TPP:4.5.1 SVN Log

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<nowiki> <nowiki>
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-r5506 | dshteyn | 2011-09-23 11:54:38 -0700 (Fri, 23 Sep 2011) | 1 line+r5647 | dshteyn | 2011-11-28 10:59:15 -0800 (Mon, 28 Nov 2011) | 1 line
-Tandem2XML: BUGFIX Fix problem when running Tandem on mgf file created with MzXML2Search, the resulting pep.xml file contained extra newline characters at the end of the spectrum name that are now being removed.+BUGFIX: correct RT model problem present in branch only (fixed in trunk).
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-r5512 | dshteyn | 2011-09-23 16:24:14 -0700 (Fri, 23 Sep 2011) | 1 line+r5648 | henryhlam | 2011-11-29 00:49:03 -0800 (Tue, 29 Nov 2011) | 1 line
-support for Agilent QTOF mzML+[SpectraST] Fix obscure bug with option passing; better error checking
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5513 | dshteyn | 2011-09-23 17:04:04 -0700 (Fri, 23 Sep 2011) | 1 line+r5653 | slagelwa | 2011-11-29 16:18:28 -0800 (Tue, 29 Nov 2011) | 3 lines
-Fix typo+Merged PTProphet.cxx from trunk into branch. David can you please check this merge was
-------------------------------------------------------------------------+successful?
-r5525 | eng_jk | 2011-10-05 16:42:41 -0700 (Wed, 05 Oct 2011) | 2 lines+
- +
-quick mod to Patrick's buffer overrun fix (for non-sequential mzML scans); adding to 4.5 branch+
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5526 | eng_jk | 2011-10-06 14:14:46 -0700 (Thu, 06 Oct 2011) | 3 lines+r5654 | dshteyn | 2011-11-30 10:01:34 -0800 (Wed, 30 Nov 2011) | 1 line
- +
-additional cleanup of yesterday's xpress buffer overrun fix; mainly changing size of a few+
-allocated arrays which only affects mzML files with with non-sequential native IDs.+
 +PTMProphet: undo Joe's bad merge commit.
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5539 | henryhlam | 2011-10-10 20:08:54 -0700 (Mon, 10 Oct 2011) | 1 line+r5657 | henryhlam | 2011-12-05 01:13:19 -0800 (Mon, 05 Dec 2011) | 1 line
-[SpectraST] Fix rare error when S/N calculation failed due to too few peaks outside precursor region (trunk r5501)+[SpectraST] Fix SpectraSTPeakList::shiftAllPeaks problem - change branch 4.5 so that when it gets merged into trunk, PTMProphet will have the right version to call
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-r5540 | henryhlam | 2011-10-10 20:12:27 -0700 (Mon, 10 Oct 2011) | 1 line+r5658 | henryhlam | 2011-12-05 01:15:36 -0800 (Mon, 05 Dec 2011) | 1 line
-[mzParser] Pound-include stdint.h and catch return values for smooth compiling (trunk r5530)+[SpectraST] Consider all charges when library spectrum has charge 0. This change is already in trunk.
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-r5541 | henryhlam | 2011-10-10 20:15:16 -0700 (Mon, 10 Oct 2011) | 1 line+r5659 | henryhlam | 2011-12-05 01:17:23 -0800 (Mon, 05 Dec 2011) | 1 line
-[util] Catch return values for smooth compiling (trunk r5532)+[SpectraST] Fix uninitialized value causing wrong Nreps when building best-replicate library
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-r5542 | henryhlam | 2011-10-10 20:18:11 -0700 (Mon, 10 Oct 2011) | 1 line+r5660 | henryhlam | 2011-12-05 01:19:26 -0800 (Mon, 05 Dec 2011) | 1 line
-[Tandem2XML] Fix wrong enzyme specificity for Lys-C (trunk r5533)+[SpectraST] Fix extremely minor memory leak, offending pointer not used anyway
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-r5543 | henryhlam | 2011-10-10 20:23:42 -0700 (Mon, 10 Oct 2011) | 1 line+r5673 | real_procopio | 2011-12-14 13:07:40 -0800 (Wed, 14 Dec 2011) | 1 line
-Move RefreshParser ahead of PeptideProphet to safeguard against some search engines' mangling the protein names and/or omitting NTT/NMC (trunk r5534)+[new] Utility script to rename Mascot F files to original mz(X)ML base name
