modified interfaces for SVMs, still a
	  problem with inheritance.

2006-10-11  Soeren Sonnenburg <sonne@debian.org>

	* kernel/CommUlongStringKernel.cpp, kernel/SimpleKernel.h,
	  kernel/SparseGaussianKernel.cpp, kernel/SparseGaussianKernel.h,
	  kernel/SparseKernel.h, kernel/SparseLinearKernel.cpp,
	  kernel/SparseLinearKernel.h, kernel/SparseNormSquaredKernel.cpp,
	  kernel/SparseNormSquaredKernel.h, kernel/SparsePolyKernel.cpp,
	  kernel/SparsePolyKernel.h, kernel/SpectrumKernel.cpp,
	  kernel/SpectrumKernel.h, kernel/SpektrumKernel.cpp,
	  kernel/SpektrumKernel.h, lib/suffixarray, lib/suffixarrays:
	* kernel/CommUlongStringKernel.h, kernel/SimpleKernel.h,
	  kernel/SparseKernel.h, kernel/SparseRealKernel.h,
	  kernel/SparseRealKernel.i, kernel/SpektrumKernel.cpp,
	  kernel/SpektrumKernel.h, kernel/StringKernel.h:

2006-10-10  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* classifier/svm/SVM.i, classifier/svm/SVM_light.i,
	  features/Features.i, features/RealFeatures.i: modified swig
	  interfaces to work with SVM module
	* classifier/Classifier.i, classifier/svm/SVM.i,
	  features/ByteFeatures.i, features/Features.i,
	  features/SimpleFeatures.i, kernel/Kernel.i,
	  kernel/KernelMachine.i, kernel/WeightedDegreeCharKernel.h:
	  modified Classifier and KernelMachine to be modules in order to
	  get the director proxy classes right.

2006-10-10  Soeren Sonnenburg <sonne@debian.org>

	* .generate_link_dependencies.py:

2006-10-10  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* kernel/Kernel.i: added swig director support
	* features/Features.i: modified Features

2006-10-10  Soeren Sonnenburg <sonne@debian.org>

	* .generate_link_dependencies.py, Makefile, features/allFeatures.i:
	  +fixed makefile for swig

2006-10-10  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* features/Features.i, features/__init__.py,
	  kernel/CommWordKernel.i, kernel/GaussianKernel.i,
	  kernel/HistogramWordKernel.i, kernel/Kernel.i,
	  kernel/PolyMatchCharKernel.i, kernel/PolyMatchWordKernel.i,
	  kernel/SimpleKernel.i, kernel/SparseGaussianKernel.i,
	  kernel/SparseKernel.i, kernel/SparseRealKernel.i,
	  kernel/StringKernel.i, kernel/WeightedDegreeCharKernel.i,
	  kernel/__init__.py: modified some interfaces

2006-10-10  Soeren Sonnenburg <sonne@debian.org>

	* Makefile:
	* classifier/Classifier.i, classifier/KNN.i,
	  classifier/KernelPerceptron.i, classifier/LDA.i,
	  classifier/LPM.i, classifier/LinearClassifier.i,
	  classifier/Perceptron.i, classifier/PluginEstimate.i,
	  classifier/svm/LibSVM.i, classifier/svm/SVM.i,
	  classifier/svm/SVM_light.i, distributions/Distribution.i,
	  features/Alphabet.i, features/ByteFeatures.i,
	  features/CharFeatures.i, features/CombinedFeatures.i,
	  features/FKFeatures.i, features/Features.i, features/Labels.i,
	  features/MindyGramFeatures.i, features/RealFeatures.i,
	  features/RealFileFeatures.i, features/ShortFeatures.i,
	  features/SimpleFeatures.i, features/SparseFeatures.i,
	  features/SparseRealFeatures.i, features/StringFeatures.i,
	  features/TOPFeatures.i, features/WordFeatures.i,
	  features/allFeatures.i, kernel/AUCKernel.i,
	  kernel/CharPolyKernel.i, kernel/Chi2Kernel.i,
	  kernel/CombinedKernel.i, kernel/CommUlongStringKernel.i,
	  kernel/CommWordKernel.i, kernel/CommWordStringKernel.i,
	  kernel/CustomKernel.i, kernel/DiagKernel.i,
	  kernel/FixedDegreeCharKernel.i, kernel/GaussianKernel.i,
	  kernel/HistogramWordKernel.i, kernel/Kernel.i,
	  kernel/KernelMachine.i, kernel/LinearByteKernel.i,
	  kernel/LinearCharKernel.i, kernel/LinearKernel.i,
	  kernel/LinearWordKernel.i, kernel/LocalityImprovedCharKernel.i,
	  kernel/MindyGramKernel.i, kernel/PolyKernel.i,
	  kernel/PolyMatchCharKernel.i, kernel/PolyMatchWordKernel.i,
	  kernel/SalzbergWordKernel.i, kernel/SigmoidKernel.i,
	  kernel/SimpleKernel.i, kernel/SimpleLocalityImprovedCharKernel.i,
	  kernel/SparseGaussianKernel.i, kernel/SparseKernel.i,
	  kernel/SparseLinearKernel.i, kernel/SparseNormSquaredKernel.i,
	  kernel/SparsePolyKernel.i, kernel/SparseRealKernel.i,
	  kernel/StringKernel.i, kernel/WDCharKernel.i,
	  kernel/WeightedDegreeCharKernel.i,
	  kernel/WeightedDegreeCharKernelPolyA.i,
	  kernel/WeightedDegreePositionCharKernel.i,
	  kernel/WordMatchKernel.i, lib/Cache.i, lib/DynArray.i,
	  lib/File.i, lib/List.i, lib/Mathmatics.i, lib/Parallel.i,
	  lib/Signal.i, lib/SimpleFile.i, lib/Time.i, lib/Trie.i,
	  lib/Version.i, lib/common.i, lib/config.i, lib/io.i,
	  lib/lapack.i: + refactoring swig... now everything is broken
	* kernel/SpektrumKernel.cpp, kernel/SpektrumKernel.h: spektrum
	  kernel based on SA (not working yet)
	* lib/suffixarrays/.ltp-sa-nsl.cpp.swp:
	* lib/suffixarrays, lib/suffixarrays/.ltp-sa-nsl.cpp.swp,
	  lib/suffixarrays/BWT.cpp, lib/suffixarrays/BWT.h,
	  lib/suffixarrays/BoundedRangeWeight.cpp,
	  lib/suffixarrays/BoundedRangeWeight.h,
	  lib/suffixarrays/ChildTable.cpp, lib/suffixarrays/ChildTable.h,
	  lib/suffixarrays/ConstantWeight.cpp,
	  lib/suffixarrays/ConstantWeight.h, lib/suffixarrays/DataType.h,
	  lib/suffixarrays/ESA.cpp, lib/suffixarrays/ESA.h,
	  lib/suffixarrays/ErrorCode.h,
	  lib/suffixarrays/ExpDecayWeight.cpp,
	  lib/suffixarrays/ExpDecayWeight.h,
	  lib/suffixarrays/I_LCPFactory.h, lib/suffixarrays/I_SAFactory.h,
	  lib/suffixarrays/I_WeightFactory.h,
	  lib/suffixarrays/InductionSort.cpp,
	  lib/suffixarrays/InductionSort.h, lib/suffixarrays/IntroSort.h,
	  lib/suffixarrays/KSpectrumWeight.cpp,
	  lib/suffixarrays/KSpectrumWeight.h, lib/suffixarrays/LCP.cpp,
	  lib/suffixarrays/LCP.h, lib/suffixarrays/MSufSort.cpp,
	  lib/suffixarrays/MSufSort.h, lib/suffixarrays/SConstruct,
	  lib/suffixarrays/Stack.h, lib/suffixarrays/W_kasai_lcp.cpp,
	  lib/suffixarrays/W_kasai_lcp.h, lib/suffixarrays/W_msufsort.cpp,
	  lib/suffixarrays/W_msufsort.h: +suffix arrays
	* ChangeLog, README.developer, TODO, classifier/svm/SVM.i,
	  features/CharFeatures.h, features/RealFeatures.h,
	  features/SimpleFeatures.h, features/StringFeatures.h,
	  features/WordFeatures.h, guilib/GUIKernel.cpp,
	  kernel/AUCKernel.cpp, kernel/AUCKernel.h, kernel/ByteKernel.h,
	  kernel/ByteKernel.i, kernel/CanberraWordKernel.cpp,
	  kernel/CanberraWordKernel.h, kernel/CharKernel.h,
	  kernel/CharKernel.i, kernel/CharPolyKernel.cpp,
	  kernel/CharPolyKernel.h, kernel/Chi2Kernel.cpp,
	  kernel/Chi2Kernel.h, kernel/CommWordKernel.cpp,
	  kernel/CommWordKernel.h, kernel/FixedDegreeCharKernel.cpp,
	  kernel/FixedDegreeCharKernel.h, kernel/GaussianKernel.cpp,
	  kernel/GaussianKernel.h, kernel/GaussianKernel.i,
	  kernel/HammingWordKernel.cpp, kernel/HammingWordKernel.h,
	  kernel/HistogramWordKernel.cpp, kernel/HistogramWordKernel.h,
	  kernel/LinearByteKernel.cpp, kernel/LinearByteKernel.h,
	  kernel/LinearCharKernel.cpp, kernel/LinearCharKernel.h,
	  kernel/LinearKernel.cpp, kernel/LinearKernel.h,
	  kernel/LinearWordKernel.cpp, kernel/LinearWordKernel.h,
	  kernel/LocalityImprovedCharKernel.cpp,
	  kernel/LocalityImprovedCharKernel.h,
	  kernel/ManhattenWordKernel.cpp, kernel/ManhattenWordKernel.h,
	  kernel/PolyKernel.cpp, kernel/PolyKernel.h,
	  kernel/PolyMatchCharKernel.cpp, kernel/PolyMatchCharKernel.h,
	  kernel/PolyMatchWordKernel.cpp, kernel/PolyMatchWordKernel.h,
	  kernel/RealKernel.h, kernel/RealKernel.i,
	  kernel/SalzbergWordKernel.cpp, kernel/SalzbergWordKernel.h,
	  kernel/ShortKernel.h, kernel/ShortKernel.i,
	  kernel/SigmoidKernel.cpp, kernel/SigmoidKernel.h,
	  kernel/SimpleKernel.h, kernel/SimpleKernel.i,
	  kernel/SimpleLocalityImprovedCharKernel.cpp,
	  kernel/SimpleLocalityImprovedCharKernel.h, kernel/StringKernel.h,
	  kernel/WDCharKernel.cpp, kernel/WDCharKernel.h,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreeCharKernel.i,
	  kernel/WeightedDegreeCharKernelPolyA.cpp,
	  kernel/WeightedDegreeCharKernelPolyA.h,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h,
	  kernel/WeightedDegreePositionCharKernel.i, kernel/WordKernel.h,
	  kernel/WordKernel.i, kernel/WordMatchKernel.cpp,
	  kernel/WordMatchKernel.h: +make use of templates wherever
	  possible,
	  this removes all the {Byte,Char,Word,Real}Kernel* fils

