TPP:4.5.1 SVN Log

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 += Changes since 4.5.0 release =
-= Trunk Check Ins As of 10/24/2011 =+ <nowiki>
 +------------------------------------------------------------------------
 +r5506 | dshteyn | 2011-09-23 11:54:38 -0700 (Fri, 23 Sep 2011) | 1 line
-<nowiki>+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.
-Revision: 5567+------------------------------------------------------------------------
-Author: henryhlam+r5512 | dshteyn | 2011-09-23 16:24:14 -0700 (Fri, 23 Sep 2011) | 1 line
-Date: 10:16:00 PM, Sunday, October 23, 2011+
-Message:+
-[SpectraST] High-mass accuracy MS2 support: frag type of CID-QTOF and HCD. Change to shuffleAllPeaks which is used by PTMProphet+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTConstants.hpp+
-Modified : /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTCreateParams.cpp+
-Modified : /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.cpp+
-Modified : /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.hpp+
-Modified : /trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphet.cxx+
-Revision: 5565+support for Agilent QTOF mzML
-Author: mhoopmann+------------------------------------------------------------------------
-Date: 3:15:24 PM, Friday, October 21, 2011+r5513 | dshteyn | 2011-09-23 17:04:04 -0700 (Fri, 23 Sep 2011) | 1 line
-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 : /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h+
-Modified : /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp+
-Modified : /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzxmlhandler.cpp+
-Revision: 5561+Fix typo
-Author: real_procopio+------------------------------------------------------------------------
-Date: 5:24:09 PM, Thursday, October 20, 2011+r5525 | eng_jk | 2011-10-05 16:42:41 -0700 (Wed, 05 Oct 2011) | 2 lines
-Message:+
-[Petunia] Added version checking upon login; warn users if using an old version of TPP+
-----+
-Modified : /trunk/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl+
-Revision: 5560+quick mod to Patrick's buffer overrun fix (for non-sequential mzML scans); adding to 4.5 branch
-Author: dshteyn+
-Date: 2:56:38 PM, Thursday, October 20, 2011+
-Message:+
-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).+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphet.cxx+
-Modified : /trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphet.h+
-Modified : /trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphetMain.cxx+
-Modified : /trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphetParser.cxx+
-Modified : /trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphetParser.h+
-Revision: 5558+------------------------------------------------------------------------
-Author: henryhlam+r5526 | eng_jk | 2011-10-06 14:14:46 -0700 (Thu, 06 Oct 2011) | 3 lines
-Date: 2:06:59 AM, Thursday, October 20, 2011+
-Message:+
-[SpectraST] New clustering algorithm. Saves memory, prevent deep recursion.+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTMzLibIndex.cpp+
-Modified : /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTSpLibImporter.cpp+
-Modified : /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTSpLibImporter.hpp+
-Revision: 5557+additional cleanup of yesterday's xpress buffer overrun fix; mainly changing size of a few
-Author: henryhlam+allocated arrays which only affects mzML files with with non-sequential native IDs.
-Date: 2:01:34 AM, Thursday, October 20, 2011+
-Message:+
-[SpectraST] Allow import of non-peptide from MSP format+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTMspLibImporter.cpp+
-Revision: 5556+------------------------------------------------------------------------
-Author: henryhlam+r5539 | henryhlam | 2011-10-10 20:08:54 -0700 (Mon, 10 Oct 2011) | 1 line
-Date: 1:59:58 AM, Thursday, October 20, 2011+
-Message:+
-[SpectraST] Consider all charges when library spectrum has charge 0+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTQuery.cpp+
-Revision: 5555+[SpectraST] Fix rare error when S/N calculation failed due to too few peaks outside precursor region (trunk r5501)
-Author: henryhlam+------------------------------------------------------------------------
-Date: 1:52:25 AM, Thursday, October 20, 2011+r5540 | henryhlam | 2011-10-10 20:12:27 -0700 (Mon, 10 Oct 2011) | 1 line
-Message:+
-[SpectraST] Allow users to specify their own m/z range for MRM transitions (Q3)+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTCreateParams.cpp+
-Modified : /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTCreateParams.hpp+
-Modified : /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.cpp+
-Modified : /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.hpp+
-Modified : /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTSpLibImporter.cpp+
-Revision: 5553+[mzParser] Pound-include stdint.h and catch return values for smooth compiling (trunk r5530)
-Author: real_procopio+------------------------------------------------------------------------
-Date: 5:02:11 PM, Wednesday, October 19, 2011+r5541 | henryhlam | 2011-10-10 20:15:16 -0700 (Mon, 10 Oct 2011) | 1 line
-Message:+
-[dta2mzxml] Change 'plustwo' option to include lowest charge state found for a given scan; also make sure output is real mzXML+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/mzXML/converters/dta2mzxml/Dta2mzXML.cpp+
-Modified : /trunk/trans_proteomic_pipeline/src/mzXML/converters/dta2mzxml/Dta2mzXML.h+
-Modified : /trunk/trans_proteomic_pipeline/src/mzXML/converters/dta2mzxml/main.cpp+
-Revision: 5552+[util] Catch return values for smooth compiling (trunk r5532)
-Author: eng_jk+------------------------------------------------------------------------
-Date: 12:59:35 PM, Tuesday, October 18, 2011+r5542 | henryhlam | 2011-10-10 20:18:11 -0700 (Mon, 10 Oct 2011) | 1 line
-Message:+
-replicate branch 5551 checkin to trunk for xpress/mzML fix+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideUpdateParser/XPressPeptideUpdateParserMain.cxx+
-Modified : /trunk/trans_proteomic_pipeline/src/common/util.cxx+
-Revision: 5548+[Tandem2XML] Fix wrong enzyme specificity for Lys-C (trunk r5533)
-Author: slagelwa+------------------------------------------------------------------------
-Date: 3:22:56 PM, Friday, October 14, 2011+r5543 | henryhlam | 2011-10-10 20:23:42 -0700 (Mon, 10 Oct 2011) | 1 line
-Message:+
-* 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+
-----+
-Modified : /trunk/trans_proteomic_pipeline/extern/hpctools/grid/templates/sequest.params+
-Modified : /trunk/trans_proteomic_pipeline/extern/hpctools/grid/templates/tandem.params+
-Revision: 5538+Move RefreshParser ahead of PeptideProphet to safeguard against some search engines' mangling the protein names and/or omitting NTT/NMC (trunk r5534)
-Author: henryhlam+------------------------------------------------------------------------
-Date: 12:43:02 AM, Monday, October 10, 2011+r5544 | henryhlam | 2011-10-10 20:25:26 -0700 (Mon, 10 Oct 2011) | 1 line
-Message:+
-[Enzyme] Equate tryptic with trypsin+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Enzyme/ProteolyticEnzyme/ProteolyticEnzyme.cxx+
-Revision: 5537+[InteractParser] Fix OMSSA's problem with n-term mods (trunk r5535)
-Author: henryhlam+------------------------------------------------------------------------
-Date: 12:35:35 AM, Monday, October 10, 2011+r5545 | henryhlam | 2011-10-10 20:27:17 -0700 (Mon, 10 Oct 2011) | 1 line
-Message:+
-[PeptideProphet] More finely divided bins for error rate estimates. Important for modern, large datasets.+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Validation/MixtureModel/MixtureModel.cxx+
-Revision: 5536+[Enzyme] Equate tryptic with trypsin (trunk r5538)
-Author: henryhlam+------------------------------------------------------------------------
-Date: 12:32:35 AM, Monday, October 10, 2011+r5546 | henryhlam | 2011-10-10 20:30:09 -0700 (Mon, 10 Oct 2011) | 1 line
-Message:+
-[InterProphet] More finely divided bins for error rate estimates. Important for modern, large datasets.+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/InterProphet.cxx+
-Revision: 5535+[InterProphet] More finely divided bins for error rate estimates. Important for modern, large datasets. (trunk r5536)
-Author: henryhlam+------------------------------------------------------------------------
-Date: 12:19:18 AM, Monday, October 10, 2011+r5547 | henryhlam | 2011-10-10 22:48:06 -0700 (Mon, 10 Oct 2011) | 1 line
-Message:+
-[InteractParser] Fix OMSSA's problem with n-term mods+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx+
-Revision: 5534+[PeptideProphet] More finely divided bins for error rate estimates. Important for modern, large datasets. (trunk r5537)
-Author: henryhlam+------------------------------------------------------------------------
-Date: 12:12:16 AM, Monday, October 10, 2011+r5549 | slagelwa | 2011-10-17 14:31:27 -0700 (Mon, 17 Oct 2011) | 1 line
-Message:+
-[xinteract] Move RefreshParser ahead of PeptideProphet to safeguard against some search engines' mangling the protein names and/or omitting NTT/NMC+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Visualization/xinteract/xinteract.cxx+
-Revision: 5533+Increased size of buffer for holding fasta header lines as per recommendation by David Trudgian.
-Author: henryhlam+------------------------------------------------------------------------
-Date: 12:02:43 AM, Monday, October 10, 2011+r5550 | slagelwa | 2011-10-17 14:41:42 -0700 (Mon, 17 Oct 2011) | 1 line
-Message:+
-[Tandem2XML] Fix wrong enzyme specificity for Lys-C+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Tandem2XML/TandemParamsParser.cxx+
-Revision: 5532+Cut&paste in cygwin inserted newline
-Author: henryhlam+------------------------------------------------------------------------
-Date: 11:59:27 PM, Sunday, October 09, 2011+r5551 | eng_jk | 2011-10-18 12:14:31 -0700 (Tue, 18 Oct 2011) | 4 lines
-Message:+
-[util] Catch return values for smooth compiling+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/util/calculate_pi.cpp+
-Revision: 5531+Fix for mzML files when viewing xpress chromatograms through the ProteinProphet to XPressCGIProteinDisplayParser.cgi binary.
-Author: henryhlam+No notion of file extensions exist in that path and mzXML files were always assumed. This fix simply has the cgi try mzML
-Date: 11:57:02 PM, Sunday, October 09, 2011+file extension if the mzXML file is not found.
-Message:+
-[MzXML2Search] Option to remove charge-reduced precursors for ETD spectra (useful for search engines that do not have that feature)+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Parsers/MzXML2Search/MzXML2Search.cxx+
-Revision: 5530+------------------------------------------------------------------------
-Author: henryhlam+r5554 | henryhlam | 2011-10-20 01:36:19 -0700 (Thu, 20 Oct 2011) | 1 line
-Date: 10:03:18 PM, Sunday, October 09, 2011+
-Message:+
-[mzParser] Pound-include stdint.h and catch return values for smooth compiling+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h+
-Modified : /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp+
-Modified : /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzxmlhandler.cpp+
-Revision: 5529+[SpectraST] Allow users to specify their own m/z range for MRM transitions (Q3)
-Author: henryhlam+------------------------------------------------------------------------
-Date: 10:00:49 PM, Sunday, October 09, 2011+r5559 | real_procopio | 2011-10-20 12:20:06 -0700 (Thu, 20 Oct 2011) | 1 line
-Message:+
-[util] Catch return values for smooth compiling+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/util/pep_dbcount.cpp+
-Modified : /trunk/trans_proteomic_pipeline/src/util/translateDNA2AA-FASTA.cpp+
-Revision: 5528+merging trunk changes from rev 5553
-Author: eng_jk+------------------------------------------------------------------------
-Date: 2:18:53 PM, Thursday, October 06, 2011+r5562 | real_procopio | 2011-10-20 17:27:40 -0700 (Thu, 20 Oct 2011) | 1 line
-Message:+
-change deflines to include which reading frame as part of accession+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/util/translateDNA2AA-FASTA.cpp+
-Revision: 5527+[Petunia] merging rev 5561 from trunk
-Author: eng_jk+------------------------------------------------------------------------
-Date: 2:16:52 PM, Thursday, October 06, 2011+r5563 | real_procopio | 2011-10-21 13:40:59 -0700 (Fri, 21 Oct 2011) | 1 line
-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 : /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx+
-Modified : /trunk/trans_proteomic_pipeline/src/common/constants.h+
-Revision: 5524+[Petunia] Added support for Bruker .yep and .baf files, as well as mzXML output to msconvert; Expanded Libra normalization channel option to 8
-Author: eng_jk+------------------------------------------------------------------------
-Date: 4:36:44 PM, Wednesday, October 05, 2011+r5564 | mhoopmann | 2011-10-21 15:10:06 -0700 (Fri, 21 Oct 2011) | 1 line
-Message:+
-quick mod to Patrick's buffer overrun fix (for non-sequential mzML scans)+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx+
-Revision: 5523+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.
-Author: ppatrick+------------------------------------------------------------------------
-Date: 2:09:52 PM, Wednesday, October 05, 2011+r5566 | real_procopio | 2011-10-21 16:10:41 -0700 (Fri, 21 Oct 2011) | 1 line
-Message:+
-Added Supplemental Activation+
-Removed 0 intensity peaks+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/mzXML/converters/ReAdW/FilterLine.cpp+
-Modified : /trunk/trans_proteomic_pipeline/src/mzXML/converters/ReAdW/FilterLine.h+
-Modified : /trunk/trans_proteomic_pipeline/src/mzXML/converters/ReAdW/ThermoInterface.cpp+
-Revision: 5522+[Petunia] Decoy models pages should only ask for pep/protXML files as input; minor code clean-up and re-formatting
-Author: ppatrick+------------------------------------------------------------------------
-Date: 5:40:47 AM, Wednesday, October 05, 2011+r5569 | real_procopio | 2011-10-24 18:08:29 -0700 (Mon, 24 Oct 2011) | 7 lines
-Message:+
-Fixed buffer overrun in void XPressPeptideParser::validate_mzXMLfile() +
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx+
-Revision: 5521+[Petunia]
-Author: ppatrick+- Add ability to specify no output file for some commands;
-Date: 5:38:48 AM, Wednesday, October 05, 2011+- Rename files after running the Re-index mzXML tool;
-Message:+- Display file extension being searched for in File Chooser;
-Fixed buffer overruns in void XPressPeptideParser::parse(const char *xmlfile) and void XPressPeptideParser::validate_mzXMLfile()+- Add thead and tbody tags to file list table (for future jscript sorting integration);
-----+- fixed a couple of typos.
-Modified : /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx+
-Revision: 5520+------------------------------------------------------------------------
-Author: ppatrick+r5574 | real_procopio | 2011-10-26 18:48:45 -0700 (Wed, 26 Oct 2011) | 1 line
-Date: 5:35:18 AM, Wednesday, October 05, 2011+
-Message:+
-Initialized preExt to account for incorrect file names being passed.+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp+
-Revision: 5519+[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.
-Author: dshteyn+------------------------------------------------------------------------
-Date: 1:31:11 PM, Tuesday, October 04, 2011+r5580 | slagelwa | 2011-11-02 15:45:23 -0700 (Wed, 02 Nov 2011) | 3 lines
-Message:+
-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)+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Parsers/RefreshParser/RefreshParser.cxx+
-Modified : /trunk/trans_proteomic_pipeline/src/Parsers/RefreshParser/RefreshParserMain.cxx+
-Revision: 5518+Fixed a issue with uploading files on windows resulting in 0 byte files
-Author: ppatrick+
-Date: 12:29:44 PM, Tuesday, October 04, 2011+
-Message:+
-increased min peptide probability to 0.8 from 0.5+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressProteinRatioParser/XPressProteinRatioParser.cxx+
-Revision: 5517 
-Author: ppatrick 
-Date: 12:28:23 PM, Tuesday, October 04, 2011 
-Message: 
-Changed logic of xsl to speed up loading. 
----- 
-Modified : /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressCGIProteinDisplayParser/XPressCGIProteinDisplay.cxx 
-Revision: 5516+------------------------------------------------------------------------
-Author: ppatrick+r5604 | real_procopio | 2011-11-07 16:47:03 -0800 (Mon, 07 Nov 2011) | 9 lines
-Date: 8:57:14 AM, Tuesday, October 04, 2011+
-Message:+
-Changed from theoretical precursor mass to measured one to allow for narrower tolerances.+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx+
-Revision: 5515+[Petunia]
-Author: slagelwa+- New dynamic filtering box on file browser and chooser, with smart "select
-Date: 11:58:33 AM, Thursday, September 29, 2011+ all" checkbox
-Message:+- Streamlined file operations form buttons (Delete, Copy, Paste, etc)
-* now removes the log files before submission+- Do not show Clipboard div if empty
-* uses new conversion queues+- Allow users to specify data dirs with leading uppercase (e.g. C:\blah\)
-* no longer allows submissions with the --server flag and instead+- Took out 'tilde' hack for XPRESS
- uses queues+- Now using -nosticky pragma in perl CGI
-----+------------------------------------------------------------------------
-Modified : /trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qconvert+r5605 | real_procopio | 2011-11-07 16:53:48 -0800 (Mon, 07 Nov 2011) | 1 line
-Revision: 5514+New dir to store javascript files
-Author: dshteyn+------------------------------------------------------------------------
-Date: 5:04:33 PM, Friday, September 23, 2011+r5606 | real_procopio | 2011-11-07 17:02:54 -0800 (Mon, 07 Nov 2011) | 1 line
-Message:+
-Fix typo+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp+
-Revision: 5511+New Table sorting Javasript utility
-Author: dshteyn+------------------------------------------------------------------------
-Date: 4:20:07 PM, Friday, September 23, 2011+r5607 | slagelwa | 2011-11-07 22:01:50 -0800 (Mon, 07 Nov 2011) | 2 lines
-Message:+
-Adding back support for Agilent QTOF mzML+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp+
-Revision: 5510+Merged all of David's changes on trunk since the 4.5 release into 4.5 branch
-Author: slagelwa+
-Date: 3:28:18 PM, Friday, September 23, 2011+
-Message:+
-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)+------------------------------------------------------------------------
 +r5608 | slagelwa | 2011-11-08 10:23:57 -0800 (Tue, 08 Nov 2011) | 1 line
-----+4.5.1
-Modified : /trunk/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl+------------------------------------------------------------------------
-Modified : /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp+r5623 | real_procopio | 2011-11-09 17:45:53 -0800 (Wed, 09 Nov 2011) | 1 line
-Revision: 5509+[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
-Author: dshteyn+------------------------------------------------------------------------
-Date: 3:04:39 PM, Friday, September 23, 2011+r5624 | slagelwa | 2011-11-10 11:40:32 -0800 (Thu, 10 Nov 2011) | 3 lines
-Message:+
-PTMProphet: adding getVal functions for KDModel.+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/KDModel.cxx+
-Modified : /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/KDModel.h+
-Revision: 5508+Checking in David's changes on the trunk since revision 4605
-Author: dshteyn+
-Date: 2:36:13 PM, Friday, September 23, 2011+
-Message:+
-SpectraSTLIB: adding randomization of spectrum function for PTMProphet.+
-----+
-Modified : /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLibImporter.cpp+
-Modified : /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.cpp+
-Modified : /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.hpp+
-</nowiki>+
-= Branch Check Ins As of 10/24/2011 = 
-<nowiki>Revision: 5566+------------------------------------------------------------------------
-Author: real_procopio+r5632 | slagelwa | 2011-11-14 11:11:38 -0800 (Mon, 14 Nov 2011) | 4 lines
-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+Merging David's latest round of checkins on trunk with the assumption
-Author: mhoopmann+they belong here too.
-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+r5634 | slagelwa | 2011-11-14 15:59:32 -0800 (Mon, 14 Nov 2011) | 3 lines
-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+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.
-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+r5642 | slagelwa | 2011-11-16 15:09:33 -0800 (Wed, 16 Nov 2011) | 2 lines
-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+Fixing ARCH to be ARCH_FAMILY so XFORMS does the correct regex subsitution.
-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+r5644 | slagelwa | 2011-11-21 14:05:30 -0800 (Mon, 21 Nov 2011) | 2 lines
-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+Correcting issue with propertly setting up perl libpath to file perllib
-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>

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

------------------------------------------------------------------------
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