[med-svn] [crux] 04/05: Update upstream source from tag 'upstream/3.1'
Andreas Tille
tille at debian.org
Tue Dec 5 12:44:15 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository crux.
commit c023d0025ab62ff1079d5565a9a9a757953bd51f
Merge: ba23bbe e02afac
Author: Andreas Tille <tille at debian.org>
Date: Tue Dec 5 13:21:58 2017 +0100
Update upstream source from tag 'upstream/3.1'
Update to upstream version '3.1'
with Debian dir f30922d62e624fd777d0dd5b969a1d279ebdc398
AUTHORS | 5 +
CMakeLists.txt | 163 +
COPYRIGHT | 1 +
CPackConfig.cmake | 68 +
CPackSourceConfig.cmake | 73 +
INSTALL | 34 +
Makefile | 472 +
NEWS | 2 +
README | 8 +
.../Linux/ZIP/crux-3.1.Linux.x86_64/doc/Makefile | 207 +
.../doc/assign-confidence.html | 147 +
.../ZIP/crux-3.1.Linux.x86_64/doc/barista.html | 163 +
.../ZIP/crux-3.1.Linux.x86_64/doc/bullseye.html | 158 +
.../crux-3.1.Linux.x86_64/doc/cascade-search.html | 215 +
.../crux-3.1.Linux.x86_64/doc/cmake_install.cmake | 38 +
.../doc/comet-options/activation_method.html | 23 +
.../doc/comet-options/add_A_alanine.html | 15 +
.../doc/comet-options/add_B_user_amino_acid.html | 19 +
.../doc/comet-options/add_C_cysteine.html | 21 +
.../doc/comet-options/add_Cterm_peptide.html | 15 +
.../doc/comet-options/add_Cterm_protein.html | 15 +
.../doc/comet-options/add_D_aspartic_acid.html | 15 +
.../doc/comet-options/add_E_glutamic_acid.html | 15 +
.../doc/comet-options/add_F_phenylalanine.html | 15 +
.../doc/comet-options/add_G_glycine.html | 15 +
.../doc/comet-options/add_H_histidine.html | 15 +
.../doc/comet-options/add_I_isoleucine.html | 15 +
.../doc/comet-options/add_J_user_amino_acid.html | 19 +
.../doc/comet-options/add_K_lysine.html | 15 +
.../doc/comet-options/add_L_leucine.html | 15 +
.../doc/comet-options/add_M_methionine.html | 15 +
.../doc/comet-options/add_N_asparagine.html | 15 +
.../doc/comet-options/add_Nterm_peptide.html | 15 +
.../doc/comet-options/add_Nterm_protein.html | 15 +
.../doc/comet-options/add_O_ornithine.html | 15 +
.../doc/comet-options/add_P_proline.html | 15 +
.../doc/comet-options/add_Q_glutamine.html | 15 +
.../doc/comet-options/add_R_arginine.html | 15 +
.../doc/comet-options/add_S_serine.html | 15 +
.../doc/comet-options/add_T_threonine.html | 15 +
.../doc/comet-options/add_U_user_amino_acid.html | 19 +
.../doc/comet-options/add_V_valine.html | 15 +
.../doc/comet-options/add_W_tryptophan.html | 15 +
.../doc/comet-options/add_X_user_amino_acid.html | 19 +
.../doc/comet-options/add_Y_tyrosine.html | 15 +
.../doc/comet-options/add_Z_user_amino_acid.html | 19 +
.../doc/comet-options/allowed_missed_cleavage.html | 18 +
.../doc/comet-options/clear_mz_range.html | 24 +
.../doc/comet-options/clip_nterm_methionine.html | 22 +
.../doc/comet-options/combined.html | 23 +
.../doc/comet-options/comet.params | 160 +
.../doc/comet-options/content.html | 1 +
.../doc/comet-options/convertCometPHPs.py | 55 +
.../doc/comet-options/database_name.html | 21 +
.../doc/comet-options/decoy_prefix.html | 22 +
.../doc/comet-options/decoy_search.html | 29 +
.../doc/comet-options/digest_mass_range.html | 23 +
.../doc/comet-options/footer.html | 1 +
.../doc/comet-options/fragment_bin_offset.html | 31 +
.../doc/comet-options/fragment_bin_tol.html | 30 +
.../doc/comet-options/head.html | 1 +
.../doc/comet-options/index.html | 1 +
.../doc/comet-options/isotope_error.html | 28 +
.../doc/comet-options/mass_type_fragment.html | 20 +
.../doc/comet-options/mass_type_parent.html | 20 +
.../doc/comet-options/max_fragment_charge.html | 28 +
.../doc/comet-options/max_precursor_charge.html | 18 +
.../max_variable_mods_in_peptide.html | 18 +
.../doc/comet-options/minimum_intensity.html | 23 +
.../doc/comet-options/minimum_peaks.html | 21 +
.../doc/comet-options/ms_level.html | 20 +
.../comet-options/nucleotide_reading_frame.html | 28 +
.../doc/comet-options/num_enzyme_termini.html | 28 +
.../doc/comet-options/num_output_lines.html | 26 +
.../doc/comet-options/num_results.html | 22 +
.../doc/comet-options/num_threads.html | 20 +
.../doc/comet-options/output_outfiles.html | 16 +
.../doc/comet-options/output_pepxmlfile.html | 16 +
.../doc/comet-options/output_percolatorfile.html | 19 +
.../doc/comet-options/output_sqtfile.html | 16 +
.../doc/comet-options/output_sqtstream.html | 19 +
.../doc/comet-options/output_suffix.html | 25 +
.../doc/comet-options/output_txtfile.html | 52 +
.../doc/comet-options/override_charge.html | 25 +
.../doc/comet-options/peptide_mass_tolerance.html | 17 +
.../doc/comet-options/peptide_mass_units.html | 20 +
.../doc/comet-options/precursor_charge.html | 30 +
.../doc/comet-options/print_expect_score.html | 24 +
.../doc/comet-options/remove_precursor_peak.html | 25 +
.../comet-options/remove_precursor_tolerance.html | 19 +
.../doc/comet-options/require_variable_mod.html | 22 +
.../crux-3.1.Linux.x86_64/doc/comet-options/runall | 24 +
.../doc/comet-options/sample_enzyme_number.html | 22 +
.../doc/comet-options/scan_range.html | 23 +
.../doc/comet-options/search_enzyme_number.html | 46 +
.../doc/comet-options/show_fragment_ions.html | 20 +
.../doc/comet-options/skip_researching.html | 25 +
.../doc/comet-options/spectrum_batch_size.html | 28 +
.../comet-options/theoretical_fragment_ions.html | 32 +
.../doc/comet-options/topmenu.html | 1 +
.../doc/comet-options/use_A_ions.html | 18 +
.../doc/comet-options/use_B_ions.html | 18 +
.../doc/comet-options/use_C_ions.html | 18 +
.../doc/comet-options/use_NL_ions.html | 18 +
.../doc/comet-options/use_X_ions.html | 18 +
.../doc/comet-options/use_Y_ions.html | 18 +
.../doc/comet-options/use_Z_ions.html | 18 +
.../doc/comet-options/use_sparse_matrix.html | 26 +
.../doc/comet-options/variable_mod01.html | 62 +
.../doc/comet-options/variable_mod02.html | 48 +
.../doc/comet-options/variable_mod03.html | 48 +
.../doc/comet-options/variable_mod04.html | 48 +
.../doc/comet-options/variable_mod05.html | 48 +
.../doc/comet-options/variable_mod06.html | 48 +
.../doc/comet-options/variable_mod07.html | 48 +
.../doc/comet-options/variable_mod08.html | 48 +
.../doc/comet-options/variable_mod09.html | 48 +
.../Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet.html | 297 +
.../doc/commands/bullseye_standalone_to_crux.html | 74 +
.../doc/commands/hardklor_standalone_to_crux.html | 127 +
.../crux-3.1.Linux.x86_64/doc/contributors.html | 177 +
.../crux-3.1.Linux.x86_64/doc/create-docs.cmake | 127 +
.../ZIP/crux-3.1.Linux.x86_64/doc/create-docs.html | 125 +
.../ZIP/crux-3.1.Linux.x86_64/doc/default.params | 1832 +
.../ZIP/crux-3.1.Linux.x86_64/doc/demos/demo1.sh | 34 +
.../crux-3.1.Linux.x86_64/doc/demos/tsv2html.py | 77 +
.../ZIP/crux-3.1.Linux.x86_64/doc/deploy-to-web.sh | 9 +
.../ZIP/crux-3.1.Linux.x86_64/doc/download.html | 741 +
.../doc/example-files/default.params | 1676 +
.../doc/example-files/demo.ms2 | 54667 ++++
.../doc/example-files/search.target.txt | 721 +
.../doc/example-files/small-yeast.fasta | 165 +
.../doc/example-files/target.sqt | 33 +
.../crux-3.1.Linux.x86_64/doc/extract-columns.html | 131 +
.../crux-3.1.Linux.x86_64/doc/extract-rows.html | 134 +
.../Linux/ZIP/crux-3.1.Linux.x86_64/doc/faq.html | 638 +
.../doc/file-formats/barista-xml-format.html | 249 +
.../doc/file-formats/fasta-format.html | 169 +
.../doc/file-formats/features.html | 398 +
.../doc/file-formats/ms2-format.html | 283 +
