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Viewing all changes in revision 1.

Committer: Bazaar Package Importer
Author(s): Torsten Werner
Date: 2007-03-07 19:05:03 UTC
Revision ID: james.westby@ubuntu.com-20070307190503-8mt433h1n30sh5zg

Tags: upstream-0.3.2

Import upstream version 0.3.2

files added:

R

R/Makefile

R/Makefile.sed

R/README.txt

R/examples

R/examples/hmm.R

R/examples/svm_classification.R

R/examples/svr_regression.R

R/sg

R/sg/COPYING

R/sg/DESCRIPTION

R/sg/R

R/sg/R/shogun.R

R/sg/R/zzz.R

R/sg/demo

R/sg/demo/00Index

R/sg/demo/mkl_lin_sine_mix.R

R/sg/demo/mkl_sine_regression.R

R/sg/demo/string_kernel.R

R/sg/demo/wd_mkl.R

R/sg/demo/x-max_class.R

R/sg/inst

R/sg/inst/doc

R/sg/inst/doc/manual.pdf

R/sg/inst/doc/sg.Rnw

R/sg/tests

R/sg/tests/startup.R

doc

doc/Makefile

doc/doxygen

doc/doxygen/Doxyfile

doc/doxygen/footer.dpp

doc/manual

doc/manual/Makefile

doc/manual/R.txt

doc/manual/cmdline.txt

doc/manual/commands.txt

doc/manual/faq.txt

doc/manual/installation.txt

doc/manual/interfaces.txt

doc/manual/introduction.txt

doc/manual/license.txt

doc/manual/matlab.txt

doc/manual/octave.txt

doc/manual/overview.txt

doc/manual/python.txt

doc/pseudocode

doc/pseudocode/poim.txt

matlab

matlab/examples

matlab/examples/entropy.m

matlab/examples/hmm.m

matlab/examples/svm_classification.m

matlab/examples/svmlight_hang_test.m

matlab/examples/svr_regression.m

matlab/examples/test_classifier.m

matlab/examples/test_combined.m

matlab/examples/test_combined2.m

matlab/examples/test_custom_kernel.m

matlab/examples/test_gnpp_svm.m

matlab/examples/test_hmm.m

matlab/examples/test_hmm_matlab.m

matlab/examples/test_kernel_optimization.m

matlab/examples/test_knn.m

matlab/examples/test_linadd.m

matlab/examples/test_matlab_interface.m

matlab/examples/test_mkl.m

matlab/examples/test_mkl_svr.m

matlab/examples/test_mkl_svr_wrapper.m

matlab/examples/test_one_class_svm.m

matlab/examples/test_rbf_kernel.m

matlab/examples/test_regression.m

matlab/examples/test_regression_linadd.m

matlab/examples/test_regression_mkl.m

matlab/examples/test_svm.m

matlab/examples/test_svmlight_libsvm.m

matlab/examples/test_svrlight_libsvr.m

matlab/examples/test_wd_kernel.m

matlab/examples/test_wd_linadd.m

matlab/examples/test_wd_wds_parallel.m

matlab/examples/test_wdshift_kernel.m

matlab/examples/test_wdshiftphyl_kernel.m

matlab/examples/tools

matlab/examples/tools/PCACut.m

matlab/examples/tools/README

matlab/examples/tools/calcroc.m

matlab/examples/tools/calcrocscore.m

matlab/examples/tools/graph_hmm.m

matlab/examples/tools/graph_hmm2.m

matlab/examples/tools/model_to_graph.m

matlab/examples/tools/plotroc.m

matlab/examples/tools/read_feature_matrix.m

matlab/examples/tools/readroc.m

matlab/examples/tools/save_as_ascii.m

matlab/examples/tools/save_as_double.m

matlab/examples/wds_shift_interp.m

octave

octave/examples

octave/examples/hmm.m

octave/examples/spec_kernel.m

octave/examples/svm_classification.m

octave/examples/svr_regression.m

octave/examples/wd_kernel.m

octave/examples/wds_kernel.m

python

python-modular

python-modular/examples

python-modular/examples/krr.py

python-modular/examples/lda.py

python-modular/examples/multiple_svms.py

python-modular/examples/multiple_svms_matplotlib.py

python-modular/examples/numpy_commands.py

python-modular/examples/numpy_krr_matplotlib.py

python-modular/examples/numpy_krr_sinc.py

python-modular/examples/numpy_lda_matplotlib.py

python-modular/examples/numpy_svm.py

python-modular/examples/numpy_svm_matplotlib.py

python-modular/examples/numpy_svr_sinc.py

python-modular/examples/rbf_kernel.py

python-modular/examples/spec_kernel.py

python-modular/examples/stringfeatures.py

python-modular/examples/wd_kernel.py

python-modular/examples/wd_kernel_svm.py