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-r5544 | henryhlam | 2011-10-10 20:25:26 -0700 (Mon, 10 Oct 2011) | 1 line+r5674 | real_procopio | 2011-12-14 13:41:33 -0800 (Wed, 14 Dec 2011) | 7 lines
 + 
 +[petunia] Enhanced Mascot support:
 +- Added auto-renaming of Mascot F01234.dat files to original base name of mz(X)ML file
 +- Added search info on Mascot results download page
 +- Fixed issue of wget not working in Windows (caused by win32_system stripping quotes out of commands -- this is a separate fix)
 +- Fixed typo in Mascot DB filter box
-[InteractParser] Fix OMSSA's problem with n-term mods (trunk r5535) 
------------------------------------------------------------------------- 
-r5545 | henryhlam | 2011-10-10 20:27:17 -0700 (Mon, 10 Oct 2011) | 1 line 
-[Enzyme] Equate tryptic with trypsin (trunk r5538) 
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-r5546 | henryhlam | 2011-10-10 20:30:09 -0700 (Mon, 10 Oct 2011) | 1 line+r5675 | real_procopio | 2011-12-15 10:44:18 -0800 (Thu, 15 Dec 2011) | 1 line
-[InterProphet] More finely divided bins for error rate estimates. Important for modern, large datasets. (trunk r5536)+[new] Utility script to rename Mascot 'F0123..' files to original mz(X)ML base name
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-r5547 | henryhlam | 2011-10-10 22:48:06 -0700 (Mon, 10 Oct 2011) | 1 line+r5676 | real_procopio | 2011-12-15 17:02:53 -0800 (Thu, 15 Dec 2011) | 1 line
-[PeptideProphet] More finely divided bins for error rate estimates. Important for modern, large datasets. (trunk r5537)+[bugfix] Install Javascript auxiliary file for table filtering (Petunia)
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-r5549 | slagelwa | 2011-10-17 14:31:27 -0700 (Mon, 17 Oct 2011) | 1 line+r5677 | slagelwa | 2011-12-16 14:56:51 -0800 (Fri, 16 Dec 2011) | 3 lines
 + 
 +Checking in Mike's fixes for a memory issue that would cause MzXML2Search to
 +randomly fail. (Thanks for the fix Mike!)
-Increased size of buffer for holding fasta header lines as per recommendation by David Trudgian. 
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5550 | slagelwa | 2011-10-17 14:41:42 -0700 (Mon, 17 Oct 2011) | 1 line+r5678 | real_procopio | 2011-12-16 17:02:57 -0800 (Fri, 16 Dec 2011) | 1 line
-Cut&paste in cygwin inserted newline+[Petunia] Minor bugfix to decoy peps and prots processing
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-r5551 | eng_jk | 2011-10-18 12:14:31 -0700 (Tue, 18 Oct 2011) | 4 lines+r5687 | slagelwa | 2011-12-29 15:55:17 -0800 (Thu, 29 Dec 2011) | 5 lines
-Fix for mzML files when viewing xpress chromatograms through the ProteinProphet to XPressCGIProteinDisplayParser.cgi binary.+Adding a quick "hotfix" for users of InSpecT. This fix will install the
-No notion of file extensions exist in that path and mzXML files were always assumed. This fix simply has the cgi try mzML+latest code changes from Terry Farrah to the program that converts
-file extension if the mzXML file is not found.+inspect output to pep.xml for use in TPP. This fix is only needed until
 +the developers of inspect release a new version that includes these changes.
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5554 | henryhlam | 2011-10-20 01:36:19 -0700 (Thu, 20 Oct 2011) | 1 line+r5688 | slagelwa | 2011-12-30 14:45:12 -0800 (Fri, 30 Dec 2011) | 6 lines
-[SpectraST] Allow users to specify their own m/z range for MRM transitions (Q3)+Including Terry's change so that the path to the spectrum file read from the
-------------------------------------------------------------------------+inspect output isn't munged.
-r5559 | real_procopio | 2011-10-20 12:20:06 -0700 (Thu, 20 Oct 2011) | 1 line+
