MANIFEST.in
setup.py
./gui/AlignmentGUI.py
./gui/TAPIR.py
analysis/alignment/compute_full_matrix.py
analysis/alignment/extract_matrix.py
analysis/alignment/feature_alignment.py
analysis/alignment/preprocess_peakview.py
analysis/alignment/requantAlignedValues.py
analysis/data_conversion/MSE2mzML.py
analysis/data_conversion/MSE_split.py
analysis/data_conversion/featurealigner2msstats.py
analysis/data_conversion/fix_sonar.py
analysis/data_conversion/fix_swath_windows.py
analysis/data_conversion/pepxml2csv.py
analysis/data_conversion/pepxml2csv_simple.py
analysis/data_conversion/pseudoreverseDB.py
analysis/data_conversion/split_mzXML_intoSwath.py
analysis/fdr_estimation/ProtFDRTraML2Fasta.py
analysis/fdr_estimation/ProtFDRmProphet2Mayu.py
analysis/mProphet/count_pep_prot.py
analysis/mProphet/fdr_cutoff.py
analysis/misc/proteinDBmasses.py
analysis/misc/proteinDigest.py
analysis/misc/trafoXML_visualize.py
analysis/scripts/add_protein_annotation.py
analysis/scripts/convertNISTLibraryToTSV.py
analysis/scripts/copy_accesion.py
analysis/scripts/filterChrom.py
analysis/scripts/plot_alignment_tree.py
analysis/scripts/proteins_not_in_library.py
analysis/scripts/DIA/NISTParser.py
analysis/scripts/DIA/convertMassLynxTomzML.py
analysis/scripts/DIA/makeSwathFile.py
analysis/scripts/DIA/splitMSE.py
analysis/spectral_libs/spectrast2spectrast_irt.py
analysis/spectral_libs/spectrast2tsv.py
analysis/spectral_libs/spectrast_cluster.py
analysis/spectral_libs/spectrast_updateiRTs.py
analysis/spectral_libs/tsv2spectrast.py
gui/AlignmentGUI.py
gui/TAPIR.py
gui/openswathgui/__init__.py
gui/openswathgui/models/ChromatogramTransition.py
gui/openswathgui/models/MSData.py
gui/openswathgui/models/PeptideTree.py
gui/openswathgui/models/SingleChromatogramFile.py
gui/openswathgui/models/SwathRun.py
gui/openswathgui/models/SwathRunCollection.py
gui/openswathgui/models/TreeModels.py
gui/openswathgui/models/__init__.py
gui/openswathgui/views/PeptideTree.py
gui/openswathgui/views/Plot.py
gui/openswathgui/views/__init__.py
msproteomicstools.egg-info/PKG-INFO
msproteomicstools.egg-info/SOURCES.txt
msproteomicstools.egg-info/dependency_links.txt
msproteomicstools.egg-info/requires.txt
msproteomicstools.egg-info/top_level.txt
msproteomicstoolslib/__init__.py
msproteomicstoolslib/algorithms/__init__.py
msproteomicstoolslib/algorithms/PADS/MinimumSpanningTree.py
msproteomicstoolslib/algorithms/PADS/UnionFind.py
msproteomicstoolslib/algorithms/PADS/__init__.py
msproteomicstoolslib/algorithms/alignment/AlignmentAlgorithm.py
msproteomicstoolslib/algorithms/alignment/AlignmentHelper.py
msproteomicstoolslib/algorithms/alignment/AlignmentMST.py
msproteomicstoolslib/algorithms/alignment/BorderIntegration.py
msproteomicstoolslib/algorithms/alignment/FDRParameterEstimation.py
msproteomicstoolslib/algorithms/alignment/MRExperiment.py
msproteomicstoolslib/algorithms/alignment/Multipeptide.py
msproteomicstoolslib/algorithms/alignment/SplineAligner.py
msproteomicstoolslib/algorithms/alignment/__init__.py
msproteomicstoolslib/algorithms/graphs/__init__.py
msproteomicstoolslib/algorithms/graphs/graphs.py
msproteomicstoolslib/algorithms/shared/__init__.py
msproteomicstoolslib/data_structures/DDB.py
msproteomicstoolslib/data_structures/PeakGroup.py
msproteomicstoolslib/data_structures/Precursor.py
msproteomicstoolslib/data_structures/PrecursorGroup.py
msproteomicstoolslib/data_structures/Residues.py
msproteomicstoolslib/data_structures/Run.py
msproteomicstoolslib/data_structures/__init__.py
msproteomicstoolslib/data_structures/aminoacides.py
msproteomicstoolslib/data_structures/elements.py
msproteomicstoolslib/data_structures/modifications.py
msproteomicstoolslib/data_structures/modifications_default.tsv
msproteomicstoolslib/data_structures/peak.py
msproteomicstoolslib/data_structures/peptide.py
msproteomicstoolslib/format/MatrixWriters.py
msproteomicstoolslib/format/ProteinDB.py
msproteomicstoolslib/format/SWATHScoringReader.py
msproteomicstoolslib/format/TransformationCollection.py
msproteomicstoolslib/format/__init__.py
msproteomicstoolslib/format/methodDamReader.py
msproteomicstoolslib/format/methodMethReader.py
msproteomicstoolslib/format/mzXMLreader.py
msproteomicstoolslib/format/pepXMLReader.py
msproteomicstoolslib/format/speclib_db_lib.py
msproteomicstoolslib/math/LinearRegression.py
msproteomicstoolslib/math/Smoothing.py