python-modular/examples/wd_kernel_svm_linadd_batch.py

python/examples

python/examples/svm_classificaton.py

python/examples/svr_regression.py

python/examples/test_mkl.py

src

src/.generate_link_dependencies.py

src/.version.sh

src/AUTHORS

src/CONTRIBUTIONS

src/ChangeLog

src/INSTALL

src/LICENSE

src/Makefile

src/NEWS

src/README

src/README.developer

src/TODO

src/base

src/base/Parallel.cpp

src/base/Parallel.h

src/base/Parallel.i

src/base/SGObject.cpp

src/base/SGObject.h

src/base/SGObject.i

src/base/Version.cpp

src/base/Version.h

src/base/Version.i

src/classifier

src/classifier/Classifier.cpp

src/classifier/Classifier.h

src/classifier/Classifier.i

src/classifier/KNN.cpp

src/classifier/KNN.h

src/classifier/KNN.i

src/classifier/KernelPerceptron.cpp

src/classifier/KernelPerceptron.h

src/classifier/KernelPerceptron.i

src/classifier/LDA.cpp

src/classifier/LDA.h

src/classifier/LDA.i

src/classifier/LPM.cpp

src/classifier/LPM.h

src/classifier/LPM.i

src/classifier/LinearClassifier.cpp

src/classifier/LinearClassifier.h

src/classifier/LinearClassifier.i

src/classifier/Perceptron.cpp

src/classifier/Perceptron.h

src/classifier/Perceptron.i

src/classifier/PluginEstimate.cpp

src/classifier/PluginEstimate.h

src/classifier/PluginEstimate.i

src/classifier/__init__.py

src/classifier/svm

src/classifier/svm/CPLEXSVM.cpp

src/classifier/svm/CPLEXSVM.h

src/classifier/svm/GNPPSVM.cpp

src/classifier/svm/GNPPSVM.h

src/classifier/svm/GNPPSVM.i

src/classifier/svm/GPBTSVM.cpp

src/classifier/svm/GPBTSVM.h

src/classifier/svm/KerthiPrimalSVM.cpp

src/classifier/svm/KerthiPrimalSVM.h

src/classifier/svm/LibSVM.cpp

src/classifier/svm/LibSVM.h

src/classifier/svm/LibSVM.i

src/classifier/svm/LibSVM_oneclass.cpp

src/classifier/svm/LibSVM_oneclass.h

src/classifier/svm/MPD.cpp

src/classifier/svm/MPD.h

src/classifier/svm/SVM.cpp

src/classifier/svm/SVM.h

src/classifier/svm/SVM.i

src/classifier/svm/SVMLin.cpp

src/classifier/svm/SVMLin.h

src/classifier/svm/SVMLin.i

src/classifier/svm/SVM_libsvm.cpp

src/classifier/svm/SVM_libsvm.h

src/classifier/svm/__init__.py

src/classifier/svm/gnpplib.cpp

src/classifier/svm/gnpplib.h

src/classifier/svm/gpdt.cpp

src/classifier/svm/gpdt.h

src/classifier/svm/gpdtsolve.cpp

src/classifier/svm/gpdtsolve.h

src/classifier/svm/gpm.cpp

src/classifier/svm/gpm.h

src/classifier/svm/pr_loqo.cpp

src/classifier/svm/pr_loqo.h

src/classifier/svm/ssl.cpp

src/classifier/svm/ssl.h

src/configure

src/distance

src/distance/Canberra.cpp

src/distance/Canberra.h

src/distance/Canberra.i

src/distance/CanberraWordDistance.cpp

src/distance/CanberraWordDistance.h

src/distance/CanberraWordDistance.i

src/distance/Chebyshew.cpp

src/distance/Chebyshew.h

src/distance/Chebyshew.i

src/distance/Distance.cpp

src/distance/Distance.h

src/distance/Distance.i

src/distance/DistanceMachine.cpp

src/distance/DistanceMachine.h

src/distance/DistanceMachine.i

src/distance/Geodesic.cpp

src/distance/Geodesic.h

src/distance/Geodesic.i

src/distance/HammingWordDistance.cpp

src/distance/HammingWordDistance.h

src/distance/HammingWordDistance.i

src/distance/Jensen.cpp

src/distance/Jensen.h

src/distance/Jensen.i

src/distance/Manhattan.cpp

src/distance/Manhattan.h

src/distance/Manhattan.i

src/distance/ManhattanWordDistance.cpp

src/distance/ManhattanWordDistance.h

src/distance/ManhattanWordDistance.i

src/distance/Minkowski.cpp

src/distance/Minkowski.h

src/distance/Minkowski.i

src/distance/RealDistance.h

src/distance/RealDistance.i

src/distance/SimpleDistance.h

src/distance/SimpleDistance.i

src/distance/StringDistance.h

src/distance/StringDistance.i

src/distributions

src/distributions/Distribution.cpp

src/distributions/Distribution.h

src/distributions/Distribution.i

src/distributions/histogram

src/distributions/histogram/Histogram.cpp