.../doc/file-formats/parameter-file.html | 129 +
.../doc/file-formats/sample.fasta | 17 +
.../doc/file-formats/sqt-format.html | 329 +
.../doc/file-formats/txt-format.html | 1363 +
.../ZIP/crux-3.1.Linux.x86_64/doc/fileformats.html | 387 +
.../doc/generate-peptides.html | 166 +
.../doc/get-ms2-spectrum.html | 143 +
.../ZIP/crux-3.1.Linux.x86_64/doc/glossary.html | 165 +
.../ZIP/crux-3.1.Linux.x86_64/doc/hardklor.html | 168 +
.../doc/images/crux-logo-skyline.png | Bin 0 -> 6860 bytes
.../doc/images/crux-logo-text.png | Bin 0 -> 7409 bytes
.../crux-3.1.Linux.x86_64/doc/images/crux-logo.png | Bin 0 -> 20294 bytes
.../doc/images/hamburger-menu.png | Bin 0 -> 124 bytes
.../crux-3.1.Linux.x86_64/doc/images/linkicon.png | Bin 0 -> 688 bytes
.../crux-3.1.Linux.x86_64/doc/images/schematic.png | Bin 0 -> 427892 bytes
.../doc/images/stored-xcorr.png | Bin 0 -> 5136 bytes
.../doc/images/tutorialicon.png | Bin 0 -> 1134 bytes
.../Linux/ZIP/crux-3.1.Linux.x86_64/doc/index.html | 390 +
.../ZIP/crux-3.1.Linux.x86_64/doc/make-pin.html | 139 +
.../ZIP/crux-3.1.Linux.x86_64/doc/mstoolkit.html | 129 +
.../ZIP/crux-3.1.Linux.x86_64/doc/param-medic.html | 146 +
.../ZIP/crux-3.1.Linux.x86_64/doc/param-table.html | 678 +
.../ZIP/crux-3.1.Linux.x86_64/doc/percolator.html | 209 +
.../ZIP/crux-3.1.Linux.x86_64/doc/pipeline.html | 460 +
.../doc/predict-peptide-ions.html | 141 +
.../doc/print-processed-spectra.html | 141 +
.../ZIP/crux-3.1.Linux.x86_64/doc/psm-convert.html | 142 +
.../ZIP/crux-3.1.Linux.x86_64/doc/q-ranker.html | 160 +
.../crux-3.1.Linux.x86_64/doc/read-tide-index.html | 128 +
.../crux-3.1.Linux.x86_64/doc/release-notes.html | 1849 +
.../Linux/ZIP/crux-3.1.Linux.x86_64/doc/runall | 28 +
.../doc/search-for-xlinks.html | 256 +
.../crux-3.1.Linux.x86_64/doc/sort-by-column.html | 133 +
.../crux-3.1.Linux.x86_64/doc/spectral-counts.html | 152 +
.../ZIP/crux-3.1.Linux.x86_64/doc/stat-column.html | 132 +
.../Linux/ZIP/crux-3.1.Linux.x86_64/doc/styles.css | 570 +
.../crux-3.1.Linux.x86_64/doc/subtract-index.html | 138 +
.../ZIP/crux-3.1.Linux.x86_64/doc/template.html | 105 +
.../ZIP/crux-3.1.Linux.x86_64/doc/tide-index.html | 177 +
.../ZIP/crux-3.1.Linux.x86_64/doc/tide-search.html | 204 +
.../doc/tutorials/customizedsearch.html | 299 +
.../doc/tutorials/gettingstarted.html | 218 +
.../doc/tutorials/install.html | 805 +
.../doc/tutorials/search.html | 422 +
.../doc/tutorials/spectralcounts.html | 182 +
.../doc/xlink-assign-ions.html | 145 +
.../doc/xlink-score-spectrum.html | 158 +
.../Linux/ZIP/crux-3.1.Linux.x86_64/license.txt | 12 +
cmake_install.cmake | 58 +
crux_version.h | 1 +
crux_version.h.txt | 1 +
doc/Doxyfile | 1551 +
doc/PWIZ_README | 142 +
doc/crux-report.doc | Bin 0 -> 61952 bytes
doc/logo/README | 1 +
doc/logo/crux-cmyk.eps | Bin 0 -> 613534 bytes
doc/logo/crux-rgb.eps | Bin 0 -> 612666 bytes
doc/logo/crux.ai | 456 +
doc/logo/crux.png | Bin 0 -> 38669 bytes
doc/logo/crux.psd | Bin 0 -> 603834 bytes
.../design-transfer-agreement-454896-en_US.pdf | Bin 0 -> 29229 bytes
doc/logs/README | 12 +
doc/logs/analyze-log.py | 48 +
doc/logs/downloads.txt | 926 +
doc/user/CMakeLists.txt | 29 +
doc/user/Makefile | 207 +
doc/user/assign-confidence.html | 147 +
doc/user/barista.html | 163 +
doc/user/bullseye.html | 158 +
doc/user/cascade-search.html | 215 +
doc/user/cmake_install.cmake | 38 +
doc/user/comet-options/activation_method.html | 23 +
doc/user/comet-options/add_A_alanine.html | 15 +
doc/user/comet-options/add_B_user_amino_acid.html | 19 +
doc/user/comet-options/add_C_cysteine.html | 21 +
doc/user/comet-options/add_Cterm_peptide.html | 15 +
doc/user/comet-options/add_Cterm_protein.html | 15 +
doc/user/comet-options/add_D_aspartic_acid.html | 15 +
doc/user/comet-options/add_E_glutamic_acid.html | 15 +
doc/user/comet-options/add_F_phenylalanine.html | 15 +
doc/user/comet-options/add_G_glycine.html | 15 +
doc/user/comet-options/add_H_histidine.html | 15 +
doc/user/comet-options/add_I_isoleucine.html | 15 +
doc/user/comet-options/add_J_user_amino_acid.html | 19 +
doc/user/comet-options/add_K_lysine.html | 15 +
doc/user/comet-options/add_L_leucine.html | 15 +
doc/user/comet-options/add_M_methionine.html | 15 +
doc/user/comet-options/add_N_asparagine.html | 15 +
doc/user/comet-options/add_Nterm_peptide.html | 15 +
doc/user/comet-options/add_Nterm_protein.html | 15 +
doc/user/comet-options/add_O_ornithine.html | 15 +
doc/user/comet-options/add_P_proline.html | 15 +
doc/user/comet-options/add_Q_glutamine.html | 15 +
doc/user/comet-options/add_R_arginine.html | 15 +
doc/user/comet-options/add_S_serine.html | 15 +
doc/user/comet-options/add_T_threonine.html | 15 +
doc/user/comet-options/add_U_user_amino_acid.html | 19 +
doc/user/comet-options/add_V_valine.html | 15 +
doc/user/comet-options/add_W_tryptophan.html | 15 +
doc/user/comet-options/add_X_user_amino_acid.html | 19 +
doc/user/comet-options/add_Y_tyrosine.html | 15 +
doc/user/comet-options/add_Z_user_amino_acid.html | 19 +
.../comet-options/allowed_missed_cleavage.html | 18 +
doc/user/comet-options/clear_mz_range.html | 24 +
doc/user/comet-options/clip_nterm_methionine.html | 22 +
doc/user/comet-options/combined.html | 23 +
doc/user/comet-options/comet.params | 160 +
doc/user/comet-options/content.html | 1 +
doc/user/comet-options/convertCometPHPs.py | 55 +
doc/user/comet-options/database_name.html | 21 +
doc/user/comet-options/decoy_prefix.html | 22 +
doc/user/comet-options/decoy_search.html | 29 +
doc/user/comet-options/digest_mass_range.html | 23 +
doc/user/comet-options/footer.html | 1 +
doc/user/comet-options/fragment_bin_offset.html | 31 +
doc/user/comet-options/fragment_bin_tol.html | 30 +
doc/user/comet-options/head.html | 1 +
doc/user/comet-options/index.html | 1 +
doc/user/comet-options/isotope_error.html | 28 +
doc/user/comet-options/mass_type_fragment.html | 20 +
doc/user/comet-options/mass_type_parent.html | 20 +
doc/user/comet-options/max_fragment_charge.html | 28 +
doc/user/comet-options/max_precursor_charge.html | 18 +
.../max_variable_mods_in_peptide.html | 18 +
doc/user/comet-options/minimum_intensity.html | 23 +
doc/user/comet-options/minimum_peaks.html | 21 +
doc/user/comet-options/ms_level.html | 20 +
.../comet-options/nucleotide_reading_frame.html | 28 +
doc/user/comet-options/num_enzyme_termini.html | 28 +
doc/user/comet-options/num_output_lines.html | 26 +
doc/user/comet-options/num_results.html | 22 +
doc/user/comet-options/num_threads.html | 20 +
doc/user/comet-options/output_outfiles.html | 16 +
doc/user/comet-options/output_pepxmlfile.html | 16 +
doc/user/comet-options/output_percolatorfile.html | 19 +
doc/user/comet-options/output_sqtfile.html | 16 +
doc/user/comet-options/output_sqtstream.html | 19 +
doc/user/comet-options/output_suffix.html | 25 +
doc/user/comet-options/output_txtfile.html | 52 +
doc/user/comet-options/override_charge.html | 25 +
doc/user/comet-options/peptide_mass_tolerance.html | 17 +
doc/user/comet-options/peptide_mass_units.html | 20 +
doc/user/comet-options/precursor_charge.html | 30 +
doc/user/comet-options/print_expect_score.html | 24 +
doc/user/comet-options/remove_precursor_peak.html | 25 +
.../comet-options/remove_precursor_tolerance.html | 19 +
doc/user/comet-options/require_variable_mod.html | 22 +
doc/user/comet-options/runall | 24 +
doc/user/comet-options/sample_enzyme_number.html | 22 +