2006-10-08  Soeren Sonnenburg <sonne@debian.org>

	* Makefile, features/Alphabet.i, features/RealFeatures.i: +swig
	  Makefile fixes

2006-10-07  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM.h, classifier/svm/SVM_light.cpp,
	  guilib/GUISVM.h, kernel/GaussianKernel.cpp,
	  kernel/GaussianKernel.h, kernel/GaussianKernel.i,
	  kernel/Kernel.h, kernel/Kernel.i, kernel/RealKernel.h,
	  kernel/RealKernel.i, kernel/SimpleKernel.h,
	  kernel/SimpleKernel.i: +really introduce shrinking
	  +make the multiple svms example work again w/ swig
	* classifier/svm/SVM.h, classifier/svm/SVM_light.cpp,
	  gui/TextGUI.cpp, guilib/GUISVM.cpp, guilib/GUISVM.h,
	  kernel/Kernel.i: + option to disable shrinking in svm training

2006-10-06  Soeren Sonnenburg <sonne@debian.org>

	* features/Alphabet.i: +forgot the alphabet for swig

2006-10-06  Konrad Rieck <Konrad.Rieck@first.fraunhofer.de>

	* features/MindyGramFeatures.cpp, features/MindyGramFeatures.h,
	  guilib/GUIFeatures.cpp, guilib/GUIFeatures.h: fixed bugs in mindy
	  conversion routines
	* features/MindyGramFeatures.cpp, features/MindyGramFeatures.h,
	  features/StringFeatures.h, guilib/GUIFeatures.cpp,
	  guilib/GUIFeatures.h, guilib/GUIMatlab.cpp, guilib/GUIMatlab.h:
	  templates to support various conversions, e.g. string byte to
	  string ulong or string char to string word, or or or...
	* guilib/GUIMatlab.cpp: added matlab support byte matrices and cell
	  arrays of bytes

2006-10-06  Soeren Sonnenburg <sonne@debian.org>

	* features/ByteFeatures.cpp, features/CharFeatures.cpp,
	  features/CharFeatures.i, features/RealFeatures.i,
	  guilib/GUIFeatures.cpp, kernel/Kernel.i,
	  kernel/WeightedDegreeCharKernel.i, lib/Trie.h, lib/Trie.i,
	  lib/common.i: +really use alphabet for byte features
	  +freak out w/ swig
	* features/ByteFeatures.cpp, features/ByteFeatures.h: +byte
	  features now also have an alphabet
	* gui/Matlab.cpp, guilib/GUIMatlab.cpp, guilib/GUIMatlab.h:
	  +optional zero terminate the strings again as sscanf fails if we
	  don't
	* gui/Matlab.cpp, guilib/GUIMatlab.cpp, guilib/GUIMatlab.h: + make
	  getstring function not use mxGetString as it is locale sensitive
	  and
	  might screw up no ascii (0x80-0xff) chars, but do it manually
	  instead. On
	  the way I've done some input sanitizing (no more buffer overflows
	  as we now
	  use strncmp & friends everywhere + no more strlen). this also
	  save 1 byte
	  per string in stringfeatures and has different code for char
	  matrices too
	  (testme!)

