TPP:4.5.0 Release Notes

From SPCTools

Revision as of 21:35, 16 September 2011; view current revision
←Older revision | Newer revision→

Draft wiki page for the upcoming 4.5.0 release intended only for TPP developers.

Trans-Proteomic Pipeline (TPP) "Rapture" 4.5.0 Release Notes

Trans-Proteomic Pipeline (TPP) software, release 4.5.0 is a minor release containing new features, new programs, and addresses a number of issues found with 4.4.1. The software is available for Windows as well as Linux (and unofficially) through OSX source from all the usual locations (please see the section below, "Getting the software"). Most users are recommended to use the Windows installer, which installs and configures the TPP and other required software (such as a webserver). For advanced users who need to customize the TPP, or for those who run high-throughput experiments, you can download the source code. Again, most users don't need build from source, and should use the Windows installer.

Previous release notes are available at TPP:4.4.1_Release_Notes

1 New Features/Changes
2 Bug fixes and improvements
3 Miscellaneous
4 Known Issues
5 Getting the TPP Software
6 SVN Log

New Features/Changes

Bug fixes and improvements

Miscellaneous

Known Issues

None to report

Getting the TPP Software

Download the TPP version 4.5.0 native windows installer (TPP_Setup_v4_5_RAPTURE_rev_1.exe) from the Sashimi SourceForge project file release page:

 "http://sourceforge.net/projects/sashimi/files/"

Everyone is encouraged to read and contribute to our wiki, at

 "http://tools.proteomecenter.org/wiki/"

For guides to installing and using our software, please see our wiki:

 "http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP"

For downloading the source code, please go to the following link:

 "http://sourceforge.net/projects/sashimi/files/" and find the 4.4.1 source code .zip package;

or, check out the code directly from svn:

 "svn co http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-4-1"

 For building from source, please refer to the readme file in TPP/src as well as the wiki.

The TPP Team: Luis, David, Mike, Brian, Natalie, and Joe plus all other developers who contributed to this release from the ISB. Thanks to developers and users from the TPP's user community who provided feedback and code contributions.

SVN Log

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r5502 | dshteyn | 2011-09-02 02:03:18 -0700 (Fri, 02 Sep 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXIndexFile.cxx

PepXMLViewer.cgi:  Update index version
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r5501 | henryhlam | 2011-09-01 05:43:09 -0700 (Thu, 01 Sep 2011) | 1 line
Changed paths:
   M /trunk/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
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r5500 | slagelwa | 2011-08-27 08:56:04 -0700 (Sat, 27 Aug 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/common/TPPVersion.h

RC9
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r5499 | dshteyn | 2011-08-26 11:14:03 -0700 (Fri, 26 Aug 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXOptions.cxx

PepXMLViewer.cgi: Fix bug on commandline generated index which didn't print the queryString so we fake one.
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r5498 | slagelwa | 2011-08-26 08:31:55 -0700 (Fri, 26 Aug 2011) | 2 lines
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/common/TPPVersion.h

bumping the RC version

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r5497 | dshteyn | 2011-08-26 00:05:58 -0700 (Fri, 26 Aug 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXFilter.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXFilter.h
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXOptions.cxx

PepXMLViewer.cgi - serialization implemented
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r5496 | dshteyn | 2011-08-25 17:11:16 -0700 (Thu, 25 Aug 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXField.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXField.h
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXFilter.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXFilter.h
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXIndexFile.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXIndexFile.h
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXOptions.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXOptions.h
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXUtility.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXUtility.h

PepXMLViewer.cgi -  this tool had problems with boost lexical casts and serialization, replaced these with more generic functions that are easier to debug and work now.
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r5495 | slagelwa | 2011-08-25 13:01:55 -0700 (Thu, 25 Aug 2011) | 26 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/MANIFEST
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/Makefile.PL
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amztppd (from /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amztppserver:5481)
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amztppd.conf
   D /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amztppserver
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Client.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Credentials.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/EC2Manager.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/S3Manager.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/SearchService.pm

* Changed name of amztppserver to the more standard amztppd
* Changed to use the upstart init daemon on Ubuntu to start (and keep
  respawning) the amztpp daemon
* Now checkst to make sure that when getting the # running instances that
  if the EC2 API returns something other than a list it doesn't crash
* Changed/added error message if a file to be uploaded doesn't actually
  exist
* Changed timeout on nodes to 10 minutes to equal the same timeout on
  the client (and reduce the opportunity of nodes running longer than
  needed)
* Fixed/changed the algorithm for deciding to start more nodes.  Now
  starts nodes if pending > running & pending > started
* Message handles for services being executed are now written to the file
  system and removed after the service is completed.  This is done to
  so that if  the daemon unexpectly quits and is restarted the message isn't
  ignored for the timeout but instead is just removed.
* uses checksum of file instead of checksum of gzipped file.  (Didn't know
  that the same file contents in two different files results in different
  gzipped checksums.)
* Shutdown only on exit now, always make sure srv message is deleted in
  case it is interrupted by an exit or signal, and always put the file
  to S3.
* New "-s" option for tppamzd to control whether or not to shutdown on
  exit


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r5494 | real_procopio | 2011-08-24 17:59:51 -0700 (Wed, 24 Aug 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms2.cxx

[lorikeet] Make this works under Windows, for now...
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r5493 | dshteyn | 2011-08-23 15:11:41 -0700 (Tue, 23 Aug 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXParser.cxx

PepXMLViewer.cgi: fix crash when empty filtered set is returned.
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r5492 | slagelwa | 2011-08-22 15:37:17 -0700 (Mon, 22 Aug 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/SearchResult/MyrimatchResult.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/SearchResult/MyrimatchResult.h

Merged David's trunk fixes for PeptideProphetParser: update to correct problem with latest version of Myrimatch which removed some scores in the reports.
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r5491 | dshteyn | 2011-08-19 14:04:18 -0700 (Fri, 19 Aug 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp

mzParser:  Handling of highMZ lowMZ values for Agilent QTOF.
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r5490 | dshteyn | 2011-08-17 15:55:23 -0700 (Wed, 17 Aug 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/SearchResult/MyrimatchResult.cxx
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/SearchResult/MyrimatchResult.h

PeptideProphetParser: update to correct problem with latest version of Myrimatch which removed some scores in the reports.
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r5489 | slagelwa | 2011-08-17 12:17:09 -0700 (Wed, 17 Aug 2011) | 7 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amztpp
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Client.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/InspectService.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/MyrimatchService.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/OMSSAService.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/SearchService.pm

* Make sure relative filenames in databases are treated correctly. 
* Changed algorithm on when new instances are started.  Now starts
  a new instance when the # running < # max and # pending > # running. Which
  might spawn extra instances due to eventual consistancy but shouldn't spawn
  more than can be processed. 
  

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r5488 | slagelwa | 2011-08-17 09:57:57 -0700 (Wed, 17 Aug 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/common/TPPVersion.h

Going for RC7 (and what I hope is a *real* release candidate)
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r5487 | slagelwa | 2011-08-16 16:58:47 -0700 (Tue, 16 Aug 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXIndexFile.cxx

Revert back to using <int> instead of <long long> for the column maps and indexes 
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r5486 | slagelwa | 2011-08-15 15:29:58 -0700 (Mon, 15 Aug 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Makefile

Fixed pwiz fetching (needed to do it in BINMODE for windows)
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r5485 | slagelwa | 2011-08-15 14:30:29 -0700 (Mon, 15 Aug 2011) | 2 lines
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/installer_win32/TPP_installer.nsi
   M /branches/4-5/trans_proteomic_pipeline/src/Makefile
   M /branches/4-5/trans_proteomic_pipeline/src/common/TPPVersion.h

Last changes to installer that needed checked in

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r5484 | eng_jk | 2011-08-11 11:36:24 -0700 (Thu, 11 Aug 2011) | 3 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/util/subsetdb1.cpp

Add -e option to subsetdb for Andreas to allow for export of entries that do not match -N strings.
Previously, the -N no-match strings only filtered out matches that passed the -M match strings.

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r5483 | real_procopio | 2011-08-10 16:37:13 -0700 (Wed, 10 Aug 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl

Added IPROPHET option to ProteinProphet; fixed bug that FileChooser to fail when pressing 'Enter' to switch directory; minor formatting fix to PepC page
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r5482 | slagelwa | 2011-08-10 14:28:37 -0700 (Wed, 10 Aug 2011) | 2 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amztpp

setting missing svn keywords property

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r5481 | slagelwa | 2011-08-10 14:21:37 -0700 (Wed, 10 Aug 2011) | 2 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS.pm

fixing revision tag

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r5480 | slagelwa | 2011-08-10 14:15:57 -0700 (Wed, 10 Aug 2011) | 11 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amztpp
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amztppserver
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Client.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/EC2Manager.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/OMSSAService.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Report.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/SQSManager.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/SearchService.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS.pm

Significant changes across the board that haven't been checked in.

* Include EC2 name in working directory on instance to distinguish it
* Fixed omssa path/files issues
* Changed how polling of SQS message queues are tallied
* Forking of upload/downloads
* Fixed paths issue in pep.xml files
* Cache directory changes



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r5479 | real_procopio | 2011-08-08 12:35:03 -0700 (Mon, 08 Aug 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl

[petunia] Make Tandem the default pipeline; added option to run Tandem2XML immediately after searching
------------------------------------------------------------------------
r5478 | slagelwa | 2011-08-03 14:39:30 -0700 (Wed, 03 Aug 2011) | 8 lines
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/installer_win32/TPP_files.nsh
   M /branches/4-5/trans_proteomic_pipeline/installer_win32/TPP_installer.nsi
   M /branches/4-5/trans_proteomic_pipeline/installer_win32/TPP_proteowizard.nsh
   M /branches/4-5/trans_proteomic_pipeline/installer_win32/checkPerl.nsh
   D /branches/4-5/trans_proteomic_pipeline/installer_win32/tpp_perlVersionCheck.bat

* Fixed proteowizard files (now that I understand how the macro works)
* Fixed issue with perl version test.  Problem was that it was running
  a bat script that might or might not be there.  So I simplified it by
  instead just running perl -M5.8.8 which tests the version using perl's
  built in "use version" feature.  Gets rid of the hairy "perl | perl" in
  the bat script.
* Check perl version, apache, in the requirements function prior to
  installing
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r5477 | slagelwa | 2011-08-02 15:09:43 -0700 (Tue, 02 Aug 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/installer_win32/TPP_installer.nsi
   A /branches/4-5/trans_proteomic_pipeline/installer_win32/TPP_proteowizard.nsh

Moved msconvert/pwiz files to its own file.  Updated the list of dlls based on feedback from pwiz folks
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r5476 | slagelwa | 2011-08-02 15:07:19 -0700 (Tue, 02 Aug 2011) | 3 lines
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Makefile

* added exporTPP.pl (well, maybe)
* to make it easier for builts, there now is a target that will download pwiz for you.  It gets downloaded 
  into winpwiz, so that it can be used to build the windows installer
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r5475 | real_procopio | 2011-08-02 12:24:25 -0700 (Tue, 02 Aug 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl

[Petunia] Henry's SpectraST changes: took out obsolete user options; added decoy-related options and Append To Library feature
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r5474 | slagelwa | 2011-08-02 11:21:42 -0700 (Tue, 02 Aug 2011) | 2 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/grid/Makefile

* fixed params/ templates confusion

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r5473 | slagelwa | 2011-08-02 11:18:35 -0700 (Tue, 02 Aug 2011) | 4 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/grid/Makefile
   M /trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qsequest
   M /trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qtandem
   D /trunk/trans_proteomic_pipeline/extern/hpctools/grid/params
   A /trunk/trans_proteomic_pipeline/extern/hpctools/grid/templates/mascot.params (from /trunk/trans_proteomic_pipeline/extern/hpctools/grid/params/mascot.params:5472)
   A /trunk/trans_proteomic_pipeline/extern/hpctools/grid/templates/sequest.params (from /trunk/trans_proteomic_pipeline/extern/hpctools/grid/params/sequest.params:5472)

* Cleaned up duplicate params/ templates/ directories
* Updated qtandem to handle .gz files
 

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r5472 | henryhlam | 2011-08-02 00:31:34 -0700 (Tue, 02 Aug 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/Peptide.cpp

[SpectraST] Synch with trunk r5471 - Decoy: add two random AA plus K/R
------------------------------------------------------------------------
r5471 | henryhlam | 2011-08-02 00:28:42 -0700 (Tue, 02 Aug 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/Peptide.cpp

[SpectraST] Decoy: add two random AA plus K/R
------------------------------------------------------------------------
r5470 | henryhlam | 2011-08-02 00:22:30 -0700 (Tue, 02 Aug 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/Peptide.cpp
   M /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/Peptide.hpp
   M /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTSpLibImporter.cpp

[SpectraST] Synch with trunk r5469: Reduce chance of decoy hitting existing sequence; rand() out-of-bound fix for Windows
------------------------------------------------------------------------
r5469 | henryhlam | 2011-08-02 00:14:52 -0700 (Tue, 02 Aug 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/Peptide.cpp

[SpectraST] rand() out-of-bound fix for Windows
------------------------------------------------------------------------
r5468 | henryhlam | 2011-08-01 23:34:01 -0700 (Mon, 01 Aug 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/Peptide.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/Peptide.hpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTSpLibImporter.cpp

[SpectraST] Reduce chance of decoy hitting existing sequences leading to infinite-looping
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r5467 | slagelwa | 2011-08-01 10:54:47 -0700 (Mon, 01 Aug 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/perl_paths/perl_paths.inc

Adding exporTPP.pl
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r5466 | mhoopmann | 2011-07-29 16:33:47 -0700 (Fri, 29 Jul 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h

Updates to make mingw happy... or at least happy about TPP
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r5465 | mhoopmann | 2011-07-29 13:18:51 -0700 (Fri, 29 Jul 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Makefile

updated for mzParser changes
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r5464 | mhoopmann | 2011-07-29 13:01:13 -0700 (Fri, 29 Jul 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/Makefile

updating Makefile
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r5463 | mhoopmann | 2011-07-29 12:51:21 -0700 (Fri, 29 Jul 2011) | 1 line
Changed paths:
   A /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/Czran.cpp
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxhandler.cpp
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzxmlhandler.cpp
   D /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/zran.cpp

Wrapped zran into convenient object, improved buffering.
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r5462 | mhoopmann | 2011-07-28 09:28:27 -0700 (Thu, 28 Jul 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxhandler.cpp
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/zran.cpp

Added newlines at the ends of the files for quiet compilation.
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r5461 | mhoopmann | 2011-07-27 16:49:18 -0700 (Wed, 27 Jul 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/saxhandler.cpp
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/zran.cpp

Added buffer to random access gz parser
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r5460 | real_procopio | 2011-07-26 16:39:43 -0700 (Tue, 26 Jul 2011) | 6 lines
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/CGI/prot_wt_xml.pl

Fixed page format to fit page width, got rid of wasted space;
Minor HTML tweaks;
Added svn rev;
Code clean-up: took out unused code, re-tabbed/formatted.


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r5459 | henryhlam | 2011-07-21 18:13:32 -0700 (Thu, 21 Jul 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTCreateParams.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLibImporter.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTMzXMLLibImporter.cpp

[SpectraST] Treat sptxt as msp for import (after ensuring no file overwrite); minor fixes
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r5458 | henryhlam | 2011-07-21 18:10:37 -0700 (Thu, 21 Jul 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/SpectraSTLib.cpp
   M /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLibEntry.cpp
   M /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLibEntry.hpp
   M /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLibImporter.cpp
   M /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTMzXMLLibImporter.cpp
   M /branches/4-5/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.cpp

[SpectraST] Update to trunk r5457, including latest change of using theoretical mass for MRM
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r5457 | henryhlam | 2011-07-21 18:00:30 -0700 (Thu, 21 Jul 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLib.cpp

[SpectraST] Use theoretical mass in MRM tables -- missing change in last check-in
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r5456 | mhoopmann | 2011-07-19 13:58:13 -0700 (Tue, 19 Jul 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/saxhandler.cpp
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzxmlhandler.cpp
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/zran.cpp

Updated declarations and function names to give seek/tell function macros uniqueness in mzParser.
------------------------------------------------------------------------
r5455 | mhoopmann | 2011-07-15 16:07:01 -0700 (Fri, 15 Jul 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/saxhandler.cpp

renamed SAXHandler class to mzpSAXHandler to prevent conflicts with SAXHandler in PepXMLViewer
------------------------------------------------------------------------
r5454 | mhoopmann | 2011-07-15 11:41:34 -0700 (Fri, 15 Jul 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatioPeptideParser/ASAPRatioPeptideParser.cxx

trying again
------------------------------------------------------------------------
r5453 | mhoopmann | 2011-07-15 10:45:30 -0700 (Fri, 15 Jul 2011) | 1 line
Changed paths:
   A /branches/4-5/trans_proteomic_pipeline/extern/ra_gzstream
   A /branches/4-5/trans_proteomic_pipeline/extern/ra_gzstream/random_access_compressed_ifstream.cpp
   A /branches/4-5/trans_proteomic_pipeline/extern/ra_gzstream/random_access_compressed_ifstream.hpp

Broke this out of pwiz for convenient testing/use. Many TPP tools need random access gz parsing without using any actual pwiz structures or functions.
------------------------------------------------------------------------
r5452 | mhoopmann | 2011-07-15 09:45:41 -0700 (Fri, 15 Jul 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatioPeptideParser/ASAPRatioPeptideParser.cxx

Got a little carried away. Put the correct header back.
------------------------------------------------------------------------
r5451 | henryhlam | 2011-07-14 19:40:43 -0700 (Thu, 14 Jul 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLib.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLibEntry.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLibEntry.hpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.cpp

[SpectraST] MRM table prints theoretical (not observed), accurate (to 4 decimal places) mass for Q3
------------------------------------------------------------------------
r5450 | mhoopmann | 2011-07-14 16:23:01 -0700 (Thu, 14 Jul 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Quantitation/Libra/LibraPeptideParser/LibraPeptideParser.cxx

Fixed case where cygwin path was interfering with guessing file type. Now replicates original behavior (prior to mzParser) of assuming mzXML when file cannot be found because of cygpath
------------------------------------------------------------------------
r5449 | mhoopmann | 2011-07-14 14:57:16 -0700 (Thu, 14 Jul 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Comet2XML/Comet2xml.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Mascot2XML/MascotConverter.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Mascot2XML/MascotConverter.h
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/SearchResult/ProDataComponent.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sequest2XML/CombineOut.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sequest2XML/CombineOut.h
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sequest2XML/Out2XML.h
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sequest2XML/Sequest2XML.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Tandem2XML/TandemResultsParser.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Tandem2XML/TandemResultsParser.h
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/MzXML2Search/MzXML2Search.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/Parser/TagListComparator.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPCGIDisplay/ASAPRatioProteinCGIDisplayParser.h
   M /branches/4-5/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatioPeptideParser/ASAPRatioPeptideParser.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatioPeptideParser/ASAPRatioPeptideParser.h
   M /branches/4-5/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatioProteinRatioParser/ASAPRatioGroupPeptideParser.h
   M /branches/4-5/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_pepFns.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_pepFns.h
   M /branches/4-5/trans_proteomic_pipeline/src/Quantitation/Libra/LibraPeptideParser/LibraConditionHandler.cpp
   M /branches/4-5/trans_proteomic_pipeline/src/Quantitation/Option.h
   M /branches/4-5/trans_proteomic_pipeline/src/Quantitation/Q3/Q3ProteinRatioParser/Q3GroupPeptideParser.h
   M /branches/4-5/trans_proteomic_pipeline/src/Quantitation/XPress/XPressGroupPeptideParser.h
   M /branches/4-5/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.h
   M /branches/4-5/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideUpdateParser/XPressPeptideUpdateParserMain.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms2.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/Pep3D/BasenameParser.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/Pep3D/Pep3DParser.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/Pep3D/Pep3D_functions.h
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/Pep3D/cgi_Pep3D_xml/cgi_Pep3D_xml.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/Pep3D/cgi_getCidData.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXField.cxx
   M /branches/4-5/trans_proteomic_pipeline/src/mzXML/tools/readmzXML/readmzXML.cpp
   M /branches/4-5/trans_proteomic_pipeline/src/util/dta-xml.cpp
   M /branches/4-5/trans_proteomic_pipeline/src/util/getSpectrum.cpp
   M /branches/4-5/trans_proteomic_pipeline/src/util/mzxml2dta1.cpp
   M /branches/4-5/trans_proteomic_pipeline/src/util/runsearch1.cpp

Verifying and fixing any ramp->mzParser headers.
------------------------------------------------------------------------
r5448 | pcbrefugee | 2011-07-13 17:48:06 -0700 (Wed, 13 Jul 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl

[pentunia] added a link on the PepC page to the PepC paper, which is now on PubMed
------------------------------------------------------------------------
r5447 | pcbrefugee | 2011-07-13 17:38:50 -0700 (Wed, 13 Jul 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl

[pentunia] added a link on the PepC page to the PepC paper, which is now on PubMed
------------------------------------------------------------------------
r5446 | slagelwa | 2011-07-13 15:05:09 -0700 (Wed, 13 Jul 2011) | 2 lines
Changed paths:
   A /trunk/trans_proteomic_pipeline/extern/hpctools/ec2
   A /trunk/trans_proteomic_pipeline/extern/hpctools/ec2/bundle_ec2_image.sh
   A /trunk/trans_proteomic_pipeline/extern/hpctools/ec2/launch_ec2_image.sh
   A /trunk/trans_proteomic_pipeline/extern/hpctools/ec2/publish_ec2_image.sh
   A /trunk/trans_proteomic_pipeline/extern/hpctools/ec2/setup_ec2_image.sh

Finally checking in the new EC2 AMI scripts

------------------------------------------------------------------------
r5445 | mhoopmann | 2011-07-13 13:22:46 -0700 (Wed, 13 Jul 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp

Fix intermittent extension tokenizer bug.
------------------------------------------------------------------------
r5444 | mhoopmann | 2011-07-13 13:05:33 -0700 (Wed, 13 Jul 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/tpp_hostname/tpp_hostname.cpp

pointing header to mzParser instead of ramp
------------------------------------------------------------------------
r5443 | mhoopmann | 2011-07-12 15:47:49 -0700 (Tue, 12 Jul 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp

Silencing error messages for a blissfully ignorant world of data analysis.
------------------------------------------------------------------------
r5442 | mhoopmann | 2011-07-12 15:00:17 -0700 (Tue, 12 Jul 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp

fixed rampValidFileType to process extensionless files.
------------------------------------------------------------------------
r5441 | mhoopmann | 2011-07-07 14:09:53 -0700 (Thu, 07 Jul 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp

Changed rampValidFileType to stop complaining when .mz(X)ML.gz files are used.
------------------------------------------------------------------------
r5440 | mhoopmann | 2011-06-30 10:30:57 -0700 (Thu, 30 Jun 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/BasicSpectrum.cpp
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h
   M /branches/4-5/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp

Activated the code for referencableParamGroup tracking. Added parameters for storing spectrum polarity and profile status. Note, these values are/were not considered in RAMP, so are not identified through the RAMP wrapper.
------------------------------------------------------------------------
r5439 | slagelwa | 2011-06-29 21:00:45 -0700 (Wed, 29 Jun 2011) | 28 lines
Changed paths:
   A /branches/4-5/trans_proteomic_pipeline/installer_win32/CheckApacheServer.nsh
   A /branches/4-5/trans_proteomic_pipeline/installer_win32/CheckIISServer.nsh
   D /branches/4-5/trans_proteomic_pipeline/installer_win32/CheckWebServer.nsh
   M /branches/4-5/trans_proteomic_pipeline/installer_win32/TPP_files.nsh
   M /branches/4-5/trans_proteomic_pipeline/installer_win32/TPP_installer.nsi
   M /branches/4-5/trans_proteomic_pipeline/installer_win32/checkPerl.nsh

Refactored the installer.  The most significant change is that there is now
a components section in the installer, and msconvert is one of the components
that can be selected/deselected.  This is all due to the new click thru
licensing needed to install msconvert with the vendor libraries.

Other changes include:

* The old help dialog is now a installer page that users see prior to
the components page

* Apache/IIS checks are done when leaving the component page

* msconvert license acceptance check when leaving the component page
and msconvert selected

* Apache and IIS are also components on the component page.  With a 
little crude nsis scripting the selection boxes are exclusive.

* Dialog is presented with IIS choosen that really makes sure they
want to do this before its installed.  If IIS is not installed they
have the choice to keep going.

* The perl check is done at the beginning of the TPP installation 
instead of the end.  Seems to make sense to check for this before
installing a bunch of files.



------------------------------------------------------------------------
r5438 | slagelwa | 2011-06-29 20:52:01 -0700 (Wed, 29 Jun 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/common/TPPVersion.h

Updating the version to RC #2
------------------------------------------------------------------------
r5437 | real_procopio | 2011-06-20 18:23:15 -0700 (Mon, 20 Jun 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl

[Petunia] Pass correct centroiding filter to msconvert; allow msconvert to convert wiff files, .d and .raw directories to mzML
------------------------------------------------------------------------
r5436 | real_procopio | 2011-06-17 11:44:08 -0700 (Fri, 17 Jun 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/installer_win32/TPP_files.nsh

[exporTPP] New TPP experiment export tool
------------------------------------------------------------------------
r5435 | real_procopio | 2011-06-17 11:30:41 -0700 (Fri, 17 Jun 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/Comet/comet-fastadb/comet-fastadb1.cxx

[exporTPP] Adding html comments for easier scrubbing of page by exporTPP.pl
------------------------------------------------------------------------
r5434 | real_procopio | 2011-06-17 11:25:12 -0700 (Fri, 17 Jun 2011) | 1 line
Changed paths:
   A /branches/4-5/trans_proteomic_pipeline/perl/exporTPP.pl

[exporTPP] New TPP experiment export tool
------------------------------------------------------------------------
r5433 | real_procopio | 2011-06-16 15:57:28 -0700 (Thu, 16 Jun 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/installer_win32/TPP_files.nsh

[windows installer] Adding Sqt2XML
------------------------------------------------------------------------
r5432 | real_procopio | 2011-06-16 15:55:18 -0700 (Thu, 16 Jun 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/installer_win32/TPP_files.nsh

[windows installer] Adding Sqt2XML
------------------------------------------------------------------------
r5431 | dshteyn | 2011-06-15 14:36:17 -0700 (Wed, 15 Jun 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/RefreshParser/RefreshParser.cxx
   M /trunk/trans_proteomic_pipeline/src/Parsers/RefreshParser/RefreshParser.h

RefreshParser: I->L conversion on peptide and proteins to map to all indistinguishable peptides in the proteins.
------------------------------------------------------------------------
r5430 | dshteyn | 2011-06-10 14:20:09 -0700 (Fri, 10 Jun 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/installer_win32/TPP_files.nsh

iModelParser.cgi for windows installation
------------------------------------------------------------------------
r5429 | pcbrefugee | 2011-06-09 17:57:22 -0700 (Thu, 09 Jun 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/TPPvc8.sln
   M /trunk/trans_proteomic_pipeline/src/tpplib/tpplibvc8.vcproj

[VC8 build] add saxtandemhandler.cxx, don't use mzParser vcproj after all
------------------------------------------------------------------------
r5428 | pcbrefugee | 2011-06-09 16:47:58 -0700 (Thu, 09 Jun 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/gsl.vcproj
   M /trunk/trans_proteomic_pipeline/extern/gsl_vc8.vcproj

[gsl msvc build] make sure gsl config.h has include path precedence within gsl build, copy vc8 changes to vc9 file (untested)
------------------------------------------------------------------------
r5427 | pcbrefugee | 2011-06-09 15:18:32 -0700 (Thu, 09 Jun 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/build_boost_vc8.bat
   M /trunk/trans_proteomic_pipeline/extern/build_boost_vc9.bat
   M /trunk/trans_proteomic_pipeline/extern/uncompress_win_lib.bat
   A /trunk/trans_proteomic_pipeline/extern/zlib-1.2.5.tar.bz2
   M /trunk/trans_proteomic_pipeline/extern/zlib.vcproj
   M /trunk/trans_proteomic_pipeline/extern/zlibvc8.vcproj
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sqt2XML/Sqt2XML.vcproj
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sqt2XML/Sqt2XMLvc8.vcproj
   A /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser_vc8.vcproj
   M /trunk/trans_proteomic_pipeline/src/Parsers/ramp/ramp.vcproj
   M /trunk/trans_proteomic_pipeline/src/Parsers/ramp/rampvc8.vcproj
   M /trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatioPeptideParser/ASAPRatioPeptideParser2003.vcproj
   M /trunk/trans_proteomic_pipeline/src/Quantitation/Pepc/Pepc.jar
   M /trunk/trans_proteomic_pipeline/src/TPPvc8.sln
   M /trunk/trans_proteomic_pipeline/src/mzXML/converters/ReAdW/ReAdWvc8.vcproj
   M /trunk/trans_proteomic_pipeline/src/mzXML/converters/massWolf/massWolf.vcproj
   M /trunk/trans_proteomic_pipeline/src/mzXML/converters/massWolf/massWolf_VS2005.vcproj
   M /trunk/trans_proteomic_pipeline/src/mzXML/converters/massWolf/massWolf_VS2005express.vcproj
   M /trunk/trans_proteomic_pipeline/src/mzXML/converters/mzWiff/mzWiff.vcproj
   M /trunk/trans_proteomic_pipeline/src/mzXML/converters/mzWiff/mzWiff_vs2005.vcproj
   M /trunk/trans_proteomic_pipeline/src/mzXML/converters/trapper/main/trapper.vcproj
   M /trunk/trans_proteomic_pipeline/src/pwiz/pwiz.vcproj
   M /trunk/trans_proteomic_pipeline/src/pwiz/pwizvc8.vcproj
   M /trunk/trans_proteomic_pipeline/src/tpp.vsprops
   M /trunk/trans_proteomic_pipeline/src/tpplib/tpplib.vcproj
   M /trunk/trans_proteomic_pipeline/src/tpplib/tpplibvc8.vcproj

update MSVC8 build for use of zlib-1.2.5 and mzParser - probably incomplete for VC9
------------------------------------------------------------------------
r5426 | pcbrefugee | 2011-06-09 14:44:14 -0700 (Thu, 09 Jun 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h

[mzParser] use typedefs instead of define to avoid redefinition warnings, use _int32 instead of long when defining 32 bit integer type so it works in 64 bit windows
------------------------------------------------------------------------
r5425 | pcbrefugee | 2011-06-09 14:42:18 -0700 (Thu, 09 Jun 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/gsl_vc8.vcproj

[gsl] add a couple of files we weren't using before to the VC8 build
------------------------------------------------------------------------
r5424 | pcbrefugee | 2011-06-09 14:38:21 -0700 (Thu, 09 Jun 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Makefile.incl

[Makefile] help MSVC deal with inline decls in some additional GSL files we weren't using before by making a special header file for MSVC use
------------------------------------------------------------------------
r5423 | pcbrefugee | 2011-06-09 14:24:50 -0700 (Thu, 09 Jun 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/common/sysdepend.h

need to include <float.h> for _isnan decl
------------------------------------------------------------------------
r5422 | pcbrefugee | 2011-06-09 14:23:47 -0700 (Thu, 09 Jun 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/RTCatalog.cxx

[RTCalculator] casts and unused variable removal for quiet compile
------------------------------------------------------------------------
r5421 | pcbrefugee | 2011-06-09 14:20:58 -0700 (Thu, 09 Jun 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTDenoiser.cpp

[SpectraST] casts for quiet compile - log(int) is ambiguous on some compilers
------------------------------------------------------------------------
r5420 | slagelwa | 2011-06-07 10:13:46 -0700 (Tue, 07 Jun 2011) | 2 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/twa/AWS.js
   M /trunk/trans_proteomic_pipeline/extern/hpctools/twa/MyViewport.ui.js
   M /trunk/trans_proteomic_pipeline/extern/hpctools/twa/index.html
   M /trunk/trans_proteomic_pipeline/extern/hpctools/twa/welcome.html

Fixes for IE, rename title

------------------------------------------------------------------------
r5419 | slagelwa | 2011-06-01 22:19:31 -0700 (Wed, 01 Jun 2011) | 2 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/twa/AWS.js
   M /trunk/trans_proteomic_pipeline/extern/hpctools/twa/MyViewport.ui.js
   M /trunk/trans_proteomic_pipeline/extern/hpctools/twa/index.html
   M /trunk/trans_proteomic_pipeline/extern/hpctools/twa/twa.js

Improved some error handling, fixed IE bug, removed unnecessary console declarations, added important console.info() declaration for IE

------------------------------------------------------------------------
r5418 | slagelwa | 2011-06-01 16:59:29 -0700 (Wed, 01 Jun 2011) | 2 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/twa/AWS.js
   M /trunk/trans_proteomic_pipeline/extern/hpctools/twa/Makefile
   M /trunk/trans_proteomic_pipeline/extern/hpctools/twa/MyViewport.ui.js
   A /trunk/trans_proteomic_pipeline/extern/hpctools/twa/README
   A /trunk/trans_proteomic_pipeline/extern/hpctools/twa/images/reload.png
   M /trunk/trans_proteomic_pipeline/extern/hpctools/twa/index.html
   M /trunk/trans_proteomic_pipeline/extern/hpctools/twa/welcome.html

Major refit, pending some IE fixes

------------------------------------------------------------------------
r5417 | real_procopio | 2011-05-31 17:43:02 -0700 (Tue, 31 May 2011) | 1 line
Changed paths:
   M /branches/4-5/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms1.cxx

[mzParser] Moving Spectrum viewer to use mzParser (was missed on previous update)
------------------------------------------------------------------------
r5416 | pcbrefugee | 2011-05-31 13:00:39 -0700 (Tue, 31 May 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/gzstream/Makefile
   M /trunk/trans_proteomic_pipeline/src/Makefile.incl

[Makefiles] preserve compatibility with older minGW setups by testing for -static-libstdc++ support
------------------------------------------------------------------------
r5415 | slagelwa | 2011-05-27 19:49:12 -0700 (Fri, 27 May 2011) | 1 line
Changed paths:
   A /branches/4-5 (from /trunk:5414)

[branch 4.5] recreating the 4-5 branch from the trunk
------------------------------------------------------------------------
r5414 | slagelwa | 2011-05-27 19:43:52 -0700 (Fri, 27 May 2011) | 4 lines
Changed paths:
   D /branches/4-5

Removing branch.  Nobody has been using it so far and have been checking
things into the trunk.  Therefore I'm going to just recreate the branch
again.

------------------------------------------------------------------------
r5413 | mhoopmann | 2011-05-27 17:09:15 -0700 (Fri, 27 May 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h

Added readMSLevel() function to ramp-like interface.
------------------------------------------------------------------------
r5412 | mhoopmann | 2011-05-27 15:56:48 -0700 (Fri, 27 May 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp

Fix parsing bug for mzML files generated with latest version of MSconvert.
------------------------------------------------------------------------
r5411 | dshteyn | 2011-05-27 12:30:48 -0700 (Fri, 27 May 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Makefile

saxtandemhandler.h
------------------------------------------------------------------------
r5410 | dshteyn | 2011-05-27 12:22:25 -0700 (Fri, 27 May 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Tandem2XML/TandemParamsParser.h
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Tandem2XML/TandemResultsParser.h

switch to saxtandemhandler
------------------------------------------------------------------------
r5409 | dshteyn | 2011-05-27 12:21:24 -0700 (Fri, 27 May 2011) | 1 line
Changed paths:
   A /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/saxtandemhandler.cxx
   A /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/saxtandemhandler.h

Forgot to commit saxtandemhandler
------------------------------------------------------------------------
r5408 | dshteyn | 2011-05-27 11:32:59 -0700 (Fri, 27 May 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/Makefile

Adding flags to get mingw build to function.
------------------------------------------------------------------------
r5407 | dshteyn | 2011-05-26 15:48:07 -0700 (Thu, 26 May 2011) | 2 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/common/TPPVersion.h

Version update

------------------------------------------------------------------------
r5406 | dshteyn | 2011-05-26 15:47:50 -0700 (Thu, 26 May 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/perl_paths/perl_paths.inc
   M /trunk/trans_proteomic_pipeline/src/perl_paths/perl_paths.makefile

Fixing problems with mingw build.
------------------------------------------------------------------------
r5405 | slagelwa | 2011-05-25 14:36:54 -0700 (Wed, 25 May 2011) | 4 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/gzstream/Makefile

Added -static-libstc++ to linker flags.  Seems required under
the latest versions of MinGW (4.5.2).


------------------------------------------------------------------------
r5404 | slagelwa | 2011-05-25 14:02:54 -0700 (Wed, 25 May 2011) | 3 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/installer_win32/CheckWebServer.nsh

Minor quibble I noticed when testing the installer.  The message says "press Ok" but the button label is "Yes".


------------------------------------------------------------------------
r5403 | pcbrefugee | 2011-05-25 11:08:06 -0700 (Wed, 25 May 2011) | 1 line
Changed paths:
   D /trunk/trans_proteomic_pipeline/extern/zlib123-dll.tar.bz2
   M /trunk/trans_proteomic_pipeline/src/Makefile.incl

fix boost build to work with zlib125's directory structure, delete old zlib123-dll.tar.bz2
------------------------------------------------------------------------
r5402 | dshteyn | 2011-05-25 09:41:51 -0700 (Wed, 25 May 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/InterProphetParser.cxx

InterProphetParser: remove any peptideprophet or prior interprophet analysis_summary tags.
------------------------------------------------------------------------
r5401 | mhoopmann | 2011-05-20 09:32:40 -0700 (Fri, 20 May 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzxmlhandler.cpp

Added another function from RAMP.
------------------------------------------------------------------------
r5400 | dshteyn | 2011-05-18 15:10:36 -0700 (Wed, 18 May 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/InterProphetParser.cxx

InterProphetParser: BUGFIX, correct the outputting of extra </spectrum_query> tags.
------------------------------------------------------------------------
r5399 | slagelwa | 2011-05-18 11:25:26 -0700 (Wed, 18 May 2011) | 3 lines
Changed paths:
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Adding a snapshot of the new TPP Web Launcher for Amazon so I don't lose anything.


------------------------------------------------------------------------
r5398 | slagelwa | 2011-05-16 10:54:02 -0700 (Mon, 16 May 2011) | 1 line
Changed paths:
   A /branches/4-5 (from /trunk:5397)

[4.5 branch] creating branch from trunk.  Code for all 4.5.x releases lives here
------------------------------------------------------------------------
r5397 | slagelwa | 2011-05-13 16:57:14 -0700 (Fri, 13 May 2011) | 11 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Client.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Poll.pm

* Decreased the minimum time between checks for results.  The
  window was still large enough for eventual consistency 
  problems.

* Incl. ability to set max sleep time on poll

* Yet another fix to the fork/zombie issue in the client.
Now properly handles them by reaping them and *not* 
ignoring the children processes.


------------------------------------------------------------------------
r5396 | mhoopmann | 2011-05-12 17:12:12 -0700 (Thu, 12 May 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp

Workaround added for Mascot2XML. It was far easier to add an exception here than to fix that code.
------------------------------------------------------------------------
r5395 | slagelwa | 2011-05-12 14:14:14 -0700 (Thu, 12 May 2011) | 11 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Client.pm

* Burned yet again by eventual consistency.  Race condition 
existed where queues *looked* empty but werent and the client
shutdown.  Reworked main loop so that it'll poll for 5 mins
before quitting.

* Corrected signal processing issue with zombies. Similar 
issue existed in forked system() calls in the download

* Lastly, client process not quitting on signal properly


------------------------------------------------------------------------
r5394 | eng_jk | 2011-05-11 17:40:19 -0700 (Wed, 11 May 2011) | 4 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

Modifications to allow xpress to work with input mzML files with non-sequential
native scanId numbers.  Only the core XPressPeptideParser.exe has been updated;
there's no good way for the cgi gui chromatogram interface to support these data files.

------------------------------------------------------------------------
r5393 | pcbrefugee | 2011-05-11 11:36:08 -0700 (Wed, 11 May 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/Jamroot.jam
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   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/boost/lockfree/detail/prefix.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/boost/lockfree/detail/tagged_ptr.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/boost/lockfree/detail/tagged_ptr_dcas.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/boost/lockfree/detail/tagged_ptr_ptrcompression.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/boost/lockfree/fifo.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/boost/lockfree/ringbuffer.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/boost/lockfree/stack.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/boost/memory_order.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/Version.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/Version.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/passive/Jamfile.jam
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/passive/PepXMLCat.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/passive/PepXMLCat.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/passive/Pseudo2DGel.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/passive/Pseudo2DGel.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/peakdetect/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/peakdetect/MZRTField.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/peakdetect/MZRTFieldTest.cpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/peakdetect/MZTolerance.cpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/peakdetect/MZTolerance.hpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/peakdetect/MZToleranceTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/peakdetect/PeakelGrower.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/MS2Deisotoper.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/PrecursorMassFilter.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumListFactory.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumListFactoryTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_Filter.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_Filter.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_FilterTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_MetadataFixer.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_MetadataFixer.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRecalculatorTest.data/PrecursorRefineOrbi.mzML
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRefine.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_TitleMaker.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_TitleMaker.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/common/cv.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/common/cv.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/common/cvgen.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/common/cvtest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/common/diff_std.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/common/obo.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/common/obo.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/common/obotest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/common/psi-ms.obo
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/common/unit.obo
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/misc/PeakData.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/misc/PeakData.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/IOTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/MSData.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/MSDataFile.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/MSDataFile.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/MemoryMRUCache.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/Serializer_MGF.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumListCache.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumListCacheTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumList_MGF.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumList_MGF_Test.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumList_mzXML.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/Version.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/ramp/Jamfile.jam
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/ramp/ramp.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/ramp/ramp_base64.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/ramp/ramp_base64.h
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/ramp/wglob.cxx
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/ramp/wglob.h
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/DefaultReaderList.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/DelimReader.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/DelimWriter.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Diff.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Diff.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/DiffTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/IO.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/IO.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/IOTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/MascotReader.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/MascotReader.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/MascotReader_dummy.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/MzIdentML.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/MzIdentML.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/MzIdentMLFile.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/MzIdentMLFile.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/MzIdentMLTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Pep2MzIdent.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Reader.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Reader.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/References.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/ReferencesTest.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Serializer_Text.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Serializer_Text.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Serializer_Text_Test.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Serializer_mzid.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Serializer_mzid.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Serializer_mzid_Test.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Serializer_pepXML.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Serializer_pepXML_Test.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/TextWriter.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Version.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/examples.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/Digestion.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/ProteinListCache.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/ProteinListCacheTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/Serializer_FASTA.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/Serializer_FASTA_Test.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/Version.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/tradata/Version.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/Reader_ABI.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Agilent/Reader_Agilent_Test.data.tar.bz2
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Thermo/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Thermo/Reader_Thermo.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Thermo/Reader_Thermo_Detail.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Thermo/Reader_Thermo_Test.data.tar.bz2
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Thermo/SpectrumList_Thermo.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Thermo/SpectrumList_Thermo.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/ChromatogramList_Waters.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/ChromatogramList_Waters.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/Reader_Waters.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/Reader_Waters_Detail.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/Reader_Waters_Detail.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/Reader_Waters_Test.data.tar.bz2
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/Reader_Waters_Test_Legacy.data.tar.bz2
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/SpectrumList_Waters.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/SpectrumList_Waters.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/analysis/spectrum_processing.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/analysis/spectrum_processing.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/analysis/spectrum_processing_test.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/common/IterationListenerTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/common/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/common/ParamTypes.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/common/SharedCLI.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/common/cv.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/msdata/Diff.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/msdata/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/msdata/MSData.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/msdata/MSData.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/msdata/MSDataFile.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/msdata/MSDataFile.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/msdata/MSDataFileTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/chemistry/Jamfile.jam
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/chemistry/MZTolerance.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/chemistry/MZTolerance.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/chemistry/MZToleranceTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/DateTime.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/DateTimeTest.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/Environment.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/IterationListener.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/IterationListener.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/IterationListenerTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/SHA1Calculator.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/SHA1CalculatorTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/Std.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/VendorReaderTestHarness.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/mru_list.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/unit.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/ABI/Jamfile.jam
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/BaseCommon.dll
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/BaseDataAccess.dll
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/BaseError.dll
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/BaseTof.dll
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/EULA.MHDAC
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/MassHunterData.cpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/MassSpecDataReader.dll
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/agtsampleinforw.dll
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Bruker/BDal.CXt.Lc.Factory.dll
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Bruker/BDal.CXt.Lc.Interfaces.dll
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Bruker/BDal.CXt.Lc.UntU2.dll
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Bruker/BDal.CXt.Lc.dll
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Bruker/CompassXtractMS.dll
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Bruker/Interop.EDAL.SxS.manifest
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Bruker/Interop.EDAL.dll
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Bruker/Jamfile.jam
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Bruker/NTB-vc80-mt-4_3_61.dll
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Bruker/boost_regex-vc80-mt-1_33_1-BDAL_20070424.dll
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Bruker/boost_thread-vc80-mt-1_33_1-BDAL_20070424.dll
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Bruker/libfftw3-3.dll
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Bruker/libfftw3f-3.dll
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Waters/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Waters/MassLynxRaw.hpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Waters/RawData.cpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Waters/RawData.hpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Waters/RawDataTest.cpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Waters/dacserver.tli
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/EULA.MSFileReader
   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/MSFileReader.XRawfile2.SxS.manifest
   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_tools/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/commandline/Jamfile.jam
   A /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/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/common/MSDataAnalyzerApplicationTest.cpp
   M /trunk/trans_proteomic_pipeline/src/Makefile.pwiz.incl

[pwiz] synch up with official code rev 2689
------------------------------------------------------------------------
r5392 | slagelwa | 2011-05-10 11:58:41 -0700 (Tue, 10 May 2011) | 3 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amzbill
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amztpp
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amztppserver
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Report.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/SearchService.pm

Report wall time of search
use different format for pid filename

------------------------------------------------------------------------
r5391 | pcbrefugee | 2011-05-03 15:51:11 -0700 (Tue, 03 May 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreducehelper.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreducehelper.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mreport.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_c.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_hrk.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_k.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_tandem.h

[xtandem for hadoop and mpi] a few object serialization tweaks for "refine" step support
------------------------------------------------------------------------
r5390 | eng_jk | 2011-05-03 13:36:33 -0700 (Tue, 03 May 2011) | 2 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx
   M /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideUpdateParser/XPressPeptideUpdateParserMain.cxx

minor mods to increase precision of mass tol in xpress chromatogram gui; replace hydrogen mass with proton mass in code

------------------------------------------------------------------------
r5389 | mhoopmann | 2011-05-03 11:31:54 -0700 (Tue, 03 May 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/BasicSpectrum.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp
   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

Added scanIndex data member to BasicSpectrum and RAMP interface to provide sequential scan numbering independent of numbers used by instrument manufacturers.
------------------------------------------------------------------------
r5388 | eng_jk | 2011-05-02 10:52:17 -0700 (Mon, 02 May 2011) | 2 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Makefile.incl

add -static-libstdc++ compiler flag

------------------------------------------------------------------------
r5387 | eng_jk | 2011-04-27 16:26:56 -0700 (Wed, 27 Apr 2011) | 2 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/util/digestdb1.cpp

Add command line option -M to allow user to specify static mods

------------------------------------------------------------------------
r5386 | mhoopmann | 2011-04-27 09:38:29 -0700 (Wed, 27 Apr 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzxmlhandler.cpp

Fixed missing last scan indexing bug when using spectra without scan numbers. Also suppressed warning messages that appear when spectra do not have scan numbers.
------------------------------------------------------------------------
r5385 | mhoopmann | 2011-04-26 15:35:26 -0700 (Tue, 26 Apr 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp

Ack! Cleaning up test output to screen that was left in at last check-in.
------------------------------------------------------------------------
r5384 | mhoopmann | 2011-04-26 15:32:55 -0700 (Tue, 26 Apr 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp

Force spectrum object to use index number when spectrum has no scan number (for cramp functionality).
------------------------------------------------------------------------
r5383 | mhoopmann | 2011-04-25 13:44:35 -0700 (Mon, 25 Apr 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp

Default precursor scan number to 0 when not provided.
------------------------------------------------------------------------
r5382 | dshteyn | 2011-04-25 11:14:51 -0700 (Mon, 25 Apr 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Makefile.incl
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxhandler.cpp

Undo Makefile change that broke linux build.  And change mzParser to respond to -D__LINUX__ as to -DGCC.
------------------------------------------------------------------------
r5381 | pcbrefugee | 2011-04-20 17:06:42 -0700 (Wed, 20 Apr 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/Makefile

tweak for building with mingw
------------------------------------------------------------------------
r5380 | pcbrefugee | 2011-04-20 17:05:58 -0700 (Wed, 20 Apr 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h

avoid redefine of XML_STATIC for quiet compile
------------------------------------------------------------------------
r5379 | dshteyn | 2011-04-20 11:55:34 -0700 (Wed, 20 Apr 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Makefile.incl

Tweaks to compilation on Linux.
------------------------------------------------------------------------
r5378 | dshteyn | 2011-04-20 11:11:29 -0700 (Wed, 20 Apr 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Makefile
   M /trunk/trans_proteomic_pipeline/src/Makefile.incl

switch to zlib v1.2.5 and tweaks fro MingW build
------------------------------------------------------------------------
r5377 | dshteyn | 2011-04-20 11:10:24 -0700 (Wed, 20 Apr 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/installer_win32/TPP_files.nsh

update location of msconvert.exe
------------------------------------------------------------------------
r5376 | dshteyn | 2011-04-20 11:09:21 -0700 (Wed, 20 Apr 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/zlib1.dll

update zlib version to 1.2.5
------------------------------------------------------------------------
r5375 | dshteyn | 2011-04-20 11:00:47 -0700 (Wed, 20 Apr 2011) | 1 line
Changed paths:
   A /trunk/trans_proteomic_pipeline/extern/zlib125-dll.tar.bz2

switching to zlib 1.2.5
------------------------------------------------------------------------
r5374 | dshteyn | 2011-04-20 10:05:13 -0700 (Wed, 20 Apr 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxhandler.cpp

MingW compilation tweaks
------------------------------------------------------------------------
r5373 | dshteyn | 2011-04-19 16:42:07 -0700 (Tue, 19 Apr 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/Makefile

Mingw compilation
------------------------------------------------------------------------
r5372 | dshteyn | 2011-04-19 16:41:03 -0700 (Tue, 19 Apr 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/mzXML/tools/readmzXML/Makefile

Mingw compilation
------------------------------------------------------------------------
r5371 | dshteyn | 2011-04-19 15:49:46 -0700 (Tue, 19 Apr 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx
   M /trunk/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.h
   M /trunk/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParserMain.cxx

InteractParser: option for recording the retention_time_sec in pepXML.
------------------------------------------------------------------------
r5370 | slagelwa | 2011-04-19 15:11:12 -0700 (Tue, 19 Apr 2011) | 10 lines
Changed paths:
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amzbill
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amztppserver
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Client.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/EC2Manager.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/InspectService.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/SQSManager.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/TandemService.pm

* Corrected issue with SIGCHLD on server process.  system() call was
  returning "No child processes" error when started through cloud-init.  No
  longer set the sig handler to ignore
* Fixed some issues with inspect, primarily setting of the database to
  search against
* Better error checking in client responses
* Fixed typo
* Added amzbill to fetch the latest billing reports.  Script not installed
  but just part of the distro

------------------------------------------------------------------------
r5369 | slagelwa | 2011-04-15 16:16:19 -0700 (Fri, 15 Apr 2011) | 13 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amztpp
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amztppserver
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Client.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/EC2Manager.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Report.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/SQSManager.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/SearchService.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Service.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/TandemService.pm

* added reporting back into the program
   * requeues download msg in order to pass back download
     information to parent process for reporting
* amztpp no longer creates the SQS queues every time it runs
* clean no longer shuts down the nodes (use terminate to
  accomplish this)
* added back shutting down ec2 instance when server process
  ends
* debug print # visible and not visible messages in queues
* always query for ec2 instances
* others...


------------------------------------------------------------------------
r5368 | mhoopmann | 2011-04-14 12:21:48 -0700 (Thu, 14 Apr 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/BasicSpectrum.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.vcproj
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzxmlhandler.cpp

Fixed a bug that prevented spectra with a scan number of 0 from being read.
------------------------------------------------------------------------
r5367 | dshteyn | 2011-04-14 11:19:02 -0700 (Thu, 14 Apr 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/InterProphetParser.cxx

BUGFIX:  Changes to pepXML writer to correct extra tag issue when iProphet is run on pepXML that already contains iProphet tags.
------------------------------------------------------------------------
r5366 | dshteyn | 2011-04-13 09:31:32 -0700 (Wed, 13 Apr 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/InterProphetParser.cxx

InterProphetParser: BUGFIX When the pepXML already contains the iProphet tags filter them out, including the end tag.
------------------------------------------------------------------------
r5365 | pcbrefugee | 2011-04-12 17:30:06 -0700 (Tue, 12 Apr 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/find_arch.sh

set line ending to unix style (helps when running VMWare hosted linux sharing a windows source code directory)
------------------------------------------------------------------------
r5364 | pcbrefugee | 2011-04-12 16:55:16 -0700 (Tue, 12 Apr 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/Makefile
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreducehandler.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreducehelper.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreducehelper.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreducehelper_bangbang.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/masscalc.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mmotif.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mprocess.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/serialize.cpp

[mr-tandem] better logging and fixes for refinement step in mapreduce xtandem 
------------------------------------------------------------------------
r5363 | slagelwa | 2011-04-06 22:45:58 -0700 (Wed, 06 Apr 2011) | 16 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/MANIFEST
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/Makefile.PL
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amztpp
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amztppserver
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Client.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/EC2Manager.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/InspectService.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Logger.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/MyrimatchService.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/OMSSAService.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Service.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/TandemService.pm
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS.pm

* Additional updates to the documentation
* Info messages are now outputted to console (in non-debug format)
  they also now have a rudimentary formatting capability.  (Maybe one
  of these days change it over to Log::Log4perl)
* Version string is now taken out of AWS.pm
   * also added -V to server program
* Fixed die message logging in server/client
* Removed Proc::Fork dependence
* Added info messages in clean command
* Group (AMZTPP) used for instance detection
* Looks for AMI's using new naming nomenclature
* Shutdown added to server on process exit
* Added back the autostarting of instances
* Others...


------------------------------------------------------------------------
r5362 | pcbrefugee | 2011-03-31 15:48:50 -0700 (Thu, 31 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/README-MAPREDUCE
   D /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreduce_helper.py
   D /trunk/trans_proteomic_pipeline/extern/xtandem/src/xtandem_mapreduce.py

[hadoop xtandem] move launcher scripts over to the Insilicos Cloud Army project where the X!!Tandem (MPI xtandem) support scripts already live.  Change the readme-mapreduce to point users to https://ica.svn.sourceforge.net/svnroot/ica/
------------------------------------------------------------------------
r5361 | slagelwa | 2011-03-30 17:23:44 -0700 (Wed, 30 Mar 2011) | 22 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/MANIFEST
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/Makefile.PL
   D /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amzinspect
   D /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amzomssa
   D /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amztandem
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amztpp
   D /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amztppd
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amztppserver (from /trunk/trans_proteomic_pipeline/extern/hpctools/aws/bin/amztppd:4979)
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Client.pm
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Credentials.pm (from /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/Search/AWS/Credentials.pm:4979)
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/EC2Manager.pm (from /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/Search/AWS/EC2Manager.pm:4979)
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/InspectService.pm (from /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/Search/AWS/InspectService.pm:5278)
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Logger.pm (from /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/Search/Logger.pm:4979)
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/MyrimatchService.pm
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/OMSSAService.pm (from /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/Search/AWS/OMSSAService.pm:4979)
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Poll.pm (from /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/Search/AWS/Poll.pm:4998)
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Report.pm (from /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/Search/AWS/Report.pm:4979)
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/S3Manager.pm (from /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/Search/AWS/S3Manager.pm:4979)
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/SQSManager.pm (from /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/Search/AWS/SQSManager.pm:4979)
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/SearchService.pm (from /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/Search/AWS/SearchService.pm:4998)
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/Service.pm (from /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/Search/AWS/Service.pm:4979)
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS/TandemService.pm (from /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/Search/AWS/TandemService.pm:4979)
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/AWS.pm (from /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/Search/AWS.pm:4998)
   D /trunk/trans_proteomic_pipeline/extern/hpctools/aws/lib/TPP/Search
   A /trunk/trans_proteomic_pipeline/extern/hpctools/aws/t/data/myrimatch.params
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/t/data/test.fasta
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/t/data/test.fasta.phr
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/t/data/test.fasta.pin
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/t/data/test.fasta.psd
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/t/data/test.fasta.psi
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/t/data/test.fasta.psq
   M /trunk/trans_proteomic_pipeline/extern/hpctools/aws/t/data/test.mzXML

Major revision of the TPP Amazon Cloud stuff
2.0 Alpha

Changes include:

   * New command line interface, merged scripts into one client program
   * Updated documentation
   * Explict controls over background process
   * Client can do parallel upload/downloads in background
   * Support for Myrimatch
   * Uses new CloudInit boot in images
   * Uses new TPP Amazon image based on Ubuntu 10.x
   * Now creates a Amazon default security group (named SPCTools-TPP)
     if one not specified
   * Now loads Moose related modules *AFTER* processing arguments
   * Fixed issue with starting too many nodes at the beginning
   * Directory "Search" removed from packages
   * Configurable sandbox area on server
   * Server program renamed
   * Better/detailed querying of queued messages


------------------------------------------------------------------------
r5360 | dshteyn | 2011-03-28 12:18:09 -0700 (Mon, 28 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/util/translateDNA2AA-FASTA.cpp

GCC: anonymous struct warning.
------------------------------------------------------------------------
r5359 | dshteyn | 2011-03-25 16:31:27 -0700 (Fri, 25 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Makefile.incl

Makefile.incl was not checked in
------------------------------------------------------------------------
r5358 | dshteyn | 2011-03-25 16:00:08 -0700 (Fri, 25 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/SearchHit.cxx
   M /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/SearchHit.h

InteractParser: SearchHit Changes, also defines bool_hash used in RTCatalog.
------------------------------------------------------------------------
r5357 | dshteyn | 2011-03-25 15:35:21 -0700 (Fri, 25 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Makefile

Makefile changes to get all this to compile with new code and mzParser.
------------------------------------------------------------------------
r5356 | dshteyn | 2011-03-25 15:33:40 -0700 (Fri, 25 Mar 2011) | 1 line
Changed paths:
   A /trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser
   A /trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphet.cxx
   A /trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphet.h
   A /trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphetMain.cxx
   A /trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphetParser.cxx
   A /trunk/trans_proteomic_pipeline/src/Validation/PTMProphetParser/PTMProphetParser.h

PTMProphetParser: first commit
------------------------------------------------------------------------
r5355 | dshteyn | 2011-03-25 15:24:50 -0700 (Fri, 25 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/mzXML/tools/readmzXML/Makefile
   M /trunk/trans_proteomic_pipeline/src/mzXML/tools/readmzXML/readmzXML.cpp

ramp -> mzParser switch
------------------------------------------------------------------------
r5354 | dshteyn | 2011-03-25 15:15:09 -0700 (Fri, 25 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/Makefile
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLibImporter.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTMain.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPepXMLSearchOutput.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/XMLWalker.cpp

SpectraST:  Allow SpectraST to compile as lib only (no main) function so it can be used in other tools.  Also ramp ->mzParser changes.
------------------------------------------------------------------------
r5353 | dshteyn | 2011-03-25 15:05:31 -0700 (Fri, 25 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Quantitation/Q3/Q3ProteinRatioParser/Q3GroupPeptideParser.h

switch ramp -> mzParser
------------------------------------------------------------------------
r5352 | dshteyn | 2011-03-25 14:55:53 -0700 (Fri, 25 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Quantitation/Option.h

switch ramp -> mzParser
------------------------------------------------------------------------
r5351 | dshteyn | 2011-03-25 14:45:42 -0700 (Fri, 25 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressGroupPeptideParser.h
   M /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.h
   M /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideUpdateParser/XPressPeptideUpdateParserMain.cxx

XPress: switch ramp -> mzParser.
------------------------------------------------------------------------
r5350 | dshteyn | 2011-03-25 14:42:28 -0700 (Fri, 25 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatioPeptideParser/ASAPRatioPeptideParser.cxx
   M /trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatioPeptideParser/ASAPRatioPeptideParser.h
   M /trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatioPeptideParser/ASAPRatioPeptideParserMain.cxx
   M /trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatioProteinRatioParser/ASAPRatioGroupPeptideParser.h
   M /trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatioProteinRatioParser/ASAPRatioProteinRatioParser.h
   M /trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_pepFns.cxx
   M /trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_pepFns.h

ASAPRatio: switch ramp -> mzParser, add options to quantify only above certain probability.
------------------------------------------------------------------------
r5349 | dshteyn | 2011-03-25 14:13:14 -0700 (Fri, 25 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/MzXML2Search/MzXML2Search.cxx
   M /trunk/trans_proteomic_pipeline/src/Parsers/Parser/Parser.h
   M /trunk/trans_proteomic_pipeline/src/Parsers/Parser/TagListComparator.cxx
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxhandler.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/ramp/cached_ramp.h
   M /trunk/trans_proteomic_pipeline/src/Parsers/ramp/cramp.hpp

ramp -> mzParser switch.
------------------------------------------------------------------------
r5348 | mhoopmann | 2011-03-25 12:19:23 -0700 (Fri, 25 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.sln

more legacy support
------------------------------------------------------------------------
r5347 | dshteyn | 2011-03-25 10:26:36 -0700 (Fri, 25 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Comet2XML/Comet2xml.cxx
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Mascot2XML/MascotConverter.cxx
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Mascot2XML/MascotConverter.h
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/SearchResult/ProDataComponent.cxx
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sequest2XML/CombineOut.cxx
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sequest2XML/CombineOut.h
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sequest2XML/Out2XML.h
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sequest2XML/Sequest2XML.cxx
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Tandem2XML/TandemParamsParser.h
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Tandem2XML/TandemResultsParser.cxx
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Tandem2XML/TandemResultsParser.h

Search2pepXML: converted to using mzParser instead of ramp.
------------------------------------------------------------------------
r5346 | dshteyn | 2011-03-25 10:25:00 -0700 (Fri, 25 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/pICalculator.cxx

PeptideProphetParser: tweak pI model to model only +-5 stdev from mean pI for run.
------------------------------------------------------------------------
r5345 | dshteyn | 2011-03-25 10:23:34 -0700 (Fri, 25 Mar 2011) | 1 line
Changed paths:
   A /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/GradientProgram.cxx
   A /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/GradientProgram.h
   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
   A /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/RTCatalog.cxx
   A /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/RTCatalog.h
   A /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/RTCatalogParser.cxx
   A /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/RTCatalogParser.h
   A /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/RTCatalogParserMain.cxx

RTCatalogParser: tool for cataloging RTs
------------------------------------------------------------------------
r5344 | dshteyn | 2011-03-25 10:10:34 -0700 (Fri, 25 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/Pep3D/BasenameParser.cxx
   M /trunk/trans_proteomic_pipeline/src/Visualization/Pep3D/Pep3DParser.cxx
   M /trunk/trans_proteomic_pipeline/src/Visualization/Pep3D/Pep3D_functions.cxx
   M /trunk/trans_proteomic_pipeline/src/Visualization/Pep3D/Pep3D_functions.h
   M /trunk/trans_proteomic_pipeline/src/Visualization/Pep3D/cgi_Pep3D_xml/cgi_Pep3D_xml.cxx
   M /trunk/trans_proteomic_pipeline/src/Visualization/Pep3D/cgi_getCidData.cxx

Pep3D: ramp -> mzParser switch.
------------------------------------------------------------------------
r5343 | dshteyn | 2011-03-25 10:09:10 -0700 (Fri, 25 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/HeaderMRSSQ.h
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/HeaderOnly.h
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/MRSOffsetOnly.h
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/Makefile
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXField.cxx
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXField.h
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXIndexFile.cxx
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXIndexFile.h
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXNodeVecBuilder.cxx
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXNodeVecBuilder.h
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXSAXHandler.cxx
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXSAXHandler.h
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PipelineAnalysis.cxx
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PipelineAnalysis.h
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/SQOffsetOnly.h
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/SQhtmlDisplayer.h
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/XMLNode.h

PepXMLViewer: Update index to use longs to allow opening larger files. PTMProphetParser support. mzParser compatibility.
------------------------------------------------------------------------
r5342 | dshteyn | 2011-03-25 10:04:22 -0700 (Fri, 25 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.h

InteractParser: Read collision energies in all msms_run_summaries, not just the first one encountered per pepXML file.
------------------------------------------------------------------------
r5341 | dshteyn | 2011-03-25 10:03:54 -0700 (Fri, 25 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx

InteractParser: Read collision energies in all msms_run_summaries, not just the first one encountered per pepXML file.
------------------------------------------------------------------------
r5340 | pcbrefugee | 2011-03-24 14:34:35 -0700 (Thu, 24 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/installer_win32/TPP_files.nsh
   M /trunk/trans_proteomic_pipeline/installer_win32/TPP_installer.nsi

[windows installer] tweaks to handle gnuplot update in SVN ref 5124
------------------------------------------------------------------------
r5339 | mhoopmann | 2011-03-24 11:04:38 -0700 (Thu, 24 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxhandler.cpp

expanding more ramp functions
------------------------------------------------------------------------
r5338 | henryhlam | 2011-03-24 00:15:45 -0700 (Thu, 24 Mar 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/SpectraSTLib.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLib.hpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLibEntry.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLibEntry.hpp

[SpectraST] Option to output library in PAIdent format for import into PeptideAtlas
------------------------------------------------------------------------
r5337 | pcbrefugee | 2011-03-23 14:34:02 -0700 (Wed, 23 Mar 2011) | 4 lines
Changed paths:
   D /trunk/trans_proteomic_pipeline/extern/bjam_src.tgz
   D /trunk/trans_proteomic_pipeline/extern/boost_1_39_0.tar.bz2
   A /trunk/trans_proteomic_pipeline/extern/boost_1_45_0.tar.bz2
   M /trunk/trans_proteomic_pipeline/extern/boost_vc8.vcproj
   M /trunk/trans_proteomic_pipeline/extern/boost_vc9.vcproj
   M /trunk/trans_proteomic_pipeline/extern/build_boost_vc8.bat
   M /trunk/trans_proteomic_pipeline/extern/build_boost_vc9.bat
   M /trunk/trans_proteomic_pipeline/extern/common_win32/unistd.h
   M /trunk/trans_proteomic_pipeline/extern/expatvc8.vcproj
   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/installer_linux/publish_tandem_to_s3.sh
   M /trunk/trans_proteomic_pipeline/installer_linux/tandem_arch.sh
   M /trunk/trans_proteomic_pipeline/src/Makefile
   M /trunk/trans_proteomic_pipeline/src/Makefile.incl
   M /trunk/trans_proteomic_pipeline/src/TPPvc8.sln
   A /trunk/trans_proteomic_pipeline/src/find_arch.sh
   M /trunk/trans_proteomic_pipeline/src/tpp.vsprops
   M /trunk/trans_proteomic_pipeline/src/util/Makefile

[Makefiles] finer-grained $ARCH detection for cross compiling with shared source tree, so one can build side by side mingw, Ubuntu, Centos, 32 and 64 bit versions, all on the same PC under VMWare using a single copy of the source in a shared mount.
Also switches MinGW boost version to 1_45_0.
This will be a long build the first time you use it.

------------------------------------------------------------------------
r5336 | pcbrefugee | 2011-03-22 15:48:16 -0700 (Tue, 22 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Makefile.incl

[Makefile] some GCCs don't like trailing slash in -I include declarations
------------------------------------------------------------------------
r5335 | henryhlam | 2011-03-17 21:03:53 -0700 (Thu, 17 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/Makefile
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/Makefile_STANDALONE_LINUX
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTCreateParams.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTCreateParams.hpp
   A /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTDenoiser.cpp
   A /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTDenoiser.hpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLib.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLibEntry.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLibEntry.hpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTMzXMLLibImporter.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/Search/SpectraST/SpectraSTPepXMLLibImporter.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPepXMLLibImporter.hpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeptideLibIndex.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeptideLibIndex.hpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTReplicates.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTReplicates.hpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTSearch.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTSpLibImporter.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTSpLibImporter.hpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTTsvLibImporter.cpp

[SpectraST] Bracketing, Bayesian denoising (beta), option to not normalize, report TotalIonCurrent/PrecursorIntensity/OrigMaxIntensity of consensus as average of replicates rather than values of the best replicate
------------------------------------------------------------------------
r5334 | henryhlam | 2011-03-17 20:59:05 -0700 (Thu, 17 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/Peptide.cpp

[SpectraST] Treat HCD as CID, and ETD-SA as ETD in peak annotation
------------------------------------------------------------------------
r5333 | henryhlam | 2011-03-17 20:53:18 -0700 (Thu, 17 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/Lib2HTML.cpp

[SpectraST] Display Xrea (quality measure) in Lib2HTML verbose mode
------------------------------------------------------------------------
r5332 | mhoopmann | 2011-03-15 16:13:37 -0700 (Tue, 15 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore_c.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore_c.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore_k.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore_k.h

Fixed bugs relating to k-score crashes. Crashes no longer occur on Windows. However, k-score results are not exactly replicated when compared to older versions. This may be intentional by the xtandem authors, however, we should identify what is causing such changes and decide if they are appropriate for k-score.
------------------------------------------------------------------------
r5331 | dshteyn | 2011-03-09 12:50:21 -0800 (Wed, 09 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxhandler.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp

Add scan counters to use as scan numbers when this info is not available in the mzML file (e.g. Agilent QTrap Data)
------------------------------------------------------------------------
r5330 | mhoopmann | 2011-03-09 10:20:53 -0800 (Wed, 09 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h

Added cached RAMP support.
------------------------------------------------------------------------
r5329 | dshteyn | 2011-03-09 09:55:21 -0800 (Wed, 09 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/zran.cpp

mzParser: access was already defined in a unix header, renamed to gz_access
------------------------------------------------------------------------
r5328 | mhoopmann | 2011-03-08 15:48:48 -0800 (Tue, 08 Mar 2011) | 3 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.vcproj
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxhandler.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzxmlhandler.cpp
   A /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/zran.cpp

Added support for .mzXML.gz and .mzML.gz files. These are slow for the first scan read as the inflation table is built. After that the overhead is minor.

Other changes are modest increases in file reading efficiency when performing scan by scan parsing.
------------------------------------------------------------------------
r5327 | mhoopmann | 2011-03-07 16:50:17 -0800 (Mon, 07 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/BasicSpectrum.cpp
   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

Bugfix
------------------------------------------------------------------------
r5326 | mhoopmann | 2011-03-07 16:09:21 -0800 (Mon, 07 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h

Implemented readRunHeader for RAMP compatibility.
------------------------------------------------------------------------
r5325 | dshteyn | 2011-03-07 15:10:08 -0800 (Mon, 07 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/BasicSpectrum.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h

Adding FAIMS CompensationVoltage to mzParser.
------------------------------------------------------------------------
r5324 | mhoopmann | 2011-03-03 08:57:34 -0800 (Thu, 03 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/BasicSpectrum.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp
   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

Expanding the parser to capture more metadata
------------------------------------------------------------------------
r5323 | pcbrefugee | 2011-03-02 13:07:11 -0800 (Wed, 02 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Makefile

[non-windows "make install"] don't try to install optional-build Pepc components if they aren't built
------------------------------------------------------------------------
r5322 | real_procopio | 2011-03-01 15:41:14 -0800 (Tue, 01 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms2.cxx

[plot-msms] Fix typo in var name when no ms1 peaks present
------------------------------------------------------------------------
r5321 | dshteyn | 2011-03-01 12:18:45 -0800 (Tue, 01 Mar 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms2.cxx

plot-msms-js.cgi: Look for lorikeet.css in DEFAULT_HTML_DIR/css not webroot/css
------------------------------------------------------------------------
r5320 | slagelwa | 2011-02-25 16:00:54 -0800 (Fri, 25 Feb 2011) | 2 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qsequest

Checking in first stab at a new Regis specific sequest script

------------------------------------------------------------------------
r5319 | slagelwa | 2011-02-25 16:00:18 -0800 (Fri, 25 Feb 2011) | 3 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qspectrast

Now specifies the name of the spectrast log file, since it'll always
write one anyhow.

------------------------------------------------------------------------
r5318 | slagelwa | 2011-02-25 15:27:31 -0800 (Fri, 25 Feb 2011) | 2 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qconvert

Wasn't logging, missing space in the command line creation

------------------------------------------------------------------------
r5317 | slagelwa | 2011-02-25 15:26:51 -0800 (Fri, 25 Feb 2011) | 5 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qmascot

* Fixed issue with mascot using different results links
* Now reports an error when no results link returned by mascot.
It turns out that some searches return incomplete without a results
link but with a 200 OK.  Presumbably its timing out on the web server side.

------------------------------------------------------------------------
r5316 | mhoopmann | 2011-02-25 12:41:43 -0800 (Fri, 25 Feb 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore_c.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore_c.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore_hrk.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore_hrk.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore_k.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore_k.h

Updated all our plugins so that they behave as prior to cyclone. There should be no compilation errors, and no halting when running tandem.
------------------------------------------------------------------------
r5315 | mhoopmann | 2011-02-25 11:00:45 -0800 (Fri, 25 Feb 2011) | 1 line
Changed paths:
   D /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/base64.cpp

cleaning up unused file
------------------------------------------------------------------------
r5314 | mhoopmann | 2011-02-25 11:00:07 -0800 (Fri, 25 Feb 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp
   A /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/base64.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzxmlhandler.cpp

Fixed bug when parsing empty spectra in mzXML files using RAMP interface.
------------------------------------------------------------------------
r5313 | dshteyn | 2011-02-23 11:58:02 -0800 (Wed, 23 Feb 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx

InteractParser: bug fix associated with parsing OMSSA data.
------------------------------------------------------------------------
r5312 | mhoopmann | 2011-02-23 09:58:24 -0800 (Wed, 23 Feb 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzxmlhandler.cpp

Fixed bug when handling uncompressed mzXML data
------------------------------------------------------------------------
r5311 | dshteyn | 2011-02-18 17:47:28 -0800 (Fri, 18 Feb 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx

InteractParser: -P flag for OMSSA didn't fix the protein names for alternative_protein entries until this fix.
------------------------------------------------------------------------
r5310 | dshteyn | 2011-02-16 10:53:23 -0800 (Wed, 16 Feb 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx

XPressPeptideParser: Allow for proper quantitation of combined files where modified masses might be off depending on search engine and use of average vs monoisotopic mass in the search
------------------------------------------------------------------------
r5309 | slagelwa | 2011-02-16 10:34:22 -0800 (Wed, 16 Feb 2011) | 4 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qgrid_functions

By default set the umask of the job (and log files) to allow group access so
that I can debug things when they go wrong.


------------------------------------------------------------------------
r5308 | dshteyn | 2011-02-15 11:26:46 -0800 (Tue, 15 Feb 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPCGIDisplay/ASAPRatioProteinCGIDisplayParser.cxx
   M /trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPCGIDisplay/ASAPRatioProteinCGIDisplayParser.h
   M /trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/MixtureDistrFactory.cxx
   M /trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/MixtureDistrFactory.h

ASAPRatioProteinCGIDisplay: use central code for parsing search results to avoid error when parsing new search engine.
------------------------------------------------------------------------
r5307 | slagelwa | 2011-02-14 16:03:54 -0800 (Mon, 14 Feb 2011) | 8 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qspectrast

* Fixed issue with SPECTRAST variable override not being used
* Set default name for jobs
* Fixed major issue with creating libraries.  Now looks for the "-cN" flag
  to spectrast and names the qjob and qlog files using this string.  In the
  past it ended up creating hidden files named .spectrast.qjob and
  .spectrast.qlog


------------------------------------------------------------------------
r5306 | mhoopmann | 2011-02-14 12:31:20 -0800 (Mon, 14 Feb 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore_c.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore_c.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore_hrk.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore_hrk.h

Added additional scoring plugins and dealt with PLUGGABLE_SCORING flag in add_A function of mscore.cpp.
------------------------------------------------------------------------
r5305 | mhoopmann | 2011-02-10 10:20:51 -0800 (Thu, 10 Feb 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/BasicSpectrum.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.cpp
   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

Bugfixes relating to collision energy
------------------------------------------------------------------------
r5304 | pcbrefugee | 2011-02-05 23:29:58 -0800 (Sat, 05 Feb 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Makefile

[PepC] fix a bug in build when ant is present
------------------------------------------------------------------------
r5303 | slagelwa | 2011-02-02 14:20:00 -0800 (Wed, 02 Feb 2011) | 2 lines
Changed paths:
   A /trunk/trans_proteomic_pipeline/extern/hpctools/grid/params
   A /trunk/trans_proteomic_pipeline/extern/hpctools/grid/params/README
   A /trunk/trans_proteomic_pipeline/extern/hpctools/grid/params/inspect.params
   A /trunk/trans_proteomic_pipeline/extern/hpctools/grid/params/mascot.params
   A /trunk/trans_proteomic_pipeline/extern/hpctools/grid/params/omssa.params
   A /trunk/trans_proteomic_pipeline/extern/hpctools/grid/params/sequest.params
   A /trunk/trans_proteomic_pipeline/extern/hpctools/grid/params/tandem.params

Adding some default parameter file templates for the Q commands

------------------------------------------------------------------------
r5302 | slagelwa | 2011-02-02 14:17:20 -0800 (Wed, 02 Feb 2011) | 7 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qgrid_functions
   M /trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qmyrimatch
   M /trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qspectrast

* Updated submission interface
* Now checks for write permissions on database file directory as myrimatch
  can/will write a *.fasta.index file if it doesn't exist
* Quoted a lot of the shell variables in the vain attempt to support
  filenames with spaces in them


------------------------------------------------------------------------
r5301 | slagelwa | 2011-02-02 14:01:03 -0800 (Wed, 02 Feb 2011) | 2 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qmascot

update paths/queue name

------------------------------------------------------------------------
r5300 | slagelwa | 2011-02-02 14:00:09 -0800 (Wed, 02 Feb 2011) | 2 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qsequest

Beta version which submits jobs to a PBS cluster

------------------------------------------------------------------------
r5299 | mhoopmann | 2011-02-01 15:28:43 -0800 (Tue, 01 Feb 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzxmlhandler.cpp

Better handling of bogus file names.
------------------------------------------------------------------------
r5298 | mhoopmann | 2011-01-31 11:46:30 -0800 (Mon, 31 Jan 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Makefile

removing mzParser from VPATH
------------------------------------------------------------------------
r5297 | mhoopmann | 2011-01-31 11:10:01 -0800 (Mon, 31 Jan 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/Makefile
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp

bugfixes
------------------------------------------------------------------------
r5296 | real_procopio | 2011-01-28 15:40:48 -0800 (Fri, 28 Jan 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/js/aminoacid.js
   M /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/js/excanvas.min.js
   M /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/js/ion.js
   M /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/js/jquery.flot.js
   M /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/js/jquery.flot.selection.js
   M /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/js/peptide.js
   M /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/js/specview.js

Upgrading to revision r25 of Lorikeet
------------------------------------------------------------------------
r5295 | mhoopmann | 2011-01-28 11:15:35 -0800 (Fri, 28 Jan 2011) | 8 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Makefile

builds mzParser now






...(hopefully)
------------------------------------------------------------------------
r5294 | mhoopmann | 2011-01-28 11:01:38 -0800 (Fri, 28 Jan 2011) | 5 lines
Changed paths:
   A /trunk/trans_proteomic_pipeline/src/Parsers/mzParser
   A /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/BasicSpectrum.cpp
   A /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/Makefile
   A /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/RAMPface.cpp
   A /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzMLReader.cpp
   A /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.cpp
   A /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.h
   A /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.sln
   A /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzParser.vcproj
   A /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/mzp_base64.cpp
   A /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxhandler.cpp
   A /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp
   A /trunk/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzxmlhandler.cpp

Creating mzParser, an alternative to ramp. It reads mzXML and mzML without ProteoWizard (ie fast mzML reading). Includes ramp interface so that the transition is to replace the ramp.h with mzParser.h. Requires expat and zlib. To use:
1. compile mzParser.lib (libmzparser.a on linux).
2. in your source, include mzParser.h
3. link to mzParser.lib, expat.lib, zlib.lib

------------------------------------------------------------------------
r5293 | real_procopio | 2011-01-26 17:33:53 -0800 (Wed, 26 Jan 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/css/lorikeet.css
   M /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/js/specview.js

[bug] Rolling back incorrect commit!
------------------------------------------------------------------------
r5292 | real_procopio | 2011-01-26 17:27:40 -0800 (Wed, 26 Jan 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/js/specview.js

Lorikeet resources: css, images, and js code
------------------------------------------------------------------------
r5291 | real_procopio | 2011-01-26 17:27:27 -0800 (Wed, 26 Jan 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/css/lorikeet.css

Lorikeet resources: css, images, and js code
------------------------------------------------------------------------
r5290 | pcbrefugee | 2011-01-25 17:33:33 -0800 (Tue, 25 Jan 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Tandem2XML/TandemResultsParser.cxx
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Tandem2XML/TandemResultsParser.h

[Tandem2XML] integrate Brendan's fix for handling fragment mass type "average", also use our standard filename handling to correct recent change that was case sensitive and not future-proof.
------------------------------------------------------------------------
r5289 | pcbrefugee | 2011-01-18 16:38:58 -0800 (Tue, 18 Jan 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_c.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_hrk.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_k.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_tandem.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/serialize.cpp

[xtandem-hadoop] object serialization for hadoop work
------------------------------------------------------------------------
r5288 | pcbrefugee | 2011-01-18 14:58:17 -0800 (Tue, 18 Jan 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/xtandem_mapreduce.py

[xtandem-hadoop] tweak for less noisy download of tandem binary from AWS S3
------------------------------------------------------------------------
r5287 | pcbrefugee | 2011-01-18 14:53:24 -0800 (Tue, 18 Jan 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_hrk.cpp

[xtandem] add newline at end of file for quiet compile
------------------------------------------------------------------------
r5286 | pcbrefugee | 2011-01-18 14:51:58 -0800 (Tue, 18 Jan 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreducehelper.cpp

[xtandem-hadoop] tweaks for quiet compile
------------------------------------------------------------------------
r5285 | pcbrefugee | 2011-01-14 10:49:25 -0800 (Fri, 14 Jan 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/tar.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/MS2NoiseFilter.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/common/cv.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/common/cv.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/common/psi-ms.obo
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/common/unit.obo
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/IO.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/RAMPAdapter.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/ramp/ramp.h
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/DefaultReaderList.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/DelimReader.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Diff.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Diff.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/DiffTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/IO.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/IO.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/IOTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/MascotReader.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/MzIdentML.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/MzIdentML.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/MzIdentMLFile.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Pep2MzIdent.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Pep2MzIdentTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Serializer_mzid.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Serializer_mzid.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Serializer_pepXML.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Serializer_pepXML_Test.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/TextWriter.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Version.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/examples.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/examples.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/Modification.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/Modification.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/Peptide.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/Peptide.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/PeptideTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/common/cv.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/SWIG/pwiz_swigbindings_wrap.cxx
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/java/proteowizard/pwiz/RAMPAdapter/ScanHeaderStruct.java
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/java/proteowizard/pwiz/RAMPAdapter/e_contentType.java
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/java/proteowizard/pwiz/RAMPAdapter/pwiz_swigbindings.java
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/java/proteowizard/pwiz/RAMPAdapter/pwiz_swigbindingsConstants.java
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/java/proteowizard/pwiz/RAMPAdapter/pwiz_swigbindingsJNI.java
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/minimxml/XMLWriter.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/IterationListener.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/ScanFilter.cpp

[pwiz] synch up with official code rev 2465.  (note: I also merged the local changes in our rev 5279 back to the official pwiz codebase, so we're fully synched)
------------------------------------------------------------------------
r5284 | mhoopmann | 2011-01-13 15:00:18 -0800 (Thu, 13 Jan 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_hrk.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_hrk.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_k.h

Detangled mscore_hrk and mscore_k class extensions. mscore_hrk now directly extends mscore.
------------------------------------------------------------------------
r5283 | pcbrefugee | 2011-01-12 12:11:18 -0800 (Wed, 12 Jan 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreducehandler.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreducehelper.cpp

[xtandem - hadoop] - don't depend on presence of sed on hadoop nodes to tidy up path names in final result file (more efficient to do it in memory before writing the file, anyway)
------------------------------------------------------------------------
r5282 | pcbrefugee | 2011-01-07 19:26:17 -0800 (Fri, 07 Jan 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/README-MAPREDUCE
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreduce_helper.py
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreducehelper.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/xtandem_mapreduce.py

[xtandem] support for hadoop clusters that aren't hosted by Amazon Web Services.  Horribly, this involves cygwin if you want to run it on Windows.
------------------------------------------------------------------------
r5281 | real_procopio | 2011-01-04 15:10:22 -0800 (Tue, 04 Jan 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Tandem2XML/TandemResultsParser.cxx
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Tandem2XML/TandemResultsParser.h

[Tandem2XML] Add support for z,c,a,x ion series; report correct number of potential peaks based on ion series used in search
------------------------------------------------------------------------
r5280 | real_procopio | 2011-01-04 10:01:08 -0800 (Tue, 04 Jan 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/Makefile

Set the permissions on the png files (was a copy/paste error)
------------------------------------------------------------------------
r5279 | dshteyn | 2011-01-03 16:11:00 -0800 (Mon, 03 Jan 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/RAMPAdapter.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/ramp/ramp.h

Allow InteractParser (or RAMP in general) to read FAIMS Compensation Voltage from mzML filter line. TODO: need to make sure this makes it into the real PWIZ.
------------------------------------------------------------------------
r5278 | real_procopio | 2011-01-03 11:07:30 -0800 (Mon, 03 Jan 2011) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/Makefile

Corrected path to src root
------------------------------------------------------------------------
r5277 | real_procopio | 2010-12-30 17:14:37 -0800 (Thu, 30 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/installer_win32/TPP_files.nsh

Adding Lorikeet viewer to Windows installer
------------------------------------------------------------------------
r5276 | real_procopio | 2010-12-30 17:13:58 -0800 (Thu, 30 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Makefile

Adding Lorikeet viewer to Makefile
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r5275 | real_procopio | 2010-12-30 17:12:24 -0800 (Thu, 30 Dec 2010) | 1 line
Changed paths:
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/Makefile
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/css
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/css/lorikeet.css
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/images
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/images/header_lorikeet.png
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/images/header_scan.png
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/images/header_text.png
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/images/lorikeet_text_small.png
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/images/slider_handle.png
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/images/zoom_in.png
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/images/zoom_out.png
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/js
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/js/aminoacid.js
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/js/excanvas.min.js
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/js/ion.js
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/js/jquery-ui.min.js
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/js/jquery.flot.js
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/js/jquery.flot.selection.js
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/js/jquery.min.js
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/js/peptide.js
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/js/specview.js
   A /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms2.cxx

Adding Lorikeet viewer
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r5274 | pcbrefugee | 2010-12-27 16:14:15 -0800 (Mon, 27 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Makefile

htmldoc config doesn't handle MinGW, don't attempt to build it there
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r5273 | pcbrefugee | 2010-12-27 15:46:31 -0800 (Mon, 27 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sqt2XML/Sqt2XML.h

[Sqt2XML] include stdlib.h for best portability (some compilers weren't finding atoi(), etc)
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r5272 | pcbrefugee | 2010-12-27 15:45:09 -0800 (Mon, 27 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXField.cxx

cast for quiet compile
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r5271 | pcbrefugee | 2010-12-27 15:38:42 -0800 (Mon, 27 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/InterProphetParser.vcproj
   M /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/InterProphetParservc8.vcproj

[InterProphetParser] add a couple of new files to MSVC InterProphetParser build files
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r5270 | pcbrefugee | 2010-12-27 15:08:34 -0800 (Mon, 27 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Validation/DiscriminateFunction/Comet/CometDiscrimValMixtureDistr.cxx
   M /trunk/trans_proteomic_pipeline/src/Validation/DiscriminateFunction/Comet/CometDiscrimValMixtureDistr.h
   M /trunk/trans_proteomic_pipeline/src/Validation/DiscriminateFunction/DiscrimValMixtureDistr.cxx
   M /trunk/trans_proteomic_pipeline/src/Validation/DiscriminateFunction/DiscrimValMixtureDistr.h
   M /trunk/trans_proteomic_pipeline/src/Validation/DiscriminateFunction/Mascot/MascotDiscrimValMixtureDistr.cxx
   M /trunk/trans_proteomic_pipeline/src/Validation/DiscriminateFunction/Mascot/MascotDiscrimValMixtureDistr.h
   M /trunk/trans_proteomic_pipeline/src/Validation/DiscriminateFunction/ProbID/ProbIDDiscrimValMixtureDistr.cxx
   M /trunk/trans_proteomic_pipeline/src/Validation/DiscriminateFunction/ProbID/ProbIDDiscrimValMixtureDistr.h
   M /trunk/trans_proteomic_pipeline/src/Validation/DiscriminateFunction/SpectraST/SpectraSTDiscrimValMixtureDistr.cxx
   M /trunk/trans_proteomic_pipeline/src/Validation/DiscriminateFunction/SpectraST/SpectraSTDiscrimValMixtureDistr.h

C++ standard (or at least, older, portable revs of the standard) doesn't allow a ctor to call another variant of itself.  But we can use default parameter values instead to achieve the same effect.
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r5269 | pcbrefugee | 2010-12-27 14:21:35 -0800 (Mon, 27 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/MzXML2Search/MzXML2Search.cxx

[mzXML2Search] add a couple of signed/unsigned casts for quiet compile
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r5268 | pcbrefugee | 2010-12-27 13:24:06 -0800 (Mon, 27 Dec 2010) | 1 line
Changed paths:
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/ClickwrapPrompter.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/ClickwrapPrompterTest.cpp

[owiz] sigh, and couple more missed adds, probably not the last
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r5267 | pcbrefugee | 2010-12-27 13:18:21 -0800 (Mon, 27 Dec 2010) | 1 line
Changed paths:
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/MS2NoiseFilter.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRefine.cpp

[pwiz] missed a couple of adds
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r5266 | pcbrefugee | 2010-12-27 13:02:26 -0800 (Mon, 27 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/Jamroot.jam
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/boost/iostreams
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/boost/iostreams/arbitrary_positional_facade.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/boost/iostreams/filter
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/boost/iostreams/filter/base64.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools/bcp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools/bcp/CMakeLists.txt
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools/bcp/Jamfile.v2
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools/bcp/add_path.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools/bcp/bcp.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools/bcp/bcp.html
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools/bcp/bcp_imp.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools/bcp/bcp_imp.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools/bcp/copy_path.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools/bcp/file_types.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools/bcp/fileview.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools/bcp/fileview.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools/bcp/index.html
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools/bcp/licence_info.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools/bcp/licence_info.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools/bcp/main.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools/bcp/output_licence_info.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools/bcp/path_operations.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools/bcp/scan_cvs_path.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/boost_aux/tools/bcp/scan_licence.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/ext-boost.jam
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/libsvm-3.0
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/libsvm-3.0/COPYRIGHT
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/libsvm-3.0/Jamfile.jam
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/libsvm-3.0/README
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/libsvm-3.0/svm-model2code.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/libsvm-3.0/svm.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/libsvm-3.0/svm.h
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/libraries/tar.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/Version.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/Version.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/calibration/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/chromatogram_processing/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/common/DataFilter.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/common/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/eharmony/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/frequency/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/passive/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/passive/MSDataCache.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/passive/Pseudo2DGel.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/peakdetect/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/peptideid/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/proteome_processing/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/Jamfile.jam
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/MS2Deisotoper.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/MS2Deisotoper.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/MS2NoiseFilter.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/PrecursorMassFilter.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/PrecursorMassFilter.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumListFactory.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumListFactoryTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_ChargeStateCalculator.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_ChargeStateCalculatorTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_Filter.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_Filter.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_PeakFilterTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_PeakPicker.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRefine.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRefineTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/ThresholdFilter.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/analysis/spectrum_processing/ThresholdFilter.hpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/common/BrendaTissueOBO.obo
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/common/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/common/ParamTypes.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/common/ParamTypes.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/common/ParamTypesTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/misc/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/misc/PeakData.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/ChromatogramList_mzML.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/IO.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/LegacyAdapter.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/LegacyAdapterTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/RAMPAdapter.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/RAMPAdapter.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/Serializer_mzXML.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumList_MGF.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumList_MGF_Test.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumList_mzML.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumList_mzXML.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/SpectrumList_mzXML_Test.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/Version.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/examples.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/ramp/ramp.h
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/DelimReader.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/DelimWriter.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Diff.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/DiffTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/IO.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Jamfile.jam
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/MascotReader.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/MascotReader.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/MascotReader_dummy.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/MzIdentML.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/MzIdentML.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Pep2MzIdent.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Serializer_mzid.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Serializer_mzid.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Serializer_pepXML.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/TextWriter.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/Version.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/mziddata/mascotutil.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/Serializer_FASTA.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/proteome/Version.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/tradata/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/tradata/Version.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/ChromatogramList_ABI.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/Jamfile.jam
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/Reader_ABI.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/Reader_ABI.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/Reader_ABI_Detail.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/Reader_ABI_Detail.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/Reader_ABI_Test.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/Reader_ABI_Test.data.tar.bz2
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/Reader_ABI_Test.exe.config
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/SpectrumList_ABI.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/SpectrumList_ABI.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/T2D
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/T2D/Jamfile.jam
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D_Detail.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D_Detail.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D_Test.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D_Test.data.tar.bz2
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/T2D/SpectrumList_ABI_T2D.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ABI/T2D/SpectrumList_ABI_T2D.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Agilent/ChromatogramList_Agilent.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Agilent/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Agilent/Reader_Agilent_Detail.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Agilent/SpectrumList_Agilent.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Bruker
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Bruker/ChromatogramList_Bruker.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Bruker/ChromatogramList_Bruker.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Bruker/Jamfile.jam
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Bruker/Reader_Bruker.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Bruker/Reader_Bruker.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Bruker/Reader_Bruker_Detail.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Bruker/Reader_Bruker_Detail.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Bruker/Reader_Bruker_Test.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Bruker/Reader_Bruker_Test.data.tar.bz2
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Bruker/SpectrumList_Bruker.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Bruker/SpectrumList_Bruker.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/ExtendedReaderList.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Thermo/ChromatogramList_Thermo.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Thermo/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Thermo/Reader_Thermo.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Thermo/Reader_Thermo_Detail.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Thermo/SpectrumList_Thermo.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Thermo/SpectrumList_Thermo.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/ChromatogramList_Waters.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/ChromatogramList_Waters.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/Jamfile.jam
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/Reader_Waters.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/Reader_Waters.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/Reader_Waters_Detail.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/Reader_Waters_Detail.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/Reader_Waters_Test.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/Reader_Waters_Test.data.tar.bz2
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/Reader_Waters_Test_Legacy.data.tar.bz2
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/SpectrumList_Waters.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/vendor_readers/Waters/SpectrumList_Waters.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/analysis/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/analysis/spectrum_processing.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/analysis/spectrum_processing.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/analysis/spectrum_processing_test.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/common/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/common/ParamTypes.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/common/ParamTypes.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/common/ParamTypesTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/msdata/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/bindings/CLI/proteome/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/chemistry/Ion.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/chemistry/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/math/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/math/qr.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/math/round.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/minimxml/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/minimxml/SAXParser.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/minimxml/SAXParser.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/minimxml/SAXParserTest.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/ClickwrapPrompter.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/FilesystemTest.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/IterationListener.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/misc/VendorReaderTestHarness.cpp
   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/proteome/Jamfile.jam
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/utility/vendor_api
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/Jamfile.jam
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/ABI/ChromatogramList_ABI.cpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/ABI/ChromatogramList_ABI.hpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/ABI/Jamfile.jam
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/ABI/Reader_ABI.cpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/ABI/Reader_ABI.hpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/ABI/Reader_ABI_Detail.cpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/ABI/Reader_ABI_Detail.hpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/ABI/Reader_ABI_Test.cpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/ABI/SpectrumList_ABI.cpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/ABI/SpectrumList_ABI.hpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/ABI/T2D
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Bruker/ChromatogramList_Bruker.cpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Bruker/ChromatogramList_Bruker.hpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Bruker/Jamfile.jam
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Bruker/Reader_Bruker.cpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Bruker/Reader_Bruker.hpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Bruker/Reader_Bruker_Detail.cpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Bruker/Reader_Bruker_Detail.hpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Bruker/Reader_Bruker_Test.cpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Bruker/SpectrumList_Bruker.cpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Bruker/SpectrumList_Bruker.hpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Jamfile.jam
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Waters/ChromatogramList_Waters.cpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Waters/ChromatogramList_Waters.hpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Waters/Jamfile.jam
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Waters/Reader_Waters.cpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Waters/Reader_Waters.hpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Waters/Reader_Waters_Detail.cpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Waters/Reader_Waters_Detail.hpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Waters/Reader_Waters_Test.cpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Waters/SpectrumList_Waters.cpp
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/data/vendor_readers/Waters/SpectrumList_Waters.hpp
   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/Jamfile.jam
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/ABI/stub
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/BaseCommon.dll
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/BaseDataAccess.dll
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/BaseError.dll
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/BaseTof.dll
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/Documents
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/Documents/API for 3rd Party.doc
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/Documents/Instructions to use the 3rd Party Pool.doc
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/Documents/ReleaseNotes.doc
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/EULA.MHDAC
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/Jamfile.jam
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/MassHunterData.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/MassHunterData.hpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/MassHunterDataTest.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/MassSpecDataReader.dll
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Agilent/agtsampleinforw.dll
   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/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Waters/Jamfile.jam
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/Waters/stub
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/EULA.MSFileReader
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/Jamfile.jam
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/MSFileReader.XRawfile2.SxS.manifest
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/Microsoft.VC90.MFC
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/Microsoft.VC90.MFC/Microsoft.VC90.MFC.manifest
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/Microsoft.VC90.MFC/mfc90.dll
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/Microsoft.VC90.MFC/mfc90u.dll
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/Microsoft.VC90.MFC/mfcm90.dll
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/Microsoft.VC90.MFC/mfcm90u.dll
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/RawFile.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/RawFile.h
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/RawFileCOM.h
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/RawFileTest.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/RawFileTypes.h
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/RawFileValues.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/RawFileValues.h
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/ScanFilter.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/ScanFilter.h
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/ScanFilterTest.cpp
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/Thermo_CVTerms.xls
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/xrawfile2.tlh
   A /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_aux/sfcap/proctran/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_aux/sfcap/transient/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/SeeMS/Annotation.cs
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/SeeMS/Dialogs/ChromatogramListForm.cs
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/SeeMS/Dialogs/GraphForm.cs
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/SeeMS/Dialogs/SpectrumAnnotationForm.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/Manager.cs
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/SeeMS/Types.cs
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/SeeMS/seems.cs
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/commandline/Jamfile.jam
   A /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/commandline/mascot2mzid.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
   D /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/common/FullReaderList.cpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/common/FullReaderList.hpp
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/common/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/examples/Jamfile.jam
   M /trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz_tools/examples/msbenchmark.cpp
   M /trunk/trans_proteomic_pipeline/src/Makefile.pwiz.incl
   M /trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms1.cxx
   M /trunk/trans_proteomic_pipeline/src/Visualization/xinteract/xinteract.cxx
   M /trunk/trans_proteomic_pipeline/src/pwiz/pwiz.vcproj
   M /trunk/trans_proteomic_pipeline/src/pwiz/pwizvc8.vcproj
   M /trunk/trans_proteomic_pipeline/src/tpp.vsprops
   M /trunk/trans_proteomic_pipeline/src/tpp_common_debug.vsprops

Get current with ProteoWizard (SVN 2435) in anticipation of mzML read performance enhancements.  Note you'll probably need to do a "make clean-pwiz pwiz".
------------------------------------------------------------------------
r5265 | pcbrefugee | 2010-12-23 13:43:22 -0800 (Thu, 23 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/mzXML/converters/ReAdW/FilterLine.cpp

revert to previous version - last committed code cannot be built.  Missing comma in initializer list, references to class members not declared in class header, kind of a mess.
------------------------------------------------------------------------
r5264 | dshteyn | 2010-12-23 10:43:24 -0800 (Thu, 23 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Tandem2XML/TandemResultsParser.cxx

Filter out extension from Tandem spectrum names.
------------------------------------------------------------------------
r5263 | pcbrefugee | 2010-12-22 15:36:55 -0800 (Wed, 22 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mapreducehandler.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mapreducehelper.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mapreducehelper.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mapreducehelper_bangbang.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mhistogram.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mprocess.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mprocess.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore_k.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore_tandem.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/msequence.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/serialize.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/serialize.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/tandem.cpp

[xtandem] add ifdef guards around the new multinode (Hadoop/MPI) stuff - makes it easier to identify those changes against the official tandem code, and makes it easier on folks trying hard to keep boost out their builds.
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r5262 | pcbrefugee | 2010-12-22 15:34:46 -0800 (Wed, 22 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreducehelper.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mprocess.cpp

[xtandem] a couple more ifdef guards around the new multinode (Hadoop/MPI) stuff - makes it easier to identify those changes against the official tandem code, and makes it easier on folks trying hard to keep boost out their builds.
------------------------------------------------------------------------
r5261 | pcbrefugee | 2010-12-22 15:15:49 -0800 (Wed, 22 Dec 2010) | 2 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/Makefile
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreducehandler.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreducehelper.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreducehelper_bangbang.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mhistogram.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mprocess.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mprocess.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_k.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_tandem.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/msequence.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/serialize.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/serialize.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/tandem.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/xtandem.vcproj
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/xtandemvc8.vcproj

[xtandem] add ifdef guards around the new multinode (Hadoop/MPI) stuff - makes it easier to identify those changes against the official tandem code, and makes it easier on folks trying hard to keep boost out their builds.
Also add the new scoring functions to the MSVC builds.
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r5260 | pcbrefugee | 2010-12-22 15:10:07 -0800 (Wed, 22 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_hrk.cpp

add some explicit double->float casts for quiet compile
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r5259 | mhoopmann | 2010-12-22 14:48:13 -0800 (Wed, 22 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore.cpp

bugfix relating to hrK-score
------------------------------------------------------------------------
r5258 | pcbrefugee | 2010-12-22 13:37:27 -0800 (Wed, 22 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxmzmlhandler.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxmzmlhandler.h

[tandem native mzML reader] - completely untested changes to enable reading of zlib-compressed peaks in mzML, for Joe's perusal (nothing else in this directory is expected to work yet either so I don't feel bad). 
------------------------------------------------------------------------
r5257 | mhoopmann | 2010-12-22 12:42:28 -0800 (Wed, 22 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mbiomlreport.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mprocess.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mprocess.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mreport.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_c.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_c.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_hrk.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_hrk.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_k.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_k.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_tandem.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/msequtilities.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/msequtilities.h

Added two new scoring functions, and expanded virtual function declarations in mscore.h to allow more functions to be overloaded in the pluggable algorithms. Also changed A-ions to use A-dot.
------------------------------------------------------------------------
r5256 | pcbrefugee | 2010-12-20 13:04:38 -0800 (Mon, 20 Dec 2010) | 16 lines
Changed paths:
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/README
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/base64.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/base64.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/expat.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/expat_external.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/expat_external_old.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/expat_old.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/loadmspectrum.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/loadmspectrum.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/masscalc.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/masscalc.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mbiomlreport.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mbiomlreport.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mcleave.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mdomains.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mhistogram.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mmotif.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mpam.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mpam.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mplugin.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mplugin.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mpmods.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mpmods.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mprocess.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mprocess.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mrefine.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mrefine.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mreport.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mreport.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mscore.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mscore.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mscore_tandem.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mscore_tandem.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mscorepam.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mscorestate.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/msemistate.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/msequence.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/msequencecollection.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/msequencecollection.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/msequenceserver.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/msequenceserver.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/msequtilities.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/msequtilities.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mspectrum.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mspectrumcondition.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mspectrumcondition.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mtermmods.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mtermmods.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mxxcleavage.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/mxxcleavage.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/p3.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/p3mprocess.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/p3mprocess.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/p3msequenceserver.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/p3msequenceserver.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/release_notes.html
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/resource.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/saxbiomlhandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/saxbiomlhandler.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/saxgamlhandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/saxgamlhandler.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/saxhandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/saxhandler.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/saxmodhandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/saxmodhandler.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/saxmzdatahandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/saxmzdatahandler.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/saxmzmlhandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/saxmzmlhandler.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/saxmzxmlhandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/saxmzxmlhandler.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/saxsaphandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/saxsaphandler.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/saxtandeminputhandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/saxtandeminputhandler.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/saxtaxhandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/saxtaxhandler.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/stdafx.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/stdafx.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/tandem.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/xmlparameter.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/xmlparameter.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/xmltaxonomy.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_cyclone/xmltaxonomy.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/README
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/base64.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/base64.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/expat.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/expat_external.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/expat_external_old.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/expat_old.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/loadmspectrum.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/loadmspectrum.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mapreducehandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mapreducehelper.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mapreducehelper.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mapreducehelper_bangbang.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/masscalc.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/masscalc.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mbiomlreport.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mbiomlreport.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mcleave.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mdomains.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mhistogram.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mmotif.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mpam.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mpam.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mplugin.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mplugin.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mpmods.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mpmods.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mprocess.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mprocess.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mrefine.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mrefine.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mreport.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mreport.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore_k.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore_k.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore_tandem.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscore_tandem.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscorepam.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mscorestate.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/msemistate.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/msequence.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/msequencecollection.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/msequencecollection.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/msequenceserver.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/msequenceserver.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/msequtilities.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/msequtilities.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mspectrum.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mspectrumcondition.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mspectrumcondition.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mtermmods.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mtermmods.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mxxcleavage.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/mxxcleavage.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/p3.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/p3mprocess.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/p3mprocess.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/p3msequenceserver.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/p3msequenceserver.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/resource.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxbiomlhandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxbiomlhandler.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxgamlhandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxgamlhandler.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxhandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxhandler.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxmodhandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxmodhandler.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxmzdatahandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxmzdatahandler.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxmzmlhandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxmzmlhandler.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxmzxmlhandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxmzxmlhandler.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxsaphandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxsaphandler.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxtandeminputhandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxtandeminputhandler.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxtaxhandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/saxtaxhandler.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/serialize.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/serialize.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/stdafx.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/stdafx.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/tandem.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/timer.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/timer.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/xmlparameter.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/xmlparameter.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/xmltaxonomy.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/xmltaxonomy.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/xtandem.vcproj
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src_merged/xtandemvc8.vcproj

[xtandem - defork work]  Adding a couple of directories for inspection by other developers - these are *not* part of the build.

src_merged - this is my proposed but INCOMPLETE merge of current (12/1/2010) official X!Tandem code with our current src directory, as of SVN rev 5252 (so it includes my Hadoop work).  It should compile just fine but I've not tried to run any data through it yet - there are questions to be answered first.

src_cyclone - this is unaltered code from the 12/1/2010 release of X!Tandem, for comparison purposes, don't edit this, and don't expect it to compile.


RISKS

This is a long delayed update of a forked project, and I worry about possibly having tossed out changes made from the ISB/LabKey/Insilicos camp but not commented as such.  Somebody other than and in addition to me should do a careful before-and-after comparison across the whole directory.

The mscore area is of greatest concern - my sense is that there are substantial changes needed to the k score because there are substantial changes to the standard tandem scoring function since our last synch-up.   Do a 3-way diff src_merged,  src_cyclone, and src to get a feel for the changes.  The src_cyclone code really punted on this one with an ifdef for pluggable scoring that, to my eye, screams "you are falling behind".   I do wonder though how much of the new work really belongs in the mscore class instead of the mscore_tandem child class it's in now.
 
We should look hard at replacing the pwiz code with the new mzML read code, although I've not really given it the once over.  Probably doesn't do compressed peaklists at the moment if its consistent with the tandem mzXML read code.

There's a fair bit of customization on our side in mspectrumcondition.cpp, around max mass and max charge.  It looks to me like the official code is buggy, I put an email in.  Ron's response is that yes, a lot of that is cruft.  I've offered him a patch including the max mass filter.
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r5255 | ppatrick | 2010-12-20 07:57:57 -0800 (Mon, 20 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/mzXML/converters/ReAdW/FilterLine.cpp

Fixed bug in parsing filterLine containing sa (supplemental activation) param. [MS2 scans with sa where being converted as msLevel=0]
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r5254 | pcbrefugee | 2010-12-17 09:06:33 -0800 (Fri, 17 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/Parser/Parser.cxx

[general XML file handling] add a retry loop to the overwrite routine's success checker to accomodate slow file systems (such as network shares)
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r5253 | pcbrefugee | 2010-12-17 09:03:38 -0800 (Fri, 17 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTSpLibImporter.cpp

[SpecraST] a couple of int/unsigned casts for quiet compile
------------------------------------------------------------------------
r5252 | pcbrefugee | 2010-12-15 14:43:15 -0800 (Wed, 15 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreducehandler.cpp

[xtandem/hadoop] - tidier exit on success
------------------------------------------------------------------------
r5251 | pcbrefugee | 2010-12-15 13:00:34 -0800 (Wed, 15 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/uncompress_win_lib.bat

[MSVC build] add a little build-time message explaining the need for MinGW even when using MSVC, and pointing the developer at the README_WIN.txt file
------------------------------------------------------------------------
r5250 | slagelwa | 2010-12-13 16:38:52 -0800 (Mon, 13 Dec 2010) | 2 lines
Changed paths:
   D /branches/2008Express

Removing defunct branch to build TPP under Visual Studio 2008 Express

------------------------------------------------------------------------
r5249 | dshteyn | 2010-12-13 11:47:54 -0800 (Mon, 13 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx

Fix bug with output of precursor_intensity.
------------------------------------------------------------------------
r5248 | pcbrefugee | 2010-12-13 10:32:29 -0800 (Mon, 13 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Makefile

[xtandem] fix the linux "make install" target that I broke when I changed the build artifact for linux from "tandem.exe" to just "tandem"
------------------------------------------------------------------------
r5247 | pcbrefugee | 2010-12-10 17:06:33 -0800 (Fri, 10 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/installer_linux/publish_tandem_to_s3.sh
   A /trunk/trans_proteomic_pipeline/installer_linux/tandem_arch.sh

[xtandem+hadoop] move the code that identifies machine type into its own script for use by bundler and installers alike
------------------------------------------------------------------------
r5246 | dshteyn | 2010-12-10 16:26:41 -0800 (Fri, 10 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Validation/iModelParser/IModelParser.cxx
   M /trunk/trans_proteomic_pipeline/src/Validation/iModelParser/IModelParser.h

iModelParser.cgi: fix bugs with getting page to display.  Now displays but the overlapping colors of gnuplot don't work.  For best results use gnuplot 4.4
------------------------------------------------------------------------
r5245 | pcbrefugee | 2010-12-10 15:29:23 -0800 (Fri, 10 Dec 2010) | 1 line
Changed paths:
   A /trunk/trans_proteomic_pipeline/installer_linux/publish_tandem_to_s3.sh

[xtandem+hadoop] a script for building xtandem (and x!!tandem if possible) and publishing to S3 for use in EC2 or other clusters via wget
------------------------------------------------------------------------
r5244 | pcbrefugee | 2010-12-10 15:27:40 -0800 (Fri, 10 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/installer_linux/amazon_ec2_bootstrap.sh
   M /trunk/trans_proteomic_pipeline/installer_linux/amazon_ec2_installer.sh

[EC2 build] warn rather than fail when CentOS version is identified as other than 5.2
------------------------------------------------------------------------
r5243 | pcbrefugee | 2010-12-10 14:14:54 -0800 (Fri, 10 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/serialize.h

quiet a "no newline at end of file" warning
------------------------------------------------------------------------
r5242 | dshteyn | 2010-12-10 00:26:53 -0800 (Fri, 10 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXField.cxx
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PipelineAnalysis.cxx

PepXMLViewer: adding collision_energy, precursor_intensity and compensation_voltage
------------------------------------------------------------------------
r5241 | dshteyn | 2010-12-10 00:18:05 -0800 (Fri, 10 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PipelineAnalysis.cxx

PepXMLViewer: support for Crux
------------------------------------------------------------------------
r5240 | dshteyn | 2010-12-10 00:16:24 -0800 (Fri, 10 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/schema/pepXML_v117.xsd
   M /trunk/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx
   M /trunk/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.h
   M /trunk/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParserMain.cxx
   M /trunk/trans_proteomic_pipeline/src/Visualization/xinteract/xinteract.cxx

InteractParser,xinteract: new feature precursor intensity in pepXML
------------------------------------------------------------------------
r5239 | pcbrefugee | 2010-12-09 17:35:41 -0800 (Thu, 09 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/extern/xtandem/README-TPP
   M /trunk/trans_proteomic_pipeline/extern/xtandem/readme
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/Makefile
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src/README-MAPREDUCE
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreduce_helper.py
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreducehandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreducehelper.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreducehelper.h
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src/mapreducehelper_bangbang.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/masscalc.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mhistogram.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mmotif.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mprocess.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mprocess.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_k.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscore_tandem.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mscorestate.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/msemistate.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/msequence.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/msequenceserver.cpp
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/msequtilities.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/mspectrumcondition.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/saxtaxhandler.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src/serialize.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src/serialize.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/stdafx.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/tandem.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src/timer.cpp
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src/timer.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/xmlparameter.h
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/xtandem.vcproj
   A /trunk/trans_proteomic_pipeline/extern/xtandem/src/xtandem_mapreduce.py
   M /trunk/trans_proteomic_pipeline/extern/xtandem/src/xtandemvc8.vcproj
   M /trunk/trans_proteomic_pipeline/src/Makefile

[xtandem] - extending the TPP fork of X!Tandem to optionally encompass the X!!Tandem MPI capability (make target "bbtandem", needs MPICH2 devkit) and to operate under MapReduce when used with special commandline arguments (see xtandem_mapreduce.py invocation script).  Currently targeted at Amazon Web Services Elastic MapReduce service but work is ongoing to make it useful on straight-up Hadoop clusters (that is, without the amazon API frontending it).  Not fabulously well documented yet, but have a look at README-MAPREDUCE for some details.
------------------------------------------------------------------------
r5238 | dshteyn | 2010-12-09 10:50:09 -0800 (Thu, 09 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/ramp/ramp.cpp
   M /trunk/trans_proteomic_pipeline/src/Parsers/ramp/ramp.h

RAMP: adding parsing of compensationVoltage (FAIMS).
------------------------------------------------------------------------
r5237 | dshteyn | 2010-12-08 11:23:30 -0800 (Wed, 08 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/common/constants.h

pepXML schema update for collision_energy and compensation_voltage
------------------------------------------------------------------------
r5236 | dshteyn | 2010-12-08 11:18:18 -0800 (Wed, 08 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/xinteract/xinteract.cxx

xinteract: New features, report collision energy, report compensation voltage
------------------------------------------------------------------------
r5235 | dshteyn | 2010-12-08 11:08:18 -0800 (Wed, 08 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.cxx
   M /trunk/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParser.h
   M /trunk/trans_proteomic_pipeline/src/Visualization/InteractParser/InteractParserMain.cxx

InteractParser: New features, report collision energy, report compensation voltage, fix Q[111] and E[111] modification reporting in pepXML for OMSSA, max rank option to not report hits above a certain hit_rank.
------------------------------------------------------------------------
r5234 | dshteyn | 2010-12-07 15:27:09 -0800 (Tue, 07 Dec 2010) | 1 line
Changed paths:
   A /trunk/trans_proteomic_pipeline/schema/pepXML_v117.xsd

Adding collision energy and compensation voltage for FAIMS as optional attributes in pepXML schema spectrum_query
------------------------------------------------------------------------
r5233 | slagelwa | 2010-12-07 14:56:42 -0800 (Tue, 07 Dec 2010) | 4 lines
Changed paths:
   A /trunk/trans_proteomic_pipeline/schema/mzXML_3.2.xsd

Added HCD and ETD+SA to the activationMethod attribute
Added compensationVoltage to the scan element


------------------------------------------------------------------------
r5232 | slagelwa | 2010-12-07 11:13:10 -0800 (Tue, 07 Dec 2010) | 8 lines
Changed paths:
   A /trunk/trans_proteomic_pipeline/schema/mzXML_3.1.xsd

Adding mzXML 3.1 version.  This file was obtained from:

http://sashimi.sourceforge.net/schema_revision/mzXML_3.1/mzXML_3.1.xsd.

I'm presuming that this is the correct file, and that this
is the correct location in subversion for these files.


------------------------------------------------------------------------
r5231 | real_procopio | 2010-12-02 15:06:33 -0800 (Thu, 02 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/CGI/tpp_gui/nigms.jpg

New NIGMS imagem -- with thick border!
------------------------------------------------------------------------
r5230 | real_procopio | 2010-12-02 15:03:51 -0800 (Thu, 02 Dec 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/installer_win32/TPP_files.nsh

Use new NIGMS image instead of NHLBI
------------------------------------------------------------------------
r5229 | real_procopio | 2010-12-02 14:55:06 -0800 (Thu, 02 Dec 2010) | 4 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl

[Petunia]
Added mouse-over tooltips for menu items and navigation tabs;
Added NIGMS logo and credits; replacing NHLBI's

------------------------------------------------------------------------
r5228 | real_procopio | 2010-12-02 14:53:29 -0800 (Thu, 02 Dec 2010) | 1 line
Changed paths:
   A /trunk/trans_proteomic_pipeline/CGI/tpp_gui/nigms.jpg

New NIGMS image
------------------------------------------------------------------------
r5227 | real_procopio | 2010-12-01 17:11:04 -0800 (Wed, 01 Dec 2010) | 5 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl

[Petunia]
Added user input to pass parameters directly to the command-line (certain executables at this time), including simple validation;
Added support for two missing enzymes in ->pepXML, as well as semi-enzyme support;
Minor bug fix when file is not present (as opposed to unreadable).

------------------------------------------------------------------------
r5226 | slagelwa | 2010-12-01 17:03:18 -0800 (Wed, 01 Dec 2010) | 2 lines
Changed paths:
   A /trunk/trans_proteomic_pipeline/extern/hpctools/grid/templates
   A /trunk/trans_proteomic_pipeline/extern/hpctools/grid/templates/README
   A /trunk/trans_proteomic_pipeline/extern/hpctools/grid/templates/inspect.params
   A /trunk/trans_proteomic_pipeline/extern/hpctools/grid/templates/omssa.params
   A /trunk/trans_proteomic_pipeline/extern/hpctools/grid/templates/tandem.params

Added inspect.params templates and checkin in omssa, tandem, README

------------------------------------------------------------------------
r5225 | real_procopio | 2010-11-30 14:36:01 -0800 (Tue, 30 Nov 2010) | 11 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl

Adjusted Xpress defaults;
Centralized code that creates links to open files in respective viewers;
Fixed broken Set Working Dir feature, also fixed link when output is a directory;
Added direct access to switch a directory in File Browser;
Moved "timeout" link to the right to avoid overlap with update page link;
Added confirmation message when switching pipeline type;
Shortened some menu titles to save space;
Updated meaning of $in_windows and introduced $in_cygwin vars;
Removed some seemingly unused code;
Small code formatting/alignment changes.

------------------------------------------------------------------------
r5224 | real_procopio | 2010-11-30 14:33:42 -0800 (Tue, 30 Nov 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.css

Menus are now semi-transparent in Chrome
------------------------------------------------------------------------
r5223 | pcbrefugee | 2010-11-23 15:43:28 -0800 (Tue, 23 Nov 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/installer_linux/amazon_ec2_bootstrap.sh
   M /trunk/trans_proteomic_pipeline/installer_linux/amazon_ec2_installer.sh

[build] default to Ubuntu 9_x on AWS is Ubuntu distro isn't recognised (because it's Ubuntu 10-something, probably, but try 9_x tool set since it probably works fine)
------------------------------------------------------------------------
r5222 | henrylam | 2010-11-17 20:13:36 -0800 (Wed, 17 Nov 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLibEntry.cpp

[SpectraST] Shorten peak annotation to save memory during search
------------------------------------------------------------------------
r5221 | henrylam | 2010-11-17 20:05:28 -0800 (Wed, 17 Nov 2010) | 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/SpectraSTLibEntry.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLibEntry.hpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPepXMLLibImporter.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTReplicates.cpp

[SpectraST] Add massdiff information to library. Option to exclude IDs of too big massdiff.
------------------------------------------------------------------------
r5220 | henrylam | 2010-11-17 19:57:47 -0800 (Wed, 17 Nov 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTHtmlSearchOutput.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTSearchOutput.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTSearchParams.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTSimScores.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTSimScores.hpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTTxtSearchOutput.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTTxtSearchOutput.hpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTXlsSearchOutput.cpp
   M /trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTXlsSearchOutput.hpp

[SpectraST] Add headers to xls and txt search output. No-header format can still be had with -sEnxls and -sEntxt options
------------------------------------------------------------------------
r5219 | slagelwa | 2010-11-15 16:07:38 -0800 (Mon, 15 Nov 2010) | 2 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl

Added ability to upload files to a working directory.  Very useful if you happen to be running TPP on the cloud.

------------------------------------------------------------------------
r5218 | eng_jk | 2010-11-10 19:30:25 -0800 (Wed, 10 Nov 2010) | 2 lines
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/MzXML2Search/MzXML2Search.cxx

set ms2 format retention time to minutes

------------------------------------------------------------------------
r5217 | dshteyn | 2010-11-10 15:52:17 -0800 (Wed, 10 Nov 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/SearchResult/PhenyxResult.cxx

Fix parsing of Phenyx search results.
------------------------------------------------------------------------
r5216 | dshteyn | 2010-10-29 16:23:37 -0700 (Fri, 29 Oct 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Makefile

make SearchHit separate class for iProphet.
------------------------------------------------------------------------
r5215 | dshteyn | 2010-10-29 16:18:35 -0700 (Fri, 29 Oct 2010) | 1 line
Changed paths:
   M /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/InterProphet.cxx
   M /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/InterProphet.h
   M /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/InterProphetMain.cxx
   M /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/InterProphetParser.cxx
   M /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/InterProphetParser.h
   A /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/SearchHit.cxx
   A /trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/SearchHit.h

Clear out tophit hashes before recomputing. Separate SearchHit in a different class.

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TPP:4.5.0 Release Notes

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