doc/user/comet-options/scan_range.html | 23 +
doc/user/comet-options/search_enzyme_number.html | 46 +
doc/user/comet-options/show_fragment_ions.html | 20 +
doc/user/comet-options/skip_researching.html | 25 +
doc/user/comet-options/spectrum_batch_size.html | 28 +
.../comet-options/theoretical_fragment_ions.html | 32 +
doc/user/comet-options/topmenu.html | 1 +
doc/user/comet-options/use_A_ions.html | 18 +
doc/user/comet-options/use_B_ions.html | 18 +
doc/user/comet-options/use_C_ions.html | 18 +
doc/user/comet-options/use_NL_ions.html | 18 +
doc/user/comet-options/use_X_ions.html | 18 +
doc/user/comet-options/use_Y_ions.html | 18 +
doc/user/comet-options/use_Z_ions.html | 18 +
doc/user/comet-options/use_sparse_matrix.html | 26 +
doc/user/comet-options/variable_mod01.html | 62 +
doc/user/comet-options/variable_mod02.html | 48 +
doc/user/comet-options/variable_mod03.html | 48 +
doc/user/comet-options/variable_mod04.html | 48 +
doc/user/comet-options/variable_mod05.html | 48 +
doc/user/comet-options/variable_mod06.html | 48 +
doc/user/comet-options/variable_mod07.html | 48 +
doc/user/comet-options/variable_mod08.html | 48 +
doc/user/comet-options/variable_mod09.html | 48 +
doc/user/comet.html | 297 +
doc/user/commands/bullseye_standalone_to_crux.html | 74 +
doc/user/commands/hardklor_standalone_to_crux.html | 127 +
doc/user/contributors.html | 177 +
doc/user/create-docs.cmake | 127 +
doc/user/create-docs.html | 125 +
doc/user/default.params | 1832 +
doc/user/demos/demo1.sh | 34 +
doc/user/demos/tsv2html.py | 77 +
doc/user/deploy-to-web.sh | 9 +
doc/user/download.html | 741 +
doc/user/example-files/default.params | 1676 +
doc/user/example-files/demo.ms2 | 54667 ++++
doc/user/example-files/search.target.txt | 721 +
doc/user/example-files/small-yeast.fasta | 165 +
doc/user/example-files/target.sqt | 33 +
doc/user/extract-columns.html | 131 +
doc/user/extract-rows.html | 134 +
doc/user/faq.html | 638 +
doc/user/file-formats/barista-xml-format.html | 249 +
doc/user/file-formats/fasta-format.html | 169 +
doc/user/file-formats/features.html | 398 +
doc/user/file-formats/ms2-format.html | 283 +
doc/user/file-formats/parameter-file.html | 129 +
doc/user/file-formats/sample.fasta | 17 +
doc/user/file-formats/sqt-format.html | 329 +
doc/user/file-formats/txt-format.html | 1363 +
doc/user/fileformats.html | 387 +
doc/user/generate-peptides.html | 166 +
doc/user/get-ms2-spectrum.html | 143 +
doc/user/glossary.html | 165 +
doc/user/hardklor.html | 168 +
doc/user/images/crux-logo-skyline.png | Bin 0 -> 6860 bytes
doc/user/images/crux-logo-text.png | Bin 0 -> 7409 bytes
doc/user/images/crux-logo.png | Bin 0 -> 20294 bytes
doc/user/images/hamburger-menu.png | Bin 0 -> 124 bytes
doc/user/images/linkicon.png | Bin 0 -> 688 bytes
doc/user/images/schematic.png | Bin 0 -> 427892 bytes
doc/user/images/stored-xcorr.png | Bin 0 -> 5136 bytes
doc/user/images/tutorialicon.png | Bin 0 -> 1134 bytes
doc/user/index.html | 390 +
doc/user/make-pin.html | 139 +
doc/user/mstoolkit.html | 129 +
doc/user/param-medic.html | 146 +
doc/user/param-table.html | 678 +
doc/user/percolator.html | 209 +
doc/user/pipeline.html | 460 +
doc/user/predict-peptide-ions.html | 141 +
doc/user/print-processed-spectra.html | 141 +
doc/user/psm-convert.html | 142 +
doc/user/q-ranker.html | 160 +
doc/user/read-tide-index.html | 128 +
doc/user/release-notes.html | 1849 +
doc/user/runall | 28 +
doc/user/search-for-xlinks.html | 256 +
doc/user/sort-by-column.html | 133 +
doc/user/spectral-counts.html | 152 +
doc/user/stat-column.html | 132 +
doc/user/styles.css | 570 +
doc/user/subtract-index.html | 138 +
doc/user/template.html | 105 +
doc/user/tide-index.html | 177 +
doc/user/tide-search.html | 204 +
doc/user/tutorials/customizedsearch.html | 299 +
doc/user/tutorials/gettingstarted.html | 218 +
doc/user/tutorials/install.html | 805 +
doc/user/tutorials/search.html | 422 +
doc/user/tutorials/spectralcounts.html | 182 +
doc/user/xlink-assign-ions.html | 145 +
doc/user/xlink-score-spectrum.html | 158 +
ext/CMakeLists.txt | 342 +
ext/Makefile | 267 +
ext/build-comet.cmake | 10 +
ext/build_pwiz.cmake | 77 +
ext/cmake_install.cmake | 34 +
ext/create_links.sh | 44 +
ext/download-pwiz-tarball.sh | 18 +
ext/download_gflags.cmake | 66 +
ext/download_pbuffers.cmake | 65 +
ext/download_pwiz.cmake | 103 +
ext/fdstream.hpp | 184 +
ext/patch-comet.cmake | 73 +
.../XSD/mac_xdr_fix/xdr-stream-extraction.hxx | 308 +
.../XSD/mac_xdr_fix/xdr-stream-insertion.hxx | 277 +
ext/patches/boost/asio.hpp | 121 +
ext/patches/boost/asio/async_result.hpp | 96 +
ext/patches/boost/asio/basic_datagram_socket.hpp | 951 +
ext/patches/boost/asio/basic_deadline_timer.hpp | 520 +
ext/patches/boost/asio/basic_io_object.hpp | 242 +
ext/patches/boost/asio/basic_raw_socket.hpp | 942 +
ext/patches/boost/asio/basic_seq_packet_socket.hpp | 567 +
ext/patches/boost/asio/basic_serial_port.hpp | 697 +
ext/patches/boost/asio/basic_signal_set.hpp | 386 +
ext/patches/boost/asio/basic_socket.hpp | 1520 +
ext/patches/boost/asio/basic_socket_acceptor.hpp | 1138 +
ext/patches/boost/asio/basic_socket_iostream.hpp | 288 +
ext/patches/boost/asio/basic_socket_streambuf.hpp | 569 +
ext/patches/boost/asio/basic_stream_socket.hpp | 854 +
ext/patches/boost/asio/basic_streambuf.hpp | 371 +
ext/patches/boost/asio/basic_streambuf_fwd.hpp | 35 +
ext/patches/boost/asio/basic_waitable_timer.hpp | 521 +
ext/patches/boost/asio/buffer.hpp | 2241 +
ext/patches/boost/asio/buffered_read_stream.hpp | 246 +
.../boost/asio/buffered_read_stream_fwd.hpp | 27 +
ext/patches/boost/asio/buffered_stream.hpp | 260 +
ext/patches/boost/asio/buffered_stream_fwd.hpp | 27 +
ext/patches/boost/asio/buffered_write_stream.hpp | 238 +
.../boost/asio/buffered_write_stream_fwd.hpp | 27 +
ext/patches/boost/asio/buffers_iterator.hpp | 483 +
ext/patches/boost/asio/completion_condition.hpp | 220 +
ext/patches/boost/asio/connect.hpp | 825 +
ext/patches/boost/asio/coroutine.hpp | 330 +
ext/patches/boost/asio/datagram_socket_service.hpp | 434 +
ext/patches/boost/asio/deadline_timer.hpp | 42 +
ext/patches/boost/asio/deadline_timer_service.hpp | 173 +
ext/patches/boost/asio/detail/addressof.hpp | 40 +
ext/patches/boost/asio/detail/array.hpp | 40 +
ext/patches/boost/asio/detail/array_fwd.hpp | 34 +
ext/patches/boost/asio/detail/assert.hpp | 32 +
ext/patches/boost/asio/detail/atomic_count.hpp | 47 +
.../asio/detail/base_from_completion_cond.hpp | 70 +
ext/patches/boost/asio/detail/bind_handler.hpp | 491 +
.../boost/asio/detail/buffer_resize_guard.hpp | 68 +
.../boost/asio/detail/buffer_sequence_adapter.hpp | 385 +
.../boost/asio/detail/buffered_stream_storage.hpp | 128 +
ext/patches/boost/asio/detail/call_stack.hpp | 127 +
.../boost/asio/detail/chrono_time_traits.hpp | 192 +
.../boost/asio/detail/completion_handler.hpp | 83 +
ext/patches/boost/asio/detail/config.hpp | 906 +
.../boost/asio/detail/consuming_buffers.hpp | 294 +
ext/patches/boost/asio/detail/cstdint.hpp | 48 +
ext/patches/boost/asio/detail/date_time_fwd.hpp | 34 +
.../boost/asio/detail/deadline_timer_service.hpp | 229 +
ext/patches/boost/asio/detail/dependent_type.hpp | 38 +
ext/patches/boost/asio/detail/descriptor_ops.hpp | 119 +
.../boost/asio/detail/descriptor_read_op.hpp | 121 +
.../boost/asio/detail/descriptor_write_op.hpp | 121 +
ext/patches/boost/asio/detail/dev_poll_reactor.hpp | 212 +