2006-10-05  Soeren Sonnenburg <sonne@debian.org>

	* features/Alphabet.cpp, features/Alphabet.h,
	  features/StringFeatures.h, guilib/GUIMatlab.cpp: this should now
	  really fix the 8bit alphabet case
	* features/Alphabet.cpp, features/StringFeatures.h,
	  kernel/CommUlongStringKernel.cpp, kernel/CommWordKernel.cpp,
	  kernel/CommWordStringKernel.cpp: hopefully fixes spec* kernels
	  for too long strings

2006-10-03  Soeren Sonnenburg <sonne@debian.org>

	* kernel/CommUlongStringKernel.cpp, kernel/CommWordKernel.cpp,
	  kernel/CommWordStringKernel.cpp: + for very long repetitive
	  strings INT as result might not be enough (overflow)
	  -> make it a DREAL

2006-10-02  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* kernel/WeightedDegreeCharKernel.cpp, lib/Trie.cpp: Fixed two bugs
	  in the new trie code related to uninitialized variables.
	  Gu

2006-10-02  Soeren Sonnenburg <sonne@debian.org>

	* kernel/Trie.cpp, kernel/Trie.h,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h, lib/Trie.cpp, lib/Trie.h,
	  lib/Trie.i: move trie to lib (to list & dynarray)
	* classifier/svm/SVM_light.cpp: + really learn to the set accuracy
	  svm_epsilon, works with rbf/ wds+linadd /wds-linadd
	* classifier/svm/SVM_light.cpp: fully screw svm light

2006-09-29  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* kernel/WeightedDegreeCharKernel.cpp_orig,
	  kernel/WeightedDegreeCharKernel.h_orig:
	* kernel/Trie.cpp, kernel/Trie.h,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.cpp_orig,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreeCharKernel.h_orig: Major change in Weighted
	  Degree kernel (experimental):
	  
	  I moved all the trie-related code a separate class CTrie.
	  In principle, nothing should change, but I did not try it..
	  
	  Gu
	* kernel/Trie.cpp, kernel/Trie.h,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.cpp_orig,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreeCharKernel.h_orig:

2006-09-29  Soeren Sonnenburg <sonne@debian.org>

	* features/StringFeatures.h, lib/Mathmatics.h: +workaround for
	  broken powl() (powl is crashing on congo!!!)
	* features/Alphabet.cpp: +fail on unknown alphabet
	* configure:

2006-09-24  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h: +this *should* fix the
	  scoring computation function

2006-09-22  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/LibSVM_oneclass.cpp,
	  classifier/svm/LibSVM_oneclass.h, classifier/svm/SVM.cpp,
	  classifier/svm/SVM.h, classifier/svm/SVM_libsvm.cpp,
	  gui/TextGUI.cpp, guilib/GUISVM.cpp, guilib/GUISVM.h,
	  kernel/Kernel.cpp, lib/common.h: + LIBSVM_ONECLASS

2006-09-20  Soeren Sonnenburg <sonne@debian.org>

	* guilib/GUIOctave.cpp: +cell array support in octave (strings of
	  different length :)
	* classifier/svm/LibSVM.h, configure, features/Alphabet.cpp,
	  guilib/GUIPython.cpp, guilib/GUIR.cpp, guilib/GUIR.h,
	  lib/common.h: +configure now checks for math, posix threads,
	  atlas/lapack, readline
	  +compile fixes for R & python, the RAW alphabet type is now
	  RAWBYTE
	  (as it was conflicting with R)
	* configure:
	* configure:
	* configure:
	* .cpuinfo.c, INSTALL, configure: further configure updates / more
	  docu in INSTALL
	* .cpuinfo.c, configure: further configure fixes ...

2006-09-18  Soeren Sonnenburg <sonne@debian.org>

	* Makefile, configure: +make install
	  +make -C src install DESTDIR=$(pwd)/debian/
	  +fixed name for binary
	* kernel/Kernel.cpp, kernel/Kernel.h, lib/common.h: This *should*
	  fix kernel cache stuff for svmlight:
	  
	  +kernel cache indices are now checked to fit in KERNELCACHE_IDX
	  type
	  an assertion is thrown if not
	  +kernel cache is reduced to
	  totdoc*totdoc*sizeof(KERNELCACHE_ELEM) if larger
	  +KERNELCACHE_IDX is now LONG again, access operations to the
	  cache buffer do a
	  cast to KERNELCACHE_IDX, while the cache lines are limited to
	  INTs only
	  (i.e. caching max ~2^31 cache lines (~2^62 elements) is possible)

2006-09-11  Soeren Sonnenburg <sonne@debian.org>

	* configure: make configure work when $INCLUDES / $LIBS are empty
	* ChangeLog, LICENSE, configure, features/StringFeatures.h,
	  guilib/GUIOctave.cpp, lib/Mathmatics.h: + compile fixes for
	  octave
	  + modify configure to obey INCLUDES/LIBS environment variables as
	  well as
	  --libs --includes options
	  + fix compilation on g++-4.1.2
	  + note the GPL exception in LICENSE (i.e. when compiled with
	  --enable-svm-light binary is under LICENSE.SVMlight)

2006-09-06  Konrad Rieck <Konrad.Rieck@first.fraunhofer.de>

	* features/MindyGramFeatures.cpp, features/MindyGramFeatures.h,
	  gui/TextGUI.cpp, guilib/GUIFeatures.cpp, guilib/GUIKernel.cpp,
	  kernel/MindyGramKernel.cpp, kernel/MindyGramKernel.h: extended
	  Mindy support:
	  (a) embedding function: count, frequency, binary
	  (b) similarity measures: see sm.c in mindy distribution
	  (c) parameters for measures: kernel width, minkowski k, etc...

2006-09-01  Soeren Sonnenburg <sonne@debian.org>

	* gui/Matlab.cpp, guilib/GUIMatlab.cpp, guilib/GUIMatlab.h,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h: + WD und WD-Position
	  kernel scoring functions -> gibt saucoole positionsgewichtungen -
	  nieder mit MKL!