-merging trunk changes from rev 5553+(BTW, new version of inspect...expected any day with this patch)
-------------------------------------------------------------------------+
-r5562 | real_procopio | 2011-10-20 17:27:40 -0700 (Thu, 20 Oct 2011) | 1 line+
-[Petunia] merging rev 5561 from trunk 
------------------------------------------------------------------------- 
-r5563 | real_procopio | 2011-10-21 13:40:59 -0700 (Fri, 21 Oct 2011) | 1 line 
-[Petunia] Added support for Bruker .yep and .baf files, as well as mzXML output to msconvert; Expanded Libra normalization channel option to 8 
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-r5564 | mhoopmann | 2011-10-21 15:10:06 -0700 (Fri, 21 Oct 2011) | 1 line+r5690 | mhoopmann | 2012-01-04 12:32:44 -0800 (Wed, 04 Jan 2012) | 1 line
-Fixed buffer overrun when reading small spectra compressed with zlib (compression increases spectrum size in these cases, hence the overrun). Moved stdint.h to linux build as it is not part of Visual Studio.+Added check to see if requested scan exists before attempting to perform downstream functions on it.
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5566 | real_procopio | 2011-10-21 16:10:41 -0700 (Fri, 21 Oct 2011) | 1 line+r5694 | henryhlam | 2012-01-11 00:29:08 -0800 (Wed, 11 Jan 2012) | 1 line
-[Petunia] Decoy models pages should only ask for pep/protXML files as input; minor code clean-up and re-formatting+[SpectraST] Option to use the precursor intensity as rank/weight in best-replicate/consensus operation
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-r5569 | real_procopio | 2011-10-24 18:08:29 -0700 (Mon, 24 Oct 2011) | 7 lines+r5695 | henryhlam | 2012-01-11 00:33:42 -0800 (Wed, 11 Jan 2012) | 1 line
- +
-[Petunia]+
-- Add ability to specify no output file for some commands;+
-- Rename files after running the Re-index mzXML tool;+
-- Display file extension being searched for in File Chooser;+
-- Add thead and tbody tags to file list table (for future jscript sorting integration);+
-- fixed a couple of typos.+
 +[SpectraST] Follow-up to r5694: In case precursor intensity is not found or is zero, use total ion current instead
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-r5574 | real_procopio | 2011-10-26 18:48:45 -0700 (Wed, 26 Oct 2011) | 1 line+r5696 | henryhlam | 2012-01-11 00:45:20 -0800 (Wed, 11 Jan 2012) | 1 line
-[Petunia] Added function to strip base path name from a list of files (and thus shorten shell command size); implemented this for xinteract, the biggest culprit.+Back-out two accidental check-ins in r5695
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-r5580 | slagelwa | 2011-11-02 15:45:23 -0700 (Wed, 02 Nov 2011) | 3 lines+r5697 | slagelwa | 2012-01-11 16:57:22 -0800 (Wed, 11 Jan 2012) | 2 lines
- +
-Fixed a issue with uploading files on windows resulting in 0 byte files+
 +Bumped version. Added references to renamedat.pl so it gets installed correctly and the Windows installer can build.
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5604 | real_procopio | 2011-11-07 16:47:03 -0800 (Mon, 07 Nov 2011) | 9 lines+r5698 | mhoopmann | 2012-01-12 12:41:27 -0800 (Thu, 12 Jan 2012) | 1 line
- +
-[Petunia]+
-- New dynamic filtering box on file browser and chooser, with smart "select+
- all" checkbox+
-- Streamlined file operations form buttons (Delete, Copy, Paste, etc)+
-- Do not show Clipboard div if empty+
-- Allow users to specify data dirs with leading uppercase (e.g. C:\blah\)+
-- Took out 'tilde' hack for XPRESS+
-- Now using -nosticky pragma in perl CGI+
 +Expanded the RAMP-interface to include id attribute of the spectrum tag in mzML files. The header structure now has char idString[128]