ext/patches/boost/asio/detail/epoll_reactor.hpp | 244 +
ext/patches/boost/asio/detail/event.hpp | 50 +
.../asio/detail/eventfd_select_interrupter.hpp | 85 +
ext/patches/boost/asio/detail/fd_set_adapter.hpp | 41 +
ext/patches/boost/asio/detail/fenced_block.hpp | 78 +
ext/patches/boost/asio/detail/function.hpp | 40 +
.../boost/asio/detail/gcc_arm_fenced_block.hpp | 91 +
.../boost/asio/detail/gcc_hppa_fenced_block.hpp | 68 +
.../boost/asio/detail/gcc_sync_fenced_block.hpp | 65 +
.../boost/asio/detail/gcc_x86_fenced_block.hpp | 99 +
.../boost/asio/detail/handler_alloc_helpers.hpp | 82 +
.../boost/asio/detail/handler_cont_helpers.hpp | 45 +
.../boost/asio/detail/handler_invoke_helpers.hpp | 57 +
ext/patches/boost/asio/detail/handler_tracking.hpp | 161 +
.../asio/detail/handler_type_requirements.hpp | 490 +
ext/patches/boost/asio/detail/hash_map.hpp | 333 +
.../asio/detail/impl/buffer_sequence_adapter.ipp | 120 +
.../boost/asio/detail/impl/descriptor_ops.ipp | 453 +
.../boost/asio/detail/impl/dev_poll_reactor.hpp | 80 +
.../boost/asio/detail/impl/dev_poll_reactor.ipp | 447 +
.../boost/asio/detail/impl/epoll_reactor.hpp | 78 +
.../boost/asio/detail/impl/epoll_reactor.ipp | 664 +
.../detail/impl/eventfd_select_interrupter.ipp | 167 +
.../boost/asio/detail/impl/handler_tracking.ipp | 307 +
.../boost/asio/detail/impl/kqueue_reactor.hpp | 82 +
.../boost/asio/detail/impl/kqueue_reactor.ipp | 465 +
.../asio/detail/impl/pipe_select_interrupter.ipp | 126 +
ext/patches/boost/asio/detail/impl/posix_event.ipp | 49 +
ext/patches/boost/asio/detail/impl/posix_mutex.ipp | 48 +
.../boost/asio/detail/impl/posix_thread.ipp | 76 +
.../boost/asio/detail/impl/posix_tss_ptr.ipp | 48 +
.../detail/impl/reactive_descriptor_service.ipp | 210 +
.../detail/impl/reactive_serial_port_service.ipp | 153 +
.../detail/impl/reactive_socket_service_base.ipp | 269 +
.../asio/detail/impl/resolver_service_base.ipp | 132 +
.../boost/asio/detail/impl/select_reactor.hpp | 89 +
.../boost/asio/detail/impl/select_reactor.ipp | 315 +
.../boost/asio/detail/impl/service_registry.hpp | 90 +
.../boost/asio/detail/impl/service_registry.ipp | 190 +
.../boost/asio/detail/impl/signal_set_service.ipp | 649 +
ext/patches/boost/asio/detail/impl/socket_ops.ipp | 3395 +
.../asio/detail/impl/socket_select_interrupter.ipp | 177 +
.../boost/asio/detail/impl/strand_service.hpp | 120 +
.../boost/asio/detail/impl/strand_service.ipp | 178 +
.../boost/asio/detail/impl/task_io_service.hpp | 80 +
.../boost/asio/detail/impl/task_io_service.ipp | 476 +
ext/patches/boost/asio/detail/impl/throw_error.ipp | 47 +
.../boost/asio/detail/impl/timer_queue_ptime.ipp | 86 +
.../boost/asio/detail/impl/timer_queue_set.ipp | 103 +
ext/patches/boost/asio/detail/impl/win_event.ipp | 69 +
.../asio/detail/impl/win_iocp_handle_service.ipp | 527 +
.../boost/asio/detail/impl/win_iocp_io_service.hpp | 132 +
.../boost/asio/detail/impl/win_iocp_io_service.ipp | 540 +
.../detail/impl/win_iocp_serial_port_service.ipp | 182 +
.../detail/impl/win_iocp_socket_service_base.ipp | 730 +
ext/patches/boost/asio/detail/impl/win_mutex.ipp | 80 +
.../asio/detail/impl/win_object_handle_service.ipp | 446 +
.../boost/asio/detail/impl/win_static_mutex.ipp | 120 +
ext/patches/boost/asio/detail/impl/win_thread.ipp | 141 +
ext/patches/boost/asio/detail/impl/win_tss_ptr.ipp | 59 +
.../detail/impl/winrt_ssocket_service_base.ipp | 614 +
.../asio/detail/impl/winrt_timer_scheduler.hpp | 81 +
.../asio/detail/impl/winrt_timer_scheduler.ipp | 124 +
.../boost/asio/detail/impl/winsock_init.ipp | 84 +
ext/patches/boost/asio/detail/io_control.hpp | 136 +
ext/patches/boost/asio/detail/keyword_tss_ptr.hpp | 72 +
ext/patches/boost/asio/detail/kqueue_reactor.hpp | 221 +
ext/patches/boost/asio/detail/limits.hpp | 26 +
.../boost/asio/detail/local_free_on_block_exit.hpp | 59 +
.../boost/asio/detail/macos_fenced_block.hpp | 63 +
ext/patches/boost/asio/detail/mutex.hpp | 50 +
ext/patches/boost/asio/detail/noncopyable.hpp | 45 +
ext/patches/boost/asio/detail/null_event.hpp | 90 +
.../boost/asio/detail/null_fenced_block.hpp | 47 +
ext/patches/boost/asio/detail/null_mutex.hpp | 66 +
ext/patches/boost/asio/detail/null_reactor.hpp | 69 +
.../boost/asio/detail/null_signal_blocker.hpp | 71 +
.../boost/asio/detail/null_socket_service.hpp | 499 +
.../boost/asio/detail/null_static_mutex.hpp | 62 +
ext/patches/boost/asio/detail/null_thread.hpp | 63 +
ext/patches/boost/asio/detail/null_tss_ptr.hpp | 70 +
ext/patches/boost/asio/detail/object_pool.hpp | 148 +
.../boost/asio/detail/old_win_sdk_compat.hpp | 216 +
ext/patches/boost/asio/detail/op_queue.hpp | 158 +
ext/patches/boost/asio/detail/operation.hpp | 40 +
.../boost/asio/detail/pipe_select_interrupter.hpp | 91 +
ext/patches/boost/asio/detail/pop_options.hpp | 105 +
ext/patches/boost/asio/detail/posix_event.hpp | 128 +
.../boost/asio/detail/posix_fd_set_adapter.hpp | 120 +
ext/patches/boost/asio/detail/posix_mutex.hpp | 78 +
.../boost/asio/detail/posix_signal_blocker.hpp | 87 +
.../boost/asio/detail/posix_static_mutex.hpp | 66 +
ext/patches/boost/asio/detail/posix_thread.hpp | 107 +
ext/patches/boost/asio/detail/posix_tss_ptr.hpp | 81 +
ext/patches/boost/asio/detail/push_options.hpp | 138 +
.../asio/detail/reactive_descriptor_service.hpp | 324 +
.../boost/asio/detail/reactive_null_buffers_op.hpp | 90 +
.../asio/detail/reactive_serial_port_service.hpp | 236 +
.../asio/detail/reactive_socket_accept_op.hpp | 138 +
.../asio/detail/reactive_socket_connect_op.hpp | 108 +
.../boost/asio/detail/reactive_socket_recv_op.hpp | 125 +
.../asio/detail/reactive_socket_recvfrom_op.hpp | 135 +
.../asio/detail/reactive_socket_recvmsg_op.hpp | 127 +
.../boost/asio/detail/reactive_socket_send_op.hpp | 122 +
.../asio/detail/reactive_socket_sendto_op.hpp | 125 +
.../boost/asio/detail/reactive_socket_service.hpp | 459 +
.../asio/detail/reactive_socket_service_base.hpp | 452 +
ext/patches/boost/asio/detail/reactor.hpp | 32 +
ext/patches/boost/asio/detail/reactor_fwd.hpp | 42 +
ext/patches/boost/asio/detail/reactor_op.hpp | 63 +
ext/patches/boost/asio/detail/reactor_op_queue.hpp | 170 +
ext/patches/boost/asio/detail/regex_fwd.hpp | 35 +
.../boost/asio/detail/resolve_endpoint_op.hpp | 123 +
ext/patches/boost/asio/detail/resolve_op.hpp | 133 +
ext/patches/boost/asio/detail/resolver_service.hpp | 131 +
.../boost/asio/detail/resolver_service_base.hpp | 131 +
ext/patches/boost/asio/detail/scoped_lock.hpp | 103 +
ext/patches/boost/asio/detail/scoped_ptr.hpp | 81 +
.../boost/asio/detail/select_interrupter.hpp | 48 +
ext/patches/boost/asio/detail/select_reactor.hpp | 221 +
ext/patches/boost/asio/detail/service_registry.hpp | 158 +
ext/patches/boost/asio/detail/shared_ptr.hpp | 40 +
ext/patches/boost/asio/detail/signal_blocker.hpp | 46 +
ext/patches/boost/asio/detail/signal_handler.hpp | 84 +
ext/patches/boost/asio/detail/signal_init.hpp | 49 +
ext/patches/boost/asio/detail/signal_op.hpp | 51 +
.../boost/asio/detail/signal_set_service.hpp | 218 +
ext/patches/boost/asio/detail/socket_holder.hpp | 100 +
ext/patches/boost/asio/detail/socket_ops.hpp | 336 +
ext/patches/boost/asio/detail/socket_option.hpp | 318 +
.../asio/detail/socket_select_interrupter.hpp | 93 +
ext/patches/boost/asio/detail/socket_types.hpp | 406 +
.../boost/asio/detail/solaris_fenced_block.hpp | 63 +
ext/patches/boost/asio/detail/static_mutex.hpp | 54 +
