TPP:4.5.0 Release Notes

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-r5394 | eng_jk | 2011-05-11 17:40:19 -0700 (Wed, 11 May 2011) | 4 lines 
-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. 
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Line 117: Line 112:
[xtandem for hadoop and mpi] a few object serialization tweaks for "refine" step support [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 
-minor mods to increase precision of mass tol in xpress chromatogram gui; replace hydrogen mass with proton mass in code 
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Line 126: Line 118:
Added scanIndex data member to BasicSpectrum and RAMP interface to provide sequential scan numbering independent of numbers used by instrument manufacturers. 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 
- 
-add -static-libstdc++ compiler flag 
- 
------------------------------------------------------------------------- 
-r5387 | eng_jk | 2011-04-27 16:26:56 -0700 (Wed, 27 Apr 2011) | 2 lines 
-Add command line option -M to allow user to specify static mods 
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[SpectraST] Add headers to xls and txt search output. No-header format can still be had with -sEnxls and -sEntxt options [SpectraST] Add headers to xls and txt search output. No-header format can still be had with -sEnxls and -sEntxt options
- 
-r5218 | eng_jk | 2010-11-10 19:30:25 -0800 (Wed, 10 Nov 2010) | 2 lines 
- 
-set ms2 format retention time to minutes 
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Line 874: Line 854:
[SpectraST] Fix bug with rarely used spectrum plotting feature; clean up SpectraSTReplicates flow [SpectraST] Fix bug with rarely used spectrum plotting feature; clean up SpectraSTReplicates flow
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-r5208 | eng_jk | 2010-10-20 15:34:46 -0700 (Wed, 20 Oct 2010) | 3 lines 
- 
-noticed crazy scan numbers in an mzXML file (agilent .d via msconvert); this 
-small change keeps status output behaving as intended for the crazy scan #s 
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[SpectraST] For faster search, more economical insert() in SpectraSTPeakList [SpectraST] For faster search, more economical insert() in SpectraSTPeakList
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-r5206 | eng_jk | 2010-10-18 15:20:01 -0700 (Mon, 18 Oct 2010) | 2 lines 
- 
-simply change from double to single space as separating char 
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htmldoc added for export to pdf htmldoc added for export to pdf
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-r5177 | eng_jk | 2010-09-20 16:05:10 -0700 (Mon, 20 Sep 2010) | 2 lines 
- 
-add check to the initialization function to avoid possible negative index value 
- 
------------------------------------------------------------------------- 
-r5176 | eng_jk | 2010-09-20 16:03:20 -0700 (Mon, 20 Sep 2010) | 2 lines 
- 
-add check to the initialization function to avoid possible negative index value 
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[RTCalculator] add missing function return values that could cause some mysterious behavior, also add various casts and more widely portable dynamic allocations to make more compilers happy [RTCalculator] add missing function return values that could cause some mysterious behavior, also add various casts and more widely portable dynamic allocations to make more compilers happy
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-r5169 | eng_jk | 2010-09-14 16:06:20 -0700 (Tue, 14 Sep 2010) | 2 lines 
- 
-fix previous check-in 
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Line 1,019: Line 977:
Fix compilation issues with iModelParser.cgi tool. Fix compilation issues with iModelParser.cgi tool.
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-r5167 | eng_jk | 2010-09-14 11:55:39 -0700 (Tue, 14 Sep 2010) | 2 lines 
- 
-add 5158 fix to trunk 
- 
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-r5166 | eng_jk | 2010-09-14 09:38:50 -0700 (Tue, 14 Sep 2010) | 4 lines 
- 
-same single readIndex call from commit 5160 going to trunk 
-update accurate fragment ion calculations 
-remove unused pepnovo code 
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Line 1,051: Line 998:
Added updates to RTCalc in Petunia including retention time training page. Added updates to RTCalc in Petunia including retention time training page.
------------------------------------------------------------------------- 
-r5160 | eng_jk | 2010-09-10 15:35:12 -0700 (Fri, 10 Sep 2010) | 2 lines 
- 
-issue readIndex call once and use for both ms/ms and ms1 plots 
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[pwiz, ramp, plot-msms.cgi] update RAMP to use new pwiz RAMPAdapter functionality for more efficient scan number lookups, for performance boost in plot-msms CGI [pwiz, ramp, plot-msms.cgi] update RAMP to use new pwiz RAMPAdapter functionality for more efficient scan number lookups, for performance boost in plot-msms CGI
------------------------------------------------------------------------- 
-r5158 | eng_jk | 2010-09-10 12:09:13 -0700 (Fri, 10 Sep 2010) | 5 lines 
- 
-Fix error of an array not being initialized (line 2910) presumably 
-introduced in last bugfix checkin. Effect was a bunch of peptides 
-not being quantified; surprised it even produced results at all. 
- 
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Revision as of 18:42, 23 May 2011

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


Trans-Proteomic Pipeline (TPP) "<name>" 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

Contents

New Features/Changes

  • TBD

Bug fixes and improvements

  • TBD

Miscellaneous

  • TBD

Known Issues

  • None to report

Getting the TPP Software

  • Download the TPP version 4.5.0 native windows installer (TPP_Setup_v4_5_name?_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 

------------------------------------------------------------------------
r5401 | mhoopmann | 2011-05-20 09:32:40 -0700 (Fri, 20 May 2011) | 1 line

Added another function from RAMP.
------------------------------------------------------------------------
r5400 | dshteyn | 2011-05-18 15:10:36 -0700 (Wed, 18 May 2011) | 1 line

InterProphetParser: BUGFIX, correct the outputting of extra </spectrum_query> tags.
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r5399 | slagelwa | 2011-05-18 11:25:26 -0700 (Wed, 18 May 2011) | 3 lines

Adding a snapshot of the new TPP Web Launcher for Amazon so I don't lose anything.


