TPP:4.6.0 SVN Log

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-r5416 | pcbrefugee | 2011-05-31 13:00:39 -0700 (Tue, 31 May 2011) | 1 line 
- 
-[Makefiles] preserve compatibility with older minGW setups by testing for -static-libstdc++ support 
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-r5418 | slagelwa | 2011-06-01 16:59:29 -0700 (Wed, 01 Jun 2011) | 2 lines 
- 
-Major refit, pending some IE fixes 
- 
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-r5419 | slagelwa | 2011-06-01 22:19:31 -0700 (Wed, 01 Jun 2011) | 2 lines 
- 
-Improved some error handling, fixed IE bug, removed unnecessary console declarations, added important console.info() declaration for IE 
- 
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-r5420 | slagelwa | 2011-06-07 10:13:46 -0700 (Tue, 07 Jun 2011) | 2 lines 
- 
-Fixes for IE, rename title 
- 
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-r5421 | pcbrefugee | 2011-06-09 14:20:58 -0700 (Thu, 09 Jun 2011) | 1 line 
- 
-[SpectraST] casts for quiet compile - log(int) is ambiguous on some compilers 
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-r5422 | pcbrefugee | 2011-06-09 14:23:47 -0700 (Thu, 09 Jun 2011) | 1 line 
- 
-[RTCalculator] casts and unused variable removal for quiet compile 
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-r5423 | pcbrefugee | 2011-06-09 14:24:50 -0700 (Thu, 09 Jun 2011) | 1 line 
- 
-need to include <float.h> for _isnan decl 
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-r5424 | pcbrefugee | 2011-06-09 14:38:21 -0700 (Thu, 09 Jun 2011) | 1 line 
- 
-[Makefile] help MSVC deal with inline decls in some additional GSL files we weren't using before by making a special header file for MSVC use 
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-r5425 | pcbrefugee | 2011-06-09 14:42:18 -0700 (Thu, 09 Jun 2011) | 1 line 
- 
-[gsl] add a couple of files we weren't using before to the VC8 build 
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-r5426 | pcbrefugee | 2011-06-09 14:44:14 -0700 (Thu, 09 Jun 2011) | 1 line 
- 
-[mzParser] use typedefs instead of define to avoid redefinition warnings, use _int32 instead of long when defining 32 bit integer type so it works in 64 bit windows 
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-r5427 | pcbrefugee | 2011-06-09 15:18:32 -0700 (Thu, 09 Jun 2011) | 1 line 
- 
-update MSVC8 build for use of zlib-1.2.5 and mzParser - probably incomplete for VC9 
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-r5428 | pcbrefugee | 2011-06-09 16:47:58 -0700 (Thu, 09 Jun 2011) | 1 line 
- 
-[gsl msvc build] make sure gsl config.h has include path precedence within gsl build, copy vc8 changes to vc9 file (untested) 
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-r5429 | pcbrefugee | 2011-06-09 17:57:22 -0700 (Thu, 09 Jun 2011) | 1 line 
- 
-[VC8 build] add saxtandemhandler.cxx, don't use mzParser vcproj after all 
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-r5431 | dshteyn | 2011-06-15 14:36:17 -0700 (Wed, 15 Jun 2011) | 1 line 
- 
-RefreshParser: I->L conversion on peptide and proteins to map to all indistinguishable peptides in the proteins. 
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-r5433 | real_procopio | 2011-06-16 15:57:28 -0700 (Thu, 16 Jun 2011) | 1 line 
- 
-[windows installer] Adding Sqt2XML 
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-r5446 | slagelwa | 2011-07-13 15:05:09 -0700 (Wed, 13 Jul 2011) | 2 lines 
- 
-Finally checking in the new EC2 AMI scripts 
- 
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-r5448 | pcbrefugee | 2011-07-13 17:48:06 -0700 (Wed, 13 Jul 2011) | 1 line 
- 
-[pentunia] added a link on the PepC page to the PepC paper, which is now on PubMed 
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-r5451 | henryhlam | 2011-07-14 19:40:43 -0700 (Thu, 14 Jul 2011) | 1 line 
- 
-[SpectraST] MRM table prints theoretical (not observed), accurate (to 4 decimal places) mass for Q3 
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-r5457 | henryhlam | 2011-07-21 18:00:30 -0700 (Thu, 21 Jul 2011) | 1 line 
- 
-[SpectraST] Use theoretical mass in MRM tables -- missing change in last check-in 
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-r5459 | henryhlam | 2011-07-21 18:13:32 -0700 (Thu, 21 Jul 2011) | 1 line 
- 
-[SpectraST] Treat sptxt as msp for import (after ensuring no file overwrite); minor fixes 
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-r5468 | henryhlam | 2011-08-01 23:34:01 -0700 (Mon, 01 Aug 2011) | 1 line 
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-[SpectraST] Reduce chance of decoy hitting existing sequences leading to infinite-looping 
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-r5469 | henryhlam | 2011-08-02 00:14:52 -0700 (Tue, 02 Aug 2011) | 1 line 
- 
-[SpectraST] rand() out-of-bound fix for Windows 
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-r5471 | henryhlam | 2011-08-02 00:28:42 -0700 (Tue, 02 Aug 2011) | 1 line 
- 
-[SpectraST] Decoy: add two random AA plus K/R 
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-r5473 | slagelwa | 2011-08-02 11:18:35 -0700 (Tue, 02 Aug 2011) | 4 lines 
- 
-* Cleaned up duplicate params/ templates/ directories 
-* Updated qtandem to handle .gz files 
-  
- 
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-r5474 | slagelwa | 2011-08-02 11:21:42 -0700 (Tue, 02 Aug 2011) | 2 lines 
- 
-* fixed params/ templates confusion 
- 
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-r5480 | slagelwa | 2011-08-10 14:15:57 -0700 (Wed, 10 Aug 2011) | 11 lines 
- 
-Significant changes across the board that haven't been checked in. 
- 
-* Include EC2 name in working directory on instance to distinguish it 
-* Fixed omssa path/files issues 
-* Changed how polling of SQS message queues are tallied 
-* Forking of upload/downloads 
-* Fixed paths issue in pep.xml files 
-* Cache directory changes 
- 
- 
- 
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-r5481 | slagelwa | 2011-08-10 14:21:37 -0700 (Wed, 10 Aug 2011) | 2 lines 
- 
-fixing revision tag 
- 
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-r5482 | slagelwa | 2011-08-10 14:28:37 -0700 (Wed, 10 Aug 2011) | 2 lines 
- 
-setting missing svn keywords property 
- 
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-r5484 | eng_jk | 2011-08-11 11:36:24 -0700 (Thu, 11 Aug 2011) | 3 lines 
- 
-Add -e option to subsetdb for Andreas to allow for export of entries that do not match -N strings. 
-Previously, the -N no-match strings only filtered out matches that passed the -M match strings. 
- 
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-r5489 | slagelwa | 2011-08-17 12:17:09 -0700 (Wed, 17 Aug 2011) | 7 lines 
- 
-* Make sure relative filenames in databases are treated correctly.  
-* Changed algorithm on when new instances are started. Now starts 
- a new instance when the # running < # max and # pending > # running. Which 
- might spawn extra instances due to eventual consistancy but shouldn't spawn 
- more than can be processed.  
-  
- 
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-r5490 | dshteyn | 2011-08-17 15:55:23 -0700 (Wed, 17 Aug 2011) | 1 line 
- 
-PeptideProphetParser: update to correct problem with latest version of Myrimatch which removed some scores in the reports. 
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-r5491 | dshteyn | 2011-08-19 14:04:18 -0700 (Fri, 19 Aug 2011) | 1 line 
- 
-mzParser: Handling of highMZ lowMZ values for Agilent QTOF. 
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-r5495 | slagelwa | 2011-08-25 13:01:55 -0700 (Thu, 25 Aug 2011) | 26 lines 
- 
-* Changed name of amztppserver to the more standard amztppd 
-* Changed to use the upstart init daemon on Ubuntu to start (and keep 
- respawning) the amztpp daemon 
-* Now checkst to make sure that when getting the # running instances that 
- if the EC2 API returns something other than a list it doesn't crash 
-* Changed/added error message if a file to be uploaded doesn't actually 
- exist 
-* Changed timeout on nodes to 10 minutes to equal the same timeout on 
- the client (and reduce the opportunity of nodes running longer than 
- needed) 
-* Fixed/changed the algorithm for deciding to start more nodes. Now 
- starts nodes if pending > running & pending > started 
-* Message handles for services being executed are now written to the file 
- system and removed after the service is completed. This is done to 
- so that if the daemon unexpectly quits and is restarted the message isn't 
- ignored for the timeout but instead is just removed. 
-* uses checksum of file instead of checksum of gzipped file. (Didn't know 
- that the same file contents in two different files results in different 
- gzipped checksums.) 
-* Shutdown only on exit now, always make sure srv message is deleted in 
- case it is interrupted by an exit or signal, and always put the file 
- to S3. 
-* New "-s" option for tppamzd to control whether or not to shutdown on 
- exit 
- 
- 
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-r5501 | henryhlam | 2011-09-01 05:43:09 -0700 (Thu, 01 Sep 2011) | 1 line 
- 
-[SpectraST] Fix rare error when S/N calculation failed due to too few peaks outside precursor region 
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-r5504 | dshteyn | 2011-09-20 12:53:23 -0700 (Tue, 20 Sep 2011) | 1 line 
- 
-PTMProphetParser: changes to the algorithm to make it work smoother and with better results. 
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-r5507 | slagelwa | 2011-09-23 14:09:08 -0700 (Fri, 23 Sep 2011) | 1 line 
- 
-Merged branch 4.5 (r5415:5505) into the trunk 
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-r5508 | dshteyn | 2011-09-23 14:36:13 -0700 (Fri, 23 Sep 2011) | 1 line 
- 
-SpectraSTLIB: adding randomization of spectrum function for PTMProphet. 
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-r5509 | dshteyn | 2011-09-23 15:04:39 -0700 (Fri, 23 Sep 2011) | 1 line 
- 
-PTMProphet: adding getVal functions for KDModel. 
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-r5510 | slagelwa | 2011-09-23 15:28:18 -0700 (Fri, 23 Sep 2011) | 5 lines 
- 
-Re-merged 4.5 changes in trunk. SVNTortise didn't list to my "accept branch" changes when I did the merge. 
- 
-(ALSO MEANS that the trunk changes in these two files will likely be lost) 
- 
- 
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-r5511 | dshteyn | 2011-09-23 16:20:07 -0700 (Fri, 23 Sep 2011) | 1 line 
- 
-Adding back support for Agilent QTOF mzML 
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-r5514 | dshteyn | 2011-09-23 17:04:33 -0700 (Fri, 23 Sep 2011) | 2 lines 
- 
-Fix typo 
- 
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-r5515 | slagelwa | 2011-09-29 11:58:33 -0700 (Thu, 29 Sep 2011) | 6 lines 
- 
-* now removes the log files before submission 
-* uses new conversion queues 
-* no longer allows submissions with the --server flag and instead 
- uses queues 
- 
- 
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-r5516 | ppatrick | 2011-10-04 08:57:14 -0700 (Tue, 04 Oct 2011) | 2 lines 
- 
-Changed from theoretical precursor mass to measured one to allow for narrower tolerances. 
- 
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-r5517 | ppatrick | 2011-10-04 12:28:23 -0700 (Tue, 04 Oct 2011) | 2 lines 
- 
-Changed logic of xsl to speed up loading. 
- 
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-r5518 | ppatrick | 2011-10-04 12:29:44 -0700 (Tue, 04 Oct 2011) | 2 lines 
- 
-increased min peptide probability to 0.8 from 0.5 
- 
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-r5519 | dshteyn | 2011-10-04 13:31:11 -0700 (Tue, 04 Oct 2011) | 1 line 
- 
-RefreshParser: make RefreshParser mapping of semi and non trypic peptides consistent with the search engine parameters unless overridden on the commandline (per Jimmy's and Vagisha's posts to spctools-dev of Jun 10 2011) 
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-r5520 | ppatrick | 2011-10-05 05:35:18 -0700 (Wed, 05 Oct 2011) | 2 lines 
- 
-Initialized preExt to account for incorrect file names being passed. 
- 
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-r5521 | ppatrick | 2011-10-05 05:38:48 -0700 (Wed, 05 Oct 2011) | 2 lines 
- 
-Fixed buffer overruns in void XPressPeptideParser::parse(const char *xmlfile) and void XPressPeptideParser::validate_mzXMLfile() 
- 
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-r5522 | ppatrick | 2011-10-05 05:40:47 -0700 (Wed, 05 Oct 2011) | 2 lines 
- 
-Fixed buffer overrun in void XPressPeptideParser::validate_mzXMLfile()  
- 
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-r5523 | ppatrick | 2011-10-05 14:09:52 -0700 (Wed, 05 Oct 2011) | 3 lines 
- 
-Added Supplemental Activation 
-Removed 0 intensity peaks 
- 
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-r5524 | eng_jk | 2011-10-05 16:36:44 -0700 (Wed, 05 Oct 2011) | 2 lines 
- 
-quick mod to Patrick's buffer overrun fix (for non-sequential mzML scans) 
- 
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-r5527 | eng_jk | 2011-10-06 14:16:52 -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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-r5528 | eng_jk | 2011-10-06 14:18:53 -0700 (Thu, 06 Oct 2011) | 2 lines 
- 
-change deflines to include which reading frame as part of accession 
- 
