TPP:4.6.2 SVN Log
From SPCTools
This page contains a list of all source code changes made by developers for the 4.6.2 TPP release.
Trunk Changes Since 4.6.1 Merged Into 4.6 Branch (r5937:6012)
------------------------------------------------------------------------ r5937 | slagelwa | 2012-09-04 17:54:53 -0700 (Tue, 04 Sep 2012) | 3 lines Merging changes from 4.6 branch into trunk ------------------------------------------------------------------------ r5944 | slagelwa | 2012-09-24 15:01:22 -0700 (Mon, 24 Sep 2012) | 2 lines reverting to working version ------------------------------------------------------------------------ r5951 | slagelwa | 2012-09-26 15:01:37 -0700 (Wed, 26 Sep 2012) | 5 lines Merged 4.6.1 changes into trunk. (Noticed that there may have been some 4.6.0 changes also merged that had been left out as they may have been outside of the trans_proteomic_pipeline directory). ------------------------------------------------------------------------ r5952 | slagelwa | 2012-09-27 14:15:43 -0700 (Thu, 27 Sep 2012) | 4 lines Was using the -N option to set the location of the pep.xml file when in fact this really sets the basename used within the pep.xml file. ------------------------------------------------------------------------ r5953 | slagelwa | 2012-09-28 12:28:59 -0700 (Fri, 28 Sep 2012) | 2 lines bump version ------------------------------------------------------------------------ r5954 | eng_jk | 2012-10-02 10:50:54 -0700 (Tue, 02 Oct 2012) | 2 lines change chymotrypsin definition from YWFM to YWFL ------------------------------------------------------------------------ r5955 | mhoopmann | 2012-10-03 13:16:14 -0700 (Wed, 03 Oct 2012) | 2 lines Removing unneccessary call to deprecated rampTrimBaseName() ------------------------------------------------------------------------ r5956 | mhoopmann | 2012-10-04 14:44:48 -0700 (Thu, 04 Oct 2012) | 2 lines Caught exception when opening a bad mz5 file. This prevents a crash. The HDF5 trace is still printed to screen: don't know how to silence this. ------------------------------------------------------------------------ r5957 | slagelwa | 2012-10-23 16:24:17 -0700 (Tue, 23 Oct 2012) | 3 lines Now batch submits jobs to glados ------------------------------------------------------------------------ r5958 | dshteyn | 2012-10-30 16:23:20 -0700 (Tue, 30 Oct 2012) | 1 line InteractParser: more robust code for finding the data. ------------------------------------------------------------------------ r5959 | dshteyn | 2012-10-30 16:38:24 -0700 (Tue, 30 Oct 2012) | 1 line Mascot: read Mascot's expectation score. ------------------------------------------------------------------------ r5960 | dshteyn | 2012-10-30 16:38:44 -0700 (Tue, 30 Oct 2012) | 1 line Mascot: read Mascot's expectation score. ------------------------------------------------------------------------ r5961 | dshteyn | 2012-10-30 16:39:52 -0700 (Tue, 30 Oct 2012) | 1 line New Comet Support ------------------------------------------------------------------------ r5962 | dshteyn | 2012-10-30 16:40:38 -0700 (Tue, 30 Oct 2012) | 1 line New Comet Support ------------------------------------------------------------------------ r5963 | dshteyn | 2012-10-30 16:43:09 -0700 (Tue, 30 Oct 2012) | 1 line Mascot: read Mascot's expectation score. ------------------------------------------------------------------------ r5964 | dshteyn | 2012-10-30 16:44:39 -0700 (Tue, 30 Oct 2012) | 1 line PTMProphet: report that ETD mode is detected. ------------------------------------------------------------------------ r5965 | dshteyn | 2012-10-30 16:51:06 -0700 (Tue, 30 Oct 2012) | 1 line PTMProphet: default outfile is input file unless specified, n-term modified peptide bug fixed. ------------------------------------------------------------------------ r5966 | dshteyn | 2012-10-30 16:57:31 -0700 (Tue, 30 Oct 2012) | 1 line PeptideProphet: improvements and changes associated with new Comet, Mascot expect