LICENSE
MANIFEST.in
README.md
pyproject.toml
requirements.txt
setup.py
src/glycan_profiling/__init__.py
src/glycresoft/__init__.py
src/glycresoft/piped_deconvolve.py
src/glycresoft/profiler.py
src/glycresoft/scan_cache.py
src/glycresoft/symbolic_expression.py
src/glycresoft/task.py
src/glycresoft/version.py
src/glycresoft.egg-info/PKG-INFO
src/glycresoft.egg-info/SOURCES.txt
src/glycresoft.egg-info/dependency_links.txt
src/glycresoft.egg-info/entry_points.txt
src/glycresoft.egg-info/not-zip-safe
src/glycresoft.egg-info/requires.txt
src/glycresoft.egg-info/top_level.txt
src/glycresoft/_c/__init__.py
src/glycresoft/_c/cythonizer.py
src/glycresoft/_c/chromatogram_tree/__init__.py
src/glycresoft/_c/chromatogram_tree/chromatogram.pxd
src/glycresoft/_c/chromatogram_tree/chromatogram.pyx
src/glycresoft/_c/chromatogram_tree/index.c
src/glycresoft/_c/chromatogram_tree/index.pxd
src/glycresoft/_c/chromatogram_tree/index.pyx
src/glycresoft/_c/chromatogram_tree/mass_shift.c
src/glycresoft/_c/chromatogram_tree/mass_shift.pxd
src/glycresoft/_c/chromatogram_tree/mass_shift.pyx
src/glycresoft/_c/composition_distribution_model/__init__.py
src/glycresoft/_c/composition_distribution_model/utils.c
src/glycresoft/_c/composition_distribution_model/utils.pxd
src/glycresoft/_c/composition_distribution_model/utils.pyx
src/glycresoft/_c/composition_network/__init__.py
src/glycresoft/_c/composition_network/graph.c
src/glycresoft/_c/composition_network/graph.pxd
src/glycresoft/_c/composition_network/graph.pyx
src/glycresoft/_c/database/__init__.py
src/glycresoft/_c/database/mass_collection.c
src/glycresoft/_c/database/mass_collection.pxd
src/glycresoft/_c/database/mass_collection.pyx
src/glycresoft/_c/scoring/__init__.py
src/glycresoft/_c/scoring/elution_time_grouping.c
src/glycresoft/_c/scoring/elution_time_grouping.pyx
src/glycresoft/_c/scoring/shape_fitter.c
src/glycresoft/_c/scoring/shape_fitter.pyx
src/glycresoft/_c/structure/__init__.py
src/glycresoft/_c/structure/fragment_match_map.c
src/glycresoft/_c/structure/fragment_match_map.pxd
src/glycresoft/_c/structure/fragment_match_map.pyx
src/glycresoft/_c/structure/intervals.c
src/glycresoft/_c/structure/intervals.pyx
src/glycresoft/_c/structure/lru.c
src/glycresoft/_c/structure/lru.pyx
src/glycresoft/_c/structure/probability.c
src/glycresoft/_c/structure/probability.pyx
src/glycresoft/_c/structure/structure_loader.c
src/glycresoft/_c/structure/structure_loader.pxd
src/glycresoft/_c/structure/structure_loader.pyx
src/glycresoft/_c/tandem/__init__.py
src/glycresoft/_c/tandem/core_search.c
src/glycresoft/_c/tandem/core_search.pyx
src/glycresoft/_c/tandem/oxonium_ions.c
src/glycresoft/_c/tandem/oxonium_ions.pxd
src/glycresoft/_c/tandem/oxonium_ions.pyx
src/glycresoft/_c/tandem/peptide_graph.c
src/glycresoft/_c/tandem/peptide_graph.pyx
src/glycresoft/_c/tandem/spectrum_match.c
src/glycresoft/_c/tandem/spectrum_match.pxd
src/glycresoft/_c/tandem/spectrum_match.pyx
src/glycresoft/_c/tandem/tandem_scoring_helpers.c
src/glycresoft/_c/tandem/tandem_scoring_helpers.pyx
src/glycresoft/_c/tandem/target_decoy.c
src/glycresoft/_c/tandem/target_decoy.pyx
src/glycresoft/chromatogram_tree/__init__.py
src/glycresoft/chromatogram_tree/chromatogram.py
src/glycresoft/chromatogram_tree/generic.py
src/glycresoft/chromatogram_tree/grouping.py
src/glycresoft/chromatogram_tree/index.py
src/glycresoft/chromatogram_tree/mass_shift.py
src/glycresoft/chromatogram_tree/mass_shift_tree.py