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-r5529 | henryhlam | 2011-10-09 22:00:49 -0700 (Sun, 09 Oct 2011) | 1 line 
- 
-[util] Catch return values for smooth compiling 
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-r5530 | henryhlam | 2011-10-09 22:03:18 -0700 (Sun, 09 Oct 2011) | 1 line 
- 
-[mzParser] Pound-include stdint.h and catch return values for smooth compiling 
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-r5531 | henryhlam | 2011-10-09 23:57:02 -0700 (Sun, 09 Oct 2011) | 1 line 
- 
-[MzXML2Search] Option to remove charge-reduced precursors for ETD spectra (useful for search engines that do not have that feature) 
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-r5532 | henryhlam | 2011-10-09 23:59:27 -0700 (Sun, 09 Oct 2011) | 1 line 
- 
-[util] Catch return values for smooth compiling 
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-r5533 | henryhlam | 2011-10-10 00:02:43 -0700 (Mon, 10 Oct 2011) | 1 line 
- 
-[Tandem2XML] Fix wrong enzyme specificity for Lys-C 
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-r5534 | henryhlam | 2011-10-10 00:12:16 -0700 (Mon, 10 Oct 2011) | 1 line 
- 
-[xinteract] Move RefreshParser ahead of PeptideProphet to safeguard against some search engines' mangling the protein names and/or omitting NTT/NMC 
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-r5535 | henryhlam | 2011-10-10 00:19:18 -0700 (Mon, 10 Oct 2011) | 1 line 
- 
-[InteractParser] Fix OMSSA's problem with n-term mods 
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-r5536 | henryhlam | 2011-10-10 00:32:35 -0700 (Mon, 10 Oct 2011) | 1 line 
- 
-[InterProphet] More finely divided bins for error rate estimates. Important for modern, large datasets. 
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-r5537 | henryhlam | 2011-10-10 00:35:35 -0700 (Mon, 10 Oct 2011) | 1 line 
- 
-[PeptideProphet] More finely divided bins for error rate estimates. Important for modern, large datasets. 
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-r5538 | henryhlam | 2011-10-10 00:43:02 -0700 (Mon, 10 Oct 2011) | 1 line 
- 
-[Enzyme] Equate tryptic with trypsin 
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-r5548 | slagelwa | 2011-10-14 15:22:56 -0700 (Fri, 14 Oct 2011) | 4 lines 
- 
-* Set the default number of threads to 8 for tandem 
-* Include a warning in the comments that values for three  
- differential modifications are always needed 
- 
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-r5552 | eng_jk | 2011-10-18 12:59:35 -0700 (Tue, 18 Oct 2011) | 2 lines 
- 
-replicate branch 5551 checkin to trunk for xpress/mzML fix 
- 
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-r5553 | real_procopio | 2011-10-19 17:02:11 -0700 (Wed, 19 Oct 2011) | 1 line 
- 
-[dta2mzxml] Change 'plustwo' option to include lowest charge state found for a given scan; also make sure output is real mzXML 
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-r5555 | henryhlam | 2011-10-20 01:52:25 -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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-r5556 | henryhlam | 2011-10-20 01:59:58 -0700 (Thu, 20 Oct 2011) | 1 line 
- 
-[SpectraST] Consider all charges when library spectrum has charge 0 
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-r5557 | henryhlam | 2011-10-20 02:01:34 -0700 (Thu, 20 Oct 2011) | 1 line 
- 
-[SpectraST] Allow import of non-peptide from MSP format 
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-r5558 | henryhlam | 2011-10-20 02:06:59 -0700 (Thu, 20 Oct 2011) | 1 line 
- 
-[SpectraST] New clustering algorithm. Saves memory, prevent deep recursion. 
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-r5560 | dshteyn | 2011-10-20 14:56:38 -0700 (Thu, 20 Oct 2011) | 1 line 
- 
-PTMProphetParser: NEW FEATURES amino acids and mass shifts are users settable as is mz tolerance, improved classification now outperforms ASCORE, EM is now default (new option NOEM). 
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-r5561 | real_procopio | 2011-10-20 17:24:09 -0700 (Thu, 20 Oct 2011) | 1 line 
- 
-[Petunia] Added version checking upon login; warn users if using an old version of TPP 
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-r5565 | mhoopmann | 2011-10-21 15:15:24 -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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-r5567 | henryhlam | 2011-10-23 22:16:00 -0700 (Sun, 23 Oct 2011) | 1 line 
- 
-[SpectraST] High-mass accuracy MS2 support: frag type of CID-QTOF and HCD. Change to shuffleAllPeaks which is used by PTMProphet 
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-r5568 | dshteyn | 2011-10-24 10:56:36 -0700 (Mon, 24 Oct 2011) | 1 line 
- 
-PTMProphet: forgot to commit new function clearObs. 
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-r5571 | dshteyn | 2011-10-26 12:12:56 -0700 (Wed, 26 Oct 2011) | 1 line 
- 
-PepXMLViewer: Correct confusing probability column names in case of iProphet. 
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-r5572 | dshteyn | 2011-10-26 12:24:57 -0700 (Wed, 26 Oct 2011) | 1 line 
- 
-protxml2html.pl: The peptide links will now link out to PepXMLViewer instead of special separate parser. 
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-r5573 | eng_jk | 2011-10-26 16:27:35 -0700 (Wed, 26 Oct 2011) | 2 lines 
- 
-add option to dump ms1 scans as scan/mass/intensity; useful for generating plots 
- 
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-r5575 | dshteyn | 2011-11-01 10:49:27 -0700 (Tue, 01 Nov 2011) | 1 line 
- 
-RTCatalog/RTCalc/RTModel : restructure code, check for fail condition (stddev==0), add gradient peptide feature, add worklist feature. 
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-r5576 | dshteyn | 2011-11-01 12:11:00 -0700 (Tue, 01 Nov 2011) | 1 line 
- 
-Additional typedefs, should probably be centralized. 
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-r5577 | dshteyn | 2011-11-01 12:17:09 -0700 (Tue, 01 Nov 2011) | 1 line 
- 
-RTModel: Additional update functions. 
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-r5578 | dshteyn | 2011-11-01 16:15:35 -0700 (Tue, 01 Nov 2011) | 1 line 
- 
-"iModelParser.cgi: Fix output of FDR plots when available under Windows." 
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-r5579 | dshteyn | 2011-11-01 16:17:12 -0700 (Tue, 01 Nov 2011) | 2 lines 
- 
-return a default url of http://localhost/ when WEBSERVER_URL is not set. 
- 
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-r5581 | dshteyn | 2011-11-03 09:43:13 -0700 (Thu, 03 Nov 2011) | 1 line 
- 
-ProphetModel.pl bugfixes and updates. 
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-r5582 | dshteyn | 2011-11-03 12:40:58 -0700 (Thu, 03 Nov 2011) | 1 line 
- 
-Replace ~ with - to fix the whole XPress ~ character for negative mods hack problem. 
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-r5583 | dshteyn | 2011-11-03 12:54:22 -0700 (Thu, 03 Nov 2011) | 2 lines 
- 
-Fix extra paren typo 
- 
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-r5584 | pcbrefugee | 2011-11-04 14:35:26 -0700 (Fri, 04 Nov 2011) | 1 line 
- 
-[msvc RAMP] use zlib 1.2.5  
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-r5585 | pcbrefugee | 2011-11-04 14:37:14 -0700 (Fri, 04 Nov 2011) | 1 line 
- 
-tweaks for building gsl in msvc 
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-r5586 | dshteyn | 2011-11-04 14:56:44 -0700 (Fri, 04 Nov 2011) | 1 line 
- 
-XPressPeptideParser: BUGFIX handle negative mass difference 
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-r5587 | pcbrefugee | 2011-11-04 15:15:18 -0700 (Fri, 04 Nov 2011) | 1 line 
- 
-silence warnings about depecrated open(), lseek() etc 
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-r5588 | pcbrefugee | 2011-11-04 15:20:37 -0700 (Fri, 04 Nov 2011) | 1 line 
- 
-tweaks for quiet compile 
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-r5589 | pcbrefugee | 2011-11-04 15:32:45 -0700 (Fri, 04 Nov 2011) | 1 line 
- 
-[X!!Tandem] consider MPI version (OpenMPI vs others) when building X!!Tandem 
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-r5591 | dshteyn | 2011-11-04 15:46:58 -0700 (Fri, 04 Nov 2011) | 2 lines 
- 
-fix link to PepXMLViewer 
- 
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-r5593 | pcbrefugee | 2011-11-04 16:37:00 -0700 (Fri, 04 Nov 2011) | 1 line 
- 
-undo my 5588 change, actual problem was with bad implementation of stroull in windows sysdepend.h 
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-r5596 | pcbrefugee | 2011-11-07 10:02:24 -0800 (Mon, 07 Nov 2011) | 1 line 
- 
-get current with ProteoWizard: their rev 3102 with considerable performance gains for mzML reading particularly across network shares 
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-r5597 | dshteyn | 2011-11-07 10:10:12 -0800 (Mon, 07 Nov 2011) | 1 line 
- 
-xinteract: fix bug passing parameters to XPress. 
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-r5598 | eng_jk | 2011-11-07 10:46:11 -0800 (Mon, 07 Nov 2011) | 3 lines 
- 
-Add minimum probability cutoff to quantify peptides (-q command line option; -p and -P already taken) 
-Default cutoff is still at 0.5. Applies to both standard and labelfree modes 
- 
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-r5599 | pcbrefugee | 2011-11-07 11:02:19 -0800 (Mon, 07 Nov 2011) | 1 line 
- 
-quiet a "not all control paths return a value" warning 
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-r5600 | pcbrefugee | 2011-11-07 11:06:34 -0800 (Mon, 07 Nov 2011) | 1 line 
- 
-[ProteoWizard] missed a few new additions to ProteoWizard codebase 
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-r5601 | pcbrefugee | 2011-11-07 12:08:50 -0800 (Mon, 07 Nov 2011) | 1 line 
- 
-[RAMP] tweaks for using ProteoWizard's RAMPAdapter interface  
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-r5602 | pcbrefugee | 2011-11-07 13:19:26 -0800 (Mon, 07 Nov 2011) | 1 line 
- 
-[xtandem] tweak for using updated pwiz to read mzML 
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-r5603 | dshteyn | 2011-11-07 15:38:36 -0800 (Mon, 07 Nov 2011) | 1 line 
- 
-PepXMLViewer.cgi: Added link to javascript MS/MS ions viewer. 
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-r5609 | dshteyn | 2011-11-08 13:34:55 -0800 (Tue, 08 Nov 2011) | 1 line 
- 
-PTMProphetParser: Clean up PTMProphet 
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-r5610 | dshteyn | 2011-11-08 13:41:03 -0800 (Tue, 08 Nov 2011) | 1 line 
- 
-Spectrast: Function to randomize spectra. 
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-r5611 | dshteyn | 2011-11-08 13:42:20 -0800 (Tue, 08 Nov 2011) | 1 line 
- 
-Spectrast: back out Makefile change. 
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-r5612 | dshteyn | 2011-11-08 14:39:05 -0800 (Tue, 08 Nov 2011) | 1 line 
- 
-MS-GFDB support 
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-r5613 | dshteyn | 2011-11-08 14:39:47 -0800 (Tue, 08 Nov 2011) | 1 line 
- 
-MS-GFDB support 
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-r5614 | dshteyn | 2011-11-08 14:40:38 -0800 (Tue, 08 Nov 2011) | 1 line 
- 
-MS-GFDB support 
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-r5615 | dshteyn | 2011-11-08 14:56:07 -0800 (Tue, 08 Nov 2011) | 1 line 
- 
-MS-GFDB support 
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-r5617 | dshteyn | 2011-11-08 15:29:04 -0800 (Tue, 08 Nov 2011) | 1 line 
- 
-MS-GFDB support 
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-r5618 | pcbrefugee | 2011-11-08 16:59:45 -0800 (Tue, 08 Nov 2011) | 1 line 
- 
-[XPressPeptideParser] remove unneeded "struct" in "struct InputStruct" that conflicted with actual declaration of InputStruct as a class. 
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-r5619 | pcbrefugee | 2011-11-09 16:19:16 -0800 (Wed, 09 Nov 2011) | 1 line 
- 
-[pwiz] these generated files were added to SVN by mistake, deleting 
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-r5620 | pcbrefugee | 2011-11-09 16:57:33 -0800 (Wed, 09 Nov 2011) | 1 line 
- 
-[win32 build] use xcopy instead of cp -Rf for better blocking until end of copy operation when setting up gsl win32 build 
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-r5621 | pcbrefugee | 2011-11-09 17:03:34 -0800 (Wed, 09 Nov 2011) | 1 line 
- 
-[xtandem + hadoop] a few tweaks to make it easier to mimic standard x!tandem behavior on a Hadoop node for performance comparison purposes 
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-r5622 | pcbrefugee | 2011-11-09 17:10:13 -0800 (Wed, 09 Nov 2011) | 1 line 
- 
-[pwiz] add a trigger to build that generated file I just pulled from SVN 
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-r5625 | pcbrefugee | 2011-11-10 12:26:31 -0800 (Thu, 10 Nov 2011) | 1 line 
- 
-workaround for compile issue with boost::thread + mingw + gcc4.5 
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-r5626 | pcbrefugee | 2011-11-10 15:02:18 -0800 (Thu, 10 Nov 2011) | 1 line 
- 
-[pwiz] add #include <stdlib.h> to allow use of size_t in mingw gcc4.6.1 
------------------------------------------------------------------------- 
-r5627 | pcbrefugee | 2011-11-10 15:48:39 -0800 (Thu, 10 Nov 2011) | 1 line 
- 
-handle a couple more openmpi install scenarios for X!!Tandem build  
------------------------------------------------------------------------- 