ext/patches/boost/asio/detail/std_event.hpp | 178 +
ext/patches/boost/asio/detail/std_mutex.hpp | 75 +
ext/patches/boost/asio/detail/std_static_mutex.hpp | 83 +
ext/patches/boost/asio/detail/std_thread.hpp | 67 +
ext/patches/boost/asio/detail/strand_service.hpp | 144 +
ext/patches/boost/asio/detail/task_io_service.hpp | 203 +
.../asio/detail/task_io_service_operation.hpp | 78 +
.../asio/detail/task_io_service_thread_info.hpp | 42 +
ext/patches/boost/asio/detail/thread.hpp | 58 +
ext/patches/boost/asio/detail/thread_info_base.hpp | 93 +
ext/patches/boost/asio/detail/throw_error.hpp | 55 +
ext/patches/boost/asio/detail/throw_exception.hpp | 53 +
ext/patches/boost/asio/detail/timer_queue.hpp | 334 +
ext/patches/boost/asio/detail/timer_queue_base.hpp | 70 +
.../boost/asio/detail/timer_queue_ptime.hpp | 95 +
ext/patches/boost/asio/detail/timer_queue_set.hpp | 68 +
ext/patches/boost/asio/detail/timer_scheduler.hpp | 35 +
.../boost/asio/detail/timer_scheduler_fwd.hpp | 42 +
ext/patches/boost/asio/detail/tss_ptr.hpp | 71 +
ext/patches/boost/asio/detail/type_traits.hpp | 60 +
.../boost/asio/detail/variadic_templates.hpp | 63 +
ext/patches/boost/asio/detail/wait_handler.hpp | 85 +
ext/patches/boost/asio/detail/wait_op.hpp | 47 +
ext/patches/boost/asio/detail/weak_ptr.hpp | 40 +
ext/patches/boost/asio/detail/win_event.hpp | 128 +
.../boost/asio/detail/win_fd_set_adapter.hpp | 151 +
ext/patches/boost/asio/detail/win_fenced_block.hpp | 91 +
.../boost/asio/detail/win_iocp_handle_read_op.hpp | 111 +
.../boost/asio/detail/win_iocp_handle_service.hpp | 324 +
.../boost/asio/detail/win_iocp_handle_write_op.hpp | 103 +
.../boost/asio/detail/win_iocp_io_service.hpp | 317 +
.../boost/asio/detail/win_iocp_null_buffers_op.hpp | 121 +
.../boost/asio/detail/win_iocp_operation.hpp | 97 +
.../boost/asio/detail/win_iocp_overlapped_op.hpp | 90 +
.../boost/asio/detail/win_iocp_overlapped_ptr.hpp | 146 +
.../asio/detail/win_iocp_serial_port_service.hpp | 230 +
.../asio/detail/win_iocp_socket_accept_op.hpp | 167 +
.../asio/detail/win_iocp_socket_connect_op.hpp | 126 +
.../boost/asio/detail/win_iocp_socket_recv_op.hpp | 117 +
.../asio/detail/win_iocp_socket_recvfrom_op.hpp | 125 +
.../asio/detail/win_iocp_socket_recvmsg_op.hpp | 118 +
.../boost/asio/detail/win_iocp_socket_send_op.hpp | 111 +
.../boost/asio/detail/win_iocp_socket_service.hpp | 527 +
.../asio/detail/win_iocp_socket_service_base.hpp | 526 +
.../boost/asio/detail/win_iocp_thread_info.hpp | 36 +
ext/patches/boost/asio/detail/win_mutex.hpp | 80 +
.../asio/detail/win_object_handle_service.hpp | 185 +
ext/patches/boost/asio/detail/win_static_mutex.hpp | 76 +
ext/patches/boost/asio/detail/win_thread.hpp | 141 +
ext/patches/boost/asio/detail/win_tss_ptr.hpp | 81 +
ext/patches/boost/asio/detail/wince_thread.hpp | 118 +
.../boost/asio/detail/winrt_async_manager.hpp | 296 +
ext/patches/boost/asio/detail/winrt_async_op.hpp | 67 +
ext/patches/boost/asio/detail/winrt_resolve_op.hpp | 119 +
.../boost/asio/detail/winrt_resolver_service.hpp | 185 +
.../boost/asio/detail/winrt_socket_connect_op.hpp | 92 +
.../boost/asio/detail/winrt_socket_recv_op.hpp | 112 +
.../boost/asio/detail/winrt_socket_send_op.hpp | 103 +
.../boost/asio/detail/winrt_ssocket_service.hpp | 234 +
.../asio/detail/winrt_ssocket_service_base.hpp | 357 +
.../boost/asio/detail/winrt_timer_scheduler.hpp | 133 +
ext/patches/boost/asio/detail/winrt_utils.hpp | 108 +
ext/patches/boost/asio/detail/winsock_init.hpp | 130 +
ext/patches/boost/asio/detail/wrapped_handler.hpp | 293 +
ext/patches/boost/asio/error.hpp | 336 +
ext/patches/boost/asio/generic/basic_endpoint.hpp | 195 +
.../boost/asio/generic/datagram_protocol.hpp | 125 +
ext/patches/boost/asio/generic/detail/endpoint.hpp | 135 +
.../boost/asio/generic/detail/impl/endpoint.ipp | 111 +
ext/patches/boost/asio/generic/raw_protocol.hpp | 123 +
.../boost/asio/generic/seq_packet_protocol.hpp | 124 +
ext/patches/boost/asio/generic/stream_protocol.hpp | 129 +
ext/patches/boost/asio/handler_alloc_hook.hpp | 83 +
.../boost/asio/handler_continuation_hook.hpp | 56 +
ext/patches/boost/asio/handler_invoke_hook.hpp | 87 +
ext/patches/boost/asio/handler_type.hpp | 114 +
ext/patches/boost/asio/high_resolution_timer.hpp | 65 +
.../boost/asio/impl/buffered_read_stream.hpp | 360 +
.../boost/asio/impl/buffered_write_stream.hpp | 340 +
ext/patches/boost/asio/impl/connect.hpp | 430 +
ext/patches/boost/asio/impl/error.ipp | 130 +
ext/patches/boost/asio/impl/handler_alloc_hook.ipp | 79 +
ext/patches/boost/asio/impl/io_service.hpp | 156 +
ext/patches/boost/asio/impl/io_service.ipp | 157 +
ext/patches/boost/asio/impl/read.hpp | 755 +
ext/patches/boost/asio/impl/read_at.hpp | 812 +
ext/patches/boost/asio/impl/read_until.hpp | 1149 +
ext/patches/boost/asio/impl/serial_port_base.hpp | 61 +
ext/patches/boost/asio/impl/serial_port_base.ipp | 556 +
ext/patches/boost/asio/impl/spawn.hpp | 338 +
ext/patches/boost/asio/impl/src.cpp | 25 +
ext/patches/boost/asio/impl/src.hpp | 73 +
ext/patches/boost/asio/impl/use_future.hpp | 174 +
ext/patches/boost/asio/impl/write.hpp | 767 +
ext/patches/boost/asio/impl/write_at.hpp | 827 +
ext/patches/boost/asio/io_service.hpp | 772 +
ext/patches/boost/asio/ip/address.hpp | 202 +
ext/patches/boost/asio/ip/address_v4.hpp | 243 +
ext/patches/boost/asio/ip/address_v6.hpp | 248 +
ext/patches/boost/asio/ip/basic_endpoint.hpp | 265 +
ext/patches/boost/asio/ip/basic_resolver.hpp | 270 +
ext/patches/boost/asio/ip/basic_resolver_entry.hpp | 96 +
.../boost/asio/ip/basic_resolver_iterator.hpp | 262 +
ext/patches/boost/asio/ip/basic_resolver_query.hpp | 246 +
ext/patches/boost/asio/ip/detail/endpoint.hpp | 141 +
ext/patches/boost/asio/ip/detail/impl/endpoint.ipp | 206 +
ext/patches/boost/asio/ip/detail/socket_option.hpp | 571 +
ext/patches/boost/asio/ip/host_name.hpp | 44 +
ext/patches/boost/asio/ip/icmp.hpp | 117 +
ext/patches/boost/asio/ip/impl/address.hpp | 55 +
ext/patches/boost/asio/ip/impl/address.ipp | 228 +
ext/patches/boost/asio/ip/impl/address_v4.hpp | 55 +
ext/patches/boost/asio/ip/impl/address_v4.ipp | 180 +
ext/patches/boost/asio/ip/impl/address_v6.hpp | 55 +
ext/patches/boost/asio/ip/impl/address_v6.ipp | 300 +
ext/patches/boost/asio/ip/impl/basic_endpoint.hpp | 57 +
ext/patches/boost/asio/ip/impl/host_name.ipp | 56 +
ext/patches/boost/asio/ip/multicast.hpp | 193 +
ext/patches/boost/asio/ip/resolver_query_base.hpp | 132 +
ext/patches/boost/asio/ip/resolver_service.hpp | 178 +
ext/patches/boost/asio/ip/tcp.hpp | 157 +
ext/patches/boost/asio/ip/udp.hpp | 113 +
ext/patches/boost/asio/ip/unicast.hpp | 72 +
ext/patches/boost/asio/ip/v6_only.hpp | 71 +
ext/patches/boost/asio/is_read_buffered.hpp | 61 +
ext/patches/boost/asio/is_write_buffered.hpp | 61 +
ext/patches/boost/asio/local/basic_endpoint.hpp | 241 +
ext/patches/boost/asio/local/connect_pair.hpp | 106 +
ext/patches/boost/asio/local/datagram_protocol.hpp | 82 +
ext/patches/boost/asio/local/detail/endpoint.hpp | 135 +
.../boost/asio/local/detail/impl/endpoint.ipp | 130 +
ext/patches/boost/asio/local/stream_protocol.hpp | 92 +
ext/patches/boost/asio/placeholders.hpp | 125 +
ext/patches/boost/asio/posix/basic_descriptor.hpp | 492 +
.../boost/asio/posix/basic_stream_descriptor.hpp | 364 +
ext/patches/boost/asio/posix/descriptor_base.hpp | 99 +
ext/patches/boost/asio/posix/stream_descriptor.hpp | 39 +