src/glycresoft/chromatogram_tree/relation_graph.py
src/glycresoft/chromatogram_tree/utils.py
src/glycresoft/cli/__init__.py
src/glycresoft/cli/__main__.py
src/glycresoft/cli/analyze.py
src/glycresoft/cli/base.py
src/glycresoft/cli/build_db.py
src/glycresoft/cli/config.py
src/glycresoft/cli/export.py
src/glycresoft/cli/logger_config.py
src/glycresoft/cli/mzml.py
src/glycresoft/cli/tools.py
src/glycresoft/cli/utils.py
src/glycresoft/cli/validators.py
src/glycresoft/composition_distribution_model/__init__.py
src/glycresoft/composition_distribution_model/constants.py
src/glycresoft/composition_distribution_model/glycome_network_smoothing.py
src/glycresoft/composition_distribution_model/graph.py
src/glycresoft/composition_distribution_model/grid_search.py
src/glycresoft/composition_distribution_model/laplacian_smoothing.py
src/glycresoft/composition_distribution_model/observation.py
src/glycresoft/composition_distribution_model/prior_distribution.py
src/glycresoft/composition_distribution_model/utils.py
src/glycresoft/composition_distribution_model/site_model/__init__.py
src/glycresoft/composition_distribution_model/site_model/builder.py
src/glycresoft/composition_distribution_model/site_model/glycoprotein_model.py
src/glycresoft/composition_distribution_model/site_model/glycoproteome_model.py
src/glycresoft/composition_distribution_model/site_model/glycosite_model.py
src/glycresoft/config/__init__.py
src/glycresoft/config/colors.py
src/glycresoft/config/config_file.py
src/glycresoft/config/mass_shift.py
src/glycresoft/config/peptide_modification.py
src/glycresoft/config/substituent.py
src/glycresoft/database/__init__.py
src/glycresoft/database/composition_aggregation.py
src/glycresoft/database/disk_backed_database.py
src/glycresoft/database/glycan_composition_filter.py
src/glycresoft/database/index.py
src/glycresoft/database/intervals.py
src/glycresoft/database/mass_collection.py
src/glycresoft/database/analysis/__init__.py
src/glycresoft/database/analysis/analysis_migration.py
src/glycresoft/database/builder/__init__.py
src/glycresoft/database/builder/base.py
src/glycresoft/database/builder/glycan/__init__.py
src/glycresoft/database/builder/glycan/constrained_combinatorics.py
src/glycresoft/database/builder/glycan/convert_analysis.py
src/glycresoft/database/builder/glycan/glycan_combinator.py
src/glycresoft/database/builder/glycan/glycan_permutations.py
src/glycresoft/database/builder/glycan/glycan_source.py
src/glycresoft/database/builder/glycan/glycosaminoglycan_linker_generation.py
src/glycresoft/database/builder/glycan/glyspace.py
src/glycresoft/database/builder/glycan/migrate.py
src/glycresoft/database/builder/glycan/synthesis.py
src/glycresoft/database/builder/glycopeptide/__init__.py
src/glycresoft/database/builder/glycopeptide/common.py
src/glycresoft/database/builder/glycopeptide/extending_glycopeptide.py
src/glycresoft/database/builder/glycopeptide/informed_glycopeptide.py
src/glycresoft/database/builder/glycopeptide/migrate.py
src/glycresoft/database/builder/glycopeptide/naive_glycopeptide.py
src/glycresoft/database/builder/glycopeptide/proteomics/__init__.py
src/glycresoft/database/builder/glycopeptide/proteomics/fasta.py
src/glycresoft/database/builder/glycopeptide/proteomics/mzid_parser.py
src/glycresoft/database/builder/glycopeptide/proteomics/mzid_proteome.py
src/glycresoft/database/builder/glycopeptide/proteomics/peptide_permutation.py
src/glycresoft/database/builder/glycopeptide/proteomics/proteome.py