2006-08-31  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h: +support higher order scoring
	  info
	* classifier/Classifier.cpp, classifier/Classifier.h,
	  classifier/KNN.cpp, classifier/KNN.h,
	  classifier/KernelPerceptron.cpp, classifier/KernelPerceptron.h,
	  classifier/LDA.cpp, classifier/LDA.h, classifier/LPM.cpp,
	  classifier/LPM.h, classifier/LinearClassifier.cpp,
	  classifier/LinearClassifier.h, classifier/Perceptron.cpp,
	  classifier/Perceptron.h, classifier/PluginEstimate.cpp,
	  classifier/PluginEstimate.h, classifier/svm/CPLEXSVM.cpp,
	  classifier/svm/CPLEXSVM.h, classifier/svm/GPBTSVM.cpp,
	  classifier/svm/GPBTSVM.h, classifier/svm/KerthiPrimalSVM.cpp,
	  classifier/svm/KerthiPrimalSVM.h, classifier/svm/LibSVM.cpp,
	  classifier/svm/LibSVM.h, classifier/svm/MPD.cpp,
	  classifier/svm/MPD.h, classifier/svm/SVM.cpp,
	  classifier/svm/SVM.h, classifier/svm/SVM_libsvm.cpp,
	  classifier/svm/SVM_libsvm.h, classifier/svm/gpdt.cpp,
	  classifier/svm/gpdt.h, classifier/svm/gpdtsolve.cpp,
	  classifier/svm/gpdtsolve.h, classifier/svm/gpm.cpp,
	  classifier/svm/gpm.h, classifier/svm/pr_loqo.cpp,
	  classifier/svm/pr_loqo.h, distributions/Distribution.cpp,
	  distributions/Distribution.h,
	  distributions/histogram/Histogram.cpp,
	  distributions/histogram/Histogram.h, distributions/hmm/GHMM.cpp,
	  distributions/hmm/GHMM.h, distributions/hmm/HMM.cpp,
	  distributions/hmm/HMM.h, distributions/hmm/HMM_bestpath.cpp,
	  distributions/hmm/HMM_bestpath_2struct.cpp,
	  distributions/hmm/HMM_bestpath_simple.cpp,
	  distributions/hmm/LinearHMM.cpp, distributions/hmm/LinearHMM.h,
	  distributions/hmm/fibheap.cpp, distributions/hmm/fibheap.h,
	  distributions/hmm/penalty_info.cpp,
	  distributions/hmm/penalty_info.h, features/Alphabet.cpp,
	  features/Alphabet.h, features/ByteFeatures.cpp,
	  features/ByteFeatures.h, features/CharFeatures.cpp,
	  features/CharFeatures.h, features/CombinedFeatures.cpp,
	  features/CombinedFeatures.h, features/FKFeatures.cpp,
	  features/FKFeatures.h, features/Features.cpp,
	  features/Features.h, features/Labels.cpp, features/Labels.h,
	  features/MindyGramFeatures.cpp, features/MindyGramFeatures.h,
	  features/RealFeatures.cpp, features/RealFileFeatures.cpp,
	  features/RealFileFeatures.h, features/ShortFeatures.cpp,
	  features/ShortFeatures.h, features/SimpleFeatures.h,
	  features/SparseFeatures.h, features/SparseRealFeatures.cpp,
	  features/SparseRealFeatures.h, features/StringFeatures.cpp,
	  features/StringFeatures.h, features/TOPFeatures.cpp,
	  features/WordFeatures.cpp, features/WordFeatures.h, gui/GUI.cpp,
	  gui/GUI.h, gui/Matlab.cpp, gui/Octave.cpp, gui/Python.cpp,
	  gui/Python.h, gui/R.cpp, gui/TextGUI.cpp, gui/TextGUI.h,
	  guilib/GUIClassifier.cpp, guilib/GUIClassifier.h,
	  guilib/GUIFeatures.cpp, guilib/GUIFeatures.h, guilib/GUIHMM.cpp,
	  guilib/GUIHMM.h, guilib/GUIKNN.cpp, guilib/GUIKNN.h,
	  guilib/GUIKernel.cpp, guilib/GUIKernel.h, guilib/GUILabels.cpp,
	  guilib/GUILabels.h, guilib/GUIMath.cpp, guilib/GUIMath.h,
	  guilib/GUIMatlab.cpp, guilib/GUIOctave.cpp, guilib/GUIOctave.h,
	  guilib/GUIPluginEstimate.cpp, guilib/GUIPluginEstimate.h,
	  guilib/GUIPreProc.cpp, guilib/GUIPreProc.h, guilib/GUIPython.cpp,
	  guilib/GUIPython.h, guilib/GUIR.cpp, guilib/GUIR.h,
	  guilib/GUISVM.cpp, guilib/GUISVM.h, guilib/GUITime.cpp,
	  guilib/GUITime.h, kernel/AUCKernel.cpp, kernel/AUCKernel.h,
	  kernel/ByteKernel.h, kernel/CanberraWordKernel.cpp,
	  kernel/CanberraWordKernel.h, kernel/CharKernel.h,
	  kernel/CharPolyKernel.cpp, kernel/CharPolyKernel.h,
	  kernel/Chi2Kernel.cpp, kernel/Chi2Kernel.h,
	  kernel/CombinedKernel.cpp, kernel/CombinedKernel.h,
	  kernel/CommUlongStringKernel.cpp, kernel/CommUlongStringKernel.h,
	  kernel/CommWordKernel.cpp, kernel/CommWordKernel.h,
	  kernel/CommWordStringKernel.cpp, kernel/CommWordStringKernel.h,
	  kernel/ConstKernel.cpp, kernel/ConstKernel.h,
	  kernel/CustomKernel.cpp, kernel/CustomKernel.h,
	  kernel/DiagKernel.cpp, kernel/DiagKernel.h,
	  kernel/FixedDegreeCharKernel.cpp, kernel/FixedDegreeCharKernel.h,
	  kernel/GaussianKernel.cpp, kernel/GaussianKernel.h,
	  kernel/HammingWordKernel.cpp, kernel/HammingWordKernel.h,
	  kernel/HistogramWordKernel.cpp, kernel/HistogramWordKernel.h,
	  kernel/Kernel.cpp, kernel/Kernel.h, kernel/KernelMachine.cpp,
	  kernel/KernelMachine.h, kernel/LinearByteKernel.cpp,
	  kernel/LinearByteKernel.h, kernel/LinearCharKernel.cpp,
	  kernel/LinearCharKernel.h, kernel/LinearKernel.cpp,
	  kernel/LinearKernel.h, kernel/LinearWordKernel.cpp,
	  kernel/LinearWordKernel.h, kernel/LocalityImprovedCharKernel.cpp,
	  kernel/LocalityImprovedCharKernel.h,
	  kernel/ManhattenWordKernel.cpp, kernel/ManhattenWordKernel.h,
	  kernel/PolyKernel.cpp, kernel/PolyKernel.h,
	  kernel/PolyMatchCharKernel.cpp, kernel/PolyMatchCharKernel.h,
	  kernel/PolyMatchWordKernel.cpp, kernel/PolyMatchWordKernel.h,
	  kernel/RealKernel.h, kernel/SalzbergWordKernel.cpp,
	  kernel/SalzbergWordKernel.h, kernel/ShortKernel.h,
	  kernel/SigmoidKernel.cpp, kernel/SigmoidKernel.h,
	  kernel/SimpleKernel.h,
	  kernel/SimpleLocalityImprovedCharKernel.cpp,
	  kernel/SimpleLocalityImprovedCharKernel.h,
	  kernel/SparseGaussianKernel.cpp, kernel/SparseGaussianKernel.h,
	  kernel/SparseKernel.h, kernel/SparseLinearKernel.cpp,
	  kernel/SparseLinearKernel.h, kernel/SparseNormSquaredKernel.cpp,
	  kernel/SparseNormSquaredKernel.h, kernel/SparsePolyKernel.cpp,
	  kernel/SparsePolyKernel.h, kernel/SparseRealKernel.h,
	  kernel/StringKernel.h, kernel/WDCharKernel.cpp,
	  kernel/WDCharKernel.h, kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreeCharKernelPolyA.cpp,
	  kernel/WeightedDegreeCharKernelPolyA.h,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h, kernel/WordKernel.h,
	  kernel/WordMatchKernel.cpp, kernel/WordMatchKernel.h,
	  lib/Cache.h, lib/Cplex.cpp, lib/Cplex.h, lib/DynArray.h,
	  lib/File.cpp, lib/File.h, lib/List.h, lib/Mathmatics.cpp,
	  lib/Mathmatics.h, lib/Parallel.cpp, lib/Parallel.h,
	  lib/Signal.cpp, lib/Signal.h, lib/SimpleFile.h, lib/Time.cpp,
	  lib/Time.h, lib/Version.cpp, lib/Version.h, lib/common.h,
	  lib/io.cpp, lib/io.h, lib/lapack.cpp, lib/lapack.h,
	  preproc/LogPlusOne.cpp, preproc/LogPlusOne.h,
	  preproc/NormDerivativeLem3.cpp, preproc/NormDerivativeLem3.h,
	  preproc/NormOne.cpp, preproc/NormOne.h, preproc/PCACut.cpp,
	  preproc/PCACut.h, preproc/PreProc.cpp, preproc/PreProc.h,
	  preproc/PruneVarSubMean.cpp, preproc/PruneVarSubMean.h,
	  preproc/RealPreProc.h, preproc/ShortPreProc.cpp,
	  preproc/ShortPreProc.h, preproc/SimplePreProc.h,
	  preproc/SortUlongString.cpp, preproc/SortUlongString.h,
	  preproc/SortWord.cpp, preproc/SortWord.h,
	  preproc/SortWordString.cpp, preproc/SortWordString.h,
	  preproc/SparsePreProc.h, preproc/StringPreProc.h,
	  preproc/WordPreProc.cpp, preproc/WordPreProc.h,
	  regression/svr/LibSVR.cpp, regression/svr/LibSVR.h,
	  regression/svr/SVR_light.cpp, regression/svr/SVR_light.h: + now
	  alphabets are handled via the CAlphabet class,
	  + stringfeatures now require a alphabet name
	  + fixed sorting function w/ ULONGs (bug might have occured
	  with datatypes above DREAL)
	  + updated copyright info

