TPP:4.7.1 SVN Log
From SPCTools
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Changes since 4.7.0 release
Last Generated Tue May 6 12:24:24 PDT 2014
------------------------------------------------------------------------ r6427 | dshteyn | 2014-03-17 12:27:01 -0700 (Mon, 17 Mar 2014) | 1 line CGI/show_tmp_pngfile.pl: added option to keep the png file...show and not delete ------------------------------------------------------------------------ r6428 | dshteyn | 2014-03-17 12:39:25 -0700 (Mon, 17 Mar 2014) | 1 line Define GNUPLOT_BINARY with no need for GNUPLOT ------------------------------------------------------------------------ r6429 | slagelwa | 2014-03-17 14:54:54 -0700 (Mon, 17 Mar 2014) | 4 lines Streamlined use of GNUPLOT_BINARY a little bit more. Dropped use of GNUPLOT_BINARY_PIPE. ------------------------------------------------------------------------ r6430 | dshteyn | 2014-03-18 10:20:39 -0700 (Tue, 18 Mar 2014) | 1 line iModelParser.cgi: fill in correct value for score. ------------------------------------------------------------------------ r6432 | dshteyn | 2014-03-19 13:44:20 -0700 (Wed, 19 Mar 2014) | 1 line Set the default gnuplot binary to point to pgnuplot.exe on windows. ------------------------------------------------------------------------ r6433 | dshteyn | 2014-03-19 13:58:02 -0700 (Wed, 19 Mar 2014) | 1 line Fix qw issue on branch ------------------------------------------------------------------------ r6434 | dshteyn | 2014-03-19 13:59:27 -0700 (Wed, 19 Mar 2014) | 1 line Fix qw issue on branch ------------------------------------------------------------------------ r6436 | real_procopio | 2014-03-19 21:39:56 -0700 (Wed, 19 Mar 2014) | 1 line [Petunia] Applying recent trunk changes to 4.7 branch ------------------------------------------------------------------------ r6437 | slagelwa | 2014-03-20 15:08:09 -0700 (Thu, 20 Mar 2014) | 4 lines Fix the "blank" page you get when using basic authentication and you happen to open the main url without any actions. ------------------------------------------------------------------------ r6438 | real_procopio | 2014-03-20 18:07:37 -0700 (Thu, 20 Mar 2014) | 1 line [Petunia] Make it bold ------------------------------------------------------------------------ r6439 | dshteyn | 2014-03-21 11:28:31 -0700 (Fri, 21 Mar 2014) | 1 line iModelParser.cgi: fixing memory issue exposed under MingW ------------------------------------------------------------------------ r6440 | slagelwa | 2014-03-24 08:49:25 -0700 (Mon, 24 Mar 2014) | 3 lines Merged changes r6424:6425 from trunk into branch. (Though the changes are appear in the branch!!) ------------------------------------------------------------------------ r6441 | slagelwa | 2014-03-24 08:52:04 -0700 (Mon, 24 Mar 2014) | 3 lines Merged trunk changes r6423:6424 into branch ------------------------------------------------------------------------ r6442 | slagelwa | 2014-03-24 08:56:42 -0700 (Mon, 24 Mar 2014) | 3 lines Merging r6431:6435 from trunk into branch. ------------------------------------------------------------------------ r6443 | slagelwa | 2014-03-24 09:09:30 -0700 (Mon, 24 Mar 2014) | 2 lines Committing merge notices ------------------------------------------------------------------------ r6444 | slagelwa | 2014-03-24 09:13:32 -0700 (Mon, 24 Mar 2014) | 1 line Added DEV to tag ------------------------------------------------------------------------ r6445 | dshteyn | 2014-03-24 09:50:35 -0700 (Mon, 24 Mar 2014) | 1 line ASAPRatioPeptideParser: Undo change by D. T. that broke -r option ------------------------------------------------------------------------ r6446 | dshteyn | 2014-03-24 15:28:01 -0700 (Mon, 24 Mar 2014) | 1 line iProphet Page in Petunia can now run PTMProphet and Quantitation Tools. ------------------------------------------------------------------------ r6447 | dshteyn | 2014-03-24 16:34:30 -0700 (Mon, 24 Mar 2014) | 1 line iProphet: count only best prob per PSM when computing est. num. correct PSMs ------------------------------------------------------------------------ r6448 | slagelwa | 2014-03-25 12:08:57 -0700 (Tue, 25 Mar 2014) | 2 lines Upgrading Comet to 2014.01 rev. 0 ------------------------------------------------------------------------ r6449 | slagelwa | 2014-03-25 12:11:18 -0700 (Tue, 25 Mar 2014) | 2 lines Update COMET_VERSION ------------------------------------------------------------------------ r6450 | dshteyn | 2014-03-25 14:49:10 -0700 (Tue, 25 Mar 2014) | 1 line Quantitation: WARNING about multiple variable mods on same Amino Acid should appear when the masses are sufficiently different, so not to scare folks. ------------------------------------------------------------------------ r6451 | dshteyn | 2014-03-25 14:50:22 -0700 (Tue, 25 Mar 2014) | 1 line iProphet Page: Add