src/distributions/histogram/Histogram.h

src/distributions/histogram/Histogram.i

src/distributions/hmm

src/distributions/hmm/GHMM.cpp

src/distributions/hmm/GHMM.h

src/distributions/hmm/GHMM.i

src/distributions/hmm/HMM.cpp

src/distributions/hmm/HMM.h

src/distributions/hmm/HMM.i

src/distributions/hmm/LinearHMM.cpp

src/distributions/hmm/LinearHMM.h

src/distributions/hmm/LinearHMM.i

src/features

src/features/Alphabet.cpp

src/features/Alphabet.h

src/features/Alphabet.i

src/features/ByteFeatures.cpp

src/features/ByteFeatures.h

src/features/ByteFeatures.i

src/features/CharFeatures.cpp

src/features/CharFeatures.h

src/features/CharFeatures.i

src/features/CombinedFeatures.cpp

src/features/CombinedFeatures.h

src/features/CombinedFeatures.i

src/features/FKFeatures.cpp

src/features/FKFeatures.h

src/features/FKFeatures.i

src/features/Features.cpp

src/features/Features.h

src/features/Features.i

src/features/Labels.cpp

src/features/Labels.h

src/features/Labels.i

src/features/MindyGramFeatures.cpp

src/features/MindyGramFeatures.h

src/features/MindyGramFeatures.i

src/features/RealFeatures.cpp

src/features/RealFeatures.h

src/features/RealFeatures.i

src/features/RealFileFeatures.cpp

src/features/RealFileFeatures.h

src/features/RealFileFeatures.i

src/features/ShortFeatures.cpp

src/features/ShortFeatures.h

src/features/ShortFeatures.i

src/features/SimpleFeatures.h

src/features/SimpleFeatures.i

src/features/SparseFeatures.h

src/features/SparseFeatures.i

src/features/StringFeatures.cpp

src/features/StringFeatures.h

src/features/StringFeatures.i

src/features/TOPFeatures.cpp

src/features/TOPFeatures.h

src/features/TOPFeatures.i

src/features/WordFeatures.cpp

src/features/WordFeatures.h

src/features/WordFeatures.i

src/features/__init__.py

src/gui

src/gui/GUI.cpp

src/gui/GUI.h

src/gui/Matlab.cpp

src/gui/Octave.cpp

src/gui/Python.cpp

src/gui/Python.h

src/gui/R.cpp

src/gui/TextGUI.cpp

src/gui/TextGUI.h

src/guilib

src/guilib/GUIClassifier.cpp

src/guilib/GUIClassifier.h

src/guilib/GUIDistance.cpp

src/guilib/GUIDistance.h

src/guilib/GUIFeatures.cpp

src/guilib/GUIFeatures.h

src/guilib/GUIHMM.cpp

src/guilib/GUIHMM.h

src/guilib/GUIKNN.cpp

src/guilib/GUIKNN.h

src/guilib/GUIKernel.cpp

src/guilib/GUIKernel.h

src/guilib/GUILabels.cpp

src/guilib/GUILabels.h

src/guilib/GUIMath.cpp

src/guilib/GUIMath.h

src/guilib/GUIMatlab.cpp

src/guilib/GUIMatlab.h

src/guilib/GUIOctave.cpp

src/guilib/GUIOctave.h

src/guilib/GUIPluginEstimate.cpp

src/guilib/GUIPluginEstimate.h

src/guilib/GUIPreProc.cpp

src/guilib/GUIPreProc.h

src/guilib/GUIPython.cpp

src/guilib/GUIPython.h

src/guilib/GUIR.cpp

src/guilib/GUIR.h

src/guilib/GUISVM.cpp

src/guilib/GUISVM.h

src/guilib/GUITime.cpp

src/guilib/GUITime.h

src/kernel

src/kernel/AUCKernel.cpp

src/kernel/AUCKernel.h

src/kernel/AUCKernel.i

src/kernel/CanberraWordKernel.cpp

src/kernel/CanberraWordKernel.h

src/kernel/CharPolyKernel.cpp

src/kernel/CharPolyKernel.h

src/kernel/CharPolyKernel.i

src/kernel/Chi2Kernel.cpp

src/kernel/Chi2Kernel.h

src/kernel/Chi2Kernel.i

src/kernel/CombinedKernel.cpp

src/kernel/CombinedKernel.h

src/kernel/CombinedKernel.i

src/kernel/CommUlongStringKernel.cpp

src/kernel/CommUlongStringKernel.h

src/kernel/CommUlongStringKernel.i

src/kernel/CommWordKernel.cpp

src/kernel/CommWordKernel.h

src/kernel/CommWordKernel.i

src/kernel/CommWordStringKernel.cpp

src/kernel/CommWordStringKernel.h

src/kernel/CommWordStringKernel.i

src/kernel/ConstKernel.cpp

src/kernel/ConstKernel.h

src/kernel/ConstKernel.i

src/kernel/CustomKernel.cpp

src/kernel/CustomKernel.h

src/kernel/CustomKernel.i

src/kernel/DiagKernel.cpp

src/kernel/DiagKernel.h

src/kernel/DiagKernel.i

src/kernel/DistanceKernel.cpp

src/kernel/DistanceKernel.h

src/kernel/DistanceKernel.i

src/kernel/FixedDegreeCharKernel.cpp