src/glycresoft/database/builder/glycopeptide/proteomics/remove_duplicate_peptides.py
src/glycresoft/database/builder/glycopeptide/proteomics/sequence_tree.py
src/glycresoft/database/builder/glycopeptide/proteomics/share_peptides.py
src/glycresoft/database/builder/glycopeptide/proteomics/uniprot.py
src/glycresoft/database/builder/glycopeptide/proteomics/utils.py
src/glycresoft/database/composition_network/__init__.py
src/glycresoft/database/composition_network/graph.py
src/glycresoft/database/composition_network/neighborhood.py
src/glycresoft/database/composition_network/rule.py
src/glycresoft/database/composition_network/space.py
src/glycresoft/database/prebuilt/__init__.py
src/glycresoft/database/prebuilt/biosynthesis_human_n_linked.py
src/glycresoft/database/prebuilt/biosynthesis_mammalian_n_linked.py
src/glycresoft/database/prebuilt/combinatorial_human_n_linked.py
src/glycresoft/database/prebuilt/combinatorial_mammalian_n_linked.py
src/glycresoft/database/prebuilt/glycosaminoglycan_linkers.py
src/glycresoft/database/prebuilt/heparin.py
src/glycresoft/database/prebuilt/human_mucin_o_linked.py
src/glycresoft/database/prebuilt/utils.py
src/glycresoft/database/prebuilt/data/__init__.py
src/glycresoft/database/prebuilt/data/human_composition_enzyme_graph.json
src/glycresoft/database/prebuilt/data/mammalian_composition_enzyme_graph.json
src/glycresoft/database/prebuilt/data/mucin_compositions.txt
src/glycresoft/models/__init__.py
src/glycresoft/models/charge_models.py
src/glycresoft/models/features.py
src/glycresoft/models/mass_shift_models.py
src/glycresoft/models/utils.py
src/glycresoft/models/data/__init__.py
src/glycresoft/models/data/ammonium_adduct_model.json
src/glycresoft/models/data/asialo_formate_adduct_model.json
src/glycresoft/models/data/disialo_formate_adduct_model.json
src/glycresoft/models/data/methyl_loss_adduct_model.json
src/glycresoft/models/data/monosialo_formate_adduct_model.json
src/glycresoft/models/data/sialylated_charge_model.json
src/glycresoft/models/data/tetrasialo_formate_adduct_model.json
src/glycresoft/models/data/trisialo_formate_adduct_model.json
src/glycresoft/models/data/unsialylated_charge_model.json
src/glycresoft/output/__init__.py
src/glycresoft/output/annotate_spectra.py
src/glycresoft/output/csv_format.py
src/glycresoft/output/text_format.py
src/glycresoft/output/xml.py
src/glycresoft/output/report/__init__.py
src/glycresoft/output/report/base.py
src/glycresoft/output/report/glycan_lcms/__init__.py
src/glycresoft/output/report/glycan_lcms/behaviors.js
src/glycresoft/output/report/glycan_lcms/overview.templ
src/glycresoft/output/report/glycan_lcms/render.py
src/glycresoft/output/report/glycan_lcms/style.css
src/glycresoft/output/report/glycopeptide_lcmsms/__init__.py
src/glycresoft/output/report/glycopeptide_lcmsms/behaviors.js
src/glycresoft/output/report/glycopeptide_lcmsms/glycopeptide-detail-entry.templ
src/glycresoft/output/report/glycopeptide_lcmsms/glycopeptide-table.templ
src/glycresoft/output/report/glycopeptide_lcmsms/overview.templ
src/glycresoft/output/report/glycopeptide_lcmsms/protein-heading.templ
src/glycresoft/output/report/glycopeptide_lcmsms/render.py
src/glycresoft/output/report/glycopeptide_lcmsms/style.css
src/glycresoft/plotting/__init__.py
src/glycresoft/plotting/base.py
src/glycresoft/plotting/chromatogram_artist.py
src/glycresoft/plotting/colors.py
src/glycresoft/plotting/diagnostics.py
src/glycresoft/plotting/entity_bar_chart.py
src/glycresoft/plotting/glycan_visual_classification.py