-r5628 | dshteyn | 2011-11-11 12:28:05 -0800 (Fri, 11 Nov 2011) | 1 line 
- 
-cometresult.cgi: Checking QUERY_STRING for ';' 
------------------------------------------------------------------------- 
-r5629 | dshteyn | 2011-11-11 12:29:42 -0800 (Fri, 11 Nov 2011) | 1 line 
- 
-protxml2html.pl and associated tools for viewing protXML: Removed passing of commands on QUERY_STRING 
------------------------------------------------------------------------- 
-r5630 | dshteyn | 2011-11-11 12:30:19 -0800 (Fri, 11 Nov 2011) | 1 line 
- 
-tpplib_perl.pm: centralize parsing of QUERY_STRING, and checking QS for ';' 
------------------------------------------------------------------------- 
-r5631 | dshteyn | 2011-11-11 12:54:57 -0800 (Fri, 11 Nov 2011) | 1 line 
- 
-protxml2html.pl and associated tools for viewing protXML: Removed passing of commands on QUERY_STRING 
------------------------------------------------------------------------- 
-r5633 | slagelwa | 2011-11-14 15:14:47 -0800 (Mon, 14 Nov 2011) | 2 lines 
- 
-Exit on error, we're at 4.5.0 now 
- 
------------------------------------------------------------------------- 
-r5635 | slagelwa | 2011-11-14 16:08:04 -0800 (Mon, 14 Nov 2011) | 3 lines 
- 
-Fix pwiz for 4.5.0 
- 
- 
------------------------------------------------------------------------- 
-r5636 | real_procopio | 2011-11-15 16:10:31 -0800 (Tue, 15 Nov 2011) | 1 line 
- 
-[NSP Viewer] Complete overhaul of this cgi: using Perl XML:Parser module, so no more system calls to xslt; potentially thousands of times faster than the old one, since we stop parsing once we reach the end of <protein_summary_header> . Prettier output, too. 
------------------------------------------------------------------------- 
-r5637 | pcbrefugee | 2011-11-16 09:38:00 -0800 (Wed, 16 Nov 2011) | 5 lines 
- 
-Build system tweaks and a couple of disambiguating mzParser file copy/renames to make it possible to choose between RAMP+pwiz and mzParser, and to build both libs at the same time. This with an eye toward putting mzML parser maintenance burden back on ProteoWizard now that its performance problems have been fixed. Involves changing "#include <Parsers/mzParser/mzParser.h>" to just "#include <mzParser.h>" in quite a number of files. 
- 
-Just add MSDATA_XML_READER=RAMP to your "make" command and TPP will build with RAMP+pwiz in ../build/$(ARCH)-RAMP. Performance meets or exceeds mzParser on local files and is considerably better than mzParser on network shares. The main point is that given the complexity and continued development of mzML, having multiple parsers in the community is a waste of time and effort. And it leaves the door open to TPP bypassing raw->XML conversion altogether. 
- 
-Also fixed the Makefile cut and paste messiness from the ever growing list of searchResult subtyoe header files with a centralized SEARCHRESULTS_H definition, similar to DISTRIBUTIONS_H, MIXTUREDISTRS_H etc. 
------------------------------------------------------------------------- 
-r5638 | pcbrefugee | 2011-11-16 12:40:59 -0800 (Wed, 16 Nov 2011) | 1 line 
- 
-back out some experimental cruft from previous commit 
------------------------------------------------------------------------- 
-r5639 | pcbrefugee | 2011-11-16 13:29:35 -0800 (Wed, 16 Nov 2011) | 1 line 
- 
-a bit more backing out of experimental cruft from previous commit 
------------------------------------------------------------------------- 
-r5640 | pcbrefugee | 2011-11-16 14:00:42 -0800 (Wed, 16 Nov 2011) | 1 line 
- 
-rename makefile variableS MSDATA_XML_READER_* to the more generally descriptive TPP_MSDATA_READER_* 
------------------------------------------------------------------------- 
-r5641 | pcbrefugee | 2011-11-16 14:57:16 -0800 (Wed, 16 Nov 2011) | 1 line 
- 
-have Spectrast place its objects files in $(OBJ_ARCH) like everybody else so we don't mingle mzParser and RAMP builds for SpectraST by accident 
------------------------------------------------------------------------- 
-r5646 | dshteyn | 2011-11-23 11:32:16 -0800 (Wed, 23 Nov 2011) | 1 line 
- 
-BUGFIX: Correct issue with iProphet probability filtering and naming of columns. 
------------------------------------------------------------------------- 
-r5649 | henryhlam | 2011-11-29 01:01:28 -0800 (Tue, 29 Nov 2011) | 1 line 
- 
-[SpectraST] Fix obscure bug with option passing; better error checking 
------------------------------------------------------------------------- 
-r5650 | henryhlam | 2011-11-29 01:28:20 -0800 (Tue, 29 Nov 2011) | 1 line 
- 
-[SpectraST] Fix repetitive immonium annotations; Revamp immonium annotation procedure to include more than one ion for some amino acids 
------------------------------------------------------------------------- 
-r5651 | slagelwa | 2011-11-29 12:06:28 -0800 (Tue, 29 Nov 2011) | 4 lines 
- 
-* Added another check for tandem program 
-* Allow mzML files in qmascot and look for the various formats for results 
- urls in the responses from Mascot 
- 
------------------------------------------------------------------------- 
-r5652 | slagelwa | 2011-11-29 16:04:57 -0800 (Tue, 29 Nov 2011) | 4 lines 
- 
-Merging 4.5.1 branch changes into trunk (incl more than one change 
-from released 4.5.1. Fingers crossed. 
- 
- 
------------------------------------------------------------------------- 
-r5655 | dshteyn | 2011-12-02 00:09:09 -0800 (Fri, 02 Dec 2011) | 1 line 
- 
-BUGFIX: correct count of iProphet results. 
------------------------------------------------------------------------- 
-r5656 | dshteyn | 2011-12-02 00:10:26 -0800 (Fri, 02 Dec 2011) | 1 line 
- 
-MS-GFDB support: Change linear transform to get more into the right range. 
------------------------------------------------------------------------- 
-r5661 | pcbrefugee | 2011-12-05 13:53:32 -0800 (Mon, 05 Dec 2011) | 1 line 
- 
-better name for Spectrast obj build directory (formerly could conflict with Spectrast execuatble itself) 
------------------------------------------------------------------------- 
-r5662 | pcbrefugee | 2011-12-05 13:55:32 -0800 (Mon, 05 Dec 2011) | 1 line 
- 
-restore changes that got nuked by last merge-from-branch 
------------------------------------------------------------------------- 
-r5663 | pcbrefugee | 2011-12-05 14:43:37 -0800 (Mon, 05 Dec 2011) | 1 line 
- 
-remove extra copy of SpectraSTPeakList::shiftAllPeaksRandomly introduced by latest merge from branch 
------------------------------------------------------------------------- 
-r5664 | pcbrefugee | 2011-12-05 15:02:56 -0800 (Mon, 05 Dec 2011) | 1 line 
- 
-remove extra line of code intrroduced by last merge from branch (this file now compiles, I do not assert that it's correct. I do not trust automated merges.) 
------------------------------------------------------------------------- 
-r5666 | real_procopio | 2011-12-06 17:19:52 -0800 (Tue, 06 Dec 2011) | 1 line 
- 
-[decoyFASTA] Gracefully deal with empty lines in input fasta file 
------------------------------------------------------------------------- 
-r5667 | real_procopio | 2011-12-06 17:20:58 -0800 (Tue, 06 Dec 2011) | 1 line 
- 
-[decoyFASTA] dos2unix... 
------------------------------------------------------------------------- 
-r5669 | pcbrefugee | 2011-12-08 10:20:24 -0800 (Thu, 08 Dec 2011) | 1 line 
- 
-{Makefile] fix a filename case sensitivity problem that VMWare masked on my system (!) 
------------------------------------------------------------------------- 
-r5670 | slagelwa | 2011-12-09 15:56:05 -0800 (Fri, 09 Dec 2011) | 2 lines 
- 
-Use special remote convert program 
- 
------------------------------------------------------------------------- 
-r5671 | slagelwa | 2011-12-09 16:02:15 -0800 (Fri, 09 Dec 2011) | 2 lines 
- 
-Checking in correct version 
- 
------------------------------------------------------------------------- 
-r5672 | slagelwa | 2011-12-12 14:48:38 -0800 (Mon, 12 Dec 2011) | 2 lines 
- 
-Checking it old fix for omssa and signal handling 
- 
------------------------------------------------------------------------- 
-r5679 | real_procopio | 2011-12-16 17:09:52 -0800 (Fri, 16 Dec 2011) | 1 line 
- 
-[Petunia] Update trunk to current version of 4.5.x branch 
------------------------------------------------------------------------- 
-r5680 | slagelwa | 2011-12-19 16:02:30 -0800 (Mon, 19 Dec 2011) | 6 lines 
- 
-* Updated SQS queue names 
-* Fixed tests 
-* Supports EC2 regions now (requires latest Net::Amazon::EC2) 
-* Still testing... 
- 
- 
------------------------------------------------------------------------- 
-r5681 | real_procopio | 2011-12-20 15:00:31 -0800 (Tue, 20 Dec 2011) | 1 line 
- 
-[Petunia] First attempt at allowing multiple commands per user; in preparation for Cloud/cluster integration. Still more work needed... 
------------------------------------------------------------------------- 
-r5682 | slagelwa | 2011-12-20 17:03:46 -0800 (Tue, 20 Dec 2011) | 2 lines 
- 
-Merged Luis changes using svn merge (which already were merged manually checked in)  
- 
------------------------------------------------------------------------- 
-r5683 | slagelwa | 2011-12-20 18:03:20 -0800 (Tue, 20 Dec 2011) | 4 lines 
- 
-dding eol property to this file. Endlines have been changed between branch and 
- trunk and here's hoping svn can resolve that. 
- 
- 
------------------------------------------------------------------------- 
-r5684 | slagelwa | 2011-12-20 18:11:06 -0800 (Tue, 20 Dec 2011) | 2 lines 
- 
-Merged Mike's branch fixes onto trunk 
- 
------------------------------------------------------------------------- 
-r5685 | real_procopio | 2011-12-24 20:18:10 -0800 (Sat, 24 Dec 2011) | 1 line 
- 
-[Petunia] Spruced up jobs and command output page; deleting a session also deletes all of its command outputs, unless there is at least one in running status; commands output moved into user directory 
------------------------------------------------------------------------- 
-r5686 | dshteyn | 2011-12-27 16:01:53 -0800 (Tue, 27 Dec 2011) | 1 line 
- 
-InteractParser: handle more ways of representing compensationVoltage in mzXML. 
------------------------------------------------------------------------- 
-r5689 | slagelwa | 2012-01-03 10:33:54 -0800 (Tue, 03 Jan 2012) | 2 lines 
- 
-Completely revamped to work with Oracle (Sun) Grid Engine 
- 
------------------------------------------------------------------------- 
-r5691 | slagelwa | 2012-01-06 14:01:53 -0800 (Fri, 06 Jan 2012) | 11 lines 
- 
-* Updated the log output to be a little clearer and include both the job start and finish 
- time 
-* Corrected output messages when trapping exit/signals/errors. Turns out you can't 
- distinquish why SGE is killing your job (qdel vs limits). 
-* For search engines that use mgf files for input if the file already exists it doesn't 
- try to recreate it. (Running parallel search engines would cause problems with the  
- file being overwritten while a search is in progress. Come to think of it I haven't 
- completely closed this hole.) 
-* Fixed path to remoteconvert problem for qconvert 
- 
- 
------------------------------------------------------------------------- 
-r5693 | spacepod | 2012-01-10 15:59:26 -0800 (Tue, 10 Jan 2012) | 1 line 
- 
-Setting native line-ending property on xtandem code. No functional change. 
------------------------------------------------------------------------- 
-r5699 | pcbrefugee | 2012-01-12 13:02:32 -0800 (Thu, 12 Jan 2012) | 1 line 
- 
-[build] add an optional "-noreplace" arg to regenerate_VersionInfo for use in MSVC debug builds where a current timestamp just doesn't matter, and only slows the edit-build-test cycle 
------------------------------------------------------------------------- 
-r5700 | pcbrefugee | 2012-01-12 13:03:58 -0800 (Thu, 12 Jan 2012) | 1 line 
- 
-casts for quiet compile 
------------------------------------------------------------------------- 
-r5701 | pcbrefugee | 2012-01-12 13:08:21 -0800 (Thu, 12 Jan 2012) | 1 line 
- 
-[build] adding MSVC10 project files. These work with VS2010 Pro, haven't tested with Express. 
------------------------------------------------------------------------- 
-r5702 | pcbrefugee | 2012-01-12 13:28:09 -0800 (Thu, 12 Jan 2012) | 1 line 
- 
-[build] adding MSVC10 project files. These work with VS2010 Pro, haven't tested with Express. 
------------------------------------------------------------------------- 
-r5703 | pcbrefugee | 2012-01-13 14:06:13 -0800 (Fri, 13 Jan 2012) | 1 line 
- 
-[pwiz] tweak for building with OSX 10.7 
------------------------------------------------------------------------- 
-r5704 | pcbrefugee | 2012-01-13 14:07:46 -0800 (Fri, 13 Jan 2012) | 1 line 
- 
-[xtandem] tweak for building with MSVC10 
------------------------------------------------------------------------- 
-r5705 | pcbrefugee | 2012-01-13 14:11:15 -0800 (Fri, 13 Jan 2012) | 2 lines 
- 
-[Tandem2XML] convert xtandem timestamp to a proper xsd:dateTime as required by pepXML schema. For example, "2011:07:14:16:51:35" converts to "2011-07-14T16:51:35". 
- 
------------------------------------------------------------------------- 
-r5706 | pcbrefugee | 2012-01-16 16:07:55 -0800 (Mon, 16 Jan 2012) | 1 line 
- 
-tweaks to permit regression tests of pepXML originating with X!Tandem, which throws in a lot of timestamp and timing info, and calls everything a "parameter" instead of using a proper XML tag name. 
