TPP:4.5.1 SVN Log
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(Difference between revisions)
| Revision as of 20:10, 7 November 2011 JoeS (Talk | contribs) (→Branch Check Ins As of 10/24/2011) ← Previous diff |
Current revision JoeS (Talk | contribs) |
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| - | = Changes since 4.5.0 release as of 11/7/2011 = | + | = Changes since 4.5.0 release = |
| <nowiki> | <nowiki> | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| - | r5508 | dshteyn | 2011-09-23 14:36:13 -0700 (Fri, 23 Sep 2011) | 1 line | + | r5506 | dshteyn | 2011-09-23 11:54:38 -0700 (Fri, 23 Sep 2011) | 1 line |
| - | Changed paths: | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLibImporter.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.hpp | + | |
| - | SpectraSTLIB: adding randomization of spectrum function for PTMProphet. | + | Tandem2XML: BUGFIX Fix problem when running Tandem on mgf file created with MzXML2Search, the resulting pep.xml file contained extra newline characters at the end of the spectrum name that are now being removed. |
| - | ------------------------------------------------------------------------ | + | |
| - | r5509 | dshteyn | 2011-09-23 15:04:39 -0700 (Fri, 23 Sep 2011) | 1 line | + | |
| - | Changed paths: | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/KDModel.cxx | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/KDModel.h | + | |
| - | + | ||
| - | PTMProphet: adding getVal functions for KDModel. | + | |
| - | ------------------------------------------------------------------------ | + | |
| - | r5510 | slagelwa | 2011-09-23 15:28:18 -0700 (Fri, 23 Sep 2011) | 5 lines | + | |
| - | Changed paths: | + | |
| - | M /trunk/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp | + | |
| - | + | ||
| - | Re-merged 4.5 changes in trunk. SVNTortise didn't list to my "accept branch" changes when I did the merge. | + | |
| - | + | ||
| - | (ALSO MEANS that the trunk changes in these two files will likely be lost) | + | |
| - | + | ||
| - | + | ||
| - | ------------------------------------------------------------------------ | + | |
| - | r5511 | dshteyn | 2011-09-23 16:20:07 -0700 (Fri, 23 Sep 2011) | 1 line | + | |
| - | Changed paths: | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp | + | |
| - | + | ||
| - | Adding back support for Agilent QTOF mzML | + | |
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5512 | dshteyn | 2011-09-23 16:24:14 -0700 (Fri, 23 Sep 2011) | 1 line | r5512 | dshteyn | 2011-09-23 16:24:14 -0700 (Fri, 23 Sep 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp | ||
| support for Agilent QTOF mzML | support for Agilent QTOF mzML | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5513 | dshteyn | 2011-09-23 17:04:04 -0700 (Fri, 23 Sep 2011) | 1 line | r5513 | dshteyn | 2011-09-23 17:04:04 -0700 (Fri, 23 Sep 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp | ||
| Fix typo | Fix typo | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5514 | dshteyn | 2011-09-23 17:04:33 -0700 (Fri, 23 Sep 2011) | 2 lines | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp | ||
| - | |||
| - | Fix typo | ||
| - | |||
| - | ------------------------------------------------------------------------ | ||
| - | r5515 | slagelwa | 2011-09-29 11:58:33 -0700 (Thu, 29 Sep 2011) | 6 lines | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qconvert | ||
| - | |||
| - | * now removes the log files before submission | ||
| - | * uses new conversion queues | ||
| - | * no longer allows submissions with the --server flag and instead | ||
| - | uses queues | ||
| - | |||
| - | |||
| - | ------------------------------------------------------------------------ | ||
| - | r5516 | ppatrick | 2011-10-04 08:57:14 -0700 (Tue, 04 Oct 2011) | 2 lines | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx | ||
| - | |||
| - | Changed from theoretical precursor mass to measured one to allow for narrower tolerances. | ||
| - | |||
| - | ------------------------------------------------------------------------ | ||
| - | r5517 | ppatrick | 2011-10-04 12:28:23 -0700 (Tue, 04 Oct 2011) | 2 lines | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressCGIProteinDisplayParser/XPressCGIProteinDisplay.cxx | ||
| - | |||
| - | Changed logic of xsl to speed up loading. | ||
| - | |||
| - | ------------------------------------------------------------------------ | ||
| - | r5518 | ppatrick | 2011-10-04 12:29:44 -0700 (Tue, 04 Oct 2011) | 2 lines | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressProteinRatioParser/XPressProteinRatioParser.cxx | ||
| - | |||
| - | increased min peptide probability to 0.8 from 0.5 | ||
| - | |||
| - | ------------------------------------------------------------------------ | ||
| - | r5519 | dshteyn | 2011-10-04 13:31:11 -0700 (Tue, 04 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/RefreshParser/RefreshParser.cxx | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/RefreshParser/RefreshParserMain.cxx | ||
| - | |||
| - | RefreshParser: make RefreshParser mapping of semi and non trypic peptides consistent with the search engine parameters unless overridden on the commandline (per Jimmy's and Vagisha's posts to spctools-dev of Jun 10 2011) | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5520 | ppatrick | 2011-10-05 05:35:18 -0700 (Wed, 05 Oct 2011) | 2 lines | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp | ||
| - | |||
| - | Initialized preExt to account for incorrect file names being passed. | ||
| - | |||
| - | ------------------------------------------------------------------------ | ||
| - | r5521 | ppatrick | 2011-10-05 05:38:48 -0700 (Wed, 05 Oct 2011) | 2 lines | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx | ||
| - | |||
| - | Fixed buffer overruns in void XPressPeptideParser::parse(const char *xmlfile) and void XPressPeptideParser::validate_mzXMLfile() | ||
| - | |||
| - | ------------------------------------------------------------------------ | ||
| - | r5522 | ppatrick | 2011-10-05 05:40:47 -0700 (Wed, 05 Oct 2011) | 2 lines | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx | ||
| - | |||
| - | Fixed buffer overrun in void XPressPeptideParser::validate_mzXMLfile() | ||
| - | |||
| - | ------------------------------------------------------------------------ | ||
| - | r5523 | ppatrick | 2011-10-05 14:09:52 -0700 (Wed, 05 Oct 2011) | 3 lines | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/mzXML/converters/ReAdW/FilterLine.cpp | ||
| - | M /trunk/trans_proteomic_pipeline/src/mzXML/converters/ReAdW/FilterLine.h | ||
| - | M /trunk/trans_proteomic_pipeline/src/mzXML/converters/ReAdW/ThermoInterface.cpp | ||
| - | |||
| - | Added Supplemental Activation | ||
| - | Removed 0 intensity peaks | ||
| - | |||
| - | ------------------------------------------------------------------------ | ||
| - | r5524 | eng_jk | 2011-10-05 16:36:44 -0700 (Wed, 05 Oct 2011) | 2 lines | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx | ||
| - | |||
| - | quick mod to Patrick's buffer overrun fix (for non-sequential mzML scans) | ||
| - | |||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5525 | eng_jk | 2011-10-05 16:42:41 -0700 (Wed, 05 Oct 2011) | 2 lines | r5525 | eng_jk | 2011-10-05 16:42:41 -0700 (Wed, 05 Oct 2011) | 2 lines | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx | ||
| quick mod to Patrick's buffer overrun fix (for non-sequential mzML scans); adding to 4.5 branch | quick mod to Patrick's buffer overrun fix (for non-sequential mzML scans); adding to 4.5 branch | ||
| Line 139: | Line 21: | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5526 | eng_jk | 2011-10-06 14:14:46 -0700 (Thu, 06 Oct 2011) | 3 lines | r5526 | eng_jk | 2011-10-06 14:14:46 -0700 (Thu, 06 Oct 2011) | 3 lines | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/common/constants.h | ||
| additional cleanup of yesterday's xpress buffer overrun fix; mainly changing size of a few | additional cleanup of yesterday's xpress buffer overrun fix; mainly changing size of a few | ||
