TPP:4.5.1 SVN Log
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| - | </nowiki> | ||
| - | |||
| - | = Branch Check Ins As of 10/24/2011 = | ||
| - | |||
| - | <nowiki> | ||
| - | Revision: 5566 | ||
| - | Author: real_procopio | ||
| - | Date: 4:10:41 PM, Friday, October 21, 2011 | ||
| - | Message: | ||
| - | [Petunia] Decoy models pages should only ask for pep/protXML files as input; minor code clean-up and re-formatting | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl | ||
| - | |||
| - | Revision: 5564 | ||
| - | Author: mhoopmann | ||
| - | Date: 3:10:06 PM, Friday, October 21, 2011 | ||
| - | Message: | ||
| - | 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. | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzxmlhandler.cpp | ||
| - | |||
| - | Revision: 5563 | ||
| - | Author: real_procopio | ||
| - | Date: 1:40:59 PM, Friday, October 21, 2011 | ||
| - | Message: | ||
| - | [Petunia] Added support for Bruker .yep and .baf files, as well as mzXML output to msconvert; Expanded Libra normalization channel option to 8 | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl | ||
| - | |||
| - | Revision: 5562 | ||
| - | Author: real_procopio | ||
| - | Date: 5:27:40 PM, Thursday, October 20, 2011 | ||
| - | Message: | ||
| - | [Petunia] merging rev 5561 from trunk | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl | ||
| - | |||
| - | Revision: 5559 | ||
| - | Author: real_procopio | ||
| - | Date: 12:20:06 PM, Thursday, October 20, 2011 | ||
| - | Message: | ||
| - | merging trunk changes from rev 5553 | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/mzXML/converters/dta2mzxml/Dta2mzXML.cpp | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/mzXML/converters/dta2mzxml/Dta2mzXML.h | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/mzXML/converters/dta2mzxml/main.cpp | ||
| - | |||
| - | Revision: 5554 | ||
| - | Author: henryhlam | ||
| - | Date: 1:36:19 AM, Thursday, October 20, 2011 | ||
| - | Message: | ||
| - | [SpectraST] Allow users to specify their own m/z range for MRM transitions (Q3) | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTCreateParams.cpp | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTCreateParams.hpp | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.cpp | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.hpp | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTSpLibImporter.cpp | ||
| - | |||
| - | Revision: 5551 | ||
| - | Author: eng_jk | ||
| - | Date: 12:14:31 PM, Tuesday, October 18, 2011 | ||
| - | Message: | ||
| - | 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. | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideUpdateParser/XPressPeptideUpdateParserMain.cxx | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/common/util.cxx | ||
| - | |||
| - | Revision: 5550 | ||
| - | Author: slagelwa | ||
| - | Date: 2:41:42 PM, Monday, October 17, 2011 | ||
| - | Message: | ||
| - | Cut&paste in cygwin inserted newline | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/extern/xtandem/src_merged/msequenceserver.cpp | ||
| - | |||
| - | Revision: 5549 | ||
| - | Author: slagelwa | ||
| - | Date: 2:31:27 PM, Monday, October 17, 2011 | ||
| - | Message: | ||
| - | Increased size of buffer for holding fasta header lines as per recommendation by David Trudgian. | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/extern/xtandem/src/msequenceserver.cpp | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/extern/xtandem/src_cyclone/msequenceserver.cpp | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/extern/xtandem/src_merged/msequenceserver.cpp | ||
| - | |||
| - | Revision: 5547 | ||
| - | Author: henryhlam | ||
| - | Date: 10:48:06 PM, Monday, October 10, 2011 | ||
| - | Message: | ||
| - | [PeptideProphet] More finely divided bins for error rate estimates. Important for modern, large datasets. (trunk r5537) | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Validation/MixtureModel/MixtureModel.cxx | ||
| - | |||
| - | Revision: 5546 | ||
| - | Author: henryhlam | ||
| - | Date: 8:30:09 PM, Monday, October 10, 2011 | ||
| - | Message: | ||
| - | [InterProphet] More finely divided bins for error rate estimates. Important for modern, large datasets. (trunk r5536) | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/InterProphet.cxx | ||
| - | |||
| - | Revision: 5545 | ||
| - | Author: henryhlam | ||
| - | Date: 8:27:17 PM, Monday, October 10, 2011 | ||
| - | Message: | ||
| - | [Enzyme] Equate tryptic with trypsin (trunk r5538) | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Enzyme/ProteolyticEnzyme/ProteolyticEnzyme.cxx | ||
| - | |||
| - | Revision: 5544 | ||
| - | Author: henryhlam | ||
| - | Date: 8:25:26 PM, Monday, October 10, 2011 | ||
| - | Message: | ||
| - | [InteractParser] Fix OMSSA's problem with n-term mods (trunk r5535) | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx | ||
| - | |||
| - | Revision: 5543 | ||
| - | Author: henryhlam | ||
| - | Date: 8:23:42 PM, Monday, October 10, 2011 | ||
| - | Message: | ||
| - | Move RefreshParser ahead of PeptideProphet to safeguard against some search engines' mangling the protein names and/or omitting NTT/NMC (trunk r5534) | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Visualization/xinteract/xinteract.cxx | ||
| - | |||
| - | Revision: 5542 | ||
| - | Author: henryhlam | ||
| - | Date: 8:18:11 PM, Monday, October 10, 2011 | ||
| - | Message: | ||
| - | [Tandem2XML] Fix wrong enzyme specificity for Lys-C (trunk r5533) | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Tandem2XML/TandemParamsParser.cxx | ||
| - | |||
| - | Revision: 5541 | ||
| - | Author: henryhlam | ||
| - | Date: 8:15:16 PM, Monday, October 10, 2011 | ||
| - | Message: | ||
| - | [util] Catch return values for smooth compiling (trunk r5532) | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/util/calculate_pi.cpp | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/util/pep_dbcount.cpp | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/util/translateDNA2AA-FASTA.cpp | ||
| - | |||
| - | Revision: 5540 | ||
| - | Author: henryhlam | ||
| - | Date: 8:12:27 PM, Monday, October 10, 2011 | ||
| - | Message: | ||
| - | [mzParser] Pound-include stdint.h and catch return values for smooth compiling (trunk r5530) | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzxmlhandler.cpp | ||
| - | |||
| - | Revision: 5539 | ||
| - | Author: henryhlam | ||
| - | Date: 8:08:54 PM, Monday, October 10, 2011 | ||
| - | Message: | ||
| - | [SpectraST] Fix rare error when S/N calculation failed due to too few peaks outside precursor region (trunk r5501) | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.cpp | ||
| - | |||
| - | Revision: 5526 | ||
| - | Author: eng_jk | ||
| - | Date: 2:14:46 PM, Thursday, October 06, 2011 | ||
| - | Message: | ||
| - | 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. | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/common/constants.h | ||
| - | |||
| - | Revision: 5525 | ||
| - | Author: eng_jk | ||
| - | Date: 4:42:41 PM, Wednesday, October 05, 2011 | ||
| - | Message: | ||
| - | quick mod to Patrick's buffer overrun fix (for non-sequential mzML scans); adding to 4.5 branch | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx | ||
| - | |||
| - | Revision: 5513 | ||
| - | Author: dshteyn | ||
| - | Date: 5:04:04 PM, Friday, September 23, 2011 | ||
| - | Message: | ||
| - | Fix typo | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp | ||
| - | |||
| - | Revision: 5512 | ||
| - | Author: dshteyn | ||
| - | Date: 4:24:14 PM, Friday, September 23, 2011 | ||
| - | Message: | ||
| - | support for Agilent QTOF mzML | ||
| - | ---- | ||
| - | Modified : /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp | ||
| </nowiki> | </nowiki> | ||
Revision as of 20:10, 7 November 2011
Changes since 4.5.0 release as of 11/7/2011
------------------------------------------------------------------------ r5508 | dshteyn | 2011-09-23 14:36:13 -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. ------------------------------------------------------------------------ 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 Changed paths: M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp support for Agilent QTOF mzML ------------------------------------------------------------------------ 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 ------------------------------------------------------------------------ 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 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 ------------------------------------------------------------------------ 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 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 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) ------------------------------------------------------------------------ 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) ------------------------------------------------------------------------ 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) ------------------------------------------------------------------------ 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) ------------------------------------------------------------------------ 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) ------------------------------------------------------------------------ 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) ------------------------------------------------------------------------ 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) ------------------------------------------------------------------------ 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) ------------------------------------------------------------------------ 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) ------------------------------------------------------------------------ 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 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. ------------------------------------------------------------------------ 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 ------------------------------------------------------------------------ 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. 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. ------------------------------------------------------------------------ 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 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) ------------------------------------------------------------------------ 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 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 ------------------------------------------------------------------------ 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 Changed paths: M /branches/4-5/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl [Petunia] merging rev 5561 from trunk ------------------------------------------------------------------------ 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 ------------------------------------------------------------------------ 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. ------------------------------------------------------------------------ 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 ------------------------------------------------------------------------ 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 Changed paths: M /branches/4-5/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl [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. ------------------------------------------------------------------------ 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 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. ------------------------------------------------------------------------ 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 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 ------------------------------------------------------------------------ r5581 | dshteyn | 2011-11-03 09:43:13 -0700 (Thu, 03 Nov 2011) | 1 line Changed paths: M /trunk/trans_proteomic_pipeline/perl/ProphetModels.pl ProphetModel.pl bugfixes and updates. ------------------------------------------------------------------------ r5582 | dshteyn | 2011-11-03 12:40:58 -0700 (Thu, 03 Nov 2011) | 1 line Changed paths: M /trunk/trans_proteomic_pipeline/src/Visualization/xinteract/xinteract.cxx 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 Changed paths: M /trunk/trans_proteomic_pipeline/src/Visualization/xinteract/xinteract.cxx Fix extra paren typo ------------------------------------------------------------------------ r5584 | pcbrefugee | 2011-11-04 14:35:26 -0700 (Fri, 04 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 ------------------------------------------------------------------------ r5585 | pcbrefugee | 2011-11-04 14:37:14 -0700 (Fri, 04 Nov 2011) | 1 line 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 ------------------------------------------------------------------------ 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 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 ------------------------------------------------------------------------ r5588 | pcbrefugee | 2011-11-04 15:20:37 -0700 (Fri, 04 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 ------------------------------------------------------------------------ r5589 | pcbrefugee | 2011-11-04 15:32:45 -0700 (Fri, 04 Nov 2011) | 1 line 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 ------------------------------------------------------------------------ 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 A /branches/rene/src/Simulation/FragSim/include/FragSim/Peptide.h A /branches/rene/src/Simulation/FragSim/include/FragSim/ShapeStatistics.h A /branches/rene/src/Simulation/FragSim/include/FragSim/SimpleStatistics.h A /branches/rene/src/Simulation/FragSim/include/FragSim/SpectralLibrary.h A /branches/rene/src/Simulation/FragSim/include/FragSim/Spectrum.h A /branches/rene/src/Simulation/FragSim/include/FragSim/Sptxt.h A /branches/rene/src/Simulation/FragSim/include/FragSim/SptxtLibrary.h A /branches/rene/src/Simulation/FragSim/include/FragSim/SptxtPeptide.h A /branches/rene/src/Simulation/FragSim/include/FragSim/Statistics.h A /branches/rene/src/Simulation/FragSim/include/FragSim/StatisticsContainer.h A /branches/rene/src/Simulation/FragSim/include/FragSim/StatisticsFactory.h A /branches/rene/src/Simulation/FragSim/include/FragSim/TextParser.h A /branches/rene/src/Simulation/FragSim/src A /branches/rene/src/Simulation/FragSim/src/AA.C A /branches/rene/src/Simulation/FragSim/src/AminoAcid.C A /branches/rene/src/Simulation/FragSim/src/AminoAcidPairStatistics.C A /branches/rene/src/Simulation/FragSim/src/Annotation.C A /branches/rene/src/Simulation/FragSim/src/AnnotationList.C A /branches/rene/src/Simulation/FragSim/src/Definitions.C A /branches/rene/src/Simulation/FragSim/src/Enum.C A /branches/rene/src/Simulation/FragSim/src/ExtendedAnnotation.C A /branches/rene/src/Simulation/FragSim/src/FragSim.C A /branches/rene/src/Simulation/FragSim/src/IonType.C A /branches/rene/src/Simulation/FragSim/src/Makefile A /branches/rene/src/Simulation/FragSim/src/MemoryPersistent.C A /branches/rene/src/Simulation/FragSim/src/Parser.C A /branches/rene/src/Simulation/FragSim/src/Peak.C A /branches/rene/src/Simulation/FragSim/src/Peptide.C A /branches/rene/src/Simulation/FragSim/src/PeptideMatrix.C A /branches/rene/src/Simulation/FragSim/src/ShapeStatistics.C A /branches/rene/src/Simulation/FragSim/src/SimpleStatistics.C A /branches/rene/src/Simulation/FragSim/src/SpectralLibrary.C A /branches/rene/src/Simulation/FragSim/src/Spectrum.C A /branches/rene/src/Simulation/FragSim/src/Sptxt.C A /branches/rene/src/Simulation/FragSim/src/SptxtAnnotation.C A /branches/rene/src/Simulation/FragSim/src/SptxtPeptide.C A /branches/rene/src/Simulation/FragSim/src/Statistics.C A /branches/rene/src/Simulation/FragSim/src/StatisticsContainer.C A /branches/rene/src/Simulation/FragSim/src/StatisticsFactory.C A /branches/rene/src/Simulation/FragSim/src/TextParser.C first version of FragSim (MS2 simulation tool) ------------------------------------------------------------------------ r5591 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/branches/rene/extern/TernarySearchTree/tst_detail/tst_implementation.ipp A /branches/rene/extern/TernarySearchTree/tst_detail/tst_iterator_base.ipp A /branches/rene/extern/TernarySearchTree/tst_detail/tst_iterator_facade.hpp A /branches/rene/extern/TernarySearchTree/tst_detail/tst_node.hpp A /branches/rene/extern/TernarySearchTree/tst_detail/tst_search_results.ipp A /branches/rene/extern/TernarySearchTree/tst_public.doxy adding TernarySearchTree package from Rasmus Ekman needed for FragSim ------------------------------------------------------------------------ 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 Changed paths: M /branches/rene/CGI/tpp_gui/tpp_gui.pl a first Petunia version of FragSim ------------------------------------------------------------------------ r5596 | pcbrefugee | 2011-11-07 10:02:24 -0800 (Mon, 07 Nov 2011) | 1 line Changed paths: M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/Jamroot.jam M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/doc/technical/building.html M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/bcp.jam M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/boost/enum/bitfield.hpp M 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/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 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) 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 Changed paths: M /trunk/trans_proteomic_pipeline/src/mzXML/common/Base64.cpp quiet a "not all control paths return a value" warning ------------------------------------------------------------------------ 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 ------------------------------------------------------------------------