score and RTCatalog. iProphet: NSP model, semi-supervised model. ------------------------------------------------------------------------ r5967 | dshteyn | 2012-10-31 10:20:55 -0700 (Wed, 31 Oct 2012) | 1 line Hydra is still being tested. ------------------------------------------------------------------------ r5968 | dshteyn | 2012-10-31 10:25:29 -0700 (Wed, 31 Oct 2012) | 1 line No expect score for sequest ------------------------------------------------------------------------ r5969 | dshteyn | 2012-10-31 15:10:20 -0700 (Wed, 31 Oct 2012) | 1 line More descriptive error message. ------------------------------------------------------------------------ r5970 | dshteyn | 2012-10-31 15:17:05 -0700 (Wed, 31 Oct 2012) | 1 line More descriptive error message. ------------------------------------------------------------------------ r5971 | dshteyn | 2012-11-06 16:30:45 -0800 (Tue, 06 Nov 2012) | 1 line high resolution k-score support ------------------------------------------------------------------------ r5972 | real_procopio | 2012-11-09 16:51:29 -0800 (Fri, 09 Nov 2012) | 1 line [new] Script to parse and generate 'dashboard' view of pepXML and protXML models; uses js-flot libraries for client-side rendering, same as Lorikeet ------------------------------------------------------------------------ r5973 | real_procopio | 2012-11-12 17:54:58 -0800 (Mon, 12 Nov 2012) | 1 line [TPP Models] Adding the new models viewer to the build and release ------------------------------------------------------------------------ r5976 | mhoopmann | 2012-11-19 10:11:50 -0800 (Mon, 19 Nov 2012) | 4 lines Sorry, this was accidentally checked into branch earlier. Here's what was done, and is now in trunk: Added hrk-score specific check for empty spectrum prior to scoring a peptide. cleaned up comments for easier reading ------------------------------------------------------------------------ r5977 | real_procopio | 2012-11-29 13:56:52 -0800 (Thu, 29 Nov 2012) | 1 line [protXML viewer] Added use strict which, along with warnings, lead to fixing a number of bad usage of variables (misnamed, uninitialized, redeclared, and unused); also, removed some old stale code and local (regis) path comparisons. ------------------------------------------------------------------------ r5978 | real_procopio | 2012-11-29 15:21:53 -0800 (Thu, 29 Nov 2012) | 1 line [protXML viewer] Fixed links in tab-delimited output; also got rid of ineffectual if statements ------------------------------------------------------------------------ r5979 | eng_jk | 2012-11-29 15:36:59 -0800 (Thu, 29 Nov 2012) | 2 lines extend allowable enzyme string names ------------------------------------------------------------------------ r5980 | slagelwa | 2012-11-30 15:20:14 -0800 (Fri, 30 Nov 2012) | 3 lines Simple wrapper for running SuperHirn on regis ------------------------------------------------------------------------ r5981 | slagelwa | 2012-12-05 14:14:38 -0800 (Wed, 05 Dec 2012) | 46 lines Been sitting on 2.4 to long... * Changed the visibility timeout of service messages to 5 minutes. Now has a forked monitor process that bumps the visibility by 5 every 5 minutes. This way if a spot instance (or process) dies the search will go back into the pool quickly instead of waiting 12 hrs. * For all searches jobs it now invokes them with its own "system()" command in order to catch shutdown signals correctly and well, shutdown, instead of returning with a error. * Will cancel extra spot requests that haven't started if nothing else is in the service queue * Now tracks cancelled spot requests as they don't always show up as cancelled. * Broke out some of the logic to determine when to launch more instances into functions to organize it better. * Added the option ec2-util to control be able to adjust the utilization thresold(ratio) of started+running EC2 instances to pending services * If an upload from the local host fails it retries and if unsuccessful logs it as