2006-08-31  Konrad Rieck <Konrad.Rieck@first.fraunhofer.de>

	* features/MindyGramFeatures.cpp, features/StringFeatures.h:
	  debugging...
	* classifier/LDA.cpp, configure, features/MindyGramFeatures.cpp,
	  features/StringFeatures.h, guilib/GUIMatlab.cpp,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h: several minor fixes by sonne

2006-08-31  Soeren Sonnenburg <sonne@debian.org>

	* gui/Matlab.cpp, guilib/GUIMatlab.cpp, guilib/GUIMatlab.h,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreePositionCharKernel.h: + first try to get a
	  weighted scoring

2006-08-30  Soeren Sonnenburg <sonne@debian.org>

	* features/CharFeatures.cpp, features/StringFeatures.h: +hurray,
	  BYTE/RAW features are now working, however as features are now
	  set using
	  
	  sg('set_features', 'TRAIN', x, 'RAW');
	  
	  the alphabet argument should be obsolete from convert, i.e.
	  instead of
	  sg('send_command', sprintf('convert TRAIN STRING CHAR STRING
	  ULONG RAW 8 7'));
	  one should use
	  sg('send_command', sprintf('convert TRAIN STRING CHAR STRING
	  ULONG 8 7'));
	  or keep it as extra check - no ???
	* classifier/svm/Optimizer.cpp, classifier/svm/Optimizer.h,
	  classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h,
	  distributions/hmm/HMM.cpp, features/CharFeatures.cpp,
	  features/CharFeatures.h, features/CombinedFeatures.cpp,
	  features/Features.cpp, features/Features.h,
	  features/RealFeatures.h, features/ShortFeatures.cpp,
	  features/ShortFeatures.h, features/SimpleFeatures.h,
	  features/SparseRealFeatures.h, features/StringFeatures.h,
	  features/WordFeatures.cpp, features/WordFeatures.h,
	  guilib/GUIFeatures.cpp, guilib/GUIKernel.cpp,
	  guilib/GUIMatlab.cpp, kernel/Kernel.cpp, kernel/Kernel.h,
	  lib/File.cpp, lib/File.h, lib/SimpleFile.h, lib/common.h,
	  regression/svr/SVR_light.cpp, regression/svr/SVR_light.h: +LONG
	  is now definitely 64bit
	  +almost all occurances of LONG, long long, long int, long
	  were converted to INT (as this is enough)

2006-08-30  Konrad Rieck <Konrad.Rieck@first.fraunhofer.de>

	* kernel/MindyGramKernel.cpp: fixed changes in mindy interface

2006-08-30  Soeren Sonnenburg <sonne@debian.org>

	* features/StringFeatures.h, guilib/GUIMatlab.cpp, lib/common.h,
	  lib/io.h: - undo CHAR -> signed char change, as then CHAR* bla =
	  "dfadf" is a nogo on x86
	  - hopefully fix histogram creation (and thus RAW BYTE features)
	  by converting signed -> unsigned
	* features/CharFeatures.h, lib/common.h: +make CHAR case sensitive
	  and remap function return BYTE (unsigned!!!)

2006-08-30  Konrad Rieck <Konrad.Rieck@first.fraunhofer.de>

	* features/StringFeatures.h, guilib/GUIMatlab.cpp,
	  kernel/CommUlongStringKernel.cpp,
	  kernel/CommWordStringKernel.cpp, lib/common.h: fixed
	  commstring{word|ulong}kernel bugs
	* features/MindyGramFeatures.cpp, features/MindyGramFeatures.h,
	  kernel/MindyGramKernel.cpp, kernel/MindyGramKernel.h: fixed minor
	  bugs in mindy code and did code beautification

2006-08-30  Soeren Sonnenburg <sonne@debian.org>

	* features/CharFeatures.cpp, guilib/GUIFeatures.cpp,
	  guilib/GUIMatlab.cpp, guilib/GUIOctave.cpp, guilib/GUIPython.cpp,
	  guilib/GUIR.cpp, lib/common.h: relabel BYTE -> RAW (due to name
	  clash with featue type..)
	* features/CharFeatures.cpp, gui/Octave.cpp, gui/R.cpp,
	  gui/TextGUI.cpp, guilib/GUIFeatures.cpp, guilib/GUIMatlab.cpp,
	  guilib/GUIOctave.cpp, guilib/GUIPython.cpp, guilib/GUIPython.h,
	  guilib/GUIR.cpp, guilib/GUIR.h, lib/common.h: +support for non
	  DNA (BYTE,PROTEIN,...) alphabet

2006-08-29  Soeren Sonnenburg <sonne@debian.org>

	* features/StringFeatures.h, guilib/GUIKernel.cpp: +ifdef mindy
	* TODO, guilib/GUIKernel.cpp: +comm word kernel obeys normalization
	  options

2006-08-29  Konrad Rieck <Konrad.Rieck@first.fraunhofer.de>

	* features/GramFeatures.cpp, features/GramFeatures.h,
	  features/GramFeatures.i, features/MindyGramFeatures.cpp,
	  features/MindyGramFeatures.h, features/MindyGramFeatures.i,
	  guilib/GUIFeatures.cpp, guilib/GUIFeatures.h,
	  guilib/GUIKernel.cpp, kernel/MindyGramKernel.cpp,
	  kernel/MindyGramKernel.h, kernel/MindyGramKernel.i, lib/common.h:
	  rudimentary interface (features/kernel) to mindy library

2006-08-25  Soeren Sonnenburg <sonne@debian.org>

	* features/GramFeatures.cpp, features/GramFeatures.h,
	  features/GramFeatures.i, guilib/GUIFeatures.cpp,
	  guilib/GUIFeatures.h, lib/common.h: +konrads mindy lib based
	  n-gram / bag-of-words features (kernel to follow...)