src/kernel/FixedDegreeCharKernel.h

src/kernel/FixedDegreeCharKernel.i

src/kernel/GaussianKernel.cpp

src/kernel/GaussianKernel.h

src/kernel/GaussianKernel.i

src/kernel/HammingWordKernel.cpp

src/kernel/HammingWordKernel.h

src/kernel/HistogramWordKernel.cpp

src/kernel/HistogramWordKernel.h

src/kernel/HistogramWordKernel.i

src/kernel/Kernel.cpp

src/kernel/Kernel.h

src/kernel/Kernel.i

src/kernel/KernelMachine.cpp

src/kernel/KernelMachine.h

src/kernel/KernelMachine.i

src/kernel/LinearByteKernel.cpp

src/kernel/LinearByteKernel.h

src/kernel/LinearByteKernel.i

src/kernel/LinearCharKernel.cpp

src/kernel/LinearCharKernel.h

src/kernel/LinearCharKernel.i

src/kernel/LinearKernel.cpp

src/kernel/LinearKernel.h

src/kernel/LinearKernel.i

src/kernel/LinearWordKernel.cpp

src/kernel/LinearWordKernel.h

src/kernel/LinearWordKernel.i

src/kernel/LocalityImprovedCharKernel.cpp

src/kernel/LocalityImprovedCharKernel.h

src/kernel/LocalityImprovedCharKernel.i

src/kernel/ManhattenWordKernel.cpp

src/kernel/ManhattenWordKernel.h

src/kernel/MindyGramKernel.cpp

src/kernel/MindyGramKernel.h

src/kernel/MindyGramKernel.i

src/kernel/PolyKernel.cpp

src/kernel/PolyKernel.h

src/kernel/PolyKernel.i

src/kernel/PolyMatchCharKernel.cpp

src/kernel/PolyMatchCharKernel.h

src/kernel/PolyMatchCharKernel.i

src/kernel/PolyMatchWordKernel.cpp

src/kernel/PolyMatchWordKernel.h

src/kernel/PolyMatchWordKernel.i

src/kernel/SalzbergWordKernel.cpp

src/kernel/SalzbergWordKernel.h

src/kernel/SalzbergWordKernel.i

src/kernel/SigmoidKernel.cpp

src/kernel/SigmoidKernel.h

src/kernel/SigmoidKernel.i

src/kernel/SimpleKernel.h

src/kernel/SimpleKernel.i

src/kernel/SimpleLocalityImprovedCharKernel.cpp

src/kernel/SimpleLocalityImprovedCharKernel.h

src/kernel/SimpleLocalityImprovedCharKernel.i

src/kernel/SparseGaussianKernel.cpp

src/kernel/SparseGaussianKernel.h

src/kernel/SparseGaussianKernel.i

src/kernel/SparseKernel.h

src/kernel/SparseKernel.i

src/kernel/SparseLinearKernel.cpp

src/kernel/SparseLinearKernel.h

src/kernel/SparseLinearKernel.i

src/kernel/SparseNormSquaredKernel.cpp

src/kernel/SparseNormSquaredKernel.h

src/kernel/SparseNormSquaredKernel.i

src/kernel/SparsePolyKernel.cpp

src/kernel/SparsePolyKernel.h

src/kernel/SparsePolyKernel.i

src/kernel/SpectrumKernel.cpp

src/kernel/SpectrumKernel.h

src/kernel/SpectrumKernel.i

src/kernel/StringKernel.h

src/kernel/StringKernel.i

src/kernel/WeightedDegreeCharKernel.cpp

src/kernel/WeightedDegreeCharKernel.h

src/kernel/WeightedDegreeCharKernel.i

src/kernel/WeightedDegreeCharKernelPolyA.cpp

src/kernel/WeightedDegreeCharKernelPolyA.h

src/kernel/WeightedDegreeCharKernelPolyA.i

src/kernel/WeightedDegreePositionCharKernel.cpp

src/kernel/WeightedDegreePositionCharKernel.h

src/kernel/WeightedDegreePositionCharKernel.i

src/kernel/WeightedDegreePositionPhylCharKernel.cpp

src/kernel/WeightedDegreePositionPhylCharKernel.h

src/kernel/WordMatchKernel.cpp

src/kernel/WordMatchKernel.h

src/kernel/WordMatchKernel.i

src/kernel/__init__.py

src/lib

src/lib/Array.h

src/lib/Array.i

src/lib/Array2.h

src/lib/Array2.i

src/lib/Array3.h

src/lib/Array3.i

src/lib/Cache.h

src/lib/Cache.i

src/lib/Cplex.cpp

src/lib/Cplex.h

src/lib/DynamicArray.h

src/lib/DynamicArray.i

src/lib/File.cpp

src/lib/File.h

src/lib/File.i

src/lib/Library.i

src/lib/List.h

src/lib/List.i

src/lib/Mathematics.cpp

src/lib/Mathematics.h

src/lib/Mathematics.i

src/lib/ShogunException.cpp

src/lib/ShogunException.h

src/lib/ShogunException.i

src/lib/Signal.cpp

src/lib/Signal.h

src/lib/Signal.i

src/lib/SimpleFile.h

src/lib/SimpleFile.i

src/lib/Time.cpp

src/lib/Time.h

src/lib/Time.i

src/lib/Trie.cpp

src/lib/Trie.h

src/lib/Trie.i

src/lib/__init__.py

src/lib/common.h

src/lib/common.i

src/lib/io.cpp

src/lib/io.h

src/lib/io.i