an error instead of queuing it as a service and resulting in download errors. * Changed the S3 retry to 5 minutes and added a retry with a "requeue" if failure persist. Will requeue up to 10 times. * Added errors to reporting. * Fixed issue with previous results not being deleted when new search is started. * Uses real paths to files instead of absolute paths to remove links/".." that would cause problems with file locations. * Fixed an issue with mzML/mzXML files being gzipped but not sent that way due to file checksums * Files are sorted by descending size before uploading searches. * Updated/added more tests. ------------------------------------------------------------------------ r5982 | slagelwa | 2012-12-10 16:00:37 -0800 (Mon, 10 Dec 2012) | 2 lines Checking in first cut of a simple simulator for amztpp ------------------------------------------------------------------------ r5983 | mhoopmann | 2012-12-13 16:14:36 -0800 (Thu, 13 Dec 2012) | 1 line Check for minimum peak count before analyzing a spectrum, even with spectrum conditioning turned off. ------------------------------------------------------------------------ r5984 | real_procopio | 2012-12-14 18:07:21 -0800 (Fri, 14 Dec 2012) | 1 line [PepXMLViewer] Stop file checking once a) file has been detected as changed on server, or b) 4 failed attempts at getting status. ------------------------------------------------------------------------ r5985 | slagelwa | 2012-12-18 11:08:30 -0800 (Tue, 18 Dec 2012) | 2 lines Updating myrimatch ------------------------------------------------------------------------ r5986 | slagelwa | 2012-12-18 13:26:20 -0800 (Tue, 18 Dec 2012) | 3 lines Link has changed again. Continuous development...errrr ------------------------------------------------------------------------ r5987 | slagelwa | 2012-12-19 09:42:58 -0800 (Wed, 19 Dec 2012) | 2 lines Adding patch to boost so that it'll compile correctly under gcc4.7 (Ubuntu 10.12) ------------------------------------------------------------------------ r5988 | slagelwa | 2012-12-19 09:44:11 -0800 (Wed, 19 Dec 2012) | 2 lines Applying patch to boost so that it'll compile correctly under gcc4.7 (Ubuntu 10.12) ------------------------------------------------------------------------ r5989 | slagelwa | 2012-12-19 16:20:31 -0800 (Wed, 19 Dec 2012) | 5 lines Fixed problem discovered with use of strcpy() under latest glibc/gcc 4.7 on Ubunutu. According the the strcpy() references the source and destination should not overlap in memory. So I replaced it with a memmove() which does allow them to overlap. ------------------------------------------------------------------------ r5990 | slagelwa | 2012-12-19 16:24:36 -0800 (Wed, 19 Dec 2012) | 2 lines Removing debugging statements that got checked in ------------------------------------------------------------------------ r5991 | slagelwa | 2012-12-26 12:49:17 -0800 (Wed, 26 Dec 2012) | 2 lines Label it as a development/trunk version ------------------------------------------------------------------------ r5992 | slagelwa | 2012-12-26 16:34:37 -0800 (Wed, 26 Dec 2012) | 1 line Added declaration of $base_dir variable so that it builds on Windows. Now that we use strict for this perl program we need to make sure everything is declared. We're doing text replacements that insert uses of this variable into the code. ------------------------------------------------------------------------ r5993 | slagelwa | 2012-12-27 16:22:29 -0800 (Thu, 27 Dec 2012) | 7 lines * Added patch to HDF so it'll build using latest GCC under Unbuntu 10.12 (silly C++ comments in C code) * Updated Makefile to run multiple HDF patches * Updated Makefile to run multiple BOOST patches * Removed bad BOOST_INCL rule ------------------------------------------------------------------------ r5994 | slagelwa | 2012-12-28 12:45:54 -0800 (Fri, 28 Dec 2012) | 5 lines * Updated display to include more cost information. * Added download tallying of bandwidth * Improved look of chart/overall display * Working on improving cost calculations ------------------------------------------------------------------------ r5995 | eng_jk | 2013-01-04 15:30:54 -0800 (Fri, 04 Jan 2013) | 2 lines Update to latest Lorikeet viewer which fixes errors present in existing viewer in TPP. ------------------------------------------------------------------------ r5996 | slagelwa | 2013-01-04 16:02:18 -0800 (Fri, 04 Jan 2013) | 5 lines * Fixed issue with ec2 counts going negative when the number of downloads drops to zero and ec2 instances are free * Cleaned up UI a little more * More accurately calculates cost and displays it ------------------------------------------------------------------------ r5997 | eng_jk | 2013-01-04 16:23:08 -0800 (Fri, 04 Jan 2013) | 2 lines clean up source file ------------------------------------------------------------------------ r5998 | dshteyn | 2013-01-07 15:21:13 -0800 (Mon, 07 Jan 2013) | 1 line Committing changes to PTMProphet that include correct handling of static mod containing peps and simplification of PeakLists using SpectraST's PeakList object. ------------------------------------------------------------------------ r5999 | slagelwa | 2013-01-07 16:17:56 -0800 (Mon, 07 Jan 2013) | 4 lines * Added version, displays it * Fixed/finished the S3 storage cost ------------------------------------------------------------------------ r6000 | slagelwa | 2013-01-07 16:20:16 -0800 (Mon, 07 Jan 2013) | 1 line ------------------------------------------------------------------------ r6001 | eng_jk | 2013-01-07 16:21:24 -0800 (Mon, 07 Jan 2013) | 2 lines update css for lorikeet ------------------------------------------------------------------------ r6002 | slagelwa | 2013-01-09 13:15:17 -0800 (Wed, 09 Jan 2013) | 2 lines Adding new script ------------------------------------------------------------------------ r6003 | slagelwa | 2013-01-11 11:52:16 -0800 (Fri, 11 Jan 2013) | 6 lines * Renamed top directory to amztpp. Why not call it what it is. * Fixed an issue where it was missing Win32::ShellQuote dependency on Windows. * Bumped the version to 2.4.1 ------------------------------------------------------------------------ r6004 | slagelwa | 2013-01-11 12:03:31 -0800 (Fri, 11 Jan 2013) | 3 lines * Renamed top directory to amztpp using svn mv ------------------------------------------------------------------------ r6005 | slagelwa | 2013-01-11 13:07:37 -0800 (Fri, 11 Jan 2013) | 4 lines Adding LGPL v2 license (same as TPP) as we use ExtJS's open source license and need to meet the requirements ------------------------------------------------------------------------ r6006 | slagelwa | 2013-01-11 14:11:05 -0800 (Fri, 11 Jan 2013) | 4 lines * Fixing the number of tests skipped. Not bumping the version for this change, its still 2.4.1. ------------------------------------------------------------------------ r6007 | slagelwa | 2013-01-15 16:35:16 -0800 (Tue, 15 Jan 2013) | 9 lines * Added a license file * Fixed an issue where the myrimatch and inspect log files wheren't being linked correctly for displaying results * Fixed an issue with base_name paths not being updated which led to spectrum not being displayed in Petunia. ------------------------------------------------------------------------ r6008 | eng_jk | 2013-01-16 12:17:56 -0800 (Wed, 16 Jan 2013) | 5 lines Updated to Lorikeet rev 50. Added "Exp. m/z" mass to 2nd line of Lorikeet header. Modified plot-msms-js.cgi to use calculated mass in place of experimental mass if PepMass is not passed on URL; for MS1 plotting. ------------------------------------------------------------------------ r6009 | henryhlam | 2013-01-16 20:38:37 -0800 (Wed, 16 Jan 2013) | 1 line [SpectraST] New -cq option for cutoff by FDR (q-value) when importing from pep.xml ------------------------------------------------------------------------ r6010 | dshteyn | 2013-01-17 13:06:21 -0800 (Thu, 17 Jan 2013) | 1 line PTMProphet: adding version info output to pepXML. ------------------------------------------------------------------------ r6011 | slagelwa | 2013-01-17 13:20:11 -0800 (Thu, 17 Jan 2013) | 6 lines Merging any changes (which there aren't any) of the 4.6 branch to the trunk. This is done to update the merge info so we can merge trunk changes back to 4.6. ------------------------------------------------------------------------