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r5398 | slagelwa | 2011-05-16 10:54:02 -0700 (Mon, 16 May 2011) | 1 line

[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

* 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

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

* 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




------------------------------------------------------------------------
r5393 | pcbrefugee | 2011-05-11 11:36:08 -0700 (Wed, 11 May 2011) | 1 line

[pwiz] synch up with official code rev 2689

------------------------------------------------------------------------
r5391 | pcbrefugee | 2011-05-03 15:51:11 -0700 (Tue, 03 May 2011) | 1 line

[xtandem for hadoop and mpi] a few object serialization tweaks for "refine" step support


------------------------------------------------------------------------
r5389 | mhoopmann | 2011-05-03 11:31:54 -0700 (Tue, 03 May 2011) | 1 line

Added scanIndex data member to BasicSpectrum and RAMP interface to provide sequential scan numbering independent of numbers used by instrument manufacturers.


------------------------------------------------------------------------
r5386 | mhoopmann | 2011-04-27 09:38:29 -0700 (Wed, 27 Apr 2011) | 1 line

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

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

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

Default precursor scan number to 0 when not provided.
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r5382 | dshteyn | 2011-04-25 11:14:51 -0700 (Mon, 25 Apr 2011) | 1 line

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

tweak for building with mingw
------------------------------------------------------------------------
r5380 | pcbrefugee | 2011-04-20 17:05:58 -0700 (Wed, 20 Apr 2011) | 1 line

avoid redefine of XML_STATIC for quiet compile
------------------------------------------------------------------------
r5379 | dshteyn | 2011-04-20 11:55:34 -0700 (Wed, 20 Apr 2011) | 1 line

Tweaks to compilation on Linux.
------------------------------------------------------------------------
r5378 | dshteyn | 2011-04-20 11:11:29 -0700 (Wed, 20 Apr 2011) | 1 line

switch to zlib v1.2.5 and tweaks fro MingW build
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r5377 | dshteyn | 2011-04-20 11:10:24 -0700 (Wed, 20 Apr 2011) | 1 line

update location of msconvert.exe
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r5376 | dshteyn | 2011-04-20 11:09:21 -0700 (Wed, 20 Apr 2011) | 1 line

update zlib version to 1.2.5
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r5375 | dshteyn | 2011-04-20 11:00:47 -0700 (Wed, 20 Apr 2011) | 1 line

switching to zlib 1.2.5
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r5374 | dshteyn | 2011-04-20 10:05:13 -0700 (Wed, 20 Apr 2011) | 1 line

MingW compilation tweaks
------------------------------------------------------------------------
r5373 | dshteyn | 2011-04-19 16:42:07 -0700 (Tue, 19 Apr 2011) | 1 line

Mingw compilation
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r5372 | dshteyn | 2011-04-19 16:41:03 -0700 (Tue, 19 Apr 2011) | 1 line

Mingw compilation
------------------------------------------------------------------------
r5371 | dshteyn | 2011-04-19 15:49:46 -0700 (Tue, 19 Apr 2011) | 1 line

InteractParser: option for recording the retention_time_sec in pepXML.

------------------------------------------------------------------------
r5369 | slagelwa | 2011-04-15 16:16:19 -0700 (Fri, 15 Apr 2011) | 13 lines

* 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

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

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

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

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

[mr-tandem] better logging and fixes for refinement step in mapreduce xtandem

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r5362 | pcbrefugee | 2011-03-31 15:48:50 -0700 (Thu, 31 Mar 2011) | 1 line

[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/

------------------------------------------------------------------------
r5360 | dshteyn | 2011-03-28 12:18:09 -0700 (Mon, 28 Mar 2011) | 1 line

GCC: anonymous struct warning.
------------------------------------------------------------------------
r5359 | dshteyn | 2011-03-25 16:31:27 -0700 (Fri, 25 Mar 2011) | 1 line

Makefile.incl was not checked in
------------------------------------------------------------------------
r5358 | dshteyn | 2011-03-25 16:00:08 -0700 (Fri, 25 Mar 2011) | 1 line

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

Makefile changes to get all this to compile with new code and mzParser.
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r5356 | dshteyn | 2011-03-25 15:33:40 -0700 (Fri, 25 Mar 2011) | 1 line

PTMProphetParser: first commit
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r5355 | dshteyn | 2011-03-25 15:24:50 -0700 (Fri, 25 Mar 2011) | 1 line

ramp -> mzParser switch
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r5354 | dshteyn | 2011-03-25 15:15:09 -0700 (Fri, 25 Mar 2011) | 1 line