src/lib/lapack.cpp

src/lib/lapack.h

src/lib/lapack.i

src/lib/numpy.i

src/lib/suffixarray

src/lib/suffixarray/BWT.cpp

src/lib/suffixarray/BWT.h

src/lib/suffixarray/BoundedRangeWeight.cpp

src/lib/suffixarray/BoundedRangeWeight.h

src/lib/suffixarray/ChildTable.cpp

src/lib/suffixarray/ChildTable.h

src/lib/suffixarray/ConstantWeight.cpp

src/lib/suffixarray/ConstantWeight.h

src/lib/suffixarray/DataType.h

src/lib/suffixarray/ESA.cpp

src/lib/suffixarray/ESA.h

src/lib/suffixarray/ErrorCode.h

src/lib/suffixarray/ExpDecayWeight.cpp

src/lib/suffixarray/ExpDecayWeight.h

src/lib/suffixarray/I_LCPFactory.h

src/lib/suffixarray/I_SAFactory.h

src/lib/suffixarray/I_WeightFactory.h

src/lib/suffixarray/InductionSort.cpp

src/lib/suffixarray/InductionSort.h

src/lib/suffixarray/IntroSort.h

src/lib/suffixarray/KSpectrumWeight.cpp

src/lib/suffixarray/KSpectrumWeight.h

src/lib/suffixarray/LCP.cpp

src/lib/suffixarray/LCP.h

src/lib/suffixarray/MSufSort.cpp

src/lib/suffixarray/MSufSort.h

src/lib/suffixarray/SConstruct

src/lib/suffixarray/Stack.h

src/lib/suffixarray/W_kasai_lcp.cpp

src/lib/suffixarray/W_kasai_lcp.h

src/lib/suffixarray/W_msufsort.cpp

src/lib/suffixarray/W_msufsort.h

src/lib/versionstring.h

src/preproc

src/preproc/LogPlusOne.cpp

src/preproc/LogPlusOne.h

src/preproc/LogPlusOne.i

src/preproc/NormDerivativeLem3.cpp

src/preproc/NormDerivativeLem3.h

src/preproc/NormDerivativeLem3.i

src/preproc/NormOne.cpp

src/preproc/NormOne.h

src/preproc/NormOne.i

src/preproc/PCACut.cpp

src/preproc/PCACut.h

src/preproc/PCACut.i

src/preproc/PreProc.cpp

src/preproc/PreProc.h

src/preproc/PreProc.i

src/preproc/PruneVarSubMean.cpp

src/preproc/PruneVarSubMean.h

src/preproc/PruneVarSubMean.i

src/preproc/RealPreProc.h

src/preproc/RealPreProc.i

src/preproc/ShortPreProc.cpp

src/preproc/ShortPreProc.h

src/preproc/ShortPreProc.i

src/preproc/SimplePreProc.h

src/preproc/SimplePreProc.i

src/preproc/SortUlongString.cpp

src/preproc/SortUlongString.h

src/preproc/SortUlongString.i

src/preproc/SortWord.cpp

src/preproc/SortWord.h

src/preproc/SortWord.i

src/preproc/SortWordString.cpp

src/preproc/SortWordString.h

src/preproc/SortWordString.i

src/preproc/SparsePreProc.h

src/preproc/SparsePreProc.i

src/preproc/StringPreProc.h

src/preproc/StringPreProc.i

src/preproc/WordPreProc.cpp

src/preproc/WordPreProc.h

src/preproc/WordPreProc.i

src/regression

src/regression/KRR.cpp

src/regression/KRR.h

src/regression/KRR.i

src/regression/Regression.i

src/regression/svr

src/regression/svr/LibSVR.cpp

src/regression/svr/LibSVR.h

src/regression/svr/LibSVR.i

src/sg.m

src/structure

src/structure/DynProg.cpp

src/structure/DynProg.h

src/structure/DynProg.i

src/structure/Plif.cpp

src/structure/Plif.h

src/structure/Plif.i

src/structure/PlifArray.cpp

src/structure/PlifArray.h

src/structure/PlifArray.i

src/structure/PlifBase.h

src/structure/PlifBase.i

src/structure/Structure.i

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added added

removed removed

R/examples/hmm.R

R/examples/svm_classification.R

R/examples/svr_regression.R

R/sg/DESCRIPTION

R/sg/R/shogun.R

R/sg/demo/00Index

R/sg/demo/mkl_lin_sine_mix.R

R/sg/demo/mkl_sine_regression.R

R/sg/demo/string_kernel.R

R/sg/demo/wd_mkl.R

R/sg/demo/x-max_class.R

R/sg/inst/doc/manual.pdf

R/sg/inst/doc/sg.Rnw

R/sg/tests/startup.R

doc/doxygen/Doxyfile

doc/manual/Makefile

doc/manual/R.txt

doc/manual/cmdline.txt

doc/manual/commands.txt

doc/manual/faq.txt

doc/manual/installation.txt

doc/manual/interfaces.txt

doc/manual/introduction.txt

doc/manual/license.txt

doc/manual/matlab.txt

doc/manual/octave.txt

doc/manual/overview.txt

doc/manual/python.txt

doc/pseudocode/

doc/pseudocode/poim.txt

matlab/examples/

matlab/examples/entropy.m

matlab/examples/hmm.m

matlab/examples/svm_classification.m