2006-08-09  Soeren Sonnenburg <sonne@debian.org>

	* configure: +new experimental configure (should work on macbook
	  pro's)

2006-07-14  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* kernel/WeightedDegreePositionCharKernel.cpp:

2006-07-01  Soeren Sonnenburg <sonne@debian.org>

	* configure: +compile fix for matlab+osx

2006-06-30  Soeren Sonnenburg <sonne@debian.org>

	* ChangeLog:

2006-06-29  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/SVM_light.cpp, guilib/GUIMatlab.cpp,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreePositionCharKernel.cpp: +fix entropy
	  function
	  +use SLOWBUTMEMEFFICIENT in reactivate_inactive_examples
	  +fix: use normalization when requested w/ WDPosition kernel
	  +fix: shift of length 0 resulted in unitialized vec array
	  (WDPosition kernel)
	  +tons of fixes in WD kernel:
	  1. linadd should work again
	  2. batch computation implemented and works
	  3. mkl does at least not crash and leads to same objective value
	  (but output on test set is different)
	  4. used remap() function w/ alphabet from character features
	  (should speed up a lot)
	  5. removed has_floats from Trie structure (saves some mem)
	  
	  however WD+mismatch functions seem to not work, MKL w/ WD shift
	  kernel might work but need example!
	* kernel/WeightedDegreeCharKernel.cpp:

2006-06-28  Soeren Sonnenburg <sonne@debian.org>

	* kernel/WeightedDegreePositionCharKernel.cpp: good news: this
	  kernel is now really really working (except for maybe MKL -
	  i.e. someone needs to test it w/ MKL!), however it works with NON
	  CONSTANT
	  SHIFTS, with and w/o batch computation, with
	  FASTBUTMEMHUNGRY/SLOWBUTMEMEFFICIENT
	  the added (advanced!) example shows the usage. note: batch
	  computation is emulated
	  when the combined kernel is used (by using linadd/ if that is not
	  available linadd
	  is emulated)
	* classifier/svm/SVM_light.cpp, kernel/LinearByteKernel.cpp,
	  kernel/LinearCharKernel.cpp, kernel/LinearWordKernel.cpp,
	  kernel/WordMatchKernel.cpp, lib/common.h: +LONGDREAL -> LONGREAL
	  +call delete_optimization after svm training, this fixes the
	  'zero output on when init_kernel_optimization is forgotten' issue

2006-06-26  Soeren Sonnenburg <sonne@debian.org>

	* configure: - mpisvm
	  + lots of documentation ...

2006-06-25  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* kernel/WeightedDegreePositionCharKernel.cpp: experimental code
	  for protein sequences ...
	  G

2006-06-25  Soeren Sonnenburg <sonne@debian.org>

	* lib/Mathmatics.cpp: + compile fix for cygwin W32 arch

2006-06-23  Soeren Sonnenburg <sonne@debian.org>

	* kernel/GaussianKernel.i, kernel/RealKernel.i,
	  kernel/SimpleKernel.i:
	* kernel/GaussianKernel.cpp, kernel/GaussianKernel.h:
	* classifier/svm/LibSVM.i, classifier/svm/SVM_light.i:
	* features/RealFeatures.i:
	* features/CharFeatures.i, features/RealFeatures.i,
	  features/SimpleFeatures.i, lib/common.i: just cleanups

2006-06-23  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* features/RealFeatures.h: changed include order
	* kernel/GaussianKernel.i: modified
	* features/RealFeatures.i: i
	* features/__init__.py: added new submodule
	* features/SimpleFeatures.i: added %template directive to solve the
	  issublcass(RealFatures,SimpleFeatures) problem
	* features/allFeatures.i: combined interface file for Features,
	  SimpleFeatures and RealFeatures.
	* features/Features.i, features/RealFeatures.i,
	  features/__init__.py, kernel/GaussianKernel.i,
	  kernel/__init__.py: added GaussianKernel interface
	* features/RealFeatures.i: new constructor added

2006-06-23  Soeren Sonnenburg <sonne@debian.org>

	* features/RealFeatures.h:
	* features/RealFeatures.h: + realfeatures

2006-06-22  Soeren Sonnenburg <sonne@debian.org>

	* lib/common.i:

2006-06-22  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* features/CharFeatures.i: added include common.i
	* lib/__init__.py: added module init
	* features/CharFeatures.i, kernel/WeightedDegreeCharKernel.i,
	  lib/common.i: added some stuff
	* lib/common.i: modified common interface
	* classifier/svm/SVM_light.i, lib/common.i, swigfiles: removed
	  swigfiles dir

2006-06-21  Soeren Sonnenburg <sonne@debian.org>

	* gui/Octave.cpp, guilib/GUIOctave.cpp, guilib/GUIOctave.h,
	  kernel/CommWordStringKernel.h, lib/Mathmatics.h: +hmm example
	  working in octave / several hmm fixes + svm_classify_example ...
	* distributions/hmm/HMM.cpp, gui/Matlab.cpp, guilib/GUIMatlab.cpp,
	  guilib/GUIMatlab.h: + fixed hmm w/ matlab
	  + nice hmm matlab example

2006-06-21  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* features/Labels.i, features/SimpleFeatures.i,
	  kernel/CharKernel.i, kernel/SimpleKernel.i,
	  kernel/WeightedDegreeCharKernel.i,
	  kernel/WeightedDegreePositionCharKernel.i: fixed even some more
	  lib/common.i issues
	* classifier/svm/SVM.i, classifier/svm/SVM_light.i,
	  features/CharFeatures.i, features/Features.i, kernel/Kernel.i,
	  lib/common.i: fixed some include paths

2006-06-21  Soeren Sonnenburg <sonne@debian.org>

	* configure, guilib/GUIOctave.cpp: +octave set/get_features fixes
	  +examples for svm/svr w/ octave
	* lib/lapack.c, lib/lapack.cpp: c -> cpp

2006-06-20  Soeren Sonnenburg <sonne@debian.org>

	* lib/lapack.c, lib/lapack.h, preproc/PCACut.cpp: + use extern "C"
	  for lapack functions
	  + simplified python svm/svr examples -> now on webpage
	* classifier/svm/pr_loqo.cpp, configure, lib/Mathmatics.cpp,
	  lib/Mathmatics.h, lib/io.h, lib/lapack.c, lib/lapack.h,
	  preproc/PCACut.cpp: + fix c++ compiler detection on macs
	  + various workarounds for blas/lapack on macosx ... it does not
	  work :/
	  - disable lapack on macs and print a warning

2006-06-19  Soeren Sonnenburg <sonne@debian.org>

	* lib/Mathmatics.cpp, lib/lapack.h, preproc/PCACut.cpp: +further
	  lapack osx compilation fixes

2006-06-19  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* kernel/Kernel.i, kernel/WeightedDegreeCharKernel.i,
	  kernel/WeightedDegreePositionCharKernel.i, lib/common.i:
	  centralized swig helper datastructures in common.i
	* .generate_link_dependencies.py: cpointer added to none dependend
	  files

2006-06-19  Soeren Sonnenburg <sonne@debian.org>

	* Makefile, classifier/LDA.cpp, configure, lib/Mathmatics.cpp,
	  lib/Mathmatics.h: + allow compiling w/ lapack/blas on osx
	  + workaround clapack_dpotrf not beeing defined (needs check!!)