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

switch ramp -> mzParser
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r5352 | dshteyn | 2011-03-25 14:55:53 -0700 (Fri, 25 Mar 2011) | 1 line

switch ramp -> mzParser
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r5351 | dshteyn | 2011-03-25 14:45:42 -0700 (Fri, 25 Mar 2011) | 1 line

XPress: switch ramp -> mzParser.
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r5350 | dshteyn | 2011-03-25 14:42:28 -0700 (Fri, 25 Mar 2011) | 1 line

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

ramp -> mzParser switch.
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r5348 | mhoopmann | 2011-03-25 12:19:23 -0700 (Fri, 25 Mar 2011) | 1 line

more legacy support
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r5347 | dshteyn | 2011-03-25 10:26:36 -0700 (Fri, 25 Mar 2011) | 1 line

Search2pepXML: converted to using mzParser instead of ramp.
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r5346 | dshteyn | 2011-03-25 10:25:00 -0700 (Fri, 25 Mar 2011) | 1 line

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

RTCatalogParser: tool for cataloging RTs
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r5344 | dshteyn | 2011-03-25 10:10:34 -0700 (Fri, 25 Mar 2011) | 1 line

Pep3D: ramp -> mzParser switch.
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r5343 | dshteyn | 2011-03-25 10:09:10 -0700 (Fri, 25 Mar 2011) | 1 line

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

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

InteractParser: Read collision energies in all msms_run_summaries, not just the first one encountered per pepXML file.
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r5340 | pcbrefugee | 2011-03-24 14:34:35 -0700 (Thu, 24 Mar 2011) | 1 line

[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

expanding more ramp functions
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r5338 | henryhlam | 2011-03-24 00:15:45 -0700 (Thu, 24 Mar 2011) | 1 line

[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

[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

[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

[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
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r5334 | henryhlam | 2011-03-17 20:59:05 -0700 (Thu, 17 Mar 2011) | 1 line

[SpectraST] Treat HCD as CID, and ETD-SA as ETD in peak annotation
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r5333 | henryhlam | 2011-03-17 20:53:18 -0700 (Thu, 17 Mar 2011) | 1 line

[SpectraST] Display Xrea (quality measure) in Lib2HTML verbose mode
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r5332 | mhoopmann | 2011-03-15 16:13:37 -0700 (Tue, 15 Mar 2011) | 1 line

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

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

Added cached RAMP support.
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r5329 | dshteyn | 2011-03-09 09:55:21 -0800 (Wed, 09 Mar 2011) | 1 line

mzParser: access was already defined in a unix header, renamed to gz_access
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r5328 | mhoopmann | 2011-03-08 15:48:48 -0800 (Tue, 08 Mar 2011) | 3 lines

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

Bugfix
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r5326 | mhoopmann | 2011-03-07 16:09:21 -0800 (Mon, 07 Mar 2011) | 1 line

Implemented readRunHeader for RAMP compatibility.
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r5325 | dshteyn | 2011-03-07 15:10:08 -0800 (Mon, 07 Mar 2011) | 1 line

Adding FAIMS CompensationVoltage to mzParser.
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r5324 | mhoopmann | 2011-03-03 08:57:34 -0800 (Thu, 03 Mar 2011) | 1 line

Expanding the parser to capture more metadata
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r5323 | pcbrefugee | 2011-03-02 13:07:11 -0800 (Wed, 02 Mar 2011) | 1 line

[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

[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

plot-msms-js.cgi: Look for lorikeet.css in DEFAULT_HTML_DIR/css not webroot/css

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r5316 | mhoopmann | 2011-02-25 12:41:43 -0800 (Fri, 25 Feb 2011) | 1 line

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

cleaning up unused file
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r5314 | mhoopmann | 2011-02-25 11:00:07 -0800 (Fri, 25 Feb 2011) | 1 line

Fixed bug when parsing empty spectra in mzXML files using RAMP interface.
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r5313 | dshteyn | 2011-02-23 11:58:02 -0800 (Wed, 23 Feb 2011) | 1 line

InteractParser: bug fix associated with parsing OMSSA data.
------------------------------------------------------------------------
r5312 | mhoopmann | 2011-02-23 09:58:24 -0800 (Wed, 23 Feb 2011) | 1 line

Fixed bug when handling uncompressed mzXML data
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r5311 | dshteyn | 2011-02-18 17:47:28 -0800 (Fri, 18 Feb 2011) | 1 line

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

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

------------------------------------------------------------------------
r5308 | dshteyn | 2011-02-15 11:26:46 -0800 (Tue, 15 Feb 2011) | 1 line

ASAPRatioProteinCGIDisplay: use central code for parsing search results to avoid error when parsing new search engine.
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r5307 | slagelwa | 2011-02-14 16:03:54 -0800 (Mon, 14 Feb 2011) | 8 lines

* 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

Added additional scoring plugins and dealt with PLUGGABLE_SCORING flag in add_A function of mscore.cpp.
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r5305 | mhoopmann | 2011-02-10 10:20:51 -0800 (Thu, 10 Feb 2011) | 1 line

Bugfixes relating to collision energy
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r5304 | pcbrefugee | 2011-02-05 23:29:58 -0800 (Sat, 05 Feb 2011) | 1 line