matlab/examples/svmlight_hang_test.m

matlab/examples/svr_regression.m

matlab/examples/test_classifier.m

matlab/examples/test_combined.m

matlab/examples/test_combined2.m

matlab/examples/test_custom_kernel.m

matlab/examples/test_gnpp_svm.m

matlab/examples/test_hmm.m

matlab/examples/test_hmm_matlab.m

matlab/examples/test_kernel_optimization.m

matlab/examples/test_knn.m

matlab/examples/test_linadd.m

matlab/examples/test_matlab_interface.m

matlab/examples/test_mkl.m

matlab/examples/test_mkl_svr.m

matlab/examples/test_mkl_svr_wrapper.m

matlab/examples/test_one_class_svm.m

matlab/examples/test_rbf_kernel.m

matlab/examples/test_regression.m

matlab/examples/test_regression_linadd.m

matlab/examples/test_regression_mkl.m

matlab/examples/test_svm.m

matlab/examples/test_svmlight_libsvm.m

matlab/examples/test_svrlight_libsvr.m

matlab/examples/test_wd_kernel.m

matlab/examples/test_wd_linadd.m

matlab/examples/test_wd_wds_parallel.m

matlab/examples/test_wdshift_kernel.m

matlab/examples/test_wdshiftphyl_kernel.m

matlab/examples/tools/

matlab/examples/tools/PCACut.m

matlab/examples/tools/README

matlab/examples/tools/calcroc.m

matlab/examples/tools/calcrocscore.m

matlab/examples/tools/graph_hmm.m

matlab/examples/tools/graph_hmm2.m

matlab/examples/tools/model_to_graph.m

matlab/examples/tools/plotroc.m

matlab/examples/tools/read_feature_matrix.m

matlab/examples/tools/readroc.m

matlab/examples/tools/save_as_ascii.m

matlab/examples/tools/save_as_double.m

matlab/examples/wds_shift_interp.m

octave/examples/

octave/examples/hmm.m

octave/examples/spec_kernel.m

octave/examples/svm_classification.m

octave/examples/svr_regression.m

octave/examples/wd_kernel.m

octave/examples/wds_kernel.m

python-modular/

python-modular/examples/

python-modular/examples/krr.py

python-modular/examples/lda.py

python-modular/examples/multiple_svms.py

python-modular/examples/multiple_svms_matplotlib.py

python-modular/examples/numpy_commands.py

python-modular/examples/numpy_krr_matplotlib.py

python-modular/examples/numpy_krr_sinc.py

python-modular/examples/numpy_lda_matplotlib.py

python-modular/examples/numpy_svm.py

python-modular/examples/numpy_svm_matplotlib.py

python-modular/examples/numpy_svr_sinc.py

python-modular/examples/rbf_kernel.py

python-modular/examples/spec_kernel.py

python-modular/examples/stringfeatures.py

python-modular/examples/wd_kernel.py

python-modular/examples/wd_kernel_svm.py

python-modular/examples/wd_kernel_svm_linadd_batch.py

python/examples/

python/examples/svm_classificaton.py

python/examples/svr_regression.py

python/examples/test_mkl.py

src/.generate_link_dependencies.py

src/.version.sh

src/CONTRIBUTIONS

src/README.developer

src/base/Parallel.cpp

src/base/Parallel.h

src/base/Parallel.i

src/base/SGObject.cpp

src/base/SGObject.h

src/base/SGObject.i

src/base/Version.cpp

src/base/Version.h

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src/classifier/

src/classifier/Classifier.cpp

src/classifier/Classifier.h

src/classifier/Classifier.i

src/classifier/KNN.cpp

src/classifier/KNN.h

src/classifier/KNN.i

src/classifier/KernelPerceptron.cpp

src/classifier/KernelPerceptron.h

src/classifier/KernelPerceptron.i

src/classifier/LDA.cpp

src/classifier/LDA.h

src/classifier/LDA.i

src/classifier/LPM.cpp

src/classifier/LPM.h

src/classifier/LPM.i

src/classifier/LinearClassifier.cpp

src/classifier/LinearClassifier.h

src/classifier/LinearClassifier.i

src/classifier/Perceptron.cpp

src/classifier/Perceptron.h

src/classifier/Perceptron.i

src/classifier/PluginEstimate.cpp

src/classifier/PluginEstimate.h

src/classifier/PluginEstimate.i

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src/classifier/svm/

src/classifier/svm/CPLEXSVM.cpp

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src/classifier/svm/GNPPSVM.cpp