------------------------------------------------------------------------- 
-r5707 | spacepod | 2012-01-16 16:15:13 -0800 (Mon, 16 Jan 2012) | 1 line 
- 
-Calling out the errno.h include, as some *nix flavors don't do this automatically 
------------------------------------------------------------------------- 
-r5708 | dshteyn | 2012-01-17 13:09:36 -0800 (Tue, 17 Jan 2012) | 1 line 
- 
-D3 javascript library for compareProts.pl (for now). 
------------------------------------------------------------------------- 
-r5710 | henryhlam | 2012-01-18 00:37:28 -0800 (Wed, 18 Jan 2012) | 1 line 
- 
-[mzParser] Initialize collisionEnergy field to zero to avoid having uninitialized meaningless numbers showing up in library entries 
------------------------------------------------------------------------- 
-r5712 | spacepod | 2012-01-19 16:36:09 -0800 (Thu, 19 Jan 2012) | 1 line 
- 
-Deleting standalone makefile for readmzXML tool and moving build into main Makefile. Build was breaking on OS X 10.7 64-bit, and there was no apparent need for duplicating the complexity of the main Makefile again in the standalone one. Feel free to roll this back if it breaks anything. 
------------------------------------------------------------------------- 
-r5713 | spacepod | 2012-01-19 16:39:10 -0800 (Thu, 19 Jan 2012) | 1 line 
- 
-Deleting accidental commit of development target in Makefile. 
------------------------------------------------------------------------- 
-r5715 | dshteyn | 2012-01-23 11:44:33 -0800 (Mon, 23 Jan 2012) | 1 line 
- 
-PepXMLViewer, ASAPRatio: get PepXMLViewer to recognize wavelet smoothing in ASAPRatio. 
------------------------------------------------------------------------- 
-r5716 | dshteyn | 2012-01-23 11:45:09 -0800 (Mon, 23 Jan 2012) | 1 line 
- 
-PepXMLViewer, ASAPRatio: get PepXMLViewer to recognize wavelet smoothing in ASAPRatio. 
------------------------------------------------------------------------- 
-r5717 | dshteyn | 2012-01-23 11:47:24 -0800 (Mon, 23 Jan 2012) | 1 line 
- 
-Build: Get the build to work under CentOS with xtandem and PepC compiling. 
------------------------------------------------------------------------- 
-r5718 | dshteyn | 2012-01-23 11:49:37 -0800 (Mon, 23 Jan 2012) | 1 line 
- 
-Build: Get the build to work under CentOS with xtandem and PepC compiling. 
------------------------------------------------------------------------- 
-r5719 | dshteyn | 2012-01-23 11:51:07 -0800 (Mon, 23 Jan 2012) | 1 line 
- 
-mzxml2search: init variable for start and end scan 
------------------------------------------------------------------------- 
-r5720 | dshteyn | 2012-01-23 11:53:31 -0800 (Mon, 23 Jan 2012) | 1 line 
- 
-RAMP: mismatch new-delete fixed. 
------------------------------------------------------------------------- 
-r5721 | dshteyn | 2012-01-23 11:57:13 -0800 (Mon, 23 Jan 2012) | 1 line 
- 
-PepXMLViewer, ASAPRatio: get PepXMLViewer to recognize wavelet smoothing in ASAPRatio. 
------------------------------------------------------------------------- 
-r5722 | dshteyn | 2012-01-23 11:58:12 -0800 (Mon, 23 Jan 2012) | 1 line 
- 
-PepXMLViewer, ASAPRatio: get PepXMLViewer to recognize wavelet smoothing in ASAPRatio. 
------------------------------------------------------------------------- 
-r5723 | dshteyn | 2012-01-23 11:59:59 -0800 (Mon, 23 Jan 2012) | 1 line 
- 
-PepXMLViewer, ASAPRatio: get PepXMLViewer to recognize wavelet smoothing in ASAPRatio. 
------------------------------------------------------------------------- 
-r5724 | dshteyn | 2012-01-23 12:02:03 -0800 (Mon, 23 Jan 2012) | 1 line 
- 
-PTMProphet: default now updates the pepXML file with most likely modifications, option NOUPDATE retains original behavior. 
------------------------------------------------------------------------- 
-r5725 | dshteyn | 2012-01-23 12:06:56 -0800 (Mon, 23 Jan 2012) | 1 line 
- 
-perl_paths: modified for changine compareProts as it now needs to point to d3.js. 
------------------------------------------------------------------------- 
-r5726 | dshteyn | 2012-01-23 12:10:19 -0800 (Mon, 23 Jan 2012) | 1 line 
- 
-compareProts.pl: Now does a lot more, including outputting a D3 interactive plot for browsing proteins incommons between pairs or files. 
------------------------------------------------------------------------- 
-r5727 | slagelwa | 2012-01-23 12:35:36 -0800 (Mon, 23 Jan 2012) | 4 lines 
- 
-* qmascot: Fixed up mascot parameters a bit 
-* qtandem: not all grid engines have a parallel engine called threads  
-* qsequest: working again 
- 
------------------------------------------------------------------------- 
-r5728 | slagelwa | 2012-01-23 12:37:24 -0800 (Mon, 23 Jan 2012) | 6 lines 
- 
-- added the pvm start/stop scripts for qsequest 
-- no longer use "notify" option. This option sends a USR1 signal  
- right before the job is stopped due to priority/load. Some of the 
- subprocesses exit when they get this signal. 
-  
- 
------------------------------------------------------------------------- 
-r5729 | dshteyn | 2012-01-23 14:23:56 -0800 (Mon, 23 Jan 2012) | 1 line 
- 
-D3.js : Tweak d3 library to respond better to wousewheel zooms. 
------------------------------------------------------------------------- 
-r5730 | dshteyn | 2012-01-23 15:36:52 -0800 (Mon, 23 Jan 2012) | 1 line 
- 
-Remove building of SRMProphet (not yet public). 
------------------------------------------------------------------------- 
-r5731 | dshteyn | 2012-01-23 15:41:36 -0800 (Mon, 23 Jan 2012) | 1 line 
- 
-Fix bad function call 
------------------------------------------------------------------------- 
-r5733 | dshteyn | 2012-01-23 21:56:45 -0800 (Mon, 23 Jan 2012) | 1 line 
- 
-Fix broken build due to misplaced comments. 
------------------------------------------------------------------------- 
-r5734 | dshteyn | 2012-01-26 14:49:10 -0800 (Thu, 26 Jan 2012) | 1 line 
- 
-PTMProphet: NOUPDATE option implemented, default now updates the mods to most likely sites; auto-detect ETD or CID and set the appropriate ion types, bugfix on modification info for static mods with an additional variable mod on the same position (mass was wrongly computed before). 
------------------------------------------------------------------------- 
-r5735 | dshteyn | 2012-01-27 09:59:40 -0800 (Fri, 27 Jan 2012) | 1 line 
- 
-mzParser: BUGFIX activationMethod was not being populates. 
------------------------------------------------------------------------- 
-r5736 | slagelwa | 2012-02-01 12:47:15 -0800 (Wed, 01 Feb 2012) | 4 lines 
- 
-* Changed "threads" pvm to "serial" to align with name of pe on aegir 
-* Fixed issue in qsequest with bash numerical comparision 
-* Fixed issue in qsequest with input and output dir comparision 
- 
------------------------------------------------------------------------- 
-r5739 | slagelwa | 2012-02-01 23:15:19 -0800 (Wed, 01 Feb 2012) | 6 lines 
- 
-Major revision. Modified file storage in S3 to match what's on filesystem 
-and use the "standard" key naming mechansim by most 3rd party programs. 
-This saves the hassle of dealing with updating paths everywhere and means 
-that you can "browse" the repository using other tools. Links still 
-present a problem, but they do anyhow for all 3rd party apps. 
- 
------------------------------------------------------------------------ ------------------------------------------------------------------------
r5744 | dshteyn | 2012-02-07 16:38:46 -0800 (Tue, 07 Feb 2012) | 1 line r5744 | dshteyn | 2012-02-07 16:38:46 -0800 (Tue, 07 Feb 2012) | 1 line
Line 1,267: Line 356:
Modifications to Makefile(s), headers, and sources to support building with hdf5 and mzParser changes in mingw Modifications to Makefile(s), headers, and sources to support building with hdf5 and mzParser changes in mingw
------------------------------------------------------------------------ ------------------------------------------------------------------------
-</nowiki>+r5803 | slagelwa | 2012-04-19 14:57:34 -0700 (Thu, 19 Apr 2012) | 1 line
 + 
 +[branch 4.6] creating the 4-6 branch from the trunk
 +------------------------------------------------------------------------
 +r5804 | slagelwa | 2012-04-20 15:41:21 -0700 (Fri, 20 Apr 2012) | 2 lines
 + 
 +* Fixed the patching of hdf5
 +* Set the version/build
 +------------------------------------------------------------------------
 +r5809 | slagelwa | 2012-04-30 15:46:10 -0700 (Mon, 30 Apr 2012) | 2 lines
 + 
 +Merging changes added on 4.5.2 branch after release
 + 
 +------------------------------------------------------------------------
 +r5811 | slagelwa | 2012-05-01 11:00:39 -0700 (Tue, 01 May 2012) | 3 lines
 + 
 +Merging David Shteynbergs recent change on the trunk into 4.6.
 + 
 + 
 +------------------------------------------------------------------------
 +r5812 | slagelwa | 2012-05-02 10:14:31 -0700 (Wed, 02 May 2012) | 2 lines
 + 
 +Adding rules for createChargeFile, mergeCharges and fileDownloader
 + 
 +------------------------------------------------------------------------
 +r5813 | slagelwa | 2012-05-02 12:01:45 -0700 (Wed, 02 May 2012) | 3 lines
 + 
 +Tabs. Wicked. Tricksy. False. We hates Tabs.
 + 
 + 
 +------------------------------------------------------------------------
 +r5814 | slagelwa | 2012-05-02 14:18:46 -0700 (Wed, 02 May 2012) | 2 lines
 + 
 +.pl.pl should be .pl
 + 
 +------------------------------------------------------------------------
 +r5815 | slagelwa | 2012-05-03 10:53:21 -0700 (Thu, 03 May 2012) | 1 line
 + 
 +Adding PTM prophet to Windows installer file list
 +------------------------------------------------------------------------
 +r5816 | real_procopio | 2012-05-03 12:00:41 -0700 (Thu, 03 May 2012) | 1 line
 + 
 +Added basic Amazon EC2 Management page: can register/delete keys and check status; Show 'no jobs' in Jobs status tooltip if none have been launched.
 +------------------------------------------------------------------------
 +r5819 | real_procopio | 2012-05-04 15:39:06 -0700 (Fri, 04 May 2012) | 1 line
 + 
 +[petunia] Added PTMProphet page (with a hack until the executable can handle output file as a parameter)
 +------------------------------------------------------------------------
 +r5821 | slagelwa | 2012-05-04 17:26:19 -0700 (Fri, 04 May 2012) | 2 lines
 + 
 +Merging David's changes that were checked in on the trunk
 + 
 +------------------------------------------------------------------------
 +r5832 | slagelwa | 2012-05-07 10:47:28 -0700 (Mon, 07 May 2012) | 2 lines
 + 
 +Merging in David's latest check in on trunk into 4.6
 + 
 +------------------------------------------------------------------------
 +r5833 | real_procopio | 2012-05-07 11:02:18 -0700 (Mon, 07 May 2012) | 1 line
 + 
 +[Petunia] Fix reported bug when converting multiple files to pepXML using semi-cleavage specificity
 +------------------------------------------------------------------------
 +r5835 | dshteyn | 2012-05-07 12:07:59 -0700 (Mon, 07 May 2012) | 1 line
 + 
 +updateAllPaths.pl: switch to '\' to '/' for updating
 +------------------------------------------------------------------------
 +r5836 | dshteyn | 2012-05-07 12:10:59 -0700 (Mon, 07 May 2012) | 1 line
 + 
 +Makefile for building PTMProphet MULTIPLEX
 +------------------------------------------------------------------------
 +r5838 | slagelwa | 2012-05-07 13:16:44 -0700 (Mon, 07 May 2012) | 2 lines
 + 
 +Fixing compile issue with NEWPATH
 + 
 +------------------------------------------------------------------------
 +r5840 | slagelwa | 2012-05-07 16:32:35 -0700 (Mon, 07 May 2012) | 2 lines
 + 
 +Merging another of David's changes in.
 + 
 +------------------------------------------------------------------------
 +r5841 | real_procopio | 2012-05-07 16:40:47 -0700 (Mon, 07 May 2012) | 1 line
 + 
 +[Petunia] Specify output file to PTMProphet
 +------------------------------------------------------------------------
 +r5842 | real_procopio | 2012-05-08 14:46:46 -0700 (Tue, 08 May 2012) | 1 line
 + 
 +[plot-msms-js] Bugfix: do not attempt to populate ms1 data unless we are reading an mz[X]ML file
 +------------------------------------------------------------------------
 +r5843 | real_procopio | 2012-05-09 12:35:26 -0700 (Wed, 09 May 2012) | 1 line
 + 
 +[Petunia] Fixed auto-refresh of page when submitting a job in Windows; Added ability to delete a single command output log file; Updated userTimeoutRecovery for new log files; Fixed small typo on PTMProphet page.
 +------------------------------------------------------------------------
 +r5844 | dshteyn | 2012-05-09 14:54:13 -0700 (Wed, 09 May 2012) | 1 line
 + 
 +ProphetModels.pl: BUGFIX double counting uniques
 +------------------------------------------------------------------------
 +r5845 | slagelwa | 2012-05-09 15:18:09 -0700 (Wed, 09 May 2012) | 5 lines
 + 
 +Commented out EC2 special case in Makefile. Its no longer the default to
 +detect that you are building on a EC2 node and need a special move to handle
 +issues with using S3FS. If you need/want this functionality either uncomment
 +the line in the Makefile.incl, or add the define on the command line.
 + 
 +------------------------------------------------------------------------
 +r5846 | real_procopio | 2012-05-09 15:44:49 -0700 (Wed, 09 May 2012) | 1 line
 + 
 +[Petunia] Add blinking baloney when checking status on jobs page; Made MULTIPLEX the default for PTMProphet (as per DDS)