msproteomicstoolslib/math/__init__.py
msproteomicstoolslib/math/chauvenet.py
msproteomicstoolslib/util/__init__.py
msproteomicstoolslib/util/assertions.py
msproteomicstoolslib/util/gnuplot.py
msproteomicstoolslib/util/latex.py
msproteomicstoolslib/util/logs.py
msproteomicstoolslib/util/progress.py
msproteomicstoolslib/util/utils.py
test/__init__.py
test/test_import.py
test/test_mzXMLReader.py
test/algorithms_test/test_Alignment.py
test/algorithms_test/test_AlignmentMST.py
test/algorithms_test/test_FDRParameterEstimation.py
test/algorithms_test/test_graphs.py
test/algorithms_test/test_multipeptides.py
test/analysis_test/__init__.py
test/analysis_test/test_compute_full_matrix.py
test/analysis_test/test_damMethodReader.py
test/analysis_test/test_featurealignment.py
test/analysis_test/test_pepxml2csv.py
test/analysis_test/test_pseudoreverseDB.py
test/analysis_test/test_requantAlignedValues.py
test/analysis_test/test_spectrast2tsv.py
test/data/ABSciex_expected_output.csv
test/data/ABSciex_testInput.dam
test/data/ABSciex_testInput2.dam
test/data/ABSciex_testInput3.dam
test/data/computeFullMatrix_1_input.csv
test/data/computeFullMatrix_1_output.tsv
test/data/feature_alignment_1_openswath_output_cluster_ids.csv
test/data/feature_alignment_1_openswath_output_matrix.csv
test/data/feature_alignment_2_output_1_ids.csv
test/data/feature_alignment_2_output_2_matrix.csv
test/data/feature_alignment_3_openswath_input.csv
test/data/feature_alignment_3_openswath_output_cluster_ids.csv
test/data/feature_alignment_5_peakview_output_matrix.csv
test/data/feature_alignment_6_output_1_ids.csv
test/data/feature_alignment_6_output_2_matrix.csv
test/data/feature_alignment_7_openswath_input.csv
test/data/feature_alignment_7_output_1_ids.csv
test/data/feature_alignment_7_output_2_matrix.csv
test/data/feature_alignment_7_output_3.csv
test/data/feature_alignment_openswath_input_1.csv
test/data/feature_alignment_peakview_input_2.csv
test/data/imputeValues_1_output.csv
test/data/imputeValues_1_output_matrix.csv
test/data/imputeValues_3_output.csv
test/data/imputeValues_3_output_matrix.csv
test/data/imputeValues_5_output.csv
test/data/imputeValues_5_output_matrix.csv
test/data/imputeValues_6_output.csv
test/data/imputeValues_6_output_matrix.csv
test/data/imputeValues_7_output.csv
test/data/imputeValues_7_output_matrix.csv
test/data/imputeValues_8_output.csv
test/data/imputeValues_8_output_matrix.csv
test/data/labeling_file.txt
test/data/methodDamReader_1_output.csv
test/data/methodDamReader_2_output.csv
test/data/methodDamReader_3_output.csv
test/data/modsfile_test.txt
test/data/pepxml2csv.expected_out.csv
test/data/smallDB.fasta
test/data/spectrast2tsv_1_openswath_out.csv
test/data/spectrast2tsv_2_openswath_out.csv
test/data/swaths_file.txt
test/data/test.pep.xml
test/data/test_pseudoreverse.expected_out.fasta
test/data/test_pseudoreverse.fasta
test/data/testfile.small.mzXML
test/data/testlib.sptxt
test/data/gui/README
test/data/gui/dataset1.chrom.mzML
test/data/gui/dataset1.csv
test/data/gui/dataset1.yaml
test/data/gui/dataset2.csv
test/data/gui/dataset2_description.TraML
test/data/gui/dataset2_description.csv
test/data/gui/dataset2_file1.mzML
test/data/gui/dataset2_file2.mzML
test/data/gui/dataset2_file3.mzML
test/data/gui/dataset2_simple_description.csv
test/data/imputeValues/imputeValues_1_input.csv
test/data/imputeValues/imputeValues_5_input.csv
test/data/imputeValues/imputeValues_7_input.csv
test/data/imputeValues/imputeValues_8_input.csv
test/data/imputeValues/r003_small/split_olgas_K121102_003_SW_PA1_earlyexp.chrom.mzML
test/data/imputeValues/r003_small/transformation-0_0-0_0.tr
test/data/imputeValues/r004_small/split_olgas_otherfile.chrom.mzML
test/data/imputeValues/r004_small/transformation-0_1-0_0.tr
test/data_structures_test/__init__.py
test/data_structures_test/test_aminoacides.py
test/data_structures_test/test_elements.py
test/data_structures_test/test_modifications.py
test/data_structures_test/test_peakgroup.py
test/data_structures_test/test_peptide.py
test/data_structures_test/test_precursor.py
test/data_structures_test/test_run.py
test/format_test/__init__.py
test/format_test/test_ProteinDB.py
test/format_test/test_SWATHScoringReader.py
test/format_test/test_methodDamReader.py
test/integration_test/test_Integration.py
test/math_test/test_Smoothing.py
test/util_test/__init__.py
test/util_test/test_logs.py