src/classifier/svm/GNPPSVM.h

src/classifier/svm/GNPPSVM.i

src/classifier/svm/GPBTSVM.cpp

src/classifier/svm/GPBTSVM.h

src/classifier/svm/KerthiPrimalSVM.cpp

src/classifier/svm/KerthiPrimalSVM.h

src/classifier/svm/LibSVM.cpp

src/classifier/svm/LibSVM.h

src/classifier/svm/LibSVM.i

src/classifier/svm/LibSVM_oneclass.cpp

src/classifier/svm/LibSVM_oneclass.h

src/classifier/svm/MPD.cpp

src/classifier/svm/MPD.h

src/classifier/svm/SVM.cpp

src/classifier/svm/SVM.h

src/classifier/svm/SVM.i

src/classifier/svm/SVMLin.cpp

src/classifier/svm/SVMLin.h

src/classifier/svm/SVMLin.i

src/classifier/svm/SVM_libsvm.cpp

src/classifier/svm/SVM_libsvm.h

src/classifier/svm/__init__.py

src/classifier/svm/gnpplib.cpp

src/classifier/svm/gnpplib.h

src/classifier/svm/gpdt.cpp

src/classifier/svm/gpdt.h

src/classifier/svm/gpdtsolve.cpp

src/classifier/svm/gpdtsolve.h

src/classifier/svm/gpm.cpp

src/classifier/svm/gpm.h

src/classifier/svm/pr_loqo.cpp

src/classifier/svm/pr_loqo.h

src/classifier/svm/ssl.cpp

src/classifier/svm/ssl.h

src/distance/Canberra.cpp

src/distance/Canberra.h

src/distance/Canberra.i

src/distance/CanberraWordDistance.cpp

src/distance/CanberraWordDistance.h

src/distance/CanberraWordDistance.i

src/distance/Chebyshew.cpp

src/distance/Chebyshew.h

src/distance/Chebyshew.i

src/distance/Distance.cpp

src/distance/Distance.h

src/distance/Distance.i

src/distance/DistanceMachine.cpp

src/distance/DistanceMachine.h

src/distance/DistanceMachine.i

src/distance/Geodesic.cpp

src/distance/Geodesic.h

src/distance/Geodesic.i

src/distance/HammingWordDistance.cpp

src/distance/HammingWordDistance.h

src/distance/HammingWordDistance.i

src/distance/Jensen.cpp

src/distance/Jensen.h

src/distance/Jensen.i

src/distance/Manhattan.cpp

src/distance/Manhattan.h

src/distance/Manhattan.i

src/distance/ManhattanWordDistance.cpp

src/distance/ManhattanWordDistance.h

src/distance/ManhattanWordDistance.i

src/distance/Minkowski.cpp

src/distance/Minkowski.h

src/distance/Minkowski.i

src/distance/RealDistance.h

src/distance/RealDistance.i

src/distance/SimpleDistance.h

src/distance/SimpleDistance.i

src/distance/StringDistance.h

src/distance/StringDistance.i

src/distributions/

src/distributions/Distribution.cpp

src/distributions/Distribution.h

src/distributions/Distribution.i

src/distributions/histogram/

src/distributions/histogram/Histogram.cpp

src/distributions/histogram/Histogram.h

src/distributions/histogram/Histogram.i

src/distributions/hmm/

src/distributions/hmm/GHMM.cpp

src/distributions/hmm/GHMM.h

src/distributions/hmm/GHMM.i

src/distributions/hmm/HMM.cpp

src/distributions/hmm/HMM.h

src/distributions/hmm/HMM.i

src/distributions/hmm/LinearHMM.cpp

src/distributions/hmm/LinearHMM.h

src/distributions/hmm/LinearHMM.i

src/features/Alphabet.cpp

src/features/Alphabet.h

src/features/Alphabet.i

src/features/ByteFeatures.cpp

src/features/ByteFeatures.h

src/features/ByteFeatures.i

src/features/CharFeatures.cpp

src/features/CharFeatures.h

src/features/CharFeatures.i

src/features/CombinedFeatures.cpp

src/features/CombinedFeatures.h

src/features/CombinedFeatures.i

src/features/FKFeatures.cpp

src/features/FKFeatures.h

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src/features/Features.cpp

src/features/Features.h

src/features/Features.i

src/features/Labels.cpp

src/features/Labels.h

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src/features/MindyGramFeatures.cpp

src/features/MindyGramFeatures.h

src/features/MindyGramFeatures.i

src/features/RealFeatures.cpp

src/features/RealFeatures.h

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src/features/RealFileFeatures.cpp

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src/features/ShortFeatures.cpp

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src/features/SimpleFeatures.h

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src/features/SparseFeatures.h

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src/features/StringFeatures.cpp

src/features/StringFeatures.h

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src/features/TOPFeatures.cpp

src/features/TOPFeatures.h

src/features/TOPFeatures.i

src/features/WordFeatures.cpp

src/features/WordFeatures.h

src/features/WordFeatures.i

src/features/__init__.py

src/gui/GUI.cpp

src/gui/Matlab.cpp

src/gui/Octave.cpp

src/gui/Python.cpp

src/gui/Python.h

src/gui/TextGUI.cpp

src/gui/TextGUI.h

src/guilib/GUIClassifier.cpp

src/guilib/GUIClassifier.h

src/guilib/GUIDistance.cpp

src/guilib/GUIDistance.h

src/guilib/GUIFeatures.cpp

src/guilib/GUIFeatures.h

src/guilib/GUIHMM.cpp

src/guilib/GUIHMM.h

src/guilib/GUIKNN.cpp

src/guilib/GUIKNN.h

src/guilib/GUIKernel.cpp

src/guilib/GUIKernel.h

src/guilib/GUILabels.cpp

src/guilib/GUILabels.h

src/guilib/GUIMath.cpp

src/guilib/GUIMath.h

src/guilib/GUIMatlab.cpp

src/guilib/GUIMatlab.h

src/guilib/GUIOctave.cpp

src/guilib/GUIOctave.h

src/guilib/GUIPluginEstimate.cpp

src/guilib/GUIPluginEstimate.h

src/guilib/GUIPreProc.cpp

src/guilib/GUIPreProc.h

src/guilib/GUIPython.cpp

src/guilib/GUIPython.h

src/guilib/GUIR.cpp

src/guilib/GUIR.h

src/guilib/GUISVM.cpp

src/guilib/GUISVM.h

src/guilib/GUITime.cpp

src/guilib/GUITime.h

src/kernel/AUCKernel.cpp

src/kernel/AUCKernel.h

src/kernel/AUCKernel.i

src/kernel/CanberraWordKernel.cpp

src/kernel/CanberraWordKernel.h

src/kernel/CharPolyKernel.cpp

src/kernel/CharPolyKernel.h

src/kernel/CharPolyKernel.i

src/kernel/Chi2Kernel.cpp

src/kernel/Chi2Kernel.h

src/kernel/Chi2Kernel.i

src/kernel/CombinedKernel.cpp

src/kernel/CombinedKernel.h

src/kernel/CombinedKernel.i

src/kernel/CommUlongStringKernel.cpp

src/kernel/CommUlongStringKernel.h

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src/kernel/CommWordKernel.cpp