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5605 | real_procopio | 2011-11-07 16:53:48 -0800 (Mon, 07 Nov 2011) | 1 line+r5709 | henryhlam | 2012-01-18 00:19:41 -0800 (Wed, 18 Jan 2012) | 1 line
-New dir to store javascript files+[SpectraST] Set fragmentation type to CID by default (instead of leaving it blank) when importing from NIST libraries; allow user to set to others by -cI option
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-r5606 | real_procopio | 2011-11-07 17:02:54 -0800 (Mon, 07 Nov 2011) | 1 line+r5711 | henryhlam | 2012-01-18 00:58:24 -0800 (Wed, 18 Jan 2012) | 1 line
-New Table sorting Javasript utility+[SpectraST] Follow-up to r5709, fix compiling error
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-r5607 | slagelwa | 2011-11-07 22:01:50 -0800 (Mon, 07 Nov 2011) | 2 lines+r5714 | henryhlam | 2012-01-20 01:10:25 -0800 (Fri, 20 Jan 2012) | 1 line
- +
-Merged all of David's changes on trunk since the 4.5 release into 4.5 branch+
 +[SpectraST] Annotation defaults to CID if unrecognized fragmentation type is encountered.
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5608 | slagelwa | 2011-11-08 10:23:57 -0800 (Tue, 08 Nov 2011) | 1 line+r5732 | slagelwa | 2012-01-23 16:01:37 -0800 (Mon, 23 Jan 2012) | 3 lines
-4.5.1 +Merged Luis's trunk changes into branch as per his request. This is an overhaul
-------------------------------------------------------------------------+that displays the NSP bin info that no longer uses xslt.
-r5623 | real_procopio | 2011-11-09 17:45:53 -0800 (Wed, 09 Nov 2011) | 1 line+
-[Petunia] Toggle visible checkboxes only: Support for older versions of the perl CGI module, where the <label> tag is the parent of the <input> tag 
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5624 | slagelwa | 2011-11-10 11:40:32 -0800 (Thu, 10 Nov 2011) | 3 lines+r5737 | slagelwa | 2012-02-01 13:14:07 -0800 (Wed, 01 Feb 2012) | 2 lines
- +
-Checking in David's changes on the trunk since revision 4605+
 +When I did a previous merge from trunk I didn't do a top level check in. This check in just updates the merge property.
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5632 | slagelwa | 2011-11-14 11:11:38 -0800 (Mon, 14 Nov 2011) | 4 lines+r5738 | slagelwa | 2012-02-01 13:20:20 -0800 (Wed, 01 Feb 2012) | 4 lines
-Merging David's latest round of checkins on trunk with the assumption+Merged refision 5646, contains dshteyn bug fix
-they belong here too.+"Correct issue with iProphet probability filtering and naming of columns."
------------------------------------------------------------------------ ------------------------------------------------------------------------
-r5634 | slagelwa | 2011-11-14 15:59:32 -0800 (Mon, 14 Nov 2011) | 3 lines+r5741 | real_procopio | 2012-02-02 17:30:16 -0800 (Thu, 02 Feb 2012) | 1 line
- +
-Trying again. Last checkin with David's changed were not committed. This checkin also includes the stdlib.h addition in pwiz done by Brian so that it will compile on gcc 4.6.1.+
- +
- +
-------------------------------------------------------------------------+
-r5642 | slagelwa | 2011-11-16 15:09:33 -0800 (Wed, 16 Nov 2011) | 2 lines+
- +
-Fixing ARCH to be ARCH_FAMILY so XFORMS does the correct regex subsitution.+
- +
-------------------------------------------------------------------------+
-r5644 | slagelwa | 2011-11-21 14:05:30 -0800 (Mon, 21 Nov 2011) | 2 lines+
- +
-Correcting issue with propertly setting up perl libpath to file perllib+
 +Add warning if (legacy) mzXML converter is not found on system before attempting to convert, and suggest using msconvert; Move such page to a less prominent place in tab menu; Tone down libraries warning on mscovert page.
------------------------------------------------------------------------ ------------------------------------------------------------------------
</nowiki> </nowiki>

Revision as of 18:35, 6 February 2012

Changes since 4.5.0 release 

------------------------------------------------------------------------
r5647 | dshteyn | 2011-11-28 10:59:15 -0800 (Mon, 28 Nov 2011) | 1 line

BUGFIX: correct RT model problem present in branch only (fixed in trunk).
------------------------------------------------------------------------
r5648 | henryhlam | 2011-11-29 00:49:03 -0800 (Tue, 29 Nov 2011) | 1 line

[SpectraST] Fix obscure bug with option passing; better error checking
------------------------------------------------------------------------
r5653 | slagelwa | 2011-11-29 16:18:28 -0800 (Tue, 29 Nov 2011) | 3 lines

Merged PTProphet.cxx from trunk into branch. David can you please check this merge was
successful?

------------------------------------------------------------------------
r5654 | dshteyn | 2011-11-30 10:01:34 -0800 (Wed, 30 Nov 2011) | 1 line

PTMProphet: undo Joe's bad merge commit.
------------------------------------------------------------------------
r5657 | henryhlam | 2011-12-05 01:13:19 -0800 (Mon, 05 Dec 2011) | 1 line

[SpectraST] Fix SpectraSTPeakList::shiftAllPeaks problem - change branch 4.5 so that when it gets merged into trunk, PTMProphet will have the right version to call
------------------------------------------------------------------------
r5658 | henryhlam | 2011-12-05 01:15:36 -0800 (Mon, 05 Dec 2011) | 1 line

[SpectraST] Consider all charges when library spectrum has charge 0. This change is already in trunk.
------------------------------------------------------------------------
r5659 | henryhlam | 2011-12-05 01:17:23 -0800 (Mon, 05 Dec 2011) | 1 line

[SpectraST] Fix uninitialized value causing wrong Nreps when building best-replicate library
------------------------------------------------------------------------
r5660 | henryhlam | 2011-12-05 01:19:26 -0800 (Mon, 05 Dec 2011) | 1 line

[SpectraST] Fix extremely minor memory leak, offending pointer not used anyway
------------------------------------------------------------------------
r5673 | real_procopio | 2011-12-14 13:07:40 -0800 (Wed, 14 Dec 2011) | 1 line

[new] Utility script to rename Mascot F files to original mz(X)ML base name
------------------------------------------------------------------------
r5674 | real_procopio | 2011-12-14 13:41:33 -0800 (Wed, 14 Dec 2011) | 7 lines

[petunia] Enhanced Mascot support:
- Added auto-renaming of Mascot F01234.dat files to original base name of mz(X)ML file
- Added search info on Mascot results download page
- Fixed issue of wget not working in Windows (caused by win32_system stripping quotes out of commands -- this is a separate fix)
- Fixed typo in Mascot DB filter box


------------------------------------------------------------------------
r5675 | real_procopio | 2011-12-15 10:44:18 -0800 (Thu, 15 Dec 2011) | 1 line

[new] Utility script to rename Mascot 'F0123..' files to original mz(X)ML base name
------------------------------------------------------------------------
r5676 | real_procopio | 2011-12-15 17:02:53 -0800 (Thu, 15 Dec 2011) | 1 line

[bugfix] Install Javascript auxiliary file for table filtering (Petunia)
------------------------------------------------------------------------
r5677 | slagelwa | 2011-12-16 14:56:51 -0800 (Fri, 16 Dec 2011) | 3 lines

Checking in Mike's fixes for a memory issue that would cause MzXML2Search to 
randomly fail.  (Thanks for the fix Mike!)