 +------------------------------------------------------------------------
 +r5847 | real_procopio | 2012-05-09 15:59:18 -0700 (Wed, 09 May 2012) | 1 line
 + 
 +[PepXMLViewer] Default ions2 link to Lorikeet, hide the link to old viewer (still available via Pick Columns)
 +------------------------------------------------------------------------
 +r5848 | slagelwa | 2012-05-09 16:22:10 -0700 (Wed, 09 May 2012) | 14 lines
 + 
 +Correction for building tandem w/pthreads as it was missing a dll.
 + 
 +Turns out that in the past we were linking to the Windows version of threads
 +even though we were building it in a Unix like environment provided by MinGW.
 +This was accomplished by setting the define MSVC to fool the tandem build to
 +think it was in a pure Windows environment...which of course is was not. This no
 +longer works since the newest version of tandem has added some additional MS
 +specific code (vector math)that is unavailable to MinGW. So instead of changing
 +the tandem code to allow MS threads but not the math stuff I instead just built
 +a pthreads version.
 + 
 +Problem is that pthreads can only be build with a dynamic library (well *almost*
 +true but for our purposes it might as well be). So we now include the pthreads
 +dll in the installer.
 +------------------------------------------------------------------------
 +r5849 | dshteyn | 2012-05-10 11:32:39 -0700 (Thu, 10 May 2012) | 1 line
 + 
 +Increase precision for reported intensities so even the tiny peaks can be seen...helpful for PTM assignment that depends on the small peaks
 +------------------------------------------------------------------------
 +r5850 | real_procopio | 2012-05-10 13:42:43 -0700 (Thu, 10 May 2012) | 1 line
 + 
 +[Tandem2XML] Re-indented entire file for readibility, no functional change
 +------------------------------------------------------------------------
 +r5851 | real_procopio | 2012-05-10 14:33:38 -0700 (Thu, 10 May 2012) | 1 line
 + 
 +[Petunia] Avoid doing the blinky thing on initial page load; also made blinking code more elegant (these things matter, yo!)
 +------------------------------------------------------------------------
 +r5853 | dshteyn | 2012-05-11 16:03:09 -0700 (Fri, 11 May 2012) | 1 line
 + 
 +XPressPeptideParser: was slow, much faster using cached_ramp
 +------------------------------------------------------------------------
 +r5854 | dshteyn | 2012-05-11 16:05:54 -0700 (Fri, 11 May 2012) | 1 line
 + 
 +Commented out code causing an Infinite Recurrence
 +------------------------------------------------------------------------
 +r5855 | dshteyn | 2012-05-14 12:59:55 -0700 (Mon, 14 May 2012) | 1 line
 + 
 +PTMProphet: Tweaking the algorithm to improve model
 +------------------------------------------------------------------------
 +r5856 | dshteyn | 2012-05-14 13:01:43 -0700 (Mon, 14 May 2012) | 1 line
 + 
 +New function for PTMProphet that remembers the peaks already matched
 +------------------------------------------------------------------------
 +r5857 | spacepod | 2012-05-14 13:05:59 -0700 (Mon, 14 May 2012) | 1 line
 + 
 +Removing zlib from build prerequisites on OS X; otherwise on make will error out on OS X (no target for -lz). zlib is still included in the linker flags for os x X!Tandem. NOTE: if zlib is not needed for some special platform such as mingw, it would be cleanest to remove this logic and simply remove ZLIB_LIB from the xtandem prereq list in both TPP and extern/xtandem makefiles.
 +------------------------------------------------------------------------
 +r5858 | dshteyn | 2012-05-14 14:15:45 -0700 (Mon, 14 May 2012) | 1 line
 + 
 +PTMProphetMpx: tweak to the model improves performance
 +------------------------------------------------------------------------
 +r5860 | dshteyn | 2012-05-14 15:28:57 -0700 (Mon, 14 May 2012) | 1 line
 + 
 +PTMProphet: model tweak
 +------------------------------------------------------------------------
 +r5862 | real_procopio | 2012-05-14 20:08:45 -0700 (Mon, 14 May 2012) | 1 line
 + 
 +[LibraPeptideParser] Re-formatting code so it can be read by human beings, no functional change
 +------------------------------------------------------------------------
 +r5864 | pcbrefugee | 2012-05-15 13:34:38 -0700 (Tue, 15 May 2012) | 1 line
 + 
 +Branch copy of fix for an infinite recursion bug I introduced in trunk, change 5637 (Nov 2011). I missed it because I tend to use RAMP+pwiz instead of mzparser, surprising that it took anyone else this long to notice. Just a one liner to fix. Also backing out change 5854 to cached_ramp.h which was an attempt to fix this, and which led to performance hits in XPress and Libra (5853 is addressed XPress performance with changes equivalent to the #defines in cached_ramp.h, but Libra is still dinged)
 +------------------------------------------------------------------------
 +r5865 | real_procopio | 2012-05-15 14:20:38 -0700 (Tue, 15 May 2012) | 1 line
 + 
 +[mascotout.pl] Added error message if file not found; also added html footer with TPP version
 +------------------------------------------------------------------------
 +r5866 | real_procopio | 2012-05-15 14:26:09 -0700 (Tue, 15 May 2012) | 1 line
 + 
 +[lorikeet] Fix typos on parameter names for n- and c-terMods
 +------------------------------------------------------------------------
 +r5867 | real_procopio | 2012-05-15 17:00:33 -0700 (Tue, 15 May 2012) | 1 line
 + 
 +[PepXMLViewer] Fix webserver accessible file path
 +------------------------------------------------------------------------
 +r5868 | dshteyn | 2012-05-15 17:34:29 -0700 (Tue, 15 May 2012) | 1 line
 + 
 +PTMProphet: further tweaks to enhance performance of the model
 +------------------------------------------------------------------------
 +r5869 | dshteyn | 2012-05-16 11:16:19 -0700 (Wed, 16 May 2012) | 1 line
 + 
 +tpp_gui.pl: Jobs page sorted by the Session with most recent job executed. Jobs within each session sorted in stack order. Makes it easier to find your job.
 +------------------------------------------------------------------------
 +r5870 | spacepod | 2012-05-16 11:38:09 -0700 (Wed, 16 May 2012) | 1 line
 + 
 +Minor cleanup: removing rouge tab character from Makefile.incl to prevent possible future make issues
 +------------------------------------------------------------------------
 +r5871 | dshteyn | 2012-05-16 15:41:18 -0700 (Wed, 16 May 2012) | 1 line
 + 
 +ASAPRatio: Remove debugging output
 +------------------------------------------------------------------------
 +r5872 | mhoopmann | 2012-05-16 16:30:55 -0700 (Wed, 16 May 2012) | 3 lines
 + 
 +Updated mzXML parser to treat startMz and endMz attributes as synonymous to lowMz and highMz
 + 
 + 
 +------------------------------------------------------------------------
 +r5873 | mhoopmann | 2012-05-16 16:36:05 -0700 (Wed, 16 May 2012) | 3 lines
 + 
 +conditional check on setting high and low mz
 + 
 + 
 +------------------------------------------------------------------------
 +r5874 | real_procopio | 2012-05-16 16:49:12 -0700 (Wed, 16 May 2012) | 1 line
 + 
 +[mzParser] start low, end high high as a kite!
 +------------------------------------------------------------------------
 +r5875 | real_procopio | 2012-05-17 11:39:14 -0700 (Thu, 17 May 2012) | 1 line
 + 
 +[Petunia] MULTIPLEX no longer an option in PTMProphet
 +------------------------------------------------------------------------
 +r5876 | dshteyn | 2012-05-17 11:50:47 -0700 (Thu, 17 May 2012) | 1 line
 + 
 +PTMProphetParser: Switching to Binomial Distribution to compute probability to site being modified. Default settings: disable EM, enable MULTIPLEX
 +------------------------------------------------------------------------
 +r5879 | dshteyn | 2012-05-20 22:12:40 -0700 (Sun, 20 May 2012) | 1 line
 + 
 +PTMProphet: Fix bug in enumerating all combinations of mods. Replaced recurring function with an iterative procedure.
 +------------------------------------------------------------------------
 +r5880 | spacepod | 2012-05-24 15:16:33 -0700 (Thu, 24 May 2012) | 2 lines
 + 
 +Small xtandem commandline build update: if only building TPP's xtandem in an otherwise clean source tree, be sure that the TPP's build directory is created too.
 + 
 +------------------------------------------------------------------------
 +r5882 | dshteyn | 2012-05-29 15:48:03 -0700 (Tue, 29 May 2012) | 1 line
 + 
 +use a library to get current directory...system call to pwd stopped working
 +------------------------------------------------------------------------
 +r5883 | dshteyn | 2012-05-29 16:49:56 -0700 (Tue, 29 May 2012) | 1 line
 + 
 +updateAllPaths.pl: Need to close open filehandles in windows to allow overwriting the existing file.
 +------------------------------------------------------------------------
 +r5884 | dshteyn | 2012-05-29 17:00:56 -0700 (Tue, 29 May 2012) | 1 line
 + 
 +put rename back in...it wasn't the problem
 +------------------------------------------------------------------------
 +r5885 | dshteyn | 2012-05-29 17:13:04 -0700 (Tue, 29 May 2012) | 1 line
 + 
 +PTMProphet: Fix crash on peptides with modified 'n' written in the mod peptide tag.
 +------------------------------------------------------------------------
 +r5886 | slagelwa | 2012-05-30 11:38:30 -0700 (Wed, 30 May 2012) | 1 line
 + 
 +Bumping RC #
 +------------------------------------------------------------------------
 +r5888 | real_procopio | 2012-06-01 12:57:42 -0700 (Fri, 01 Jun 2012) | 1 line
 + 
 +[Tandem2XML] Deal with quick acetyl mods, default in Tandem as of 2010.01.01.1
 +------------------------------------------------------------------------
 +r5889 | mhoopmann | 2012-06-01 13:20:17 -0700 (Fri, 01 Jun 2012) | 1 line
 + 
 +Minor changes to make sure tandem_native is identical with and without PLUGGABLE_SCORING. There is one remaining #ifdef PLUGGABLE_SCORING in mscore, however, it is handled in such a way that it should be identical when using "native". Tests show identical hyperscores, evalues, and peptide results. However, the section with the #ifdef PLUGGABLE_SCORING is not called at any point in any test I've tried. I cannot figure out how to trigger that section of code, which only relates to special cases for phosphosites.
 +------------------------------------------------------------------------
 +r5891 | slagelwa | 2012-06-01 15:13:24 -0700 (Fri, 01 Jun 2012) | 3 lines
 + 
 +Ubuntu's gcc doesn't like it when you don't catch the
 +return value of fread()
 + 
 +------------------------------------------------------------------------
 +r5893 | slagelwa | 2012-06-04 16:21:57 -0700 (Mon, 04 Jun 2012) | 1 line
 + 
 + 
 +------------------------------------------------------------------------
 +r5901 | slagelwa | 2012-06-12 15:29:31 -0700 (Tue, 12 Jun 2012) | 5 lines
 + 
 +Added download button to the filebrowser to allow downloading of files in a
 +directory. Multiple files are downloaded as a zip file, single files as
 +themselves.
 + 
 + 
 +------------------------------------------------------------------------
 +r5904 | slagelwa | 2012-06-18 11:49:45 -0700 (Mon, 18 Jun 2012) | 6 lines
 + 
 +Disable indexing of file system by the browser by default. With this enabled
 +it allows anyone to bypass the Petunia authentication/authoriation and both
 +list and fetch any TPP data from a system that's been left open. This certainly
 +doesn't close the door but it helps a little.
 + 
 + 
 +------------------------------------------------------------------------
 +r5905 | slagelwa | 2012-06-18 14:54:35 -0700 (Mon, 18 Jun 2012) | 3 lines
 + 
 +Increase the maximum number of threads allowed. Systems now exist with 16 or more cores. Why increase to 256? Why not?
 + 
 + 
 +------------------------------------------------------------------------
 +r5907 | real_procopio | 2012-06-19 10:55:18 -0700 (Tue, 19 Jun 2012) | 1 line
 + 
 +[Tandem2XML] Cleaner way to deal with N-term acetylation
 +------------------------------------------------------------------------
 +r5908 | mhoopmann | 2012-06-19 10:59:14 -0700 (Tue, 19 Jun 2012) | 2 lines
 + 
 +Report a,c,x,z ions (lost during upgrade to cyclone).
 +Report N-terminal protein acetylation mods with the '[' symbol.
 +------------------------------------------------------------------------
 +r5910 | dshteyn | 2012-06-22 12:33:20 -0700 (Fri, 22 Jun 2012) | 1 line
 + 
 +XPressCGIProteinDisplayParser.cgi: fix obvious security issue with passing commands in QUERY_STRING
 +------------------------------------------------------------------------
 +r5911 | dshteyn | 2012-06-22 12:34:34 -0700 (Fri, 22 Jun 2012) | 1 line
 + 
 +Remove xslt from link to XPressCGIProteinDisplayParser.cgi
 +------------------------------------------------------------------------
 +r5912 | slagelwa | 2012-06-28 10:25:42 -0700 (Thu, 28 Jun 2012) | 5 lines
 + 
 +* TPP's makefile has a "xtandem-debug" target that wasn't doing anything.
 + Fixed this by using the value of DEBUG if its set.
 +* Fixed a number of deallocation issues that valgrind was complaining about.
 + 
 + 
 +------------------------------------------------------------------------
 +r5914 | slagelwa | 2012-07-03 15:11:09 -0700 (Tue, 03 Jul 2012) | 2 lines
 + 
 +Merging Mike r5913 change into branch
 + 
 +------------------------------------------------------------------------
 + 
 + </nowiki>