src/kernel/CommWordKernel.h

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src/kernel/CommWordStringKernel.cpp

src/kernel/CommWordStringKernel.h

src/kernel/CommWordStringKernel.i

src/kernel/ConstKernel.cpp

src/kernel/ConstKernel.h

src/kernel/ConstKernel.i

src/kernel/CustomKernel.cpp

src/kernel/CustomKernel.h

src/kernel/CustomKernel.i

src/kernel/DiagKernel.cpp

src/kernel/DiagKernel.h

src/kernel/DiagKernel.i

src/kernel/DistanceKernel.cpp

src/kernel/DistanceKernel.h

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src/kernel/FixedDegreeCharKernel.cpp

src/kernel/FixedDegreeCharKernel.h

src/kernel/FixedDegreeCharKernel.i

src/kernel/GaussianKernel.cpp

src/kernel/GaussianKernel.h

src/kernel/GaussianKernel.i

src/kernel/HammingWordKernel.cpp

src/kernel/HammingWordKernel.h

src/kernel/HistogramWordKernel.cpp

src/kernel/HistogramWordKernel.h

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src/kernel/Kernel.cpp

src/kernel/Kernel.h

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src/kernel/KernelMachine.cpp

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src/kernel/LinearByteKernel.cpp

src/kernel/LinearByteKernel.h

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src/kernel/LinearCharKernel.cpp

src/kernel/LinearCharKernel.h

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src/kernel/LinearWordKernel.cpp

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src/kernel/LocalityImprovedCharKernel.cpp

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src/kernel/ManhattenWordKernel.cpp

src/kernel/ManhattenWordKernel.h

src/kernel/MindyGramKernel.cpp

src/kernel/MindyGramKernel.h

src/kernel/MindyGramKernel.i

src/kernel/PolyKernel.cpp

src/kernel/PolyKernel.h

src/kernel/PolyKernel.i

src/kernel/PolyMatchCharKernel.cpp

src/kernel/PolyMatchCharKernel.h

src/kernel/PolyMatchCharKernel.i

src/kernel/PolyMatchWordKernel.cpp

src/kernel/PolyMatchWordKernel.h

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src/kernel/SalzbergWordKernel.cpp

src/kernel/SalzbergWordKernel.h

src/kernel/SalzbergWordKernel.i

src/kernel/SigmoidKernel.cpp

src/kernel/SigmoidKernel.h

src/kernel/SigmoidKernel.i

src/kernel/SimpleKernel.h

src/kernel/SimpleKernel.i

src/kernel/SimpleLocalityImprovedCharKernel.cpp

src/kernel/SimpleLocalityImprovedCharKernel.h

src/kernel/SimpleLocalityImprovedCharKernel.i

src/kernel/SparseGaussianKernel.cpp

src/kernel/SparseGaussianKernel.h

src/kernel/SparseGaussianKernel.i

src/kernel/SparseKernel.h

src/kernel/SparseKernel.i

src/kernel/SparseLinearKernel.cpp

src/kernel/SparseLinearKernel.h

src/kernel/SparseLinearKernel.i

src/kernel/SparseNormSquaredKernel.cpp

src/kernel/SparseNormSquaredKernel.h

src/kernel/SparseNormSquaredKernel.i

src/kernel/SparsePolyKernel.cpp

src/kernel/SparsePolyKernel.h

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src/kernel/SpectrumKernel.cpp

src/kernel/SpectrumKernel.h

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src/kernel/StringKernel.h

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src/kernel/WeightedDegreeCharKernel.cpp

src/kernel/WeightedDegreeCharKernel.h

src/kernel/WeightedDegreeCharKernel.i

src/kernel/WeightedDegreeCharKernelPolyA.cpp

src/kernel/WeightedDegreeCharKernelPolyA.h

src/kernel/WeightedDegreeCharKernelPolyA.i

src/kernel/WeightedDegreePositionCharKernel.cpp

src/kernel/WeightedDegreePositionCharKernel.h

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src/kernel/WeightedDegreePositionPhylCharKernel.cpp

src/kernel/WeightedDegreePositionPhylCharKernel.h

src/kernel/WordMatchKernel.cpp

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src/kernel/WordMatchKernel.i

src/kernel/__init__.py

src/lib/Array.h

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src/lib/Array2.h

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src/lib/Cache.h

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src/lib/Cplex.cpp

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src/lib/DynamicArray.h

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src/lib/File.cpp

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src/lib/Mathematics.cpp

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src/lib/suffixarray/BWT.cpp

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src/lib/versionstring.h

src/preproc/LogPlusOne.cpp

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src/preproc/NormDerivativeLem3.cpp

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src/preproc/PCACut.cpp

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src/preproc/PreProc.cpp

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src/preproc/PruneVarSubMean.cpp

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src/preproc/RealPreProc.h

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src/preproc/SortWord.cpp

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src/preproc/SparsePreProc.h

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src/preproc/WordPreProc.cpp

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src/regression/

src/regression/KRR.cpp

src/regression/KRR.h

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src/regression/svr/

src/regression/svr/LibSVR.cpp

src/regression/svr/LibSVR.h

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src/structure/DynProg.cpp

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src/structure/PlifArray.cpp

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src/structure/PlifBase.h

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