| allocated arrays which only affects mzML files with with non-sequential native IDs. | allocated arrays which only affects mzML files with with non-sequential native IDs. | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5527 | eng_jk | 2011-10-06 14:16:52 -0700 (Thu, 06 Oct 2011) | 3 lines | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx | ||
| - | M /trunk/trans_proteomic_pipeline/src/common/constants.h | ||
| - | |||
| - | additional cleanup of yesterday's xpress buffer overrun fix; mainly changing size of a few | ||
| - | allocated arrays which only affects mzML files with with non-sequential native IDs. | ||
| - | |||
| - | ------------------------------------------------------------------------ | ||
| - | r5528 | eng_jk | 2011-10-06 14:18:53 -0700 (Thu, 06 Oct 2011) | 2 lines | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/util/translateDNA2AA-FASTA.cpp | ||
| - | |||
| - | change deflines to include which reading frame as part of accession | ||
| - | |||
| - | ------------------------------------------------------------------------ | ||
| - | r5529 | henryhlam | 2011-10-09 22:00:49 -0700 (Sun, 09 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/util/pep_dbcount.cpp | ||
| - | M /trunk/trans_proteomic_pipeline/src/util/translateDNA2AA-FASTA.cpp | ||
| - | |||
| - | [util] Catch return values for smooth compiling | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5530 | henryhlam | 2011-10-09 22:03:18 -0700 (Sun, 09 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzxmlhandler.cpp | ||
| - | |||
| - | [mzParser] Pound-include stdint.h and catch return values for smooth compiling | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5531 | henryhlam | 2011-10-09 23:57:02 -0700 (Sun, 09 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/MzXML2Search/MzXML2Search.cxx | ||
| - | |||
| - | [MzXML2Search] Option to remove charge-reduced precursors for ETD spectra (useful for search engines that do not have that feature) | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5532 | henryhlam | 2011-10-09 23:59:27 -0700 (Sun, 09 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/util/calculate_pi.cpp | ||
| - | |||
| - | [util] Catch return values for smooth compiling | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5533 | henryhlam | 2011-10-10 00:02:43 -0700 (Mon, 10 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Tandem2XML/TandemParamsParser.cxx | ||
| - | |||
| - | [Tandem2XML] Fix wrong enzyme specificity for Lys-C | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5534 | henryhlam | 2011-10-10 00:12:16 -0700 (Mon, 10 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Visualization/xinteract/xinteract.cxx | ||
| - | |||
| - | [xinteract] Move RefreshParser ahead of PeptideProphet to safeguard against some search engines' mangling the protein names and/or omitting NTT/NMC | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5535 | henryhlam | 2011-10-10 00:19:18 -0700 (Mon, 10 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx | ||
| - | |||
| - | [InteractParser] Fix OMSSA's problem with n-term mods | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5536 | henryhlam | 2011-10-10 00:32:35 -0700 (Mon, 10 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/InterProphet.cxx | ||
| - | |||
| - | [InterProphet] More finely divided bins for error rate estimates. Important for modern, large datasets. | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5537 | henryhlam | 2011-10-10 00:35:35 -0700 (Mon, 10 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Validation/MixtureModel/MixtureModel.cxx | ||
| - | |||
| - | [PeptideProphet] More finely divided bins for error rate estimates. Important for modern, large datasets. | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5538 | henryhlam | 2011-10-10 00:43:02 -0700 (Mon, 10 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Enzyme/ProteolyticEnzyme/ProteolyticEnzyme.cxx | ||
| - | |||
| - | [Enzyme] Equate tryptic with trypsin | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5539 | henryhlam | 2011-10-10 20:08:54 -0700 (Mon, 10 Oct 2011) | 1 line | r5539 | henryhlam | 2011-10-10 20:08:54 -0700 (Mon, 10 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.cpp | ||
| [SpectraST] Fix rare error when S/N calculation failed due to too few peaks outside precursor region (trunk r5501) | [SpectraST] Fix rare error when S/N calculation failed due to too few peaks outside precursor region (trunk r5501) | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5540 | henryhlam | 2011-10-10 20:12:27 -0700 (Mon, 10 Oct 2011) | 1 line | r5540 | henryhlam | 2011-10-10 20:12:27 -0700 (Mon, 10 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzxmlhandler.cpp | ||
| [mzParser] Pound-include stdint.h and catch return values for smooth compiling (trunk r5530) | [mzParser] Pound-include stdint.h and catch return values for smooth compiling (trunk r5530) | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5541 | henryhlam | 2011-10-10 20:15:16 -0700 (Mon, 10 Oct 2011) | 1 line | r5541 | henryhlam | 2011-10-10 20:15:16 -0700 (Mon, 10 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/util/calculate_pi.cpp | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/util/pep_dbcount.cpp | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/util/translateDNA2AA-FASTA.cpp | ||
| [util] Catch return values for smooth compiling (trunk r5532) | [util] Catch return values for smooth compiling (trunk r5532) | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5542 | henryhlam | 2011-10-10 20:18:11 -0700 (Mon, 10 Oct 2011) | 1 line | r5542 | henryhlam | 2011-10-10 20:18:11 -0700 (Mon, 10 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Tandem2XML/TandemParamsParser.cxx | ||
| [Tandem2XML] Fix wrong enzyme specificity for Lys-C (trunk r5533) | [Tandem2XML] Fix wrong enzyme specificity for Lys-C (trunk r5533) | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5543 | henryhlam | 2011-10-10 20:23:42 -0700 (Mon, 10 Oct 2011) | 1 line | r5543 | henryhlam | 2011-10-10 20:23:42 -0700 (Mon, 10 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Visualization/xinteract/xinteract.cxx | ||
| Move RefreshParser ahead of PeptideProphet to safeguard against some search engines' mangling the protein names and/or omitting NTT/NMC (trunk r5534) | Move RefreshParser ahead of PeptideProphet to safeguard against some search engines' mangling the protein names and/or omitting NTT/NMC (trunk r5534) | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5544 | henryhlam | 2011-10-10 20:25:26 -0700 (Mon, 10 Oct 2011) | 1 line | r5544 | henryhlam | 2011-10-10 20:25:26 -0700 (Mon, 10 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx | ||
| [InteractParser] Fix OMSSA's problem with n-term mods (trunk r5535) | [InteractParser] Fix OMSSA's problem with n-term mods (trunk r5535) | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5545 | henryhlam | 2011-10-10 20:27:17 -0700 (Mon, 10 Oct 2011) | 1 line | r5545 | henryhlam | 2011-10-10 20:27:17 -0700 (Mon, 10 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Enzyme/ProteolyticEnzyme/ProteolyticEnzyme.cxx | ||
| [Enzyme] Equate tryptic with trypsin (trunk r5538) | [Enzyme] Equate tryptic with trypsin (trunk r5538) | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5546 | henryhlam | 2011-10-10 20:30:09 -0700 (Mon, 10 Oct 2011) | 1 line | r5546 | henryhlam | 2011-10-10 20:30:09 -0700 (Mon, 10 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/InterProphet.cxx | ||
| [InterProphet] More finely divided bins for error rate estimates. Important for modern, large datasets. (trunk r5536) | [InterProphet] More finely divided bins for error rate estimates. Important for modern, large datasets. (trunk r5536) | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5547 | henryhlam | 2011-10-10 22:48:06 -0700 (Mon, 10 Oct 2011) | 1 line | r5547 | henryhlam | 2011-10-10 22:48:06 -0700 (Mon, 10 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Validation/MixtureModel/MixtureModel.cxx | ||
| [PeptideProphet] More finely divided bins for error rate estimates. Important for modern, large datasets. (trunk r5537) | [PeptideProphet] More finely divided bins for error rate estimates. Important for modern, large datasets. (trunk r5537) | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5548 | slagelwa | 2011-10-14 15:22:56 -0700 (Fri, 14 Oct 2011) | 4 lines | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/extern/hpctools/grid/templates/sequest.params | ||
| - | M /trunk/trans_proteomic_pipeline/extern/hpctools/grid/templates/tandem.params | ||
| - | |||
| - | * Set the default number of threads to 8 for tandem | ||
| - | * Include a warning in the comments that values for three | ||
| - | differential modifications are always needed | ||
| - | |||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5549 | slagelwa | 2011-10-17 14:31:27 -0700 (Mon, 17 Oct 2011) | 1 line | r5549 | slagelwa | 2011-10-17 14:31:27 -0700 (Mon, 17 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/extern/xtandem/src/msequenceserver.cpp | ||
| - | M /branches/4-5/trans_proteomic_pipeline/extern/xtandem/src_cyclone/msequenceserver.cpp | ||
| - | M /branches/4-5/trans_proteomic_pipeline/extern/xtandem/src_merged/msequenceserver.cpp | ||
| Increased size of buffer for holding fasta header lines as per recommendation by David Trudgian. | Increased size of buffer for holding fasta header lines as per recommendation by David Trudgian. | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5550 | slagelwa | 2011-10-17 14:41:42 -0700 (Mon, 17 Oct 2011) | 1 line | r5550 | slagelwa | 2011-10-17 14:41:42 -0700 (Mon, 17 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/extern/xtandem/src_merged/msequenceserver.cpp | ||
| Cut&paste in cygwin inserted newline | Cut&paste in cygwin inserted newline | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5551 | eng_jk | 2011-10-18 12:14:31 -0700 (Tue, 18 Oct 2011) | 4 lines | r5551 | eng_jk | 2011-10-18 12:14:31 -0700 (Tue, 18 Oct 2011) | 4 lines | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideUpdateParser/XPressPeptideUpdateParserMain.cxx | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/common/util.cxx | ||
| Fix for mzML files when viewing xpress chromatograms through the ProteinProphet to XPressCGIProteinDisplayParser.cgi binary. | Fix for mzML files when viewing xpress chromatograms through the ProteinProphet to XPressCGIProteinDisplayParser.cgi binary. | ||
| Line 317: | Line 76: | ||
| file extension if the mzXML file is not found. | file extension if the mzXML file is not found. | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5552 | eng_jk | 2011-10-18 12:59:35 -0700 (Tue, 18 Oct 2011) | 2 lines | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideUpdateParser/XPressPeptideUpdateParserMain.cxx | ||
| - | M /trunk/trans_proteomic_pipeline/src/common/util.cxx | ||
| - | |||
| - | replicate branch 5551 checkin to trunk for xpress/mzML fix | ||
| - | |||
| - | ------------------------------------------------------------------------ | ||
| - | r5553 | real_procopio | 2011-10-19 17:02:11 -0700 (Wed, 19 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/mzXML/converters/dta2mzxml/Dta2mzXML.cpp | ||
| - | M /trunk/trans_proteomic_pipeline/src/mzXML/converters/dta2mzxml/Dta2mzXML.h | ||
| - | M /trunk/trans_proteomic_pipeline/src/mzXML/converters/dta2mzxml/main.cpp | ||
| - | |||
| - | [dta2mzxml] Change 'plustwo' option to include lowest charge state found for a given scan; also make sure output is real mzXML | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5554 | henryhlam | 2011-10-20 01:36:19 -0700 (Thu, 20 Oct 2011) | 1 line | r5554 | henryhlam | 2011-10-20 01:36:19 -0700 (Thu, 20 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTCreateParams.cpp | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTCreateParams.hpp | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.cpp | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.hpp | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTSpLibImporter.cpp | ||
| [SpectraST] Allow users to specify their own m/z range for MRM transitions (Q3) | [SpectraST] Allow users to specify their own m/z range for MRM transitions (Q3) | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5555 | henryhlam | 2011-10-20 01:52:25 -0700 (Thu, 20 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTCreateParams.cpp | ||
| - | M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTCreateParams.hpp | ||
| - | M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.cpp | ||
| - | M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.hpp | ||
| - | M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTSpLibImporter.cpp | ||
| - | |||
| - | [SpectraST] Allow users to specify their own m/z range for MRM transitions (Q3) | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5556 | henryhlam | 2011-10-20 01:59:58 -0700 (Thu, 20 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTQuery.cpp | ||
| - | |||
| - | [SpectraST] Consider all charges when library spectrum has charge 0 | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5557 | henryhlam | 2011-10-20 02:01:34 -0700 (Thu, 20 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTMspLibImporter.cpp | ||
| - | |||
| - | [SpectraST] Allow import of non-peptide from MSP format | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5558 | henryhlam | 2011-10-20 02:06:59 -0700 (Thu, 20 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTMzLibIndex.cpp | ||
| - | M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTSpLibImporter.cpp | ||
| - | M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTSpLibImporter.hpp | ||
| - | |||
| - | [SpectraST] New clustering algorithm. Saves memory, prevent deep recursion. | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5559 | real_procopio | 2011-10-20 12:20:06 -0700 (Thu, 20 Oct 2011) | 1 line | r5559 | real_procopio | 2011-10-20 12:20:06 -0700 (Thu, 20 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/mzXML/converters/dta2mzxml/Dta2mzXML.cpp | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/mzXML/converters/dta2mzxml/Dta2mzXML.h | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/mzXML/converters/dta2mzxml/main.cpp | ||
| merging trunk changes from rev 5553 | merging trunk changes from rev 5553 | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5560 | dshteyn | 2011-10-20 14:56:38 -0700 (Thu, 20 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphet.cxx | ||
| - | M /trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphet.h | ||
| - | M /trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphetMain.cxx | ||
| - | M /trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphetParser.cxx | ||
| - | M /trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphetParser.h | ||
| - | |||
| - | PTMProphetParser: NEW FEATURES amino acids and mass shifts are users settable as is mz tolerance, improved classification now outperforms ASCORE, EM is now default (new option NOEM). | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5561 | real_procopio | 2011-10-20 17:24:09 -0700 (Thu, 20 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl | ||
| - | |||
| - | [Petunia] Added version checking upon login; warn users if using an old version of TPP | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5562 | real_procopio | 2011-10-20 17:27:40 -0700 (Thu, 20 Oct 2011) | 1 line | r5562 | real_procopio | 2011-10-20 17:27:40 -0700 (Thu, 20 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl | ||
| [Petunia] merging rev 5561 from trunk | [Petunia] merging rev 5561 from trunk | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5563 | real_procopio | 2011-10-21 13:40:59 -0700 (Fri, 21 Oct 2011) | 1 line | r5563 | real_procopio | 2011-10-21 13:40:59 -0700 (Fri, 21 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl | ||