Revision as of 22:37, 3 July 2012

Changes since 4.5.2 release 

------------------------------------------------------------------------
r5744 | dshteyn | 2012-02-07 16:38:46 -0800 (Tue, 07 Feb 2012) | 1 line

BUGFIX: didn't compile at linking step (Thanks Joe for the catch!)
------------------------------------------------------------------------
r5745 | slagelwa | 2012-02-08 13:40:39 -0800 (Wed, 08 Feb 2012) | 4 lines

Merging 4.5.2 changes into trunk.  Fingers crossed. This should merge
only new changes from the branch that aren't already in the trunk.


------------------------------------------------------------------------
r5746 | slagelwa | 2012-02-09 14:02:27 -0800 (Thu, 09 Feb 2012) | 2 lines

Updated scripts for 4.5.2 release

------------------------------------------------------------------------
r5747 | slagelwa | 2012-02-09 14:18:14 -0800 (Thu, 09 Feb 2012) | 4 lines

Create the html/js directory so that we can copy files
to it.


------------------------------------------------------------------------
r5749 | slagelwa | 2012-02-10 14:20:08 -0800 (Fri, 10 Feb 2012) | 7 lines

* Added missing documentation on "-o" flag
* Fixed issue were ec2 node log file wasn't uploaded to S3.  (Can't upload
  the log file with the md5 as we are writing to it)
* Fixed an issue with abs_path resolving symbolic links. "We will not
  resolve the link before its time".


------------------------------------------------------------------------
r5750 | slagelwa | 2012-02-15 12:21:52 -0800 (Wed, 15 Feb 2012) | 6 lines

* Fixed issue in stop pvm script where PVM enviroment variables weren't
  exported.
* Added check to remove leftover pvm pid files
* Now saves the .dta and .out files in a tgz file so petunia interface
  works again for showing top 10 hits

------------------------------------------------------------------------
r5751 | slagelwa | 2012-02-15 16:52:06 -0800 (Wed, 15 Feb 2012) | 3 lines

Updated to use the latest version of Inspect.  The one that was
being installed frequently core dumped.

------------------------------------------------------------------------
r5752 | slagelwa | 2012-02-16 13:21:48 -0800 (Thu, 16 Feb 2012) | 2 lines

Apply patch to fix buffer overflow problem in inspect

------------------------------------------------------------------------
r5753 | slagelwa | 2012-02-22 10:47:54 -0800 (Wed, 22 Feb 2012) | 7 lines

Now requests a complex resource "sequest" that should be defined on each
host of 8 that will run sequest with a value of 8.  This resource will prevent
more than one sequest job from running on the same node. Note that when you
request a PE with 8 slots you should request *1* resource as grid engine will
multiple the resource value by the # of requested slots in the PE.


------------------------------------------------------------------------
r5755 | slagelwa | 2012-03-01 14:23:12 -0800 (Thu, 01 Mar 2012) | 2 lines

Also install the qualscore lib directory

------------------------------------------------------------------------
r5756 | slagelwa | 2012-03-01 14:25:57 -0800 (Thu, 01 Mar 2012) | 2 lines

Fix copy

------------------------------------------------------------------------
r5757 | slagelwa | 2012-03-02 16:28:05 -0800 (Fri, 02 Mar 2012) | 8 lines

   * replaced Net::Amazon::EC2 with VM::EC2 and all its goodness.  Thanks,
     Lincoln Stein.  Now all we need is a VM::S3
   * EC2 region now an option
   * renamed stop() to terminate() to match EC2 API
   * minor changes to amzbill
   * Updated tests


------------------------------------------------------------------------
r5758 | slagelwa | 2012-03-06 09:05:56 -0800 (Tue, 06 Mar 2012) | 10 lines

"Mounts" a instance store disk partition on the EC2 instance.  EC2 instance
root partitions are limited to 10GB.  When amztpp was switched to using the
filesystem directly instead of a tmp directory the end result was that everything
was written to /, and this would fill up rather quickly.  Now what it does
is always creates the root directory in /mnt (always one of the instance stores)
and mount --binds it to "/" so that the path appears like a normal path.

Also removed the "-c" flag as its no longer applicable.


------------------------------------------------------------------------
r5759 | slagelwa | 2012-03-06 18:25:44 -0800 (Tue, 06 Mar 2012) | 13 lines

Installs and tests pass on Windows.

* Swapped out Proc::PID::File for File::Pid as the latter has
  a ActiveState ppm
* Modified S3Manager so only unix paths are used in S3. 
  Get/Puts convert paths appropriately depending on platform
* Lot of work on the tests.  Mainly skipping tests if they
  don't have executables installed (e.g omssa)
* Some of the t/data files were not in the tarball
* Updated the message on credentials to "missing" 
  instead of invalid
  

------------------------------------------------------------------------
r5760 | slagelwa | 2012-03-07 16:51:25 -0800 (Wed, 07 Mar 2012) | 13 lines

* Cleaned up some issues with the AWS credentials
and finished reading optional region out of them
* Fixed a minor logging issue when logdie()
* Reworked amztppd to better handle credentials and
 logging errors on them
* Log files on worker are correctly named by the
 IP address of the worker in all cases
* Updated man documenation and included --region 
 paramter
* fixed tests to use credentials instead of 
 exception


------------------------------------------------------------------------
r5763 | slagelwa | 2012-03-14 15:03:06 -0700 (Wed, 14 Mar 2012) | 7 lines

* Moved src_cyclone to src_gpm (the name cyclone will change). This is the copy
of tandem from gpm that we will modify.

* Moved src to src_hadoop.  This is the tpp modifed version of tandem (cyclone)
 that has Brian's hadoop work in it.


------------------------------------------------------------------------
r5764 | mhoopmann | 2012-03-14 15:24:36 -0700 (Wed, 14 Mar 2012) | 1 line

Updated TPP Tandem to Cyclone (Dec 2011 release)
------------------------------------------------------------------------
r5765 | mhoopmann | 2012-03-14 15:30:36 -0700 (Wed, 14 Mar 2012) | 1 line

Fixing diffs leftover from branch
------------------------------------------------------------------------
r5766 | mhoopmann | 2012-03-14 15:35:14 -0700 (Wed, 14 Mar 2012) | 1 line

Fixing makefile
------------------------------------------------------------------------
r5767 | mhoopmann | 2012-03-14 16:22:37 -0700 (Wed, 14 Mar 2012) | 1 line

Updated objects to be prefixed with mzp to avoid confusion with X!Tandem
------------------------------------------------------------------------
r5768 | mhoopmann | 2012-03-14 16:43:07 -0700 (Wed, 14 Mar 2012) | 1 line

Turned off pluggable scoring definition in the code because it is defined at compile time.
------------------------------------------------------------------------
r5769 | mhoopmann | 2012-03-14 16:48:06 -0700 (Wed, 14 Mar 2012) | 1 line

Stupid no newline at end of file message...
------------------------------------------------------------------------
r5770 | mhoopmann | 2012-03-14 16:50:00 -0700 (Wed, 14 Mar 2012) | 1 line

Added Makefile for tpp x!tandem
------------------------------------------------------------------------
r5771 | mhoopmann | 2012-03-14 16:53:12 -0700 (Wed, 14 Mar 2012) | 3 lines

Updated makefile for tandem cyclone


------------------------------------------------------------------------
r5772 | mhoopmann | 2012-03-16 09:37:01 -0700 (Fri, 16 Mar 2012) | 1 line

Force mzXML base64 conversion to always be "network" even when specified otherwise, or not at all.
------------------------------------------------------------------------
r5779 | mhoopmann | 2012-03-29 13:03:55 -0700 (Thu, 29 Mar 2012) | 3 lines

Added mz5 file support; Works natively in the ramp interface. Also made other minor bugfixes and updates.


------------------------------------------------------------------------
r5780 | mhoopmann | 2012-03-29 13:09:38 -0700 (Thu, 29 Mar 2012) | 3 lines

Added hdf5 support files.


------------------------------------------------------------------------
r5781 | mhoopmann | 2012-03-29 13:11:47 -0700 (Thu, 29 Mar 2012) | 3 lines

removing hdf5 files not needed.


------------------------------------------------------------------------
r5782 | mhoopmann | 2012-03-29 13:13:26 -0700 (Thu, 29 Mar 2012) | 3 lines

Updating the makefiles to include HDF5 addition and changes to mzParser.


------------------------------------------------------------------------
r5783 | mhoopmann | 2012-03-30 12:08:28 -0700 (Fri, 30 Mar 2012) | 3 lines

More makefile fixes for HDF5 support


------------------------------------------------------------------------
r5784 | slagelwa | 2012-04-02 10:42:37 -0700 (Mon, 02 Apr 2012) | 4 lines

* Updated handling of qsub flags
* Some sequest updates
* Added qlog for showing contents of job log file using job id

------------------------------------------------------------------------
r5785 | mhoopmann | 2012-04-02 11:19:57 -0700 (Mon, 02 Apr 2012) | 2 lines

Fixed missing newline at end of file warnings. Added reading of chromatograms.

------------------------------------------------------------------------
r5786 | mhoopmann | 2012-04-02 12:24:25 -0700 (Mon, 02 Apr 2012) | 3 lines

Fixed makefiles


------------------------------------------------------------------------
r5787 | mhoopmann | 2012-04-02 12:25:29 -0700 (Mon, 02 Apr 2012) | 3 lines

Inserted more newlines at ends of files.


------------------------------------------------------------------------
r5789 | slagelwa | 2012-04-03 10:19:49 -0700 (Tue, 03 Apr 2012) | 2 lines

Nothing to see here.  Move along.

------------------------------------------------------------------------
r5790 | mhoopmann | 2012-04-03 10:51:22 -0700 (Tue, 03 Apr 2012) | 3 lines

Adjusting the HDF5 linkage.


------------------------------------------------------------------------
r5791 | mhoopmann | 2012-04-03 11:50:50 -0700 (Tue, 03 Apr 2012) | 3 lines

Grr...


------------------------------------------------------------------------
r5792 | mhoopmann | 2012-04-03 12:16:24 -0700 (Tue, 03 Apr 2012) | 3 lines

More makefile fixes 


------------------------------------------------------------------------
r5793 | mhoopmann | 2012-04-03 13:59:17 -0700 (Tue, 03 Apr 2012) | 3 lines

reversed ordering of HDF5 libraries


------------------------------------------------------------------------
r5794 | mhoopmann | 2012-04-03 14:49:15 -0700 (Tue, 03 Apr 2012) | 3 lines

Forgot to update this as well.


------------------------------------------------------------------------
r5795 | slagelwa | 2012-04-09 15:46:29 -0700 (Mon, 09 Apr 2012) | 27 lines

* Added new amztppservice for Windows.  Manages aspects of installing
  and removing the service.  Turns out Windows doesn't like forking
  daemons.
* Makefile.PL tries to add a amztpp service on Windows
* Correct dependencies are generated in the Makefile based
  on installation platform
* Removed using CPAN ParallelManager as it blocks
  on fork() and we can't have that on Windows.  Implemented
  own non-blocking forking of upload/downloads
* Files are now stored in S3 following a Unix convention
  only and when coming from windows they are translated
* Output files are "fixed" to correct the paths when
  copying back to windows from linux
* Bootstrap process streamlined
* Better "failsafe" using startup implemented for auto
  shutting down nodes
* amztpp: can now save/delete user credentials for them
* amztpp: clean now realclean
* amztpp: only show first few files in S3 as opposed to all on
  status command
* Updated man page, fixing grammer and outdated text
* Tests updated and additional tests added
* Copyrights updated
* Added warning notice to README disclaiming any responsibility
  for expected or unexpected charges


------------------------------------------------------------------------
r5796 | real_procopio | 2012-04-10 18:03:33 -0700 (Tue, 10 Apr 2012) | 12 lines

[Petunia] Finished multiple commands monitoring:
- New jobs page, showing completed and running jobs, with links to view output, statuses are AJAX-updated
- New .jobs file to keep track of job status; only accessed/updated via file-locking
- Jobs menu title is AJAX-updated with status of all jobs, until all have been 'viewed' (also shown on tooltip with more text)
- Actions to support new AJAX requests
- Page Title shows number of running jobs (if any), AJAX-updated as well 
- Handle multiple AJAX calls in a page via arrays
- New css classes for displaying command status
- Got rid of deprecated 'wait' and 'results' pages
- Cleaned up login page


------------------------------------------------------------------------
r5797 | slagelwa | 2012-04-11 13:48:53 -0700 (Wed, 11 Apr 2012) | 5 lines

* Fixed minor bug in Myrimatch when correcting scans
* Now outputs the error when a service reports one
* Updated version


------------------------------------------------------------------------
r5798 | slagelwa | 2012-04-12 16:29:59 -0700 (Thu, 12 Apr 2012) | 4 lines

Output a error message if we can't open the directory containing the
sequest output files, instead of segmentation faulting.


------------------------------------------------------------------------
r5799 | slagelwa | 2012-04-12 16:57:48 -0700 (Thu, 12 Apr 2012) | 2 lines

Checking in change again without eclipse reformatting tabs

------------------------------------------------------------------------
r5800 | slagelwa | 2012-04-13 13:49:05 -0700 (Fri, 13 Apr 2012) | 8 lines

* Added the latest version of sequest
* Renamed the previous version to sequest27 as the architecture is
  very different (threaded vs pvm)
* Always create the mgf file in the case of seach engines that need it. 
  Previously I was only creating it if it didn't exist.  Which meant that
  when you changed your search parameters the old values were still used.


------------------------------------------------------------------------
r5801 | slagelwa | 2012-04-16 10:36:26 -0700 (Mon, 16 Apr 2012) | 3 lines

Fixing a small issue with regards to the file download retrys not actually
retrying on an error

------------------------------------------------------------------------
r5802 | slagelwa | 2012-04-18 15:34:59 -0700 (Wed, 18 Apr 2012) | 2 lines

Downgraded to HDF 1.8.6 (most recent version that builds in mingw)
Modifications to Makefile(s), headers, and sources to support building with hdf5 and mzParser changes in mingw
------------------------------------------------------------------------
r5803 | slagelwa | 2012-04-19 14:57:34 -0700 (Thu, 19 Apr 2012) | 1 line

[branch 4.6] creating the 4-6 branch from the trunk
------------------------------------------------------------------------
r5804 | slagelwa | 2012-04-20 15:41:21 -0700 (Fri, 20 Apr 2012) | 2 lines

* Fixed the patching of hdf5
* Set the version/build
------------------------------------------------------------------------
r5809 | slagelwa | 2012-04-30 15:46:10 -0700 (Mon, 30 Apr 2012) | 2 lines

Merging changes added on 4.5.2 branch after release

------------------------------------------------------------------------
r5811 | slagelwa | 2012-05-01 11:00:39 -0700 (Tue, 01 May 2012) | 3 lines

Merging David Shteynbergs recent change on the trunk into 4.6.


------------------------------------------------------------------------
r5812 | slagelwa | 2012-05-02 10:14:31 -0700 (Wed, 02 May 2012) | 2 lines

Adding rules for createChargeFile, mergeCharges and fileDownloader

------------------------------------------------------------------------
r5813 | slagelwa | 2012-05-02 12:01:45 -0700 (Wed, 02 May 2012) | 3 lines

Tabs.  Wicked. Tricksy. False.  We hates Tabs.


------------------------------------------------------------------------
r5814 | slagelwa | 2012-05-02 14:18:46 -0700 (Wed, 02 May 2012) | 2 lines

.pl.pl should be .pl

------------------------------------------------------------------------
r5815 | slagelwa | 2012-05-03 10:53:21 -0700 (Thu, 03 May 2012) | 1 line

Adding PTM prophet to Windows installer file list
------------------------------------------------------------------------
r5816 | real_procopio | 2012-05-03 12:00:41 -0700 (Thu, 03 May 2012) | 1 line

Added basic Amazon EC2 Management page: can register/delete keys and check status; Show 'no jobs' in Jobs status tooltip if none have been launched.
------------------------------------------------------------------------
r5819 | real_procopio | 2012-05-04 15:39:06 -0700 (Fri, 04 May 2012) | 1 line

[petunia] Added PTMProphet page (with a hack until the executable can handle output file as a parameter)
------------------------------------------------------------------------
r5821 | slagelwa | 2012-05-04 17:26:19 -0700 (Fri, 04 May 2012) | 2 lines

Merging David's changes that were checked in on the trunk

------------------------------------------------------------------------
r5832 | slagelwa | 2012-05-07 10:47:28 -0700 (Mon, 07 May 2012) | 2 lines

Merging in David's latest check in on trunk into 4.6

------------------------------------------------------------------------
r5833 | real_procopio | 2012-05-07 11:02:18 -0700 (Mon, 07 May 2012) | 1 line

[Petunia] Fix reported bug when converting multiple files to pepXML using semi-cleavage specificity
------------------------------------------------------------------------
r5835 | dshteyn | 2012-05-07 12:07:59 -0700 (Mon, 07 May 2012) | 1 line

updateAllPaths.pl: switch to '\' to '/' for updating 
------------------------------------------------------------------------
r5836 | dshteyn | 2012-05-07 12:10:59 -0700 (Mon, 07 May 2012) | 1 line

Makefile for building PTMProphet MULTIPLEX
------------------------------------------------------------------------
r5838 | slagelwa | 2012-05-07 13:16:44 -0700 (Mon, 07 May 2012) | 2 lines

Fixing compile issue with NEWPATH

------------------------------------------------------------------------
r5840 | slagelwa | 2012-05-07 16:32:35 -0700 (Mon, 07 May 2012) | 2 lines

Merging another of David's changes in.

------------------------------------------------------------------------
r5841 | real_procopio | 2012-05-07 16:40:47 -0700 (Mon, 07 May 2012) | 1 line

[Petunia] Specify output file to PTMProphet
------------------------------------------------------------------------
r5842 | real_procopio | 2012-05-08 14:46:46 -0700 (Tue, 08 May 2012) | 1 line

[plot-msms-js] Bugfix: do not attempt to populate ms1 data unless we are reading an mz[X]ML file
------------------------------------------------------------------------
r5843 | real_procopio | 2012-05-09 12:35:26 -0700 (Wed, 09 May 2012) | 1 line

[Petunia] Fixed auto-refresh of page when submitting a job in Windows; Added ability to delete a single command output log file; Updated userTimeoutRecovery for new log files; Fixed small typo on PTMProphet page.
------------------------------------------------------------------------
r5844 | dshteyn | 2012-05-09 14:54:13 -0700 (Wed, 09 May 2012) | 1 line

ProphetModels.pl:  BUGFIX double counting uniques
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r5845 | slagelwa | 2012-05-09 15:18:09 -0700 (Wed, 09 May 2012) | 5 lines

Commented out EC2 special case in Makefile. Its no longer the default to
detect that you are building on a EC2 node and need a special move to handle
issues with using S3FS. If you need/want this functionality either uncomment
the line in the Makefile.incl, or add the define on the command line.

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r5846 | real_procopio | 2012-05-09 15:44:49 -0700 (Wed, 09 May 2012) | 1 line

[Petunia] Add blinking baloney when checking status on jobs page; Made MULTIPLEX the default for PTMProphet (as per DDS)
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r5847 | real_procopio | 2012-05-09 15:59:18 -0700 (Wed, 09 May 2012) | 1 line

[PepXMLViewer] Default ions2 link to Lorikeet, hide the link to old viewer (still available via Pick Columns)
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r5848 | slagelwa | 2012-05-09 16:22:10 -0700 (Wed, 09 May 2012) | 14 lines

Correction for building tandem w/pthreads as it was missing a dll.

Turns out that in the past we were linking to the Windows version of threads 
even though we were building it in a Unix like environment provided by MinGW.  
This was accomplished by setting the define MSVC to fool the tandem build to
think it was in a pure Windows environment...which of course is was not. This no
longer works since the newest version of tandem has added some additional MS 
specific code (vector math)that is unavailable to MinGW.  So instead of changing
the tandem code to allow MS threads but not the math stuff I instead just built 
a pthreads version.  

Problem is that pthreads can only be build with a dynamic library (well *almost*
true but for our purposes it might as well be).  So we now include the pthreads 
dll in the installer.
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r5849 | dshteyn | 2012-05-10 11:32:39 -0700 (Thu, 10 May 2012) | 1 line

Increase precision for reported intensities so even the tiny peaks can be seen...helpful for PTM assignment that depends on the small peaks
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r5850 | real_procopio | 2012-05-10 13:42:43 -0700 (Thu, 10 May 2012) | 1 line

[Tandem2XML] Re-indented entire file for readibility, no functional change
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r5851 | real_procopio | 2012-05-10 14:33:38 -0700 (Thu, 10 May 2012) | 1 line

[Petunia] Avoid doing the blinky thing on initial page load; also made blinking code more elegant (these things matter, yo!)
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r5853 | dshteyn | 2012-05-11 16:03:09 -0700 (Fri, 11 May 2012) | 1 line

XPressPeptideParser: was slow, much faster using cached_ramp
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r5854 | dshteyn | 2012-05-11 16:05:54 -0700 (Fri, 11 May 2012) | 1 line

Commented out code causing an Infinite Recurrence
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r5855 | dshteyn | 2012-05-14 12:59:55 -0700 (Mon, 14 May 2012) | 1 line

PTMProphet: Tweaking the algorithm to improve model
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r5856 | dshteyn | 2012-05-14 13:01:43 -0700 (Mon, 14 May 2012) | 1 line

New function for PTMProphet that remembers the peaks already matched
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r5857 | spacepod | 2012-05-14 13:05:59 -0700 (Mon, 14 May 2012) | 1 line

Removing zlib from build prerequisites on OS X; otherwise on make will error out on OS X  (no target for -lz).  zlib is still included in the linker flags for os x X!Tandem.  NOTE: if zlib is not needed for some special platform such as mingw, it would be cleanest to remove this logic and simply remove ZLIB_LIB from the xtandem prereq list in both TPP and extern/xtandem makefiles.
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r5858 | dshteyn | 2012-05-14 14:15:45 -0700 (Mon, 14 May 2012) | 1 line

PTMProphetMpx: tweak to the model improves performance
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r5860 | dshteyn | 2012-05-14 15:28:57 -0700 (Mon, 14 May 2012) | 1 line

PTMProphet: model tweak
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r5862 | real_procopio | 2012-05-14 20:08:45 -0700 (Mon, 14 May 2012) | 1 line

[LibraPeptideParser] Re-formatting code so it can be read by human beings, no functional change
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r5864 | pcbrefugee | 2012-05-15 13:34:38 -0700 (Tue, 15 May 2012) | 1 line

Branch copy of fix for an infinite recursion bug I introduced in trunk, change 5637 (Nov 2011).  I missed it because I tend to use RAMP+pwiz instead of mzparser, surprising that it took anyone else this long to notice.  Just a one liner to fix.  Also backing out change 5854 to cached_ramp.h which was an attempt to fix this, and which led to performance hits in XPress and Libra (5853 is addressed XPress performance with changes equivalent to the #defines in cached_ramp.h, but Libra is still dinged)
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r5865 | real_procopio | 2012-05-15 14:20:38 -0700 (Tue, 15 May 2012) | 1 line

[mascotout.pl] Added error message if file not found; also added html footer with TPP version
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r5866 | real_procopio | 2012-05-15 14:26:09 -0700 (Tue, 15 May 2012) | 1 line

[lorikeet] Fix typos on parameter names for n- and c-terMods
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r5867 | real_procopio | 2012-05-15 17:00:33 -0700 (Tue, 15 May 2012) | 1 line

[PepXMLViewer] Fix webserver accessible file path
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r5868 | dshteyn | 2012-05-15 17:34:29 -0700 (Tue, 15 May 2012) | 1 line

PTMProphet: further tweaks to enhance performance of the model
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r5869 | dshteyn | 2012-05-16 11:16:19 -0700 (Wed, 16 May 2012) | 1 line

tpp_gui.pl: Jobs page sorted by the Session with most recent job executed.  Jobs within each session sorted in stack order.  Makes it easier to find your job.
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r5870 | spacepod | 2012-05-16 11:38:09 -0700 (Wed, 16 May 2012) | 1 line

Minor cleanup: removing rouge tab character from Makefile.incl to prevent possible future make issues
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r5871 | dshteyn | 2012-05-16 15:41:18 -0700 (Wed, 16 May 2012) | 1 line

ASAPRatio: Remove debugging output
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r5872 | mhoopmann | 2012-05-16 16:30:55 -0700 (Wed, 16 May 2012) | 3 lines

Updated mzXML parser to treat startMz and endMz attributes as synonymous to lowMz and highMz


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r5873 | mhoopmann | 2012-05-16 16:36:05 -0700 (Wed, 16 May 2012) | 3 lines

conditional check on setting high and low mz 


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r5874 | real_procopio | 2012-05-16 16:49:12 -0700 (Wed, 16 May 2012) | 1 line

[mzParser] start low, end high high as a kite!
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r5875 | real_procopio | 2012-05-17 11:39:14 -0700 (Thu, 17 May 2012) | 1 line

[Petunia] MULTIPLEX no longer an option in PTMProphet
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r5876 | dshteyn | 2012-05-17 11:50:47 -0700 (Thu, 17 May 2012) | 1 line

PTMProphetParser: Switching to Binomial Distribution to compute probability to site being modified. Default settings: disable EM, enable MULTIPLEX
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r5879 | dshteyn | 2012-05-20 22:12:40 -0700 (Sun, 20 May 2012) | 1 line

PTMProphet:  Fix bug in enumerating all combinations of mods.  Replaced recurring function with an iterative procedure.
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r5880 | spacepod | 2012-05-24 15:16:33 -0700 (Thu, 24 May 2012) | 2 lines

Small xtandem commandline build update: if only building TPP's xtandem in an otherwise clean source tree, be sure that the TPP's build directory is created too.

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r5882 | dshteyn | 2012-05-29 15:48:03 -0700 (Tue, 29 May 2012) | 1 line

use a library to get current directory...system call to pwd stopped working
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r5883 | dshteyn | 2012-05-29 16:49:56 -0700 (Tue, 29 May 2012) | 1 line

updateAllPaths.pl: Need to close open filehandles in windows to allow overwriting the existing file.
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r5884 | dshteyn | 2012-05-29 17:00:56 -0700 (Tue, 29 May 2012) | 1 line

put rename back in...it wasn't the problem
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r5885 | dshteyn | 2012-05-29 17:13:04 -0700 (Tue, 29 May 2012) | 1 line

PTMProphet: Fix crash on peptides with modified 'n' written in the mod peptide tag. 
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r5886 | slagelwa | 2012-05-30 11:38:30 -0700 (Wed, 30 May 2012) | 1 line

Bumping RC #
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r5888 | real_procopio | 2012-06-01 12:57:42 -0700 (Fri, 01 Jun 2012) | 1 line

[Tandem2XML] Deal with quick acetyl mods, default in Tandem as of 2010.01.01.1
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r5889 | mhoopmann | 2012-06-01 13:20:17 -0700 (Fri, 01 Jun 2012) | 1 line

Minor changes to make sure tandem_native is identical with and without PLUGGABLE_SCORING. There is one remaining #ifdef PLUGGABLE_SCORING in mscore, however, it is handled in such a way that it should be identical when using "native". Tests show identical hyperscores, evalues, and peptide results. However, the section with the #ifdef PLUGGABLE_SCORING is not called at any point in any test I've tried. I cannot figure out how to trigger that section of code, which only relates to special cases for phosphosites.
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r5891 | slagelwa | 2012-06-01 15:13:24 -0700 (Fri, 01 Jun 2012) | 3 lines

Ubuntu's gcc doesn't like it when you don't catch the
return value of fread()

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r5893 | slagelwa | 2012-06-04 16:21:57 -0700 (Mon, 04 Jun 2012) | 1 line


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r5901 | slagelwa | 2012-06-12 15:29:31 -0700 (Tue, 12 Jun 2012) | 5 lines

Added download button to the filebrowser to allow downloading of files in a
directory. Multiple files are downloaded as a zip file, single files as
themselves.


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r5904 | slagelwa | 2012-06-18 11:49:45 -0700 (Mon, 18 Jun 2012) | 6 lines

Disable indexing of file system by the browser by default.  With this enabled 
it allows anyone to bypass the Petunia authentication/authoriation and both 
list and fetch any TPP data from a system that's been left open.  This certainly
doesn't close the door but it helps a little.


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r5905 | slagelwa | 2012-06-18 14:54:35 -0700 (Mon, 18 Jun 2012) | 3 lines

Increase the maximum number of threads allowed.  Systems now exist with 16 or more cores.  Why increase to 256?  Why not?


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r5907 | real_procopio | 2012-06-19 10:55:18 -0700 (Tue, 19 Jun 2012) | 1 line

[Tandem2XML] Cleaner way to deal with N-term acetylation
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r5908 | mhoopmann | 2012-06-19 10:59:14 -0700 (Tue, 19 Jun 2012) | 2 lines

Report a,c,x,z ions (lost during upgrade to cyclone).
Report N-terminal protein acetylation mods with the '[' symbol.
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r5910 | dshteyn | 2012-06-22 12:33:20 -0700 (Fri, 22 Jun 2012) | 1 line

XPressCGIProteinDisplayParser.cgi: fix obvious security issue with passing commands in QUERY_STRING
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r5911 | dshteyn | 2012-06-22 12:34:34 -0700 (Fri, 22 Jun 2012) | 1 line

Remove xslt from link to XPressCGIProteinDisplayParser.cgi
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r5912 | slagelwa | 2012-06-28 10:25:42 -0700 (Thu, 28 Jun 2012) | 5 lines

* TPP's makefile has a "xtandem-debug" target that wasn't doing anything. 
  Fixed this by using the value of DEBUG if its set.
* Fixed a number of deallocation issues that valgrind was complaining about.


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r5914 | slagelