.gitignore
COPYING
COPYING.LESSER
Pipfile
Pipfile.lock
pyproject.toml
setup.cfg
setup.py
.github/workflows/publish.yml
.github/workflows/test.yml
tests/__init__.py
tests/conftest.py
tests/test_caching.py
tests/test_config.py
tests/test_const.py
tests/test_crosslinker.py
tests/test_fragment_peptides.py
tests/test_fragmentation.py
tests/test_mass.py
tests/test_modifications.py
tests/test_output_format.py
tests/test_spectra_reader.py
tests/test_synthetic_spectra.py
tests/test_utils.py
tests/test_xi_logging.py
tests/cython/__init__.py
tests/cython/test_argsort_byte_ranges.py
tests/cython/test_copy_ranges.py
tests/cython/test_fast_unique.py
tests/cython/test_inplace_reorder.py
tests/cython/test_num_lexico_permutation.py
tests/cython/test_unique_byte_ranges.py
tests/filters/__init__.py
tests/filters/test_base_filter.py
tests/filters/test_charge_reducer.py
tests/filters/test_denoise_filter.py
tests/filters/test_filters.py
tests/filters/test_isotope_detector.py
tests/filters/test_isotope_reducer.py
tests/filters/test_loss_cluster_filter.py
tests/fixtures/190410_5psm_PSM_xiFDR1.2.30.59dev.csv
tests/fixtures/B180820_06_HSA_BS3_HCD_30_top10_scans.mgf
tests/fixtures/CtermXlinkProtein.mgf
tests/fixtures/FixedMod.FASTA
tests/fixtures/ModTestProtein.FASTA
tests/fixtures/MultipleSpectra.mgf
tests/fixtures/NtermXlinkProtein.mgf
tests/fixtures/OneMiniProtein.FASTA
tests/fixtures/OneMiniProtein.mgf
tests/fixtures/P02768_HSA.FASTA
tests/fixtures/P02768_HSA.FASTA.gz
tests/fixtures/TwoPeptides.FASTA
tests/fixtures/hsa_result_dist_xiview.csv
tests/fixtures/link_site_folding.FASTA
tests/fixtures/link_site_folding.mgf
tests/fixtures/simple_test_intensities.csv
tests/fixtures/simple_test_mzs.csv
tests/fixtures/test_cl_specificity_bonus.mgf
tests/fixtures/test_run_config.json
tests/fixtures/test_run_config_mods.json
tests/fixtures/uniprot-mitochondrion_human.FASTA
tests/fixtures/uniprot-proteome_myco.FASTA
tests/fixtures/xifdr_HSA_example.csv
tests/fixtures/annotation_requests/x1_format_KKK-KKR_1-1_z1_BS3_stubs.json
tests/fixtures/annotation_requests/x1_format_KKK-KKR_1-1_z1_BS3_stubs_expected_response.json
tests/fixtures/annotation_requests/xi1_format_AKT-KMR_1-0_z3_BS3.json
tests/fixtures/annotation_requests/xi1_format_LAsdaK-TSR_z3_NAP.json
tests/fixtures/annotation_requests/xi1_format_QNCcmELFEQLGEYKFQNALLVR-KQTALVELVK_12-0_z4_BS3.json
tests/fixtures/annotation_requests/xi2_format_AKT-KMR_1-0_z3_BS3.json
tests/fixtures/annotation_requests/xi2_format_LAsdaK-TSR_z3_NAP.json
tests/fixtures/annotation_requests/xi2_format_QNCcmELFEQLGEYKFQNALLVR-KQTALVELVK_12-0_z4_BS3.json
tests/fixtures/load_test/1_HSA_SDA_AB_load_test_large.mgf
tests/fixtures/load_test/1_HSA_SDA_AB_load_test_large_linear.mgf
tests/fixtures/load_test/1_HSA_SDA_AB_load_test_small.mgf
tests/fixtures/load_test/1_HSA_SDA_AB_xi2_config.json
tests/fixtures/load_test/1_P02768.fasta
tests/fixtures/load_test/2_MITO.fasta
tests/fixtures/load_test/2_MITO_L.mgf
tests/fixtures/load_test/2_MITO_config.json
tests/fixtures/load_test/3_4_Ecoli_LS_ID2_2up_1E5.fasta
tests/fixtures/load_test/3_ecoli_BS3_LS_load_test_large.mgf
tests/fixtures/load_test/3_ecoli_BS3_LS_load_test_small.mgf
tests/fixtures/load_test/3_ecoli_BS3_LS_xi2_config.json
tests/fixtures/load_test/HSA-S_good_cl_xi1_results.csv
tests/fixtures/load_test/HSA-S_linear_xi1_results.csv
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tests/fixtures/spectra/tiny.pwiz.1.1.mzML
tests/fixtures/test_qc_files/HSA_SDA_AB_xi2_config.json
tests/fixtures/test_qc_files/rcsb_pdb_HSA-active(1ao6).fasta
tests/fixtures/test_qc_files/residue_distances_HSA-active(1ao6).csv
tests/fixtures/test_qc_files/xiFDR-2.1.2-jar-with-dependencies.jar
tests/fixtures/xi1_example_HSA_10_scans/B180820_06_HSA_BS3_HCD_30_top10_scans.mgf
tests/fixtures/xi1_example_HSA_10_scans/search_config.conf
tests/fixtures/xi1_example_HSA_10_scans/search_top10_spectra_HSA_bs3_3_Xi1.7.6.2.csv
tests/fixtures/xi1_example_HSA_10_scans/xi2_search_config.json
xicommon/__init__.py
xicommon/cache.py
xicommon/config.py
xicommon/const.py
xicommon/context_base.py
xicommon/dtypes.py
xicommon/fragment_peptides.py
xicommon/fragmentation.py
xicommon/helper.py
xicommon/mass.py
xicommon/mock_context.py
xicommon/modifications.py
xicommon/output_format.py
xicommon/simple_databases.py
xicommon/spectra_reader.py
xicommon/synthetic_spectra.py
xicommon/utils.py
xicommon/xi_logging.py
xicommon.egg-info/PKG-INFO
xicommon.egg-info/SOURCES.txt
xicommon.egg-info/dependency_links.txt
xicommon.egg-info/requires.txt
xicommon.egg-info/top_level.txt
xicommon/cython/__init__.py
xicommon/cython/argsort_byte_ranges.c
xicommon/cython/argsort_byte_ranges.pyx
xicommon/cython/compare_byte_ranges.c
xicommon/cython/compare_byte_ranges.pxd
xicommon/cython/compare_byte_ranges.pyx
xicommon/cython/copy_byte_ranges.c
xicommon/cython/copy_byte_ranges.pyx
xicommon/cython/db_uuid.c
xicommon/cython/db_uuid.pyx
xicommon/cython/fast_candidate_scores.c
xicommon/cython/fast_candidate_scores.pyx
xicommon/cython/fast_lookup.c
xicommon/cython/fast_lookup.pyx
xicommon/cython/fast_unique.c
xicommon/cython/fast_unique.pyx
xicommon/cython/fragmentation.c
xicommon/cython/fragmentation.pyx
xicommon/cython/fragmentation.pyxbld
xicommon/cython/inplace_reorder.c
xicommon/cython/inplace_reorder.pyx
xicommon/cython/isin_set.cpp
xicommon/cython/isin_set.pyx
xicommon/cython/isin_set.pyxbld
xicommon/cython/num_lexico_permutation.c
xicommon/cython/num_lexico_permutation.pyx
xicommon/cython/unique_byte_ranges.c
xicommon/cython/unique_byte_ranges.pyx
xicommon/filters/__init__.py
xicommon/filters/base_filter.py
xicommon/filters/charge_reducer.py
xicommon/filters/denoise_filter.py
xicommon/filters/isotope_detector.py
xicommon/filters/isotope_reducer.py
xicommon/filters/loss_cluster_filter.py