.../boost/asio/posix/stream_descriptor_service.hpp | 262 +
ext/patches/boost/asio/raw_socket_service.hpp | 434 +
ext/patches/boost/asio/read.hpp | 633 +
ext/patches/boost/asio/read_at.hpp | 666 +
ext/patches/boost/asio/read_until.hpp | 925 +
.../boost/asio/seq_packet_socket_service.hpp | 382 +
ext/patches/boost/asio/serial_port.hpp | 38 +
ext/patches/boost/asio/serial_port_base.hpp | 169 +
ext/patches/boost/asio/serial_port_service.hpp | 255 +
ext/patches/boost/asio/signal_set.hpp | 30 +
ext/patches/boost/asio/signal_set_service.hpp | 136 +
ext/patches/boost/asio/socket_acceptor_service.hpp | 304 +
ext/patches/boost/asio/socket_base.hpp | 522 +
ext/patches/boost/asio/spawn.hpp | 267 +
ext/patches/boost/asio/ssl.hpp | 30 +
ext/patches/boost/asio/ssl/basic_context.hpp | 42 +
ext/patches/boost/asio/ssl/context.hpp | 789 +
ext/patches/boost/asio/ssl/context_base.hpp | 169 +
ext/patches/boost/asio/ssl/context_service.hpp | 42 +
.../asio/ssl/detail/buffered_handshake_op.hpp | 112 +
ext/patches/boost/asio/ssl/detail/engine.hpp | 166 +
ext/patches/boost/asio/ssl/detail/handshake_op.hpp | 70 +
ext/patches/boost/asio/ssl/detail/impl/engine.ipp | 328 +
.../boost/asio/ssl/detail/impl/openssl_init.ipp | 147 +
ext/patches/boost/asio/ssl/detail/io.hpp | 349 +
ext/patches/boost/asio/ssl/detail/openssl_init.hpp | 103 +
.../boost/asio/ssl/detail/openssl_types.hpp | 28 +
.../boost/asio/ssl/detail/password_callback.hpp | 74 +
ext/patches/boost/asio/ssl/detail/read_op.hpp | 75 +
ext/patches/boost/asio/ssl/detail/shutdown_op.hpp | 62 +
ext/patches/boost/asio/ssl/detail/stream_core.hpp | 128 +
.../boost/asio/ssl/detail/verify_callback.hpp | 70 +
ext/patches/boost/asio/ssl/detail/write_op.hpp | 75 +
ext/patches/boost/asio/ssl/error.hpp | 72 +
ext/patches/boost/asio/ssl/impl/context.hpp | 73 +
ext/patches/boost/asio/ssl/impl/context.ipp | 952 +
ext/patches/boost/asio/ssl/impl/error.ipp | 59 +
.../boost/asio/ssl/impl/rfc2818_verification.ipp | 168 +
ext/patches/boost/asio/ssl/impl/src.hpp | 28 +
ext/patches/boost/asio/ssl/old/basic_context.hpp | 436 +
ext/patches/boost/asio/ssl/old/context_service.hpp | 176 +
.../ssl/old/detail/openssl_context_service.hpp | 388 +
.../asio/ssl/old/detail/openssl_operation.hpp | 526 +
.../asio/ssl/old/detail/openssl_stream_service.hpp | 573 +
ext/patches/boost/asio/ssl/old/stream.hpp | 503 +
ext/patches/boost/asio/ssl/old/stream_service.hpp | 186 +
.../boost/asio/ssl/rfc2818_verification.hpp | 102 +
ext/patches/boost/asio/ssl/stream.hpp | 758 +
ext/patches/boost/asio/ssl/stream_base.hpp | 54 +
ext/patches/boost/asio/ssl/stream_service.hpp | 42 +
ext/patches/boost/asio/ssl/verify_context.hpp | 75 +
ext/patches/boost/asio/ssl/verify_mode.hpp | 65 +
ext/patches/boost/asio/steady_timer.hpp | 63 +
ext/patches/boost/asio/strand.hpp | 253 +
ext/patches/boost/asio/stream_socket_service.hpp | 378 +
ext/patches/boost/asio/streambuf.hpp | 35 +
ext/patches/boost/asio/system_timer.hpp | 59 +
ext/patches/boost/asio/time_traits.hpp | 90 +
ext/patches/boost/asio/unyield.hpp | 21 +
ext/patches/boost/asio/use_future.hpp | 94 +
ext/patches/boost/asio/version.hpp | 23 +
ext/patches/boost/asio/wait_traits.hpp | 43 +
ext/patches/boost/asio/waitable_timer_service.hpp | 170 +
ext/patches/boost/asio/windows/basic_handle.hpp | 283 +
.../boost/asio/windows/basic_object_handle.hpp | 180 +
.../asio/windows/basic_random_access_handle.hpp | 378 +
.../boost/asio/windows/basic_stream_handle.hpp | 361 +
ext/patches/boost/asio/windows/object_handle.hpp | 40 +
.../boost/asio/windows/object_handle_service.hpp | 179 +
ext/patches/boost/asio/windows/overlapped_ptr.hpp | 118 +
.../boost/asio/windows/random_access_handle.hpp | 39 +
.../asio/windows/random_access_handle_service.hpp | 222 +
ext/patches/boost/asio/windows/stream_handle.hpp | 39 +
.../boost/asio/windows/stream_handle_service.hpp | 220 +
ext/patches/boost/asio/write.hpp | 620 +
ext/patches/boost/asio/write_at.hpp | 672 +
ext/patches/boost/asio/yield.hpp | 23 +
ext/patches/comet/Comet.sln | 81 +
ext/patches/comet/Comet.vcxproj | 206 +
ext/patches/comet/CometSearch/CometSearch.vcxproj | 201 +
.../comet/CometSearch/CometSearchManager.cpp | 2108 +
ext/patches/comet/MSToolkit/MSToolkitLite.vcxproj | 257 +
ext/patches/comet/MSToolkit/RAWReader.cpp | 672 +
ext/patches/google-gflags/libgflags.vcxproj | 214 +
.../protobuf/io/zero_copy_stream_impl_lite.cc | 392 +
.../protobuf/vsprojects/libprotobuf-lite.vcxproj | 163 +
.../protobuf/vsprojects/libprotobuf.vcxproj | 209 +
.../protobuf/vsprojects/libprotobuf.vcxproj.old | 1624 +
ext/patches/protobuf/vsprojects/libprotoc.vcxproj | 200 +
.../protobuf/vsprojects/libprotoc.vcxproj.old | 1600 +
ext/patches/protobuf/vsprojects/lite-test.vcxproj | 253 +
ext/patches/protobuf/vsprojects/protoc.vcxproj | 170 +
ext/patches/protobuf/vsprojects/protoc.vcxproj.old | 1328 +
.../protobuf/vsprojects/test_plugin.vcxproj | 197 +
ext/patches/protobuf/vsprojects/tests.vcxproj | 446 +
ext/post_install_pwiz.cmake | 62 +
install_manifest.txt | 189 +
license.txt | 12 +
make-version-header.cmake | 24 +
src/CMakeLists.txt | 445 +
src/Makefile | 3111 +
src/Makefile.mzidentml | 44 +
src/app/AssignConfidenceApplication.cpp | 1247 +
src/app/AssignConfidenceApplication.h | 177 +
src/app/CascadeSearchApplication.cpp | 228 +
src/app/CascadeSearchApplication.h | 89 +
src/app/CometApplication.cpp | 546 +
src/app/CometApplication.h | 102 +
src/app/ComputeQValues.cpp | 275 +
src/app/ComputeQValues.h | 98 +
src/app/ComputeQValuesLegacy.h | 46 +
src/app/CreateDocs.cpp | 598 +
src/app/CreateDocs.h | 52 +
src/app/CruxApplication.cpp | 245 +
src/app/CruxApplication.h | 159 +
src/app/CruxApplicationList.cpp | 227 +
src/app/CruxApplicationList.h | 103 +
src/app/ExtractColumns.cpp | 134 +
src/app/ExtractColumns.h | 70 +
src/app/ExtractRows.cpp | 188 +
src/app/ExtractRows.h | 70 +
src/app/GeneratePeptides.cpp | 607 +
src/app/GeneratePeptides.h | 154 +
src/app/GetMs2Spectrum.cpp | 185 +
src/app/GetMs2Spectrum.h | 86 +
src/app/MakePinApplication.cpp | 241 +
src/app/MakePinApplication.h | 88 +
src/app/PSMConvertApplication.cpp | 209 +
src/app/PSMConvertApplication.h | 72 +
src/app/ParamMedicApplication.cpp | 658 +
src/app/ParamMedicApplication.h | 165 +
src/app/PercolatorAdapter.cpp | 556 +
src/app/PercolatorAdapter.h | 140 +
src/app/PercolatorApplication.cpp | 601 +
src/app/PercolatorApplication.h | 91 +
src/app/Pipeline.cpp | 341 +
src/app/Pipeline.h | 41 +
src/app/PredictPeptideIons.cpp | 226 +
src/app/PredictPeptideIons.h | 78 +
src/app/PrintProcessedSpectra.cpp | 183 +
src/app/PrintProcessedSpectra.h | 93 +
src/app/PrintVersion.cpp | 72 +
src/app/PrintVersion.h | 57 +
src/app/ReadSpectrumRecordsApplication.cpp | 91 +
src/app/ReadSpectrumRecordsApplication.h | 70 +
src/app/ReadTideIndex.cpp | 153 +
src/app/ReadTideIndex.h | 81 +
src/app/SortColumn.cpp | 369 +
src/app/SortColumn.h | 109 +
src/app/SpectralCounts.cpp | 1148 +
src/app/SpectralCounts.h | 189 +
src/app/StatColumn.cpp | 178 +
src/app/StatColumn.h | 77 +
src/app/SubtractIndexApplication.cpp | 288 +
src/app/SubtractIndexApplication.h | 88 +
src/app/TideIndexApplication.cpp | 938 +
src/app/TideIndexApplication.h | 245 +
src/app/TideMatchSet.cpp | 647 +
src/app/TideMatchSet.h | 221 +
src/app/TideSearchApplication.cpp | 1409 +
src/app/TideSearchApplication.h | 278 +
src/app/bullseye/CKronik2.cpp | 797 +
src/app/bullseye/CKronik2.h | 340 +
src/app/bullseye/CMakeLists.txt | 48 +
src/app/bullseye/CruxBullseyeApplication.cpp | 263 +
src/app/bullseye/CruxBullseyeApplication.h | 85 +
src/app/bullseye/Makefile | 288 +
src/app/bullseye/Makefile.bullseye | 18 +
src/app/bullseye/bullseye.cpp | 465 +
src/app/bullseye/cmake_install.cmake | 34 +
src/app/bullseye/libbullseye.a | Bin 0 -> 156158 bytes
src/app/hardklor/CAveragine.cpp | 306 +
src/app/hardklor/CAveragine.h | 101 +
src/app/hardklor/CHardklor.cpp | 2280 +
src/app/hardklor/CHardklor.h | 153 +
src/app/hardklor/CHardklor2.cpp | 1484 +
src/app/hardklor/CHardklor2.h | 119 +
src/app/hardklor/CHardklorParser.cpp | 547 +
src/app/hardklor/CHardklorParser.h | 42 +
src/app/hardklor/CHardklorProtein.cpp | 73 +
src/app/hardklor/CHardklorProtein.h | 42 +
src/app/hardklor/CHardklorSetting.cpp | 198 +
src/app/hardklor/CHardklorSetting.h | 90 +
src/app/hardklor/CHardklorVariant.cpp | 100 +
src/app/hardklor/CHardklorVariant.h | 43 +
src/app/hardklor/CMakeLists.txt | 60 +
src/app/hardklor/CMercury8.cpp | 1112 +
src/app/hardklor/CMercury8.h | 77 +
src/app/hardklor/CModelLibrary.cpp | 119 +
src/app/hardklor/CModelLibrary.h | 40 +
src/app/hardklor/CNoiseReduction.cpp | 1626 +
src/app/hardklor/CNoiseReduction.h | 73 +
src/app/hardklor/CPeriodicTable.cpp | 94 +
src/app/hardklor/CPeriodicTable.h | 40 +
src/app/hardklor/CSettings.cpp | 169 +
src/app/hardklor/CSettings.h | 56 +
src/app/hardklor/CSpecAnalyze.cpp | 858 +
src/app/hardklor/CSpecAnalyze.h | 77 +
src/app/hardklor/CSplitSpectrum.cpp | 812 +
src/app/hardklor/CSplitSpectrum.h | 56 +
src/app/hardklor/CruxHardklorApplication.cpp | 308 +
src/app/hardklor/CruxHardklorApplication.h | 88 +
src/app/hardklor/FFT-HK.cpp | 227 +
src/app/hardklor/FFT-HK.h | 20 +
src/app/hardklor/FFT.cpp | 121 +
src/app/hardklor/FFT.h | 20 +
src/app/hardklor/Hardklor.dat | 109 +
src/app/hardklor/Hardklor2008.aps | Bin 0 -> 390820 bytes
src/app/hardklor/Hardklor2008.rc | 55 +
src/app/hardklor/Hardklor2008.vcproj | 370 +
src/app/hardklor/HardklorTypes.h | 140 +
src/app/hardklor/Makefile | 720 +
src/app/hardklor/Makefile.hardklor | 94 +
src/app/hardklor/README.txt | 53 +
src/app/hardklor/S2N.cpp | 340 +
src/app/hardklor/S2N.h | 16 +
src/app/hardklor/Smooth.cpp | 179 +
src/app/hardklor/Smooth.h | 15 +
src/app/hardklor/SpecAnalyzeSupport.cpp | 266 +
src/app/hardklor/SpecAnalyzeSupport.h | 136 +
src/app/hardklor/cmake_install.cmake | 34 +
src/app/hardklor/libhardklor.a | Bin 0 -> 629654 bytes
src/app/hardklor/mercury.h | 27 +
src/app/hardklor/resource.h | 17 +
src/app/hardklor/resource1.h | 16 +
src/app/q-value.cpp | 31 +
src/app/q-value.h | 56 +
src/app/qranker-barista/Barista.cpp | 2895 +
src/app/qranker-barista/Barista.h | 200 +
src/app/qranker-barista/BipartiteGraph.cpp | 106 +
src/app/qranker-barista/BipartiteGraph.h | 38 +
src/app/qranker-barista/CMakeLists.txt | 53 +
src/app/qranker-barista/CruxParser.cpp | 177 +
src/app/qranker-barista/CruxParser.h | 78 +
src/app/qranker-barista/DataSetCrux.cpp | 1369 +
src/app/qranker-barista/DataSetCrux.h | 141 +
src/app/qranker-barista/Makefile | 558 +
src/app/qranker-barista/NeuralNet.cpp | 809 +
src/app/qranker-barista/NeuralNet.h | 152 +
src/app/qranker-barista/PSMScores.cpp | 225 +
src/app/qranker-barista/PSMScores.h | 44 +
src/app/qranker-barista/PepRanker.cpp | 1431 +
src/app/qranker-barista/PepRanker.h | 149 +
src/app/qranker-barista/PepScores.cpp | 226 +
src/app/qranker-barista/PepScores.h | 45 +
src/app/qranker-barista/ProtScores.cpp | 917 +
src/app/qranker-barista/ProtScores.h | 78 +
src/app/qranker-barista/QRanker.cpp | 1281 +
src/app/qranker-barista/QRanker.h | 143 +
src/app/qranker-barista/SQTParser.cpp | 2156 +
src/app/qranker-barista/SQTParser.h | 250 +
src/app/qranker-barista/SpecFeatures.cpp | 499 +
src/app/qranker-barista/SpecFeatures.h | 97 +
src/app/qranker-barista/TabDelimParser.cpp | 777 +
src/app/qranker-barista/TabDelimParser.h | 105 +
src/app/qranker-barista/barista.html | 215 +
src/app/qranker-barista/cmake_install.cmake | 34 +
src/app/qranker-barista/libbarista.a | Bin 0 -> 1298230 bytes
src/app/tide/CMakeLists.txt | 126 +
src/app/tide/Makefile | 720 +
src/app/tide/abspath.cc | 12 +
src/app/tide/abspath.h | 8 +
src/app/tide/active_peptide_queue.cc | 347 +
src/app/tide/active_peptide_queue.h | 158 +
src/app/tide/cmake_install.cmake | 34 +
src/app/tide/compiler.h | 208 +
src/app/tide/crux_sp_spectrum.cc | 283 +
src/app/tide/crux_sp_spectrum.h | 149 +
src/app/tide/fifo_alloc.cc | 172 +
src/app/tide/fifo_alloc.h | 152 +
src/app/tide/fixed_cap_array.h | 80 +
src/app/tide/index_settings.cc | 75 +
src/app/tide/libtide-support.a | Bin 0 -> 810966 bytes
src/app/tide/make_peptides.cc | 765 +
src/app/tide/mass_constants.cc | 272 +
src/app/tide/mass_constants.h | 118 +
src/app/tide/max_mz.cc | 9 +
src/app/tide/max_mz.h | 75 +
src/app/tide/mman.c | 180 +
src/app/tide/mman.h | 55 +
src/app/tide/mod_coder.h | 38 +
src/app/tide/modifications.h | 352 +
src/app/tide/peptide.cc | 281 +
src/app/tide/peptide.h | 244 +
src/app/tide/peptide_mods3.cc | 498 +
src/app/tide/peptide_peaks.cc | 97 +
src/app/tide/protobuf/header.proto | 81 +
src/app/tide/protobuf/peptides.proto | 50 +
src/app/tide/protobuf/raw_proteins.proto | 10 +
src/app/tide/protobuf/results.proto | 30 +
src/app/tide/protobuf/spectrum.proto | 25 +
src/app/tide/protobuf/view_ms1_cmds.proto | 12 +
src/app/tide/protoobj/header.pb.cc | 3408 +
src/app/tide/protoobj/header.pb.h | 2404 +
src/app/tide/protoobj/header_pb2.py | 570 +
src/app/tide/protoobj/peptides.pb.cc | 1389 +
src/app/tide/protoobj/peptides.pb.h | 843 +
src/app/tide/protoobj/peptides_pb2.py | 242 +
src/app/tide/protoobj/raw_proteins.pb.cc | 467 +
src/app/tide/protoobj/raw_proteins.pb.h | 367 +
src/app/tide/protoobj/raw_proteins_pb2.py | 80 +
src/app/tide/protoobj/results.pb.cc | 1077 +
src/app/tide/protoobj/results.pb.h | 669 +
src/app/tide/protoobj/results_pb2.py | 184 +
src/app/tide/protoobj/spectrum.pb.cc | 675 +
src/app/tide/protoobj/spectrum.pb.h | 410 +
src/app/tide/protoobj/spectrum_pb2.py | 114 +
src/app/tide/records.h | 249 +
src/app/tide/records_to_vector-inl.h | 49 +
src/app/tide/sp_scorer.cc | 123 +
src/app/tide/sp_scorer.h | 107 +
src/app/tide/spectrum_collection.cc | 218 +
src/app/tide/spectrum_collection.h | 122 +
src/app/tide/spectrum_preprocess.h | 203 +
src/app/tide/spectrum_preprocess2.cc | 563 +
src/app/tide/theoretical_peak_pair.h | 69 +
src/app/tide/theoretical_peak_set.h | 790 +
src/app/xlink/AccurateMonoMass.cpp | 157 +
src/app/xlink/CMakeLists.txt | 61 +
src/app/xlink/LinearPeptide.cpp | 245 +
src/app/xlink/LinearPeptide.h | 145 +
src/app/xlink/LinkedIonSeries.cpp | 294 +
src/app/xlink/LinkedIonSeries.h | 139 +
src/app/xlink/LinkedPeptide.cpp | 459 +
src/app/xlink/LinkedPeptide.h | 255 +
src/app/xlink/Makefile | 909 +
src/app/xlink/README | 62 +
src/app/xlink/SearchForXLinks.cpp | 285 +
src/app/xlink/SearchForXLinks.h | 93 +
src/app/xlink/SelfLoopPeptide.cpp | 351 +
src/app/xlink/SelfLoopPeptide.h | 148 +
src/app/xlink/Weibull.cpp | 211 +
src/app/xlink/Weibull.h | 42 +
src/app/xlink/XHHC_Peptide.cpp | 238 +
src/app/xlink/XHHC_Peptide.h | 135 +
src/app/xlink/XLink.cpp | 221 +
src/app/xlink/XLink.h | 107 +
src/app/xlink/XLinkBondMap.cpp | 176 +
src/app/xlink/XLinkBondMap.h | 114 +
src/app/xlink/XLinkDatabase.cpp | 592 +
src/app/xlink/XLinkDatabase.h | 144 +