| [Petunia] Added support for Bruker .yep and .baf files, as well as mzXML output to msconvert; Expanded Libra normalization channel option to 8 | [Petunia] Added support for Bruker .yep and .baf files, as well as mzXML output to msconvert; Expanded Libra normalization channel option to 8 | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5564 | mhoopmann | 2011-10-21 15:10:06 -0700 (Fri, 21 Oct 2011) | 1 line | r5564 | mhoopmann | 2011-10-21 15:10:06 -0700 (Fri, 21 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp | ||
| - | M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzxmlhandler.cpp | ||
| - | |||
| - | Fixed buffer overrun when reading small spectra compressed with zlib (compression increases spectrum size in these cases, hence the overrun). Moved stdint.h to linux build as it is not part of Visual Studio. | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5565 | mhoopmann | 2011-10-21 15:15:24 -0700 (Fri, 21 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzxmlhandler.cpp | ||
| Fixed buffer overrun when reading small spectra compressed with zlib (compression increases spectrum size in these cases, hence the overrun). Moved stdint.h to linux build as it is not part of Visual Studio. | Fixed buffer overrun when reading small spectra compressed with zlib (compression increases spectrum size in these cases, hence the overrun). Moved stdint.h to linux build as it is not part of Visual Studio. | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5566 | real_procopio | 2011-10-21 16:10:41 -0700 (Fri, 21 Oct 2011) | 1 line | r5566 | real_procopio | 2011-10-21 16:10:41 -0700 (Fri, 21 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl | ||
| [Petunia] Decoy models pages should only ask for pep/protXML files as input; minor code clean-up and re-formatting | [Petunia] Decoy models pages should only ask for pep/protXML files as input; minor code clean-up and re-formatting | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5567 | henryhlam | 2011-10-23 22:16:00 -0700 (Sun, 23 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTConstants.hpp | ||
| - | M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTCreateParams.cpp | ||
| - | M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.cpp | ||
| - | M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.hpp | ||
| - | M /trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphet.cxx | ||
| - | |||
| - | [SpectraST] High-mass accuracy MS2 support: frag type of CID-QTOF and HCD. Change to shuffleAllPeaks which is used by PTMProphet | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5568 | dshteyn | 2011-10-24 10:56:36 -0700 (Mon, 24 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/KDModel.cxx | ||
| - | M /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/KDModel.h | ||
| - | |||
| - | PTMProphet: forgot to commit new function clearObs. | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5569 | real_procopio | 2011-10-24 18:08:29 -0700 (Mon, 24 Oct 2011) | 7 lines | r5569 | real_procopio | 2011-10-24 18:08:29 -0700 (Mon, 24 Oct 2011) | 7 lines | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl | ||
| [Petunia] | [Petunia] | ||
| Line 459: | Line 109: | ||
| - Add thead and tbody tags to file list table (for future jscript sorting integration); | - Add thead and tbody tags to file list table (for future jscript sorting integration); | ||
| - fixed a couple of typos. | - fixed a couple of typos. | ||
| - | |||
| - | ------------------------------------------------------------------------ | ||
| - | r5570 | slagelwa | 2011-10-25 11:09:28 -0700 (Tue, 25 Oct 2011) | 3 lines | ||
| - | Changed paths: | ||
| - | A /branches/rene (from /trunk/trans_proteomic_pipeline:5569) | ||
| - | |||
| - | Starting a branch for Rene to incorporate his cool simulation program. | ||
| - | |||
| - | |||
| - | ------------------------------------------------------------------------ | ||
| - | r5571 | dshteyn | 2011-10-26 12:12:56 -0700 (Wed, 26 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXField.cxx | ||
| - | M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PipelineAnalysis.cxx | ||
| - | M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/html/PepXMLViewer.html | ||
| - | |||
| - | PepXMLViewer: Correct confusing probability column names in case of iProphet. | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5572 | dshteyn | 2011-10-26 12:24:57 -0700 (Wed, 26 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/CGI/protxml2html.pl | ||
| - | |||
| - | protxml2html.pl: The peptide links will now link out to PepXMLViewer instead of special separate parser. | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5573 | eng_jk | 2011-10-26 16:27:35 -0700 (Wed, 26 Oct 2011) | 2 lines | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/mzXML/tools/readmzXML/readmzXML.cpp | ||
| - | |||
| - | add option to dump ms1 scans as scan/mass/intensity; useful for generating plots | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5574 | real_procopio | 2011-10-26 18:48:45 -0700 (Wed, 26 Oct 2011) | 1 line | r5574 | real_procopio | 2011-10-26 18:48:45 -0700 (Wed, 26 Oct 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl | ||
| [Petunia] Added function to strip base path name from a list of files (and thus shorten shell command size); implemented this for xinteract, the biggest culprit. | [Petunia] Added function to strip base path name from a list of files (and thus shorten shell command size); implemented this for xinteract, the biggest culprit. | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5575 | dshteyn | 2011-11-01 10:49:27 -0700 (Tue, 01 Nov 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/RTCalculator.cxx | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/RTCalculator.h | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/RTCalculatorMain.cxx | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/RTCatalog.cxx | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/RTCatalog.h | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/RTCatalogParser.cxx | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/RTCatalogParser.h | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/RTCatalogParserMain.cxx | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/SearchResult/SearchResult.cxx | ||
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/SearchResult/SearchResult.h | ||
| - | |||
| - | RTCatalog/RTCalc/RTModel : restructure code, check for fail condition (stddev==0), add gradient peptide feature, add worklist feature. | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5576 | dshteyn | 2011-11-01 12:11:00 -0700 (Tue, 01 Nov 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/SearchHit.h | ||
| - | |||
| - | Additional typedefs, should probably be centralized. | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5577 | dshteyn | 2011-11-01 12:17:09 -0700 (Tue, 01 Nov 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/KernelDensityRTMixtureDistr.cxx | ||
| - | M /trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/KernelDensityRTMixtureDistr.h | ||
| - | M /trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/MixtureDistr.cxx | ||
| - | M /trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/MixtureDistr.h | ||
| - | M /trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/RTMixtureDistr.cxx | ||
| - | |||
| - | RTModel: Additional update functions. | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5578 | dshteyn | 2011-11-01 16:15:35 -0700 (Tue, 01 Nov 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Validation/iModelParser/IModelParser.cxx | ||
| - | |||
| - | "iModelParser.cgi: Fix output of FDR plots when available under Windows." | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5579 | dshteyn | 2011-11-01 16:17:12 -0700 (Tue, 01 Nov 2011) | 2 lines | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/common/util.cxx | ||
| - | |||
| - | return a default url of http://localhost/ when WEBSERVER_URL is not set. | ||
| - | |||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| r5580 | slagelwa | 2011-11-02 15:45:23 -0700 (Wed, 02 Nov 2011) | 3 lines | r5580 | slagelwa | 2011-11-02 15:45:23 -0700 (Wed, 02 Nov 2011) | 3 lines | ||
| - | Changed paths: | ||
| - | M /branches/4-5/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl | ||
| Fixed a issue with uploading files on windows resulting in 0 byte files | Fixed a issue with uploading files on windows resulting in 0 byte files | ||
| Line 548: | Line 121: | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| - | r5581 | dshteyn | 2011-11-03 09:43:13 -0700 (Thu, 03 Nov 2011) | 1 line | + | r5604 | real_procopio | 2011-11-07 16:47:03 -0800 (Mon, 07 Nov 2011) | 9 lines |
| - | Changed paths: | + | |
| - | M /trunk/trans_proteomic_pipeline/perl/ProphetModels.pl | + | |
| - | ProphetModel.pl bugfixes and updates. | + | [Petunia] |
| - | ------------------------------------------------------------------------ | + | - New dynamic filtering box on file browser and chooser, with smart "select |
| - | r5582 | dshteyn | 2011-11-03 12:40:58 -0700 (Thu, 03 Nov 2011) | 1 line | + | all" checkbox |
| - | Changed paths: | + | - Streamlined file operations form buttons (Delete, Copy, Paste, etc) |
| - | M /trunk/trans_proteomic_pipeline/src/Visualization/xinteract/xinteract.cxx | + | - Do not show Clipboard div if empty |
| + | - Allow users to specify data dirs with leading uppercase (e.g. C:\blah\) | ||
| + | - Took out 'tilde' hack for XPRESS | ||
| + | - Now using -nosticky pragma in perl CGI | ||
| - | Replace ~ with - to fix the whole XPress ~ character for negative mods hack problem. | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| - | r5583 | dshteyn | 2011-11-03 12:54:22 -0700 (Thu, 03 Nov 2011) | 2 lines | + | r5605 | real_procopio | 2011-11-07 16:53:48 -0800 (Mon, 07 Nov 2011) | 1 line |
| - | Changed paths: | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Visualization/xinteract/xinteract.cxx | + | |
| - | + | ||
| - | Fix extra paren typo | + | |
| + | New dir to store javascript files | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| - | r5584 | pcbrefugee | 2011-11-04 14:35:26 -0700 (Fri, 04 Nov 2011) | 1 line | + | r5606 | real_procopio | 2011-11-07 17:02:54 -0800 (Mon, 07 Nov 2011) | 1 line |
| - | Changed paths: | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/ramp/ramp.vcproj | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/ramp/rampvc8.vcproj | + | |
| - | [msvc RAMP] use zlib 1.2.5 | + | New Table sorting Javasript utility |
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| - | r5585 | pcbrefugee | 2011-11-04 14:37:14 -0700 (Fri, 04 Nov 2011) | 1 line | + | r5607 | slagelwa | 2011-11-07 22:01:50 -0800 (Mon, 07 Nov 2011) | 2 lines |
| - | Changed paths: | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/gsl.vcproj | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/gsl_vc8.vcproj | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/uncompress_win_lib.bat | + | |
| - | M /trunk/trans_proteomic_pipeline/src/tpp.vsprops | + | |
| - | tweaks for building gsl in msvc | + | Merged all of David's changes on trunk since the 4.5 release into 4.5 branch |
| - | ------------------------------------------------------------------------ | + | |
| - | r5586 | dshteyn | 2011-11-04 14:56:44 -0700 (Fri, 04 Nov 2011) | 1 line | + | |
| - | Changed paths: | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx | + | |
| - | XPressPeptideParser: BUGFIX handle negative mass difference | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| - | r5587 | pcbrefugee | 2011-11-04 15:15:18 -0700 (Fri, 04 Nov 2011) | 1 line | + | r5608 | slagelwa | 2011-11-08 10:23:57 -0800 (Tue, 08 Nov 2011) | 1 line |
| - | Changed paths: | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/zlib.vcproj | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/zlibvc8.vcproj | + | |
| - | silence warnings about depecrated open(), lseek() etc | + | 4.5.1 |
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| - | r5588 | pcbrefugee | 2011-11-04 15:20:37 -0700 (Fri, 04 Nov 2011) | 1 line | + | r5623 | real_procopio | 2011-11-09 17:45:53 -0800 (Wed, 09 Nov 2011) | 1 line |
| - | Changed paths: | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Parsers/RefreshParser/RefreshParser.cxx | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXFilter.cxx | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXOptions.cxx | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXUtility.cxx | + | |
| - | tweaks for quiet compile | + | [Petunia] Toggle visible checkboxes only: Support for older versions of the perl CGI module, where the <label> tag is the parent of the <input> tag |
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| - | r5589 | pcbrefugee | 2011-11-04 15:32:45 -0700 (Fri, 04 Nov 2011) | 1 line | + | r5624 | slagelwa | 2011-11-10 11:40:32 -0800 (Thu, 10 Nov 2011) | 3 lines |
| - | Changed paths: | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/xtandem/src/Makefile | + | |
| - | M /trunk/trans_proteomic_pipeline/installer_linux/publish_tandem_to_s3.sh | + | |
| - | M /trunk/trans_proteomic_pipeline/installer_linux/tandem_arch.sh | + | |
| - | [X!!Tandem] consider MPI version (OpenMPI vs others) when building X!!Tandem | + | Checking in David's changes on the trunk since revision 4605 |
| - | ------------------------------------------------------------------------ | + | |
| - | r5590 | renehussong | 2011-11-04 15:46:36 -0700 (Fri, 04 Nov 2011) | 1 line | + | |
| - | Changed paths: | + | |
| - | M /branches/rene/src/Makefile | + | |
| - | A /branches/rene/src/Simulation | + | |
| - | A /branches/rene/src/Simulation/FragSim | + | |
| - | A /branches/rene/src/Simulation/FragSim/include | + | |
| - | A /branches/rene/src/Simulation/FragSim/include/FragSim | + | |
| - | A /branches/rene/src/Simulation/FragSim/include/FragSim/AA.h | + | |
| - | A /branches/rene/src/Simulation/FragSim/include/FragSim/AminoAcid.h | + | |
| - | A /branches/rene/src/Simulation/FragSim/include/FragSim/AminoAcidPairStatistics.h | + | |
| - | A /branches/rene/src/Simulation/FragSim/include/FragSim/Annotation.h | + | |
| - | A /branches/rene/src/Simulation/FragSim/include/FragSim/AnnotationList.h | + | |
| - | A /branches/rene/src/Simulation/FragSim/include/FragSim/Definitions.h | + | |
| - | A /branches/rene/src/Simulation/FragSim/include/FragSim/Enum.h | + | |
| - | A /branches/rene/src/Simulation/FragSim/include/FragSim/ExtendedAnnotation.h | + | |
| - | A /branches/rene/src/Simulation/FragSim/include/FragSim/IonType.h | + | |
| - | A /branches/rene/src/Simulation/FragSim/include/FragSim/MemoryPersistent.h | + | |
| - | A /branches/rene/src/Simulation/FragSim/include/FragSim/Parser.h | + | |
| - | A /branches/rene/src/Simulation/FragSim/include/FragSim/Peak.h | + | |
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| - | first version of FragSim (MS2 simulation tool) | ||
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| - | r5591 | dshteyn | 2011-11-04 15:46:58 -0700 (Fri, 04 Nov 2011) | 2 lines | ||
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| - | A /branches/rene/extern/TernarySearchTree/tst_public.doxy | + | |
| - | adding TernarySearchTree package from Rasmus Ekman needed for FragSim | + | Merging David's latest round of checkins on trunk with the assumption |
| - | ------------------------------------------------------------------------ | + | they belong here too. |
| - | r5593 | pcbrefugee | 2011-11-04 16:37:00 -0700 (Fri, 04 Nov 2011) | 1 line | + | |
| - | Changed paths: | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXUtility.cxx | + | |
| - | M /trunk/trans_proteomic_pipeline/src/common/sysdepend.h | + | |
| - | undo my 5588 change, actual problem was with bad implementation of stroull in windows sysdepend.h | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5594 | renehussong | 2011-11-04 18:55:14 -0700 (Fri, 04 Nov 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /branches/rene/src/Simulation/FragSim/src/FragSim.C | ||
| - | M /branches/rene/src/Simulation/FragSim/src/Sptxt.C | ||
| - | fixed immonium ion parser bug | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| - | r5595 | renehussong | 2011-11-04 19:03:26 -0700 (Fri, 04 Nov 2011) | 1 line | + | r5634 | slagelwa | 2011-11-14 15:59:32 -0800 (Mon, 14 Nov 2011) | 3 lines |
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| - | M /branches/rene/CGI/tpp_gui/tpp_gui.pl | + | |
| - | a first Petunia version of FragSim | + | Trying again. Last checkin with David's changed were not committed. This checkin also includes the stdlib.h addition in pwiz done by Brian so that it will compile on gcc 4.6.1. |
| - | ------------------------------------------------------------------------ | + | |
| - | r5596 | pcbrefugee | 2011-11-07 10:02:24 -0800 (Mon, 07 Nov 2011) | 1 line | + | |
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| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/Serializer_mzML.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/Serializer_mzXML.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumInfo.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumInfo.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumListCache.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumListCache.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumListCacheTest.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumList_MGF.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumList_MSn.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumList_MSn_Test.cpp | + | |
| - | A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumList_mz5.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumList_mzML.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumList_mzML.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumList_mzML_Test.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumList_mzXML.cpp | + | |
| - | D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/Version.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/ramp/ramp.h | + | |
| - | D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/AminoAcid.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/Digestion.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/Digestion.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/DigestionTest.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/Peptide.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/ProteinListCache.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/ProteomeData.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/Version.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/tradata/IO.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/tradata/Version.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/Jamfile.jam | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/Reader_ABI.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/Reader_ABI_Detail.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/Reader_ABI_Detail.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/Reader_ABI_Test.data.tar.bz2 | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/SpectrumList_ABI.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/SpectrumList_ABI.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/T2D/Jamfile.jam | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Agilent/ChromatogramList_Agilent.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Agilent/Jamfile.jam | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Agilent/Reader_Agilent_Detail.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Agilent/Reader_Agilent_Test.data.tar.bz2 | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Agilent/SpectrumList_Agilent.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Agilent/SpectrumList_Agilent.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Bruker/Jamfile.jam | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Bruker/Reader_Bruker.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Bruker/Reader_Bruker_Detail.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Bruker/Reader_Bruker_Detail.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Bruker/Reader_Bruker_Test.data.tar.bz2 | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Bruker/SpectrumList_Bruker.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Bruker/SpectrumList_Bruker.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Thermo/ChromatogramList_Thermo.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Thermo/Jamfile.jam | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Thermo/Reader_Thermo_Test.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Thermo/Reader_Thermo_Test.data.tar.bz2 | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Thermo/SpectrumList_Thermo.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/Jamfile.jam | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/Reader_Waters_Test.data.tar.bz2 | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/Jamfile.jam | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/analysis/spectrum_processing.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/analysis/spectrum_processing.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/analysis/spectrum_processing_test.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/common/Jamfile.jam | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/common/ParamTypes.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/common/SharedCLI.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/common/cv.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/common/map.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/common/unit.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/common/vector.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/common/virtual_map.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/msdata/MSDataFile.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/proteome/ProteomeDataFile.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/chemistry/Chemistry.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/chemistry/Chemistry.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/chemistry/ChemistryTest.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/chemistry/MZTolerance.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/chemistry/MZToleranceTest.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/minimxml/Jamfile.jam | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/minimxml/SAXParser.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/minimxml/SAXParser.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/minimxml/SAXParserTest.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/minimxml/XMLWriter.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/minimxml/XMLWriter.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/minimxml/XMLWriterTest.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/COMInitializer.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/Environment.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/Exception.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/FilesystemTest.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/Jamfile.jam | + | |
| - | A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/Singleton.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/Std.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/Stream.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/String.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/cpp_cli_utilities.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/optimized_lexical_cast.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/random_access_compressed_ifstream.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/random_access_compressed_ifstream.hpp | + | |
