TPP:4.5.2 SVN Log

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Revision as of 18:19, 6 February 2012

[edit]

Changes since 4.5.1 release 

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r5506 | dshteyn | 2011-09-23 11:54:38 -0700 (Fri, 23 Sep 2011) | 1 line

Tandem2XML: BUGFIX Fix problem when running Tandem on mgf file created with MzXML2Search, the resulting pep.xml file contained extra newline characters at the end of the spectrum name that are now being removed.
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r5512 | dshteyn | 2011-09-23 16:24:14 -0700 (Fri, 23 Sep 2011) | 1 line

support for Agilent QTOF mzML
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r5513 | dshteyn | 2011-09-23 17:04:04 -0700 (Fri, 23 Sep 2011) | 1 line

Fix typo
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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

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r5526 | eng_jk | 2011-10-06 14:14:46 -0700 (Thu, 06 Oct 2011) | 3 lines

additional cleanup of yesterday's xpress buffer overrun fix; mainly changing size of a few
allocated arrays which only affects mzML files with with non-sequential native IDs.

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r5539 | henryhlam | 2011-10-10 20:08:54 -0700 (Mon, 10 Oct 2011) | 1 line

[SpectraST] Fix rare error when S/N calculation failed due to too few peaks outside precursor region (trunk r5501)
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r5540 | henryhlam | 2011-10-10 20:12:27 -0700 (Mon, 10 Oct 2011) | 1 line

[mzParser] Pound-include stdint.h and catch return values for smooth compiling (trunk r5530)
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r5541 | henryhlam | 2011-10-10 20:15:16 -0700 (Mon, 10 Oct 2011) | 1 line

[util] Catch return values for smooth compiling (trunk r5532)
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r5542 | henryhlam | 2011-10-10 20:18:11 -0700 (Mon, 10 Oct 2011) | 1 line

[Tandem2XML] Fix wrong enzyme specificity for Lys-C (trunk r5533)
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r5543 | henryhlam | 2011-10-10 20:23:42 -0700 (Mon, 10 Oct 2011) | 1 line

Move RefreshParser ahead of PeptideProphet to safeguard against some search engines' mangling the protein names and/or omitting NTT/NMC (trunk r5534)
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r5544 | henryhlam | 2011-10-10 20:25:26 -0700 (Mon, 10 Oct 2011) | 1 line

[InteractParser] Fix OMSSA's problem with n-term mods (trunk r5535)
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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

[InterProphet] More finely divided bins for error rate estimates. Important for modern, large datasets. (trunk r5536)
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r5547 | henryhlam | 2011-10-10 22:48:06 -0700 (Mon, 10 Oct 2011) | 1 line

[PeptideProphet] More finely divided bins for error rate estimates. Important for modern, large datasets. (trunk r5537)
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r5549 | slagelwa | 2011-10-17 14:31:27 -0700 (Mon, 17 Oct 2011) | 1 line

Increased size of buffer for holding fasta header lines as per recommendation by David Trudgian.
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r5550 | slagelwa | 2011-10-17 14:41:42 -0700 (Mon, 17 Oct 2011) | 1 line

Cut&paste in cygwin inserted newline
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r5551 | eng_jk | 2011-10-18 12:14:31 -0700 (Tue, 18 Oct 2011) | 4 lines

Fix for mzML files when viewing xpress chromatograms through the ProteinProphet to XPressCGIProteinDisplayParser.cgi binary.
No notion of file extensions exist in that path and mzXML files were always assumed.  This fix simply has the cgi try mzML
file extension if the mzXML file is not found.

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r5554 | henryhlam | 2011-10-20 01:36:19 -0700 (Thu, 20 Oct 2011) | 1 line

[SpectraST] Allow users to specify their own m/z range for MRM transitions (Q3)
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r5559 | real_procopio | 2011-10-20 12:20:06 -0700 (Thu, 20 Oct 2011) | 1 line

merging trunk changes from rev 5553
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r5562 | real_procopio | 2011-10-20 17:27:40 -0700 (Thu, 20 Oct 2011) | 1 line

[Petunia] merging rev 5561 from trunk
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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

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.
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r5566 | real_procopio | 2011-10-21 16:10:41 -0700 (Fri, 21 Oct 2011) | 1 line

[Petunia] Decoy models pages should only ask for pep/protXML files as input; minor code clean-up and re-formatting
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r5569 | real_procopio | 2011-10-24 18:08:29 -0700 (Mon, 24 Oct 2011) | 7 lines

[Petunia]
- Add ability to specify no output file for some commands;
- Rename files after running the Re-index mzXML tool;
- Display file extension being searched for in File Chooser;
- Add thead and tbody tags to file list table (for future jscript sorting integration);
- fixed a couple of typos.

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r5574 | real_procopio | 2011-10-26 18:48:45 -0700 (Wed, 26 Oct 2011) | 1 line

[Petunia] Added function to strip base path name from a list of files (and thus shorten shell command size); implemented this for xinteract, the biggest culprit.
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r5580 | slagelwa | 2011-11-02 15:45:23 -0700 (Wed, 02 Nov 2011) | 3 lines

Fixed a issue with uploading files on windows resulting in 0 byte files


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r5604 | real_procopio | 2011-11-07 16:47:03 -0800 (Mon, 07 Nov 2011) | 9 lines

[Petunia]
- New dynamic filtering box on file browser and chooser, with smart "select
  all" checkbox
- Streamlined file operations form buttons (Delete, Copy, Paste, etc)
- Do not show Clipboard div if empty
- Allow users to specify data dirs with leading uppercase (e.g. C:\blah\)
- Took out 'tilde' hack for XPRESS
- Now using -nosticky pragma in perl CGI

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r5605 | real_procopio | 2011-11-07 16:53:48 -0800 (Mon, 07 Nov 2011) | 1 line

New dir to store javascript files
r5606 | real_procopio | 2011-11-07 17:02:54 -0800 (Mon, 07 Nov 2011) | 1 line

New Table sorting Javasript utility
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r5607 | slagelwa | 2011-11-07 22:01:50 -0800 (Mon, 07 Nov 2011) | 2 lines

Merged all of David's changes on trunk since the 4.5 release into 4.5 branch

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r5608 | slagelwa | 2011-11-08 10:23:57 -0800 (Tue, 08 Nov 2011) | 1 line

4.5.1 
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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
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r5624 | slagelwa | 2011-11-10 11:40:32 -0800 (Thu, 10 Nov 2011) | 3 lines

Checking in David's changes on the trunk since revision 4605


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r5632 | slagelwa | 2011-11-14 11:11:38 -0800 (Mon, 14 Nov 2011) | 4 lines

Merging David's latest round of checkins on trunk with the assumption
they belong here too.


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r5634 | slagelwa | 2011-11-14 15:59:32 -0800 (Mon, 14 Nov 2011) | 3 lines

Trying again.  Last checkin with David's changed were not committed.  This checkin also includes the stdlib.h addition in pwiz done by Brian so that it will compile on gcc 4.6.1.


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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.

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r5644 | slagelwa | 2011-11-21 14:05:30 -0800 (Mon, 21 Nov 2011) | 2 lines

Correcting issue with propertly setting up perl libpath to file perllib

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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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