src/app/xlink/XLinkIonSeriesCache.cpp | 141 +
src/app/xlink/XLinkIonSeriesCache.h | 29 +
src/app/xlink/XLinkMatch.cpp | 398 +
src/app/xlink/XLinkMatch.h | 152 +
src/app/xlink/XLinkMatchCollection.cpp | 444 +
src/app/xlink/XLinkMatchCollection.h | 169 +
src/app/xlink/XLinkPeptide.cpp | 726 +
src/app/xlink/XLinkPeptide.h | 252 +
src/app/xlink/XLinkScorer.cpp | 209 +
src/app/xlink/XLinkScorer.h | 87 +
src/app/xlink/XLinkSite.cpp | 175 +
src/app/xlink/XLinkSite.h | 79 +
src/app/xlink/XLinkablePeptide.cpp | 742 +
src/app/xlink/XLinkablePeptide.h | 284 +
src/app/xlink/XLinkablePeptideIterator.cpp | 83 +
src/app/xlink/XLinkablePeptideIterator.h | 76 +
src/app/xlink/XLinkablePeptideIteratorTopN.cpp | 169 +
src/app/xlink/XLinkablePeptideIteratorTopN.h | 83 +
src/app/xlink/cmake_install.cmake | 34 +
src/app/xlink/libxlink.a | Bin 0 -> 1224536 bytes
src/app/xlink/spectacle.pl | 331 +
src/app/xlink/xhhc.cpp | 405 +
src/app/xlink/xhhc.h | 111 +
src/app/xlink/xhhc_all.ms2 | 291285 ++++++++++++++++++
src/app/xlink/xhhc_predict_peptide_ions.cpp | 121 +
src/app/xlink/xhhc_score_peptide_spectrum.cpp | 417 +
src/app/xlink/xhhc_score_peptide_spectrum.h | 29 +
src/app/xlink/xhhc_scorer.cpp | 441 +
src/app/xlink/xhhc_scorer.h | 146 +
src/app/xlink/xhhc_search.cpp | 580 +
src/app/xlink/xlink_assign_ions.cpp | 286 +
src/app/xlink/xlink_assign_ions.h | 31 +
src/app/xlink/xlink_compute_qvalues.cpp | 282 +
src/app/xlink/xlink_compute_qvalues.h | 8 +
src/app/xlink/xlink_predict_peptide_ions.cpp | 381 +
src/app/xlink/xlink_search.cpp | 403 +
src/app/xlink/xlink_search.h | 15 +
src/cmake_install.cmake | 62 +
src/crux | Bin 0 -> 22906480 bytes
src/crux-main.cpp | 114 +
src/crux-main.h | 17 +
src/io/DelimitedFile.cpp | 825 +
src/io/DelimitedFile.h | 474 +
src/io/DelimitedFileReader.cpp | 504 +
src/io/DelimitedFileReader.h | 293 +
src/io/DelimitedFileWriter.cpp | 168 +
src/io/DelimitedFileWriter.h | 128 +
src/io/HTMLWriter.cpp | 14 +
src/io/HTMLWriter.h | 18 +
src/io/LineFileReader.cpp | 156 +
src/io/LineFileReader.h | 97 +
src/io/MSToolkitSpectrumCollection.cpp | 150 +
src/io/MSToolkitSpectrumCollection.h | 63 +
src/io/MatchCollectionParser.cpp | 211 +
src/io/MatchCollectionParser.h | 70 +
src/io/MatchColumns.cpp | 138 +
src/io/MatchColumns.h | 129 +
src/io/MatchFileReader.cpp | 403 +
src/io/MatchFileReader.h | 146 +
src/io/MatchFileWriter.cpp | 432 +
src/io/MatchFileWriter.h | 110 +
src/io/MzIdentMLReader.cpp | 361 +
src/io/MzIdentMLReader.h | 107 +
src/io/MzIdentMLWriter.cpp | 829 +
src/io/MzIdentMLWriter.h | 267 +
src/io/OutputFiles.cpp | 767 +
src/io/OutputFiles.h | 158 +
src/io/PMCDelimitedFileWriter.cpp | 709 +
src/io/PMCDelimitedFileWriter.h | 213 +
src/io/PMCPepXMLWriter.cpp | 142 +
src/io/PMCPepXMLWriter.h | 65 +
src/io/PMCSQTWriter.cpp | 160 +
src/io/PMCSQTWriter.h | 63 +
src/io/PSMReader.cpp | 29 +
src/io/PSMReader.h | 40 +
src/io/PSMWriter.cpp | 11 +
src/io/PSMWriter.h | 36 +
src/io/PWIZSpectrumCollection.cpp | 274 +
src/io/PWIZSpectrumCollection.h | 82 +
src/io/PepXMLReader.cpp | 606 +
src/io/PepXMLReader.h | 198 +
src/io/PepXMLWriter.cpp | 463 +
src/io/PepXMLWriter.h | 139 +
src/io/PinWriter.cpp | 295 +
src/io/PinWriter.h | 90 +
src/io/SQTReader.cpp | 407 +
src/io/SQTReader.h | 126 +
src/io/SQTWriter.cpp | 239 +
src/io/SQTWriter.h | 59 +
src/io/SpectrumCollection.cpp | 260 +
src/io/SpectrumCollection.h | 143 +
src/io/SpectrumCollectionFactory.cpp | 46 +
src/io/SpectrumCollectionFactory.h | 30 +
src/io/SpectrumRecordWriter.cpp | 195 +
src/io/SpectrumRecordWriter.h | 64 +
src/io/carp.cpp | 138 +
src/io/carp.h | 153 +
src/libcrux-support.a | Bin 0 -> 6144426 bytes
src/model/AbstractMatch.cpp | 142 +
src/model/AbstractMatch.h | 104 +
src/model/Database.cpp | 836 +
src/model/Database.h | 347 +
src/model/DatabasePeptideIterator.cpp | 342 +
src/model/DatabasePeptideIterator.h | 68 +
src/model/DatabaseProteinIterator.cpp | 81 +
src/model/DatabaseProteinIterator.h | 64 +
src/model/FilteredSpectrumChargeIterator.cpp | 145 +
src/model/FilteredSpectrumChargeIterator.h | 81 +
src/model/GeneratePeptidesIterator.cpp | 63 +
src/model/GeneratePeptidesIterator.h | 41 +
src/model/Ion.cpp | 1132 +
src/model/Ion.h | 473 +
src/model/IonConstraint.cpp | 473 +
src/model/IonConstraint.h | 214 +
src/model/IonFilteredIterator.cpp | 108 +
src/model/IonFilteredIterator.h | 70 +
src/model/IonSeries.cpp | 1231 +
src/model/IonSeries.h | 354 +
src/model/Match.cpp | 1110 +
src/model/Match.h | 459 +
src/model/MatchCollection.cpp | 1407 +
src/model/MatchCollection.h | 387 +
src/model/MatchCollectionIterator.cpp | 0
src/model/MatchCollectionIterator.h | 0
src/model/MatchIterator.cpp | 133 +
src/model/MatchIterator.h | 83 +
src/model/Modification.cpp | 572 +
src/model/Modification.h | 131 +
src/model/ModifiedPeptidesIterator.cpp | 238 +
src/model/ModifiedPeptidesIterator.h | 75 +
src/model/Peak.cpp | 136 +
src/model/Peak.h | 109 +
src/model/Peptide.cpp | 1275 +
src/model/Peptide.h | 490 +
src/model/PeptideConstraint.cpp | 317 +
src/model/PeptideConstraint.h | 200 +
src/model/PeptideIterator.h | 64 +
src/model/PeptideMatch.cpp | 135 +
src/model/PeptideMatch.h | 102 +
src/model/PeptideSrc.cpp | 514 +
src/model/PeptideSrc.h | 189 +
src/model/PostProcessProtein.cpp | 142 +
src/model/PostProcessProtein.h | 105 +
src/model/Protein.cpp | 940 +
src/model/Protein.h | 347 +
src/model/ProteinIndex.cpp | 174 +
src/model/ProteinIndex.h | 75 +
src/model/ProteinIndexIterator.cpp | 128 +
src/model/ProteinIndexIterator.h | 65 +
src/model/ProteinMatch.cpp | 93 +
src/model/ProteinMatch.h | 84 +
src/model/ProteinMatchCollection.cpp | 279 +
src/model/ProteinMatchCollection.h | 161 +
src/model/ProteinPeptideIterator.cpp | 525 +
src/model/ProteinPeptideIterator.h | 180 +
src/model/Scorer.cpp | 1682 +
src/model/Scorer.h | 504 +
src/model/Spectrum.cpp | 971 +
src/model/Spectrum.h | 375 +
src/model/SpectrumMatch.cpp | 103 +
src/model/SpectrumMatch.h | 101 +
src/model/SpectrumZState.cpp | 167 +
src/model/SpectrumZState.h | 134 +
src/model/match_objects.h | 36 +
src/model/objects.h | 811 +
src/parameter.cpp | 947 +
src/parameter.h | 266 +
src/util/Alphabet.cpp | 56 +
src/util/Alphabet.h | 31 +
src/util/AminoAcidUtil.cpp | 107 +
src/util/AminoAcidUtil.h | 18 +
src/util/ArgParser.cpp | 127 +
src/util/ArgParser.h | 47 +
src/util/CacheableMass.cpp | 85 +
src/util/CacheableMass.h | 68 +
src/util/CarpStreamBuf.cpp | 101 +
src/util/CarpStreamBuf.h | 72 +
src/util/FileUtils.cpp | 86 +
src/util/FileUtils.h | 28 +
src/util/GlobalParams.cpp | 197 +
src/util/GlobalParams.h | 97 +
src/util/MathUtil.cpp | 20 +
src/util/MathUtil.h | 15 +
src/util/Params.cpp | 2849 +
src/util/Params.h | 399 +
src/util/StringUtils.cpp | 139 +
src/util/StringUtils.h | 167 +
src/util/WinCrux.cpp | 193 +
src/util/WinCrux.h | 65 +
src/util/crux-utils.cpp | 1669 +
src/util/crux-utils.h | 483 +
src/util/linked_list.cpp | 370 +
src/util/linked_list.h | 145 +
src/util/mass.cpp | 307 +
src/util/mass.h | 132 +
src/util/modifications.cpp | 993 +
src/util/modifications.h | 419 +
src/util/peptide_modifications.cpp | 814 +
src/util/peptide_modifications.h | 160 +
src/util/utils.cpp | 469 +
src/util/utils.h | 247 +
src/util/windirent.h | 369 +
1265 files changed, 685777 insertions(+)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/crux.git
More information about the debian-med-commit
mailing list