------------------------------------------------------------------------
r5678 | real_procopio | 2011-12-16 17:02:57 -0800 (Fri, 16 Dec 2011) | 1 line

[Petunia] Minor bugfix to decoy peps and prots processing
------------------------------------------------------------------------
r5687 | slagelwa | 2011-12-29 15:55:17 -0800 (Thu, 29 Dec 2011) | 5 lines

Adding a quick "hotfix" for users of InSpecT.  This fix will install the
latest code changes from Terry Farrah to the program that converts 
inspect output to pep.xml for use in TPP.  This fix is only needed until
the developers of inspect release a new version that includes these changes.

------------------------------------------------------------------------
r5688 | slagelwa | 2011-12-30 14:45:12 -0800 (Fri, 30 Dec 2011) | 6 lines

Including Terry's change so that the path to the spectrum file read from the
inspect output isn't munged.

(BTW, new version of inspect...expected any day with this patch)


------------------------------------------------------------------------
r5690 | mhoopmann | 2012-01-04 12:32:44 -0800 (Wed, 04 Jan 2012) | 1 line

Added check to see if requested scan exists before attempting to perform downstream functions on it.
------------------------------------------------------------------------
r5694 | henryhlam | 2012-01-11 00:29:08 -0800 (Wed, 11 Jan 2012) | 1 line

[SpectraST] Option to use the precursor intensity as rank/weight in best-replicate/consensus operation
------------------------------------------------------------------------
r5695 | henryhlam | 2012-01-11 00:33:42 -0800 (Wed, 11 Jan 2012) | 1 line

[SpectraST] Follow-up to r5694: In case precursor intensity is not found or is zero, use total ion current instead
------------------------------------------------------------------------
r5696 | henryhlam | 2012-01-11 00:45:20 -0800 (Wed, 11 Jan 2012) | 1 line

Back-out two accidental check-ins in r5695
------------------------------------------------------------------------
r5697 | slagelwa | 2012-01-11 16:57:22 -0800 (Wed, 11 Jan 2012) | 2 lines

Bumped version.  Added references to renamedat.pl so it gets installed correctly and the Windows installer can build.

------------------------------------------------------------------------
r5698 | mhoopmann | 2012-01-12 12:41:27 -0800 (Thu, 12 Jan 2012) | 1 line

Expanded the RAMP-interface to include id attribute of the spectrum tag in mzML files. The header structure now has char idString[128]
------------------------------------------------------------------------
r5709 | henryhlam | 2012-01-18 00:19:41 -0800 (Wed, 18 Jan 2012) | 1 line

[SpectraST] Set fragmentation type to CID by default (instead of leaving it blank) when importing from NIST libraries; allow user to set to others by -cI option
------------------------------------------------------------------------
r5711 | henryhlam | 2012-01-18 00:58:24 -0800 (Wed, 18 Jan 2012) | 1 line

[SpectraST] Follow-up to r5709, fix compiling error
------------------------------------------------------------------------
r5714 | henryhlam | 2012-01-20 01:10:25 -0800 (Fri, 20 Jan 2012) | 1 line

[SpectraST] Annotation defaults to CID if unrecognized fragmentation type is encountered.
------------------------------------------------------------------------
r5732 | slagelwa | 2012-01-23 16:01:37 -0800 (Mon, 23 Jan 2012) | 3 lines

Merged Luis's trunk changes into branch as per his request.  This is an overhaul
that displays the NSP bin info that no longer uses xslt.

------------------------------------------------------------------------
r5737 | slagelwa | 2012-02-01 13:14:07 -0800 (Wed, 01 Feb 2012) | 2 lines

When I did a previous merge from trunk I didn't do a top level check in.  This check in just updates the merge property.

------------------------------------------------------------------------
r5738 | slagelwa | 2012-02-01 13:20:20 -0800 (Wed, 01 Feb 2012) | 4 lines

Merged refision 5646, contains dshteyn bug fix
"Correct issue with iProphet probability filtering and naming of columns."


------------------------------------------------------------------------
r5741 | real_procopio | 2012-02-02 17:30:16 -0800 (Thu, 02 Feb 2012) | 1 line

Add warning if (legacy) mzXML converter is not found on system before attempting to convert, and suggest using msconvert; Move such page to a less prominent place in tab menu; Tone down libraries warning on mscovert page.
------------------------------------------------------------------------
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