[PepC] fix a bug in build when ant is present

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r5299 | mhoopmann | 2011-02-01 15:28:43 -0800 (Tue, 01 Feb 2011) | 1 line

Better handling of bogus file names.
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r5298 | mhoopmann | 2011-01-31 11:46:30 -0800 (Mon, 31 Jan 2011) | 1 line

removing mzParser from VPATH
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r5297 | mhoopmann | 2011-01-31 11:10:01 -0800 (Mon, 31 Jan 2011) | 1 line

bugfixes
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r5296 | real_procopio | 2011-01-28 15:40:48 -0800 (Fri, 28 Jan 2011) | 1 line

Upgrading to revision r25 of Lorikeet
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r5295 | mhoopmann | 2011-01-28 11:15:35 -0800 (Fri, 28 Jan 2011) | 8 lines

builds mzParser now


...(hopefully)
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r5294 | mhoopmann | 2011-01-28 11:01:38 -0800 (Fri, 28 Jan 2011) | 5 lines

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

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r5293 | real_procopio | 2011-01-26 17:33:53 -0800 (Wed, 26 Jan 2011) | 1 line

[bug] Rolling back incorrect commit!
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r5292 | real_procopio | 2011-01-26 17:27:40 -0800 (Wed, 26 Jan 2011) | 1 line

Lorikeet resources: css, images, and js code
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r5291 | real_procopio | 2011-01-26 17:27:27 -0800 (Wed, 26 Jan 2011) | 1 line

Lorikeet resources: css, images, and js code
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r5290 | pcbrefugee | 2011-01-25 17:33:33 -0800 (Tue, 25 Jan 2011) | 1 line

[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.
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r5289 | pcbrefugee | 2011-01-18 16:38:58 -0800 (Tue, 18 Jan 2011) | 1 line

[xtandem-hadoop] object serialization for hadoop work
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r5288 | pcbrefugee | 2011-01-18 14:58:17 -0800 (Tue, 18 Jan 2011) | 1 line

[xtandem-hadoop] tweak for less noisy download of tandem binary from AWS S3
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r5287 | pcbrefugee | 2011-01-18 14:53:24 -0800 (Tue, 18 Jan 2011) | 1 line

[xtandem] add newline at end of file for quiet compile
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r5286 | pcbrefugee | 2011-01-18 14:51:58 -0800 (Tue, 18 Jan 2011) | 1 line

[xtandem-hadoop] tweaks for quiet compile
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r5285 | pcbrefugee | 2011-01-14 10:49:25 -0800 (Fri, 14 Jan 2011) | 1 line

[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

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

[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)
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r5282 | pcbrefugee | 2011-01-07 19:26:17 -0800 (Fri, 07 Jan 2011) | 1 line

[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.
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r5281 | real_procopio | 2011-01-04 15:10:22 -0800 (Tue, 04 Jan 2011) | 1 line

[Tandem2XML] Add support for z,c,a,x ion series; report correct number of potential peaks based on ion series used in search
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r5280 | real_procopio | 2011-01-04 10:01:08 -0800 (Tue, 04 Jan 2011) | 1 line

Set the permissions on the png files (was a copy/paste error)
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r5279 | dshteyn | 2011-01-03 16:11:00 -0800 (Mon, 03 Jan 2011) | 1 line

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.
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r5278 | real_procopio | 2011-01-03 11:07:30 -0800 (Mon, 03 Jan 2011) | 1 line

Corrected path to src root
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r5277 | real_procopio | 2010-12-30 17:14:37 -0800 (Thu, 30 Dec 2010) | 1 line

Adding Lorikeet viewer to Windows installer
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r5276 | real_procopio | 2010-12-30 17:13:58 -0800 (Thu, 30 Dec 2010) | 1 line

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

Adding Lorikeet viewer
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r5274 | pcbrefugee | 2010-12-27 16:14:15 -0800 (Mon, 27 Dec 2010) | 1 line

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

[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

cast for quiet compile
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r5271 | pcbrefugee | 2010-12-27 15:38:42 -0800 (Mon, 27 Dec 2010) | 1 line

[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

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

[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

[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

[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

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".
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r5265 | pcbrefugee | 2010-12-23 13:43:22 -0800 (Thu, 23 Dec 2010) | 1 line

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.
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r5264 | dshteyn | 2010-12-23 10:43:24 -0800 (Thu, 23 Dec 2010) | 1 line

Filter out extension from Tandem spectrum names.
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r5263 | pcbrefugee | 2010-12-22 15:36:55 -0800 (Wed, 22 Dec 2010) | 1 line

[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

[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.
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r5261 | pcbrefugee | 2010-12-22 15:15:49 -0800 (Wed, 22 Dec 2010) | 2 lines

[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

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

bugfix relating to hrK-score
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r5258 | pcbrefugee | 2010-12-22 13:37:27 -0800 (Wed, 22 Dec 2010) | 1 line

[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

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

[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.
------------------------------------------------------------------------
r5255 | ppatrick | 2010-12-20 07:57:57 -0800 (Mon, 20 Dec 2010) | 1 line

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

[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

[SpecraST] a couple of int/unsigned casts for quiet compile
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r5252 | pcbrefugee | 2010-12-15 14:43:15 -0800 (Wed, 15 Dec 2010) | 1 line

[xtandem/hadoop] - tidier exit on success
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r5251 | pcbrefugee | 2010-12-15 13:00:34 -0800 (Wed, 15 Dec 2010) | 1 line

[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
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r5250 | slagelwa | 2010-12-13 16:38:52 -0800 (Mon, 13 Dec 2010) | 2 lines

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

Fix bug with output of precursor_intensity.
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r5248 | pcbrefugee | 2010-12-13 10:32:29 -0800 (Mon, 13 Dec 2010) | 1 line

[xtandem] fix the linux "make install" target that I broke when I changed the build artifact for linux from "tandem.exe" to just "tandem"
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r5247 | pcbrefugee | 2010-12-10 17:06:33 -0800 (Fri, 10 Dec 2010) | 1 line

[xtandem+hadoop] move the code that identifies machine type into its own script for use by bundler and installers alike
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r5246 | dshteyn | 2010-12-10 16:26:41 -0800 (Fri, 10 Dec 2010) | 1 line

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

[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
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r5244 | pcbrefugee | 2010-12-10 15:27:40 -0800 (Fri, 10 Dec 2010) | 1 line

[EC2 build] warn rather than fail when CentOS version is identified as other than 5.2
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r5243 | pcbrefugee | 2010-12-10 14:14:54 -0800 (Fri, 10 Dec 2010) | 1 line

quiet a "no newline at end of file" warning
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r5242 | dshteyn | 2010-12-10 00:26:53 -0800 (Fri, 10 Dec 2010) | 1 line

PepXMLViewer: adding collision_energy, precursor_intensity and compensation_voltage
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r5241 | dshteyn | 2010-12-10 00:18:05 -0800 (Fri, 10 Dec 2010) | 1 line

PepXMLViewer: support for Crux
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r5240 | dshteyn | 2010-12-10 00:16:24 -0800 (Fri, 10 Dec 2010) | 1 line

InteractParser,xinteract: new feature precursor intensity in pepXML
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r5239 | pcbrefugee | 2010-12-09 17:35:41 -0800 (Thu, 09 Dec 2010) | 1 line

[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.
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r5238 | dshteyn | 2010-12-09 10:50:09 -0800 (Thu, 09 Dec 2010) | 1 line

RAMP: adding parsing of compensationVoltage (FAIMS).
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r5237 | dshteyn | 2010-12-08 11:23:30 -0800 (Wed, 08 Dec 2010) | 1 line

pepXML schema update for collision_energy and compensation_voltage
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r5236 | dshteyn | 2010-12-08 11:18:18 -0800 (Wed, 08 Dec 2010) | 1 line

xinteract: New features, report collision energy, report compensation voltage
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r5235 | dshteyn | 2010-12-08 11:08:18 -0800 (Wed, 08 Dec 2010) | 1 line

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.
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r5234 | dshteyn | 2010-12-07 15:27:09 -0800 (Tue, 07 Dec 2010) | 1 line

Adding collision energy and compensation voltage for FAIMS as optional attributes in pepXML schema spectrum_query
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r5233 | slagelwa | 2010-12-07 14:56:42 -0800 (Tue, 07 Dec 2010) | 4 lines

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

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

New NIGMS imagem -- with thick border!
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r5230 | real_procopio | 2010-12-02 15:03:51 -0800 (Thu, 02 Dec 2010) | 1 line

Use new NIGMS image instead of NHLBI
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r5229 | real_procopio | 2010-12-02 14:55:06 -0800 (Thu, 02 Dec 2010) | 4 lines

[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

New NIGMS image
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r5227 | real_procopio | 2010-12-01 17:11:04 -0800 (Wed, 01 Dec 2010) | 5 lines

[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).

------------------------------------------------------------------------
r5225 | real_procopio | 2010-11-30 14:36:01 -0800 (Tue, 30 Nov 2010) | 11 lines

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

Menus are now semi-transparent in Chrome
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r5223 | pcbrefugee | 2010-11-23 15:43:28 -0800 (Tue, 23 Nov 2010) | 1 line

[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)
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r5222 | henrylam | 2010-11-17 20:13:36 -0800 (Wed, 17 Nov 2010) | 1 line

[SpectraST] Shorten peak annotation to save memory during search
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r5221 | henrylam | 2010-11-17 20:05:28 -0800 (Wed, 17 Nov 2010) | 1 line

[SpectraST] Add massdiff information to library. Option to exclude IDs of too big massdiff.
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r5220 | henrylam | 2010-11-17 19:57:47 -0800 (Wed, 17 Nov 2010) | 1 line

[SpectraST] Add headers to xls and txt search output. No-header format can still be had with -sEnxls and -sEntxt options

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r5217 | dshteyn | 2010-11-10 15:52:17 -0800 (Wed, 10 Nov 2010) | 1 line

Fix parsing of Phenyx search results.
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r5216 | dshteyn | 2010-10-29 16:23:37 -0700 (Fri, 29 Oct 2010) | 1 line

make SearchHit separate class for iProphet.
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r5215 | dshteyn | 2010-10-29 16:18:35 -0700 (Fri, 29 Oct 2010) | 1 line

Clear out tophit hashes before recomputing. Separate SearchHit in a different class. 
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r5214 | slagelwa | 2010-10-25 10:20:36 -0700 (Mon, 25 Oct 2010) | 1 line

[4.4.1 release] tagging release from branch
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r5213 | henrylam | 2010-10-22 02:49:33 -0700 (Fri, 22 Oct 2010) | 1 line

[SpectraST] Similarity clustering feature -- work in progress
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r5212 | henrylam | 2010-10-22 02:34:59 -0700 (Fri, 22 Oct 2010) | 1 line

[SpectraST] Partial revert to old insertForSearch behavior to keep search results invariant
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r5211 | henrylam | 2010-10-20 21:24:03 -0700 (Wed, 20 Oct 2010) | 1 line

[SpectraST] Add feature: ProbTable (-cT option) can retrieve entries of any charge by leaving out the /<charge> in the table
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r5210 | henrylam | 2010-10-20 21:14:02 -0700 (Wed, 20 Oct 2010) | 1 line

[SpectraST] Add option to record all raw spectra going into a consensus; RawSpectrum/RawSpectra field now excludes .charge
------------------------------------------------------------------------
r5209 | henrylam | 2010-10-20 20:23:39 -0700 (Wed, 20 Oct 2010) | 1 line

[SpectraST] Fix bug with rarely used spectrum plotting feature; clean up SpectraSTReplicates flow

------------------------------------------------------------------------
r5207 | henrylam | 2010-10-19 03:31:40 -0700 (Tue, 19 Oct 2010) | 1 line

[SpectraST] For faster search, more economical insert() in SpectraSTPeakList

------------------------------------------------------------------------
r5205 | dshteyn | 2010-10-18 10:45:43 -0700 (Mon, 18 Oct 2010) | 1 line

Use | as another separator for getting the protein name
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r5204 | henrylam | 2010-10-18 03:07:07 -0700 (Mon, 18 Oct 2010) | 1 line

[SpectraST] Enable several new ways of retrieving entries from SpectraSTMzLibIndex: delayed read, sort by s/n
------------------------------------------------------------------------
r5203 | henrylam | 2010-10-18 03:01:07 -0700 (Mon, 18 Oct 2010) | 1 line

[SpectraST] Add (hidden) option of limiting number of peaks of library spectrum used in searching
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r5202 | henrylam | 2010-10-18 01:00:42 -0700 (Mon, 18 Oct 2010) | 1 line

[MzXML2Search] Change interpretation of -A option when the scan has no activationMethod field in the mzXML file
------------------------------------------------------------------------
r5201 | henrylam | 2010-10-18 00:35:16 -0700 (Mon, 18 Oct 2010) | 1 line

[ramp] Parse activationMethod in <scan> element -- msconvert put it there, not in <precursorMz>
------------------------------------------------------------------------
r5200 | pcbrefugee | 2010-10-14 11:47:28 -0700 (Thu, 14 Oct 2010) | 1 line

[documentation] update the windows build notes to reflect the fact that one needs MinGW to configure certain libraries before MSVC can be used for building TPP
------------------------------------------------------------------------
r5199 | dctrud | 2010-10-14 01:50:34 -0700 (Thu, 14 Oct 2010) | 1 line

[ASAPRatioProteinRatioParser] Removing cacheing changes from r4884 as can cause crashes on some input due to out of memory
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r5198 | dshteyn | 2010-10-12 10:35:08 -0700 (Tue, 12 Oct 2010) | 1 line

Back out unfinished parts that broke the build.
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r5197 | dshteyn | 2010-10-12 10:32:05 -0700 (Tue, 12 Oct 2010) | 1 line

Backing out system specific checkin that shouldn't've been, retaining the CLEVEL stuff
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r5196 | pcbrefugee | 2010-10-12 09:37:03 -0700 (Tue, 12 Oct 2010) | 1 line

[xtandem] fixed a bug that caused all groups in the output file to have identical "sumI" and "maxI" intensity values when configured with "spectrum, use conditioning"="no".  Also submitted a patch to the official X!Tandem project.
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r5195 | dshteyn | 2010-10-11 17:28:27 -0700 (Mon, 11 Oct 2010) | 1 line

Petunia: Add feature for setting CLEVEL parameter on Analyze Peptides page
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r5194 | dshteyn | 2010-10-11 17:25:24 -0700 (Mon, 11 Oct 2010) | 1 line

Fix option parsing bug
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r5193 | dshteyn | 2010-10-11 17:23:20 -0700 (Mon, 11 Oct 2010) | 1 line

Fix options parsing bug 
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r5185 | slagelwa | 2010-09-29 15:23:50 -0700 (Wed, 29 Sep 2010) | 2 lines

4.4.1 fixes, including installer changes on perl, missing msconvert files, SpectraST fixes by Henry and fixes by Jimmy

------------------------------------------------------------------------
r5184 | pcbrefugee | 2010-09-24 14:31:23 -0700 (Fri, 24 Sep 2010) | 5 lines

tweaks for building on Debian, which is the basis of the Amazon Elastic Map Reduce service
recognize Debian 5.0.3, fall through to Ununtu 8 handling for that
S3Fuse cache in /mnt instead of /mnt - less likely to fill the local volume
don't use sudo if you're already root (normally harmless except that debian hasn't got sudo and you're already root anyway)

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r5182 | rbs66 | 2010-09-22 14:47:10 -0700 (Wed, 22 Sep 2010) | 1 line

Added full path to rm command.
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r5181 | slagelwa | 2010-09-21 10:35:54 -0700 (Tue, 21 Sep 2010) | 2 lines

Fixing placement of '@' in htmldoc make command

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r5180 | dshteyn | 2010-09-20 16:30:19 -0700 (Mon, 20 Sep 2010) | 1 line

no autoconf
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r5179 | dshteyn | 2010-09-20 16:18:07 -0700 (Mon, 20 Sep 2010) | 1 line

htmldoc added for export to pdf
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r5178 | dshteyn | 2010-09-20 16:16:53 -0700 (Mon, 20 Sep 2010) | 1 line

htmldoc added for export to pdf

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r5175 | pcbrefugee | 2010-09-14 17:37:49 -0700 (Tue, 14 Sep 2010) | 1 line

[iModelParser] oops, hit the wrong header file in last commit
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r5174 | pcbrefugee | 2010-09-14 17:34:12 -0700 (Tue, 14 Sep 2010) | 1 line

[iModelParser] destructor was deleting a string it hadn't allocated
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r5173 | pcbrefugee | 2010-09-14 17:27:13 -0700 (Tue, 14 Sep 2010) | 1 line

[iModelParser] remove redundant iModelParser:: within iModelParser class declaration
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r5172 | pcbrefugee | 2010-09-14 17:26:26 -0700 (Tue, 14 Sep 2010) | 1 line

[ModelParser] fix memory leak
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r5171 | pcbrefugee | 2010-09-14 17:03:10 -0700 (Tue, 14 Sep 2010) | 1 line

tweak my previous tweak.  Crossplatform is hard!
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r5170 | pcbrefugee | 2010-09-14 16:30:50 -0700 (Tue, 14 Sep 2010) | 1 line

[RTCalculator] add missing function return values that could cause some mysterious behavior, also add various casts and more widely portable dynamic allocations to make more compilers happy

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r5168 | dshteyn | 2010-09-14 16:02:08 -0700 (Tue, 14 Sep 2010) | 1 line

Fix compilation issues with iModelParser.cgi tool.

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r5165 | dshteyn | 2010-09-13 17:17:49 -0700 (Mon, 13 Sep 2010) | 1 line

Fix compilation problem and logic for detecting obs_charge_distr reported by Natalie
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r5164 | rbs66 | 2010-09-10 16:52:39 -0700 (Fri, 10 Sep 2010) | 1 line

Removed duplicate line from last update.
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r5163 | rbs66 | 2010-09-10 16:28:26 -0700 (Fri, 10 Sep 2010) | 1 line

Updated to display iProb links in Petunia that lead to analysis results for iProphet pep xml files.
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r5162 | rbs66 | 2010-09-10 16:23:18 -0700 (Fri, 10 Sep 2010) | 1 line

Added commands for iModelParser.cgi, the iProphet pep xml viewer in Petunia.
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r5161 | rbs66 | 2010-09-10 16:18:56 -0700 (Fri, 10 Sep 2010) | 1 line

Added updates to RTCalc in Petunia including retention time training page.

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r5159 | pcbrefugee | 2010-09-10 13:56:18 -0700 (Fri, 10 Sep 2010) | 1 line

[pwiz, ramp, plot-msms.cgi] update RAMP to use new pwiz RAMPAdapter functionality for more efficient scan number lookups, for performance boost in plot-msms CGI

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r5157 | dshteyn | 2010-09-09 11:36:51 -0700 (Thu, 09 Sep 2010) | 1 line

Implementing additional functions for peptide parameters borrowed from Elude.  Output file option.  Cleanup of ANN specification (now done using 1 file).
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r5156 | pcbrefugee | 2010-09-03 10:16:32 -0700 (Fri, 03 Sep 2010) | 1 line

change a statically allocated buffer to dynamic - could cause problems with stack-allocated ogzstream
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r5155 | dshteyn | 2010-09-02 11:29:23 -0700 (Thu, 02 Sep 2010) | 1 line

Use one file to reference all neural net stuff.
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r5154 | dshteyn | 2010-09-02 09:57:16 -0700 (Thu, 02 Sep 2010) | 1 line

New peptide features based on Elude model. Capture neural network parameter index in a separate file.
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r5153 | slagelwa | 2010-09-01 14:35:32 -0700 (Wed, 01 Sep 2010) | 2 lines

* Perl check now presents a "abort/retry/ignore" dialog if the perl check fails -- allowing users to continue the installation in the event this a failed perl check...fails
* Remove annoying "\" in the main window dialog.  I shouldn't do this but...
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r5152 | slagelwa | 2010-09-01 14:32:41 -0700 (Wed, 01 Sep 2010) | 1 line

Fix perl 5.12 test.  Added comment about a cleaner way to do the test, but did not make the change.
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r5151 | rbs66 | 2010-08-30 17:06:15 -0700 (Mon, 30 Aug 2010) | 1 line

Added backwards compatibility with older pep xml file versions.
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r5150 | rbs66 | 2010-08-30 17:03:50 -0700 (Mon, 30 Aug 2010) | 1 line

CHanged to work with new modified util functions.
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r5149 | rbs66 | 2010-08-30 17:02:54 -0700 (Mon, 30 Aug 2010) | 1 line

Updated xml schema to 116.
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r5148 | rbs66 | 2010-08-30 17:01:06 -0700 (Mon, 30 Aug 2010) | 1 line

Added tags for Model Parser updated to schema.
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r5147 | slagelwa | 2010-08-30 13:48:52 -0700 (Mon, 30 Aug 2010) | 2 lines

Fixing SVN add issue

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r5146 | henrylam | 2010-08-29 20:49:31 -0700 (Sun, 29 Aug 2010) | 1 line

[SpectraST] Updated XREA calculation
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r5145 | henrylam | 2010-08-29 20:14:43 -0700 (Sun, 29 Aug 2010) | 1 line

[SpectraST] Fix re-annotation crash; ensure m/z order of peak list; minor stylistic changes
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r5144 | pcbrefugee | 2010-08-27 17:26:23 -0700 (Fri, 27 Aug 2010) | 1 line

this stops the unneeded fann/gsl rebuilds my last change caused on the linux side
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r5143 | pcbrefugee | 2010-08-27 16:44:15 -0700 (Fri, 27 Aug 2010) | 1 line

don't try to run ant if it's not installed
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r5142 | pcbrefugee | 2010-08-27 15:59:36 -0700 (Fri, 27 Aug 2010) | 1 line

clear up potential malloc/free/new/delete confusion by refactoring some path manipulation routines in util.h to return std::string instead
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r5141 | pcbrefugee | 2010-08-27 14:37:40 -0700 (Fri, 27 Aug 2010) | 1 line

build the FANN and GSL libs even if the directory already exists (as when MSVC build is performed before MinGW build)
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r5140 | pcbrefugee | 2010-08-27 14:10:30 -0700 (Fri, 27 Aug 2010) | 1 line

[ModelParser] GCC 4 wouldn't compile "sprintf(tmp, tag->getAttributeValue(tmp));" due to "error: format not a string literal and no format arguments".  Upon inspection there's a memory leak as well as a potential crash from naively using the possibly NULL result of tag->getAttributeValue(), and a probable buffer overrun as well, I cleaned these up. 
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r5139 | pcbrefugee | 2010-08-27 12:13:45 -0700 (Fri, 27 Aug 2010) | 1 line

deal with a strict GCC 4 warning for failure to check fgets return value
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r5138 | rbs66 | 2010-08-27 10:48:03 -0700 (Fri, 27 Aug 2010) | 1 line

Fixed function call where string length was passed instead of its entire possible size. Deleted a couple comments.
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r5137 | rbs66 | 2010-08-26 16:36:59 -0700 (Thu, 26 Aug 2010) | 1 line

Quick recommit to fix minor Java bug with charge tab selection.
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r5136 | rbs66 | 2010-08-26 16:15:22 -0700 (Thu, 26 Aug 2010) | 1 line

Fixed some minor memory problems and tricky incorrect file path bug.
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r5135 | slagelwa | 2010-08-26 15:44:38 -0700 (Thu, 26 Aug 2010) | 3 lines

Use -terse when on the sun grid engine to mimic output functionality that
happens in PBS

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r5134 | pcbrefugee | 2010-08-26 14:27:32 -0700 (Thu, 26 Aug 2010) | 1 line

add Crux support to MSVC builds
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r5133 | pcbrefugee | 2010-08-26 13:59:46 -0700 (Thu, 26 Aug 2010) | 2 lines

remove useless null pointer checks before free and delete (free and delete handle NULL just fine, this just slows down some very heavily used code)
remove useless nulling of pointers in destructors (worse than useless, actually - potentially hides double-free problems in calling code)
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r5132 | rbs66 | 2010-08-25 15:41:42 -0700 (Wed, 25 Aug 2010) | 1 line

Recommitting changes that had problems merging.
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r5131 | rbs66 | 2010-08-25 15:34:26 -0700 (Wed, 25 Aug 2010) | 2 lines

Recommitted due to problems merging.
Originally updated to write roc curve data and error data for individual charges, for use with Model Parser updates.
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r5130 | dshteyn | 2010-08-25 15:33:53 -0700 (Wed, 25 Aug 2010) | 1 line

Safer Array freeing
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r5129 | dshteyn | 2010-08-25 15:32:44 -0700 (Wed, 25 Aug 2010) | 1 line

Make scan parsing from Mascot case insensitive
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r5128 | dshteyn | 2010-08-25 15:31:21 -0700 (Wed, 25 Aug 2010) | 1 line

Crux support
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r5127 | dshteyn | 2010-08-25 15:30:29 -0700 (Wed, 25 Aug 2010) | 1 line

Crux support
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r5126 | dshteyn | 2010-08-25 15:29:41 -0700 (Wed, 25 Aug 2010) | 1 line

Support for Crux
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r5125 | dshteyn | 2010-08-25 15:26:49 -0700 (Wed, 25 Aug 2010) | 1 line

Use CLEVEL in crux too
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r5124 | slagelwa | 2010-08-25 15:04:31 -0700 (Wed, 25 Aug 2010) | 2 lines

[merge 4.4] Merging head of 4.4 branch back into trunk

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