src/glycresoft/plotting/lcms_map.py
src/glycresoft/plotting/lcms_surface.py
src/glycresoft/plotting/map_glycan_network.py
src/glycresoft/plotting/plot_glycoforms.py
src/glycresoft/plotting/sequence_fragment_logo.py
src/glycresoft/plotting/spectral_annotation.py
src/glycresoft/plotting/summaries.py
src/glycresoft/plotting/svg_utils.py
src/glycresoft/plotting/utils.py
src/glycresoft/scoring/__init__.py
src/glycresoft/scoring/base.py
src/glycresoft/scoring/charge_state.py
src/glycresoft/scoring/chromatogram_solution.py
src/glycresoft/scoring/isotopic_fit.py
src/glycresoft/scoring/mass_shift_scoring.py
src/glycresoft/scoring/shape_fitter.py
src/glycresoft/scoring/spacing_fitter.py
src/glycresoft/scoring/utils.py
src/glycresoft/scoring/elution_time_grouping/__init__.py
src/glycresoft/scoring/elution_time_grouping/cross_run.py
src/glycresoft/scoring/elution_time_grouping/linear_regression.py
src/glycresoft/scoring/elution_time_grouping/model.py
src/glycresoft/scoring/elution_time_grouping/pipeline.py
src/glycresoft/scoring/elution_time_grouping/recalibrator.py
src/glycresoft/scoring/elution_time_grouping/reviser.py
src/glycresoft/scoring/elution_time_grouping/structure.py
src/glycresoft/serialize/__init__.py
src/glycresoft/serialize/analysis.py
src/glycresoft/serialize/base.py
src/glycresoft/serialize/chromatogram.py
src/glycresoft/serialize/config.py
src/glycresoft/serialize/connection.py
src/glycresoft/serialize/identification.py
src/glycresoft/serialize/migration.py
src/glycresoft/serialize/param.py
src/glycresoft/serialize/serializer.py
src/glycresoft/serialize/spectrum.py
src/glycresoft/serialize/tandem.py
src/glycresoft/serialize/utils.py
src/glycresoft/serialize/hypothesis/__init__.py
src/glycresoft/serialize/hypothesis/generic.py
src/glycresoft/serialize/hypothesis/glycan.py
src/glycresoft/serialize/hypothesis/hypothesis.py
src/glycresoft/serialize/hypothesis/peptide.py
src/glycresoft/structure/__init__.py
src/glycresoft/structure/denovo.py
src/glycresoft/structure/enums.py
src/glycresoft/structure/fragment_match_map.py
src/glycresoft/structure/lru.py
src/glycresoft/structure/probability.py
src/glycresoft/structure/scan.py
src/glycresoft/structure/structure_loader.py
src/glycresoft/structure/utils.py
src/glycresoft/tandem/__init__.py
src/glycresoft/tandem/coelute.py
src/glycresoft/tandem/identified_structure.py
src/glycresoft/tandem/localize.py
src/glycresoft/tandem/oxonium_ions.py
src/glycresoft/tandem/process_dispatcher.py
src/glycresoft/tandem/ref.py
src/glycresoft/tandem/reporter.py
src/glycresoft/tandem/spectrum_evaluation.py
src/glycresoft/tandem/spectrum_graph.py
src/glycresoft/tandem/temp_store.py
src/glycresoft/tandem/workflow.py
src/glycresoft/tandem/workload.py
src/glycresoft/tandem/chromatogram_mapping/__init__.py
src/glycresoft/tandem/chromatogram_mapping/aggregation.py
src/glycresoft/tandem/chromatogram_mapping/base.py
src/glycresoft/tandem/chromatogram_mapping/chromatogram.py
src/glycresoft/tandem/chromatogram_mapping/graph.py
src/glycresoft/tandem/chromatogram_mapping/mapper.py
src/glycresoft/tandem/chromatogram_mapping/representer.py
src/glycresoft/tandem/chromatogram_mapping/revision.py
src/glycresoft/tandem/evaluation_dispatch/__init__.py
src/glycresoft/tandem/evaluation_dispatch/evaluation.py
src/glycresoft/tandem/evaluation_dispatch/process.py
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src/glycresoft/tandem/evaluation_dispatch/utils.py