2006-06-18  Soeren Sonnenburg <sonne@debian.org>

	* d-bug.py:
	* classifier/svm/gpdtsolve.h, classifier/svm/gpm.h: +forgotten
	  necessary files
	* Makefile, classifier/svm/GPBTSVM.cpp, classifier/svm/gpdt.cpp,
	  classifier/svm/gpdt.h, classifier/svm/gpdtsolve.cpp, configure,
	  distributions/Distribution.h, features/CharFeatures.cpp,
	  features/CharFeatures.h, features/CharFeatures.i,
	  features/SimpleFeatures.h, features/SimpleFeatures.i,
	  kernel/Kernel.cpp, kernel/Kernel.h, kernel/Kernel.i,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreeCharKernel.i, lib/versionstring.i: using
	  swig one can now train a svm like this:
	  
	  import kernel.WeightedDegreeCharKernel as wd
	  import features.CharFeatures as cf
	  import features.Labels as lab
	  import classifier.svm.SVM_light as svm
	  
	  dA = wd.doubleArray(5)
	  dA[0] = 0.167
	  dA[1] = 0.25
	  dA[2] = 0.5
	  dA[3] = 0.25
	  dA[4] = 0.167
	  f=cf.CCharFeatures(cf.DNA,'ACGTAAACCGGT',4,3)
	  kernel = wd.CWeightedDegreeCharKernel(f,f,10,dA,2,0,True,False,1)
	  
	  trainlabels = lab.CLabels(3)
	  trainlabels.set_int_label(0,1)
	  trainlabels.set_int_label(1,-1)
	  trainlabels.set_int_label(2,-1)
	  
	  s = svm.CSVMLight()
	  s.set_labels(trainlabels)
	  s.set_kernel(kernel)
	  result = s.train();
	  print result

2006-06-16  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* classifier/svm/SVM.i, kernel/Kernel.i,
	  kernel/WeightedDegreeCharKernel.i,
	  kernel/WeightedDegreePositionCharKernel.i: updated a few
	  interfaces

2006-06-16  Soeren Sonnenburg <sonne@debian.org>

	* Makefile: +make swigclean
	* configure: yet another python build fix
	* configure:
	* configure: +fix linking in python interface, disable svm light
	  msg for now
	* Makefile: +check entries in .svn/ and always update versionstring
	  if a newer entry file exist
	* Makefile: - make doc
	* Makefile, configure: +updated the example to the one used in the
	  talk
	  +now R sources should really install
	* configure: -ccache

2006-06-16  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* Makefile: removed gcc --dumpversion

2006-06-16  Soeren Sonnenburg <sonne@debian.org>

	* README, classifier/svm/SVM_light.cpp, classifier/svm/SVM_light.h,
	  configure, gui/R.cpp, gui/TextGUI.cpp, guilib/GUIClassifier.cpp,
	  guilib/GUIKernel.cpp, guilib/GUIKernel.h, guilib/GUIR.cpp,
	  guilib/GUIR.h, guilib/GUISVM.cpp, kernel/CombinedKernel.cpp,
	  kernel/CommUlongStringKernel.cpp, kernel/CommWordKernel.cpp,
	  kernel/CommWordStringKernel.cpp, kernel/Kernel.cpp,
	  kernel/Kernel.h, kernel/WDCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernelPolyA.cpp,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  regression/svr/SVR_light.cpp, regression/svr/SVR_light.h: + R
	  vignette
	  + configure option --disable-svm-light
	  + print out warning when confiuring w/ svmlight

2006-06-15  Soeren Sonnenburg <sonne@debian.org>

	* CONTRIBUTIONS, ChangeLog, HISTORY, LICENSE.SVMlight, gui/R.cpp,
	  guilib/GUIHMM.cpp, guilib/GUIR.cpp, guilib/GUIR.h,
	  lib/Mathmatics.cpp: + documented contributions form joachims,
	  chen lin, smola etc
	  + create math object to get its constructor called (this screwed
	  up the HMM since oct-2004) -> HMM training is now working again
	  + get_viterbi_path and other functions for HMM
	  + a running HMM example
	* .version.sh, AUTHORS, CONTRIBUTIONS, INSTALL, README,
	  README.developer, classifier/Classifier.cpp,
	  classifier/Classifier.h, classifier/KNN.cpp, classifier/KNN.h,
	  classifier/KernelPerceptron.cpp, classifier/KernelPerceptron.h,
	  classifier/LDA.cpp, classifier/LDA.h, classifier/LPM.cpp,
	  classifier/LPM.h, classifier/LinearClassifier.cpp,
	  classifier/LinearClassifier.h, classifier/Perceptron.cpp,
	  classifier/Perceptron.h, classifier/PluginEstimate.cpp,
	  classifier/PluginEstimate.h, classifier/svm/CPLEXSVM.cpp,
	  classifier/svm/CPLEXSVM.h, classifier/svm/GPBTSVM.cpp,
	  classifier/svm/GPBTSVM.h, classifier/svm/KerthiPrimalSVM.cpp,
	  classifier/svm/KerthiPrimalSVM.h, classifier/svm/LibSVM.cpp,
	  classifier/svm/LibSVM.h, classifier/svm/MPD.cpp,
	  classifier/svm/MPD.h, classifier/svm/Optimizer.cpp,
	  classifier/svm/Optimizer.h, classifier/svm/SVM.cpp,
	  classifier/svm/SVM.h, classifier/svm/SVM_libsvm.cpp,
	  classifier/svm/SVM_libsvm.h, classifier/svm/SVM_light.cpp,
	  classifier/svm/SVM_light.h, classifier/svm/gpdt.cpp,
	  classifier/svm/gpdt.h, classifier/svm/gpdtsolve.cpp,
	  classifier/svm/gpm.cpp, classifier/svm/pr_loqo.cpp,
	  classifier/svm/pr_loqo.h, distributions/Distribution.cpp,
	  distributions/Distribution.h,
	  distributions/histogram/Histogram.cpp,
	  distributions/histogram/Histogram.h, distributions/hmm/GHMM.cpp,
	  distributions/hmm/GHMM.h, distributions/hmm/HMM.cpp,
	  distributions/hmm/HMM.h, distributions/hmm/HMM_bestpath.cpp,
	  distributions/hmm/HMM_bestpath_2struct.cpp,
	  distributions/hmm/HMM_bestpath_simple.cpp,
	  distributions/hmm/LinearHMM.cpp, distributions/hmm/LinearHMM.h,
	  distributions/hmm/fibheap.cpp, distributions/hmm/fibheap.h,
	  distributions/hmm/penalty_info.cpp,
	  distributions/hmm/penalty_info.h, features/ByteFeatures.cpp,
	  features/ByteFeatures.h, features/CharFeatures.cpp,
	  features/CharFeatures.h, features/CombinedFeatures.cpp,
	  features/CombinedFeatures.h, features/FKFeatures.cpp,
	  features/FKFeatures.h, features/Features.cpp,
	  features/Features.h, features/Labels.cpp, features/Labels.h,
	  features/RealFeatures.cpp, features/RealFeatures.h,
	  features/RealFileFeatures.cpp, features/RealFileFeatures.h,
	  features/ShortFeatures.cpp, features/ShortFeatures.h,
	  features/SimpleFeatures.h, features/SparseFeatures.h,
	  features/SparseRealFeatures.cpp, features/SparseRealFeatures.h,
	  features/StringFeatures.cpp, features/StringFeatures.h,
	  features/TOPFeatures.cpp, features/TOPFeatures.h,
	  features/WordFeatures.cpp, features/WordFeatures.h, gui/GUI.cpp,
	  gui/GUI.h, gui/Matlab.cpp, gui/Octave.cpp, gui/Python.cpp,
	  gui/Python.h, gui/R.cpp, gui/TextGUI.cpp, gui/TextGUI.h,
	  guilib/GUIClassifier.cpp, guilib/GUIClassifier.h,
	  guilib/GUIFeatures.cpp, guilib/GUIFeatures.h, guilib/GUIHMM.cpp,
	  guilib/GUIHMM.h, guilib/GUIKNN.cpp, guilib/GUIKNN.h,
	  guilib/GUIKernel.cpp, guilib/GUIKernel.h, guilib/GUILabels.cpp,
	  guilib/GUILabels.h, guilib/GUIMath.cpp, guilib/GUIMath.h,
	  guilib/GUIMatlab.cpp, guilib/GUIMatlab.h, guilib/GUIOctave.cpp,
	  guilib/GUIOctave.h, guilib/GUIPluginEstimate.cpp,
	  guilib/GUIPluginEstimate.h, guilib/GUIPreProc.cpp,
	  guilib/GUIPreProc.h, guilib/GUIPython.cpp, guilib/GUIPython.h,
	  guilib/GUIR.cpp, guilib/GUIR.h, guilib/GUISVM.cpp,
	  guilib/GUISVM.h, guilib/GUITime.cpp, guilib/GUITime.h,
	  kernel/AUCKernel.cpp, kernel/AUCKernel.h, kernel/ByteKernel.h,
	  kernel/CanberraWordKernel.cpp, kernel/CanberraWordKernel.h,
	  kernel/CharKernel.h, kernel/CharPolyKernel.cpp,
	  kernel/CharPolyKernel.h, kernel/Chi2Kernel.cpp,
	  kernel/Chi2Kernel.h, kernel/CombinedKernel.cpp,
	  kernel/CombinedKernel.h, kernel/CommUlongStringKernel.cpp,
	  kernel/CommUlongStringKernel.h, kernel/CommWordKernel.cpp,
	  kernel/CommWordKernel.h, kernel/CommWordStringKernel.cpp,
	  kernel/CommWordStringKernel.h, kernel/ConstKernel.cpp,
	  kernel/ConstKernel.h, kernel/CustomKernel.cpp,
	  kernel/CustomKernel.h, kernel/DiagKernel.cpp,
	  kernel/DiagKernel.h, kernel/FixedDegreeCharKernel.cpp,
	  kernel/FixedDegreeCharKernel.h, kernel/GaussianKernel.cpp,
	  kernel/GaussianKernel.h, kernel/HammingWordKernel.cpp,
	  kernel/HammingWordKernel.h, kernel/HistogramWordKernel.cpp,
	  kernel/HistogramWordKernel.h, kernel/Kernel.cpp, kernel/Kernel.h,
	  kernel/KernelMachine.cpp, kernel/KernelMachine.h,
	  kernel/LinearByteKernel.cpp, kernel/LinearByteKernel.h,
	  kernel/LinearCharKernel.cpp, kernel/LinearCharKernel.h,
	  kernel/LinearKernel.cpp, kernel/LinearKernel.h,
	  kernel/LinearWordKernel.cpp, kernel/LinearWordKernel.h,
	  kernel/LocalityImprovedCharKernel.cpp,
	  kernel/LocalityImprovedCharKernel.h,
	  kernel/ManhattenWordKernel.cpp, kernel/ManhattenWordKernel.h,
	  kernel/PolyKernel.cpp, kernel/PolyKernel.h,
	  kernel/PolyMatchCharKernel.cpp, kernel/PolyMatchCharKernel.h,
	  kernel/PolyMatchWordKernel.cpp, kernel/PolyMatchWordKernel.h,
	  kernel/RealKernel.h, kernel/SalzbergWordKernel.cpp,
	  kernel/SalzbergWordKernel.h, kernel/ShortKernel.h,
	  kernel/SigmoidKernel.cpp, kernel/SigmoidKernel.h,
	  kernel/SimpleKernel.h,
	  kernel/SimpleLocalityImprovedCharKernel.cpp,
	  kernel/SimpleLocalityImprovedCharKernel.h,
	  kernel/SparseGaussianKernel.cpp, kernel/SparseGaussianKernel.h,
	  kernel/SparseKernel.h, kernel/SparseLinearKernel.cpp,
	  kernel/SparseLinearKernel.h, kernel/SparseNormSquaredKernel.cpp,
	  kernel/SparseNormSquaredKernel.h, kernel/SparsePolyKernel.cpp,
	  kernel/SparsePolyKernel.h, kernel/SparseRealKernel.h,
	  kernel/StringKernel.h, kernel/WDCharKernel.cpp,
	  kernel/WDCharKernel.h, kernel/WeightedDegreeCharKernel.cpp,
	  kernel/WeightedDegreeCharKernel.h,
	  kernel/WeightedDegreeCharKernelPolyA.cpp,
	  kernel/WeightedDegreeCharKernelPolyA.h,
	  kernel/WeightedDegreePositionCharKernel.cpp,
	  kernel/WeightedDegreePositionCharKernel.h, kernel/WordKernel.h,
	  kernel/WordMatchKernel.cpp, kernel/WordMatchKernel.h,
	  lib/Cache.h, lib/Cplex.cpp, lib/Cplex.h, lib/DynArray.h,
	  lib/File.cpp, lib/File.h, lib/List.h, lib/Mathmatics.cpp,
	  lib/Mathmatics.h, lib/Parallel.cpp, lib/Parallel.h,
	  lib/Signal.cpp, lib/Signal.h, lib/SimpleFile.h, lib/Time.cpp,
	  lib/Time.h, lib/Version.cpp, lib/Version.h, lib/common.h,
	  lib/io.cpp, lib/io.h, lib/lapack.h, preproc/LogPlusOne.cpp,
	  preproc/LogPlusOne.h, preproc/NormDerivativeLem3.cpp,
	  preproc/NormDerivativeLem3.h, preproc/NormOne.cpp,
	  preproc/NormOne.h, preproc/PCACut.cpp, preproc/PCACut.h,
	  preproc/PreProc.cpp, preproc/PreProc.h,
	  preproc/PruneVarSubMean.cpp, preproc/PruneVarSubMean.h,
	  preproc/RealPreProc.h, preproc/ShortPreProc.cpp,
	  preproc/ShortPreProc.h, preproc/SimplePreProc.h,
	  preproc/SortUlongString.cpp, preproc/SortUlongString.h,
	  preproc/SortWord.cpp, preproc/SortWord.h,
	  preproc/SortWordString.cpp, preproc/SortWordString.h,
	  preproc/SparsePreProc.h, preproc/StringPreProc.h,
	  preproc/WordPreProc.cpp, preproc/WordPreProc.h,
	  regression/svr/LibSVR.cpp, regression/svr/LibSVR.h,
	  regression/svr/SVR_light.cpp, regression/svr/SVR_light.h, svm:

2006-06-13  Fabio De Bona <Fabio.De.Bona@tuebingen.mpg.de>

	* gui/R.cpp, guilib/GUIR.cpp, guilib/GUIR.h: added length parameter
	  to set_features

2006-06-12  Soeren Sonnenburg <sonne@debian.org>

	* configure: +make configure executable

2006-06-11  Soeren Sonnenburg <sonne@debian.org>

	* Makefile, configure, gui/R.cpp, guilib/GUIPython.cpp,
	  guilib/GUIR.cpp, guilib/GUIR.h: + make char features work with
	  numarray (work around bug in numarray and take type info from
	  self->descr->type_num
	  + set/get_svm in R interf.
	  + make clean should not mess around in .svn

2006-06-08  Soeren Sonnenburg <sonne@debian.org>

	* classifier/svm/MPD.h, configure, gui/R.cpp, guilib/GUIFeatures.h,
	  guilib/GUILabels.h, guilib/GUIR.cpp, lib/io.cpp: - -fforce-mem
	  from configure
	  + make R interface work with matrices (not just 1d-vectors) and
	  string matrices
	  + overload CIO::message for R to use Rprintf / Reprintf

2006-06-06  Gunnar Raetsch <Gunnar.Raetsch@tuebingen.mpg.de>

	* deletemetoo: gu's 2nd test.
	  G
	* deletemetoo: gu's test.
	  G

2006-06-05  Soeren Sonnenburg <sonne@debian.org>

	* gui/R.cpp, guilib/GUIR.cpp: + classification example
	* .:

