TPP:4.5.1 SVN Log

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Changes since 4.5.0 release 

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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).
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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
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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?

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

PTMProphet: undo Joe's bad merge commit.
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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
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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.
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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
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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
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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
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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


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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
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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)
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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!)

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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
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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.

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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)


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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.
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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
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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
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r5696 | henryhlam | 2012-01-11 00:45:20 -0800 (Wed, 11 Jan 2012) | 1 line

Back-out two accidental check-ins in r5695
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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.

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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]
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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
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r5711 | henryhlam | 2012-01-18 00:58:24 -0800 (Wed, 18 Jan 2012) | 1 line

[SpectraST] Follow-up to r5709, fix compiling error
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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.
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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.

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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.

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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."


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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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