4.6 Branch Changes Post Merge of Trunk
------------------------------------------------------------------------ r5949 | dshteyn | 2012-09-25 14:50:36 -0700 (Tue, 25 Sep 2012) | 1 line Mascot2XML: 5 digit scan numbers ------------------------------------------------------------------------ r5974 | mhoopmann | 2012-11-14 13:42:26 -0800 (Wed, 14 Nov 2012) | 1 line Added hrk-score specific check for empty spectrum prior to scoring a peptide. ------------------------------------------------------------------------ r5975 | mhoopmann | 2012-11-14 13:50:50 -0800 (Wed, 14 Nov 2012) | 1 line cleaned up comments for easier reading ------------------------------------------------------------------------ r6012 | slagelwa | 2013-01-17 16:50:24 -0800 (Thu, 17 Jan 2013) | 4 lines Merged (manually) changes from -r5937:HEAD on the trunk into 4.6 in preparation for a 4.6.2 release. ------------------------------------------------------------------------ r6013 | slagelwa | 2013-01-18 10:42:29 -0800 (Fri, 18 Jan 2013) | 1 line Addresses a compiler issue under Windows/MingW. With Linux g++ version 4.1.2 the overloaded constructor construct is allowed but with g++ 4.6.2 on MingW it complains about having a constructor call itself. Regardless its unnecessary to have both constructors since the definition is assigning a default value to the last parameter anyhow. ------------------------------------------------------------------------ r6014 | real_procopio | 2013-01-18 13:25:37 -0800 (Fri, 18 Jan 2013) | 1 line [Mascot2XML] Fix reported buffer overflow bug (Courtesy of Phil Charles) ------------------------------------------------------------------------ r6015 | real_procopio | 2013-01-22 17:19:52 -0800 (Tue, 22 Jan 2013) | 1 line [comet-fastadb] Do not error out in case of unknown enzyme; warn instead; removed old revision history, placed SVN ID in header instead; small color changes to markAA and messages. ------------------------------------------------------------------------ r6016 | real_procopio | 2013-01-23 17:17:47 -0800 (Wed, 23 Jan 2013) | 1 line [SpectraST] Fix potential bug with peptide sequence comparison (courtesy of http://www.viva64.com/en/b/0156/ ) ------------------------------------------------------------------------ r6017 | real_procopio | 2013-01-23 17:31:26 -0800 (Wed, 23 Jan 2013) | 1 line [Tandem2XML] Do not add path if full path passed in; also corrected a logic error in path insertion (last one courtesy of http://www.viva64.com/en/b/0156/ ) ------------------------------------------------------------------------ r6018 | real_procopio | 2013-01-23 17:33:39 -0800 (Wed, 23 Jan 2013) | 1 line [PepXMLViewer] Fix faulty substring search (courtesy of http://www.viva64.com/en/b/0156/ ) ------------------------------------------------------------------------ r6019 | real_procopio | 2013-01-23 17:34:44 -0800 (Wed, 23 Jan 2013) | 1 line [crypt] Fix erroneous index (courtesy of http://www.viva64.com/en/b/0156/ ) ------------------------------------------------------------------------ r6020 | real_procopio | 2013-01-23 17:39:18 -0800 (Wed, 23 Jan 2013) | 1 line [Mascot2XML] Reformat code; fix logic error (partially masked by bad formatting -- (courtesy of http://www.viva64.com/en/b/0156/ ) ------------------------------------------------------------------------ r6021 | slagelwa | 2013-01-24 17:18:50 -0800 (Thu, 24 Jan 2013) | 4 lines Recognize OMSSA generated pepXML files. OMSAA uses the older DOCTYPE dtd declaration in its XML output instead of using the newer XML schema