| - | D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/ABI/Jamfile.jam | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/ABI/T2D/T2D_Data.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFile.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/ABI/WiffFileTest.cpp | + | |
| - | D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/Documents | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/MassHunterData.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/MassHunterData.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Bruker/CompassData.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Bruker/CompassData.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Bruker/Jamfile.jam | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Waters/MassLynxRaw.hpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/Jamfile.jam | + | |
| - | D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/Microsoft.VC90.MFC | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/RawFile.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/RawFile.h | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/RawFileValues.h | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/ScanFilter.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/ScanFilter.h | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/ScanFilterTest.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/xrawfile2.tli | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/SeeMS/Annotation.cs | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/SeeMS/DataSource.cs | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/SeeMS/Dialogs/AnnotationPanels.Designer.cs | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/SeeMS/Dialogs/OpenDataSourceDialog.cs | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/SeeMS/Dialogs/SpectrumListForm.cs | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/SeeMS/Jamfile.jam | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/SeeMS/Manager.cs | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/SeeMS/Properties/AssemblyInfo.cs | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/SeeMS/STL_Containers.dll | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/SeeMS/seems.csproj | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/commandline/Jamfile.jam | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/commandline/chainsaw.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/commandline/idconvert.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/commandline/mascot2mzid.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/commandline/msaccess.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/commandline/msconvert.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/commandline/mspicture.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/commandline/mzidtxt.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/commandline/pep2mzid.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/commandline/tab2mzid.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/examples/Jamfile.jam | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/examples/write_mzid_example_files.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/examples/write_proteome_example_files.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Makefile | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Makefile.pwiz.incl | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Quantitation/Pepc/Pepc.jar | + | |
| - | A /trunk/trans_proteomic_pipeline/src/pwiz/generate-version.pl | + | |
| - | M /trunk/trans_proteomic_pipeline/src/pwiz/pwiz.vcproj | + | |
| - | D /trunk/trans_proteomic_pipeline/src/pwiz/pwiz_Version.cpp | + | |
| - | M /trunk/trans_proteomic_pipeline/src/pwiz/pwizvc8.vcproj | + | |
| - | get current with ProteoWizard: their rev 3102 with considerable performance gains for mzML reading particularly across network shares | ||
| - | ------------------------------------------------------------------------ | ||
| - | r5597 | dshteyn | 2011-11-07 10:10:12 -0800 (Mon, 07 Nov 2011) | 1 line | ||
| - | Changed paths: | ||
| - | M /trunk/trans_proteomic_pipeline/src/Visualization/xinteract/xinteract.cxx | ||
| - | xinteract: fix bug passing parameters to XPress. | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| - | r5598 | eng_jk | 2011-11-07 10:46:11 -0800 (Mon, 07 Nov 2011) | 3 lines | + | r5642 | slagelwa | 2011-11-16 15:09:33 -0800 (Wed, 16 Nov 2011) | 2 lines |
| - | Changed paths: | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.h | + | |
| - | M /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParserMain.cxx | + | |
| - | M /trunk/trans_proteomic_pipeline/src/common/constants.h | + | |
| - | Add minimum probability cutoff to quantify peptides (-q command line option; -p and -P already taken) | + | Fixing ARCH to be ARCH_FAMILY so XFORMS does the correct regex subsitution. |
| - | Default cutoff is still at 0.5. Applies to both standard and labelfree modes | + | |
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| - | r5599 | pcbrefugee | 2011-11-07 11:02:19 -0800 (Mon, 07 Nov 2011) | 1 line | + | r5644 | slagelwa | 2011-11-21 14:05:30 -0800 (Mon, 21 Nov 2011) | 2 lines |
| - | Changed paths: | + | |
| - | M /trunk/trans_proteomic_pipeline/src/mzXML/common/Base64.cpp | + | |
| - | quiet a "not all control paths return a value" warning | + | Correcting issue with propertly setting up perl libpath to file perllib |
| - | ------------------------------------------------------------------------ | + | |
| - | r5600 | pcbrefugee | 2011-11-07 11:06:34 -0800 (Mon, 07 Nov 2011) | 1 line | + | |
| - | Changed paths: | + | |
| - | A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/common/UnimodTest.cpp | + | |
| - | A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/ChromatogramList_mz5.cpp | + | |
| - | A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/Serializer_mz5.hpp | + | |
| - | A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumList_mz5.cpp | + | |
| - | A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumList_mz5_Test.cpp | + | |
| - | A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/shared_map.hpp | + | |
| - | [ProteoWizard] missed a few new additions to ProteoWizard codebase | ||
| ------------------------------------------------------------------------ | ------------------------------------------------------------------------ | ||
| </nowiki> | </nowiki> | ||
Current revision
[edit]
Changes since 4.5.0 release
------------------------------------------------------------------------ r5506 | dshteyn | 2011-09-23 11:54:38 -0700 (Fri, 23 Sep 2011) | 1 line Tandem2XML: BUGFIX Fix problem when running Tandem on mgf file created with MzXML2Search, the resulting pep.xml file contained extra newline characters at the end of the spectrum name that are now being removed. ------------------------------------------------------------------------ r5512 | dshteyn | 2011-09-23 16:24:14 -0700 (Fri, 23 Sep 2011) | 1 line support for Agilent QTOF mzML ------------------------------------------------------------------------ r5513 | dshteyn | 2011-09-23 17:04:04 -0700 (Fri, 23 Sep 2011) | 1 line Fix typo ------------------------------------------------------------------------ r5525 | eng_jk | 2011-10-05 16:42:41 -0700 (Wed, 05 Oct 2011) | 2 lines quick mod to Patrick's buffer overrun fix (for non-sequential mzML scans); adding to 4.5 branch ------------------------------------------------------------------------ r5526 | eng_jk | 2011-10-06 14:14:46 -0700 (Thu, 06 Oct 2011) | 3 lines additional cleanup of yesterday's xpress buffer overrun fix; mainly changing size of a few allocated arrays which only affects mzML files with with non-sequential native IDs. ------------------------------------------------------------------------ r5539 | henryhlam | 2011-10-10 20:08:54 -0700 (Mon, 10 Oct 2011) | 1 line [SpectraST] Fix rare error when S/N calculation failed due to too few peaks outside precursor region (trunk r5501) ------------------------------------------------------------------------ r5540 | henryhlam | 2011-10-10 20:12:27 -0700 (Mon, 10 Oct 2011) | 1 line [mzParser] Pound-include stdint.h and catch return values for smooth compiling (trunk r5530) ------------------------------------------------------------------------ r5541 | henryhlam | 2011-10-10 20:15:16 -0700 (Mon, 10 Oct 2011) | 1 line [util] Catch return values for smooth compiling (trunk r5532) ------------------------------------------------------------------------ r5542 | henryhlam | 2011-10-10 20:18:11 -0700 (Mon, 10 Oct 2011) | 1 line [Tandem2XML] Fix wrong enzyme specificity for Lys-C (trunk r5533) ------------------------------------------------------------------------ r5543 | henryhlam | 2011-10-10 20:23:42 -0700 (Mon, 10 Oct 2011) | 1 line Move RefreshParser ahead of PeptideProphet to safeguard against some search engines' mangling the protein names and/or omitting NTT/NMC (trunk r5534) ------------------------------------------------------------------------ r5544 | henryhlam | 2011-10-10 20:25:26 -0700 (Mon, 10 Oct 2011) | 1 line [InteractParser] Fix OMSSA's problem with n-term mods (trunk r5535) ------------------------------------------------------------------------ r5545 | henryhlam | 2011-10-10 20:27:17 -0700 (Mon, 10 Oct 2011) | 1 line [Enzyme] Equate tryptic with trypsin (trunk r5538) ------------------------------------------------------------------------ r5546 | henryhlam | 2011-10-10 20:30:09 -0700 (Mon, 10 Oct 2011) | 1 line [InterProphet] More finely divided bins for error rate estimates. Important for modern, large datasets. (trunk r5536) ------------------------------------------------------------------------ r5547 | henryhlam | 2011-10-10 22:48:06 -0700 (Mon, 10 Oct 2011) | 1 line [PeptideProphet] More finely divided bins for error rate estimates. Important for modern, large datasets. (trunk r5537) ------------------------------------------------------------------------ r5549 | slagelwa | 2011-10-17 14:31:27 -0700 (Mon, 17 Oct 2011) | 1 line Increased size of buffer for holding fasta header lines as per recommendation by David Trudgian. ------------------------------------------------------------------------ r5550 | slagelwa | 2011-10-17 14:41:42 -0700 (Mon, 17 Oct 2011) | 1 line Cut&paste in cygwin inserted newline ------------------------------------------------------------------------ r5551 | eng_jk | 2011-10-18 12:14:31 -0700 (Tue, 18 Oct 2011) | 4 lines Fix for mzML files when viewing xpress chromatograms through the ProteinProphet to XPressCGIProteinDisplayParser.cgi binary. No notion of file extensions exist in that path and mzXML files were always assumed. This fix simply has the cgi try mzML file extension if the mzXML file is not found. ------------------------------------------------------------------------ r5554 | henryhlam | 2011-10-20 01:36:19 -0700 (Thu, 20 Oct 2011) | 1 line [SpectraST] Allow users to specify their own m/z range for MRM transitions (Q3) ------------------------------------------------------------------------ r5559 | real_procopio | 2011-10-20 12:20:06 -0700 (Thu, 20 Oct 2011) | 1 line merging trunk changes from rev 5553 ------------------------------------------------------------------------ r5562 | real_procopio | 2011-10-20 17:27:40 -0700 (Thu, 20 Oct 2011) | 1 line [Petunia] merging rev 5561 from trunk ------------------------------------------------------------------------ r5563 | real_procopio | 2011-10-21 13:40:59 -0700 (Fri, 21 Oct 2011) | 1 line [Petunia] Added support for Bruker .yep and .baf files, as well as mzXML output to msconvert; Expanded Libra normalization channel option to 8 ------------------------------------------------------------------------ r5564 | mhoopmann | 2011-10-21 15:10:06 -0700 (Fri, 21 Oct 2011) | 1 line Fixed buffer overrun when reading small spectra compressed with zlib (compression increases spectrum size in these cases, hence the overrun). Moved stdint.h to linux build as it is not part of Visual Studio. ------------------------------------------------------------------------ r5566 | real_procopio | 2011-10-21 16:10:41 -0700 (Fri, 21 Oct 2011) | 1 line [Petunia] Decoy models pages should only ask for pep/protXML files as input; minor code clean-up and re-formatting ------------------------------------------------------------------------ r5569 | real_procopio | 2011-10-24 18:08:29 -0700 (Mon, 24 Oct 2011) | 7 lines [Petunia] - Add ability to specify no output file for some commands; - Rename files after running the Re-index mzXML tool; - Display file extension being searched for in File Chooser; - Add thead and tbody tags to file list table (for future jscript sorting integration); - fixed a couple of typos. ------------------------------------------------------------------------ r5574 | real_procopio | 2011-10-26 18:48:45 -0700 (Wed, 26 Oct 2011) | 1 line [Petunia] Added function to strip base path name from a list of files (and thus shorten shell command size); implemented this for xinteract, the biggest culprit. ------------------------------------------------------------------------ r5580 | slagelwa | 2011-11-02 15:45:23 -0700 (Wed, 02 Nov 2011) | 3 lines Fixed a issue with uploading files on windows resulting in 0 byte files ------------------------------------------------------------------------ r5604 | real_procopio | 2011-11-07 16:47:03 -0800 (Mon, 07 Nov 2011) | 9 lines [Petunia] - New dynamic filtering box on file browser and chooser, with smart "select all" checkbox - Streamlined file operations form buttons (Delete, Copy, Paste, etc) - Do not show Clipboard div if empty - Allow users to specify data dirs with leading uppercase (e.g. C:\blah\) - Took out 'tilde' hack for XPRESS - Now using -nosticky pragma in perl CGI ------------------------------------------------------------------------ r5605 | real_procopio | 2011-11-07 16:53:48 -0800 (Mon, 07 Nov 2011) | 1 line New dir to store javascript files ------------------------------------------------------------------------ r5606 | real_procopio | 2011-11-07 17:02:54 -0800 (Mon, 07 Nov 2011) | 1 line New Table sorting Javasript utility ------------------------------------------------------------------------ r5607 | slagelwa | 2011-11-07 22:01:50 -0800 (Mon, 07 Nov 2011) | 2 lines Merged all of David's changes on trunk since the 4.5 release into 4.5 branch ------------------------------------------------------------------------ r5608 | slagelwa | 2011-11-08 10:23:57 -0800 (Tue, 08 Nov 2011) | 1 line 4.5.1 ------------------------------------------------------------------------ r5623 | real_procopio | 2011-11-09 17:45:53 -0800 (Wed, 09 Nov 2011) | 1 line [Petunia] Toggle visible checkboxes only: Support for older versions of the perl CGI module, where the <label> tag is the parent of the <input> tag ------------------------------------------------------------------------ r5624 | slagelwa | 2011-11-10 11:40:32 -0800 (Thu, 10 Nov 2011) | 3 lines Checking in David's changes on the trunk since revision 4605 ------------------------------------------------------------------------ r5632 | slagelwa | 2011-11-14 11:11:38 -0800 (Mon, 14 Nov 2011) | 4 lines Merging David's latest round of checkins on trunk with the assumption they belong here too. ------------------------------------------------------------------------ r5634 | slagelwa | 2011-11-14 15:59:32 -0800 (Mon, 14 Nov 2011) | 3 lines Trying again. Last checkin with David's changed were not committed. This checkin also includes the stdlib.h addition in pwiz done by Brian so that it will compile on gcc 4.6.1. ------------------------------------------------------------------------ r5642 | slagelwa | 2011-11-16 15:09:33 -0800 (Wed, 16 Nov 2011) | 2 lines Fixing ARCH to be ARCH_FAMILY so XFORMS does the correct regex subsitution. ------------------------------------------------------------------------ r5644 | slagelwa | 2011-11-21 14:05:30 -0800 (Mon, 21 Nov 2011) | 2 lines Correcting issue with propertly setting up perl libpath to file perllib ------------------------------------------------------------------------