an option to launch ProteinProphet, ------------------------------------------------------------------------ r6452 | dshteyn | 2014-03-25 14:53:52 -0700 (Tue, 25 Mar 2014) | 1 line PTMProphet: bug for detection of nterm_mod. ------------------------------------------------------------------------ r6455 | dshteyn | 2014-03-26 12:13:01 -0700 (Wed, 26 Mar 2014) | 1 line xinteract: soften error message to a warning and only when they try to use ptmprophet without iprophet ------------------------------------------------------------------------ r6456 | dshteyn | 2014-03-26 12:14:44 -0700 (Wed, 26 Mar 2014) | 1 line tpp_gui.pl: fix bug with deleted pepXMLs on windows when using unmerged analysis in runXinteract, cleaner auto-naming scheme for runXinteract. ------------------------------------------------------------------------ r6457 | dshteyn | 2014-03-26 12:18:20 -0700 (Wed, 26 Mar 2014) | 1 line BUGFIX: correct time reporting in xinteract -D_USE_32BIT_TIME_T ------------------------------------------------------------------------ r6460 | dshteyn | 2014-03-27 18:55:16 -0700 (Thu, 27 Mar 2014) | 1 line iProphet: Rewrite spectrum_query index to make unique for quantitation tools. ------------------------------------------------------------------------ r6461 | dshteyn | 2014-03-27 22:56:14 -0700 (Thu, 27 Mar 2014) | 1 line ASAPRatio: Use iProphet probs if present. When running gnuplot test for existence of the png file image before deleting the temporaries. ------------------------------------------------------------------------ r6462 | dshteyn | 2014-03-28 11:02:16 -0700 (Fri, 28 Mar 2014) | 1 line GNUPLOT flush with unset output to help the image file flushing issue under windows ------------------------------------------------------------------------ r6464 | slagelwa | 2014-03-28 16:04:49 -0700 (Fri, 28 Mar 2014) | 5 lines David' been tracking a weird bug with gnuplot. He's traced it down to a change where I removed the unused GNUPLOT_PIPE but inadvertly changed the binary name. Fingers crossed this works... ------------------------------------------------------------------------ r6465 | slagelwa | 2014-03-28 16:18:17 -0700 (Fri, 28 Mar 2014) | 5 lines Merged r6458:6459 Jimmys change on trunk into branch. Looks to be a small conflict when I did it. From what I could see there were some warning messages in the branch version that weren't in the trunk. Just took the trunk version. ------------------------------------------------------------------------ r6466 | slagelwa | 2014-03-28 16:21:46 -0700 (Fri, 28 Mar 2014) | 2 lines Merged r6462:6463 change on trunk into branch ------------------------------------------------------------------------ r6467 | dshteyn | 2014-04-02 11:25:03 -0700 (Wed, 02 Apr 2014) | 1 line PepXMLViewer.cgi: MZRatio is reported as a link only in html mode now, simple value every other mode. ------------------------------------------------------------------------ r6468 | dshteyn | 2014-04-02 12:13:24 -0700 (Wed, 02 Apr 2014) | 1 line iProphet: Fix FPKM message bug. ------------------------------------------------------------------------ r6472 | slagelwa | 2014-04-14 13:48:22 -0700 (Mon, 14 Apr 2014) | 1 line Corrects problem which results in a incomplete pep.xml file when the -r option is not used. ------------------------------------------------------------------------ r6473 | dshteyn | 2014-04-15 13:56:21 -0700 (Tue, 15 Apr 2014) | 1 line Sqt2XML: fix bug when empty lines happen in an Sqt, don't quit..skip to next spectrum_query, reported on spctools-discuss ------------------------------------------------------------------------ r6474 | real_procopio | 2014-04-15 19:07:15 -0700 (Tue, 15 Apr 2014) | 1 line [Petunia] (re-)Simplifying iProphet page by taking out PTM and ProteinProphet options; also removed code that was copy/pasted into PTMProphet page but had no actual function; made Comet the default engine; removed (rarely used) advanced options for ProteinProphet in xinteract page; made PPM the default unit for AccMass model; Added link to Mayu. ------------------------------------------------------------------------ r6477 | real_procopio | 2014-04-16 18:37:38 -0700 (Wed, 16 Apr 2014) | 1 line [Petunia] Added 'no spaces' validation for filepaths and other parameters; make sure iProphet page actually catches errors; moved Mayu link and added link to Comet project page; added warning if speclibs dir does not exist; added option to report probs for decoy hits in PepProph; change 'Paste' button color after click to indicate it is working. ------------------------------------------------------------------------ r6500 | real_procopio | 2014-04-30 15:49:41 -0700 (Wed, 30 Apr 2014) | 1 line [plotspectrast] Added support for mzML (courtesy of DDS) ------------------------------------------------------------------------