declaration. ------------------------------------------------------------------------ r6024 | slagelwa | 2013-01-25 10:59:04 -0800 (Fri, 25 Jan 2013) | 2 lines Be a little more precise ------------------------------------------------------------------------ r6026 | slagelwa | 2013-01-28 15:38:56 -0800 (Mon, 28 Jan 2013) | 5 lines No need to write the alternate protein twice. It gets written out later in the code. This fixes an issue when running InteractParser on OMSSA results and then getting duplicate alternate proteins for a peptide. ------------------------------------------------------------------------ r6029 | slagelwa | 2013-01-29 11:59:12 -0800 (Tue, 29 Jan 2013) | 6 lines Merging in David's recent trunk changes: "InteractParser: auto-correct raw data paths, OMSSA auto correct protein names, remove shtml file generation." ------------------------------------------------------------------------ r6030 | slagelwa | 2013-01-29 12:09:38 -0800 (Tue, 29 Jan 2013) | 5 lines Merging David's trunk changes into branch: "InteractParser: auto-correct five digit scan numbers." ------------------------------------------------------------------------ r6033 | slagelwa | 2013-01-29 15:48:52 -0800 (Tue, 29 Jan 2013) | 5 lines Merging trunk change by David: "InteractParser: fix problem with Comet's msms_run_summary tag" ------------------------------------------------------------------------ r6034 | slagelwa | 2013-01-30 10:03:55 -0800 (Wed, 30 Jan 2013) | 5 lines Merging changes made by David on trunk: "InteractParser: auto-correct raw data paths, OMSSA auto correct protein names, remove shtml file generation." ------------------------------------------------------------------------ r6035 | dshteyn | 2013-01-30 15:09:57 -0800 (Wed, 30 Jan 2013) | 1 line ProteinProphet:BUGFIX corrected problem with wrong protein descriptions being displayed next to other proteins (reported by Rene.) ------------------------------------------------------------------------ r6036 | slagelwa | 2013-01-30 15:23:00 -0800 (Wed, 30 Jan 2013) | 3 lines Document changes to function. ------------------------------------------------------------------------ r6037 | dshteyn | 2013-01-30 15:28:00 -0800 (Wed, 30 Jan 2013) | 1 line Petunia: enable decoyFastaGenerator.pl page ------------------------------------------------------------------------ r6038 | dshteyn | 2013-01-30 15:30:53 -0800 (Wed, 30 Jan 2013) | 1 line Petunia: enable decoyFastaGenerator.pl page ------------------------------------------------------------------------ r6039 | dshteyn | 2013-01-30 15:37:39 -0800 (Wed, 30 Jan 2013) | 1 line Petunia: enable decoyFastaGenerator.pl page ------------------------------------------------------------------------ r6040 | dshteyn | 2013-01-30 15:40:05 -0800 (Wed, 30 Jan 2013) | 1 line Petunia: decoyFastaGenerator.pl page ------------------------------------------------------------------------ r6041 | dshteyn | 2013-01-30 15:54:29 -0800 (Wed, 30 Jan 2013) | 1 line Undo PTMProphet change commit accidentally. ------------------------------------------------------------------------ r6042 | dshteyn | 2013-01-30 16:07:48 -0800 (Wed, 30 Jan 2013) | 1 line Petunia: change decoyFastaGenerator.pl calls. ------------------------------------------------------------------------ r6043 | real_procopio | 2013-01-31 14:24:08 -0800 (Thu, 31 Jan 2013) | 1 line [plot-msms] Fix incorrect increment operator (courtesy of http://www.viva64.com/en/b/0156/ ); add SVN revision ------------------------------------------------------------------------ r6044 | real_procopio | 2013-01-31 14:34:37 -0800 (Thu, 31 Jan 2013) | 1 line [Out2XML] Use correct size for array (courtesy of http://www.viva64.com/en/b/0156/ ) ------------------------------------------------------------------------ r6045 | real_procopio | 2013-01-31 14:37:03 -0800 (Thu, 31 Jan 2013) | 1 line [RTCalculator] Initialize variable that may potentially not get a value before comparison (courtesy of http://www.viva64.com/en/b/0156/ ) ------------------------------------------------------------------------ r6046 | real_procopio | 2013-01-31 14:41:18 -0800 (Thu, 31 Jan 2013) | 1 line [KernelDensityRTMixtureDistr] Remove unused if/else logic (courtesy of http://www.viva64.com/en/b/0156/ ) ------------------------------------------------------------------------ r6047 | real_procopio | 2013-01-31 14:51:14 -0800 (Thu, 31 Jan 2013) | 1 line [MixtureModel] Initialize variable (courtesy of http://www.viva64.com/en/b/0156/ ) ------------------------------------------------------------------------ r6048 | dshteyn | 2013-01-31 14:54:18 -0800 (Thu, 31 Jan 2013) | 1 line InteractParser: fix segfault on unknown enzyme. Auto update ntt and nmc info based on sample_enzyme tag when recognized. ------------------------------------------------------------------------ r6049 | real_procopio | 2013-01-31 15:00:17 -0800 (Thu, 31 Jan 2013) | 1 line [Dta2mzXML] Fix faulty substring search (courtesy of http://www.viva64.com/en/b/0156/ ); also got rid of lots of whitespace and added SVN rev ------------------------------------------------------------------------ r6050 | real_procopio | 2013-01-31 15:06:00 -0800 (Thu, 31 Jan 2013) | 1 line [ModelParser] Throw a meaningful error if input file is not found; added SVN rev ------------------------------------------------------------------------ r6051 | real_procopio | 2013-01-31 17:36:09 -0800 (Thu, 31 Jan 2013) | 1 line [comet-fastadb] Implement on-page error reporting via javascript; Forget specified enzyme if not recognized; Removed a bare pointer and redundant logic in NXST check (courtesy of http://www.viva64.com/en/b/0156/ ) ------------------------------------------------------------------------ r6052 | real_procopio | 2013-01-31 17:54:36 -0800 (Thu, 31 Jan 2013) | 1 line [TPP Models] Make sure sens and error plots for each charge state have different vriable names in jscript; take out regis reference ------------------------------------------------------------------------ r6055 | dshteyn | 2013-02-01 12:04:28 -0800 (Fri, 01 Feb 2013) | 1 line ModificationInfo: create some additional space in the string to accomodate modifications with more digits to prevent crash on some files. ------------------------------------------------------------------------ r6056 | slagelwa | 2013-02-01 13:55:56 -0800 (Fri, 01 Feb 2013) | 5 lines Added Trypsin/P as it wasn't being recognized. Also included a link in the comments to the onotology page for the cleavage agents that are used by Proteowizard/other search engines -- for reference. ------------------------------------------------------------------------ r6057 | dshteyn | 2013-02-01 16:04:10 -0800 (Fri, 01 Feb 2013) | 1 line BUGFIX: InteractParser memory issue. ------------------------------------------------------------------------ r6059 | slagelwa | 2013-02-04 09:55:35 -0800 (Mon, 04 Feb 2013) | 3 lines Updated link to UniProtKB (API change?) and removed broken link to SGD. ------------------------------------------------------------------------ r6060 | dshteyn | 2013-02-04 11:38:31 -0800 (Mon, 04 Feb 2013) | 1 line InteractParser: -a now changes the paths even for all base_names. ------------------------------------------------------------------------ r6061 | dshteyn | 2013-02-04 11:46:05 -0800 (Mon, 04 Feb 2013) | 1 line ProteinProphet: when 0 peptides found, generate output file with 0 proteins output. ------------------------------------------------------------------------ r6062 | dshteyn | 2013-02-04 16:52:45 -0800 (Mon, 04 Feb 2013) | 1 line InteractParser: allow outputfile to be nameed with a prefix equal to the input file. ------------------------------------------------------------------------ r6063 | dshteyn | 2013-02-04 22:37:11 -0800 (Mon, 04 Feb 2013) | 1 line InteractParser: fix pyro mod only if mod_nterm_mass is not NULL (meaning it has not been fixed yet). ------------------------------------------------------------------------