src/glycresoft/tandem/glycan/__init__.py
src/glycresoft/tandem/glycan/composition_matching.py
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src/glycresoft/tandem/glycan/scoring/__init__.py
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src/glycresoft/tandem/glycan/scoring/signature_ion_scoring.py
src/glycresoft/tandem/glycan/scoring/binomial_coverage/__init__.py
src/glycresoft/tandem/glycan/scoring/binomial_coverage/matcher.py
src/glycresoft/tandem/glycan/scoring/binomial_coverage/score_components.py
src/glycresoft/tandem/glycopeptide/__init__.py
src/glycresoft/tandem/glycopeptide/chromatogram_graph.py
src/glycresoft/tandem/glycopeptide/core_search.py
src/glycresoft/tandem/glycopeptide/glycopeptide_matcher.py
src/glycresoft/tandem/glycopeptide/identified_structure.py
src/glycresoft/tandem/glycopeptide/matcher.py
src/glycresoft/tandem/glycopeptide/dynamic_generation/__init__.py
src/glycresoft/tandem/glycopeptide/dynamic_generation/journal.py
src/glycresoft/tandem/glycopeptide/dynamic_generation/mixture.py
src/glycresoft/tandem/glycopeptide/dynamic_generation/multipart_fdr.py
src/glycresoft/tandem/glycopeptide/dynamic_generation/peptide_graph.py
src/glycresoft/tandem/glycopeptide/dynamic_generation/search_space.py
src/glycresoft/tandem/glycopeptide/dynamic_generation/searcher.py
src/glycresoft/tandem/glycopeptide/dynamic_generation/workflow.py
src/glycresoft/tandem/glycopeptide/scoring/__init__.py
src/glycresoft/tandem/glycopeptide/scoring/base.py
src/glycresoft/tandem/glycopeptide/scoring/binomial_score.py
src/glycresoft/tandem/glycopeptide/scoring/coverage_weighted_binomial.py
src/glycresoft/tandem/glycopeptide/scoring/glycan_signature_ions.py
src/glycresoft/tandem/glycopeptide/scoring/intensity_scorer.py
src/glycresoft/tandem/glycopeptide/scoring/pair_amino_acids_scoring.py
src/glycresoft/tandem/glycopeptide/scoring/peak_vector.py
src/glycresoft/tandem/glycopeptide/scoring/precursor_mass_accuracy.py
src/glycresoft/tandem/glycopeptide/scoring/simple_score.py
src/glycresoft/tandem/match_between_runs/__init__.py
src/glycresoft/tandem/match_between_runs/dataset.py
src/glycresoft/tandem/match_between_runs/match_between.py
src/glycresoft/tandem/peptide/__init__.py
src/glycresoft/tandem/peptide/scoring/__init__.py
src/glycresoft/tandem/peptide/scoring/base.py
src/glycresoft/tandem/peptide/scoring/intensity_score.py
src/glycresoft/tandem/peptide/scoring/localize.py
src/glycresoft/tandem/peptide/scoring/simple_score.py
src/glycresoft/tandem/spectrum_match/__init__.py
src/glycresoft/tandem/spectrum_match/solution_set.py
src/glycresoft/tandem/spectrum_match/spectrum_match.py
src/glycresoft/tandem/target_decoy/__init__.py
src/glycresoft/tandem/target_decoy/base.py
src/glycresoft/tandem/target_decoy/svm.py
src/glycresoft/trace/__init__.py
src/glycresoft/trace/evaluate.py
src/glycresoft/trace/extract.py
src/glycresoft/trace/match.py
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tests/test_composition_network.py
tests/test_constrained_combinatorics.py
tests/test_core_search.py
tests/test_fasta_glycopeptide.py
tests/test_glycan_chromatogram_analyzer.py
tests/test_glycan_combinator.py
tests/test_glycan_prebuilt.py
tests/test_glycan_source.py
tests/test_glycopeptide_scorers.py
tests/test_glycopeptide_search.py
tests/test_mzid_glycopeptide.py
tests/test_rt_model.py
tests/test_sample_consumer.py
tests/test_structure_loader.py
tests/test_symbolic_expression.py
tests/test_target_decoy.py
tests/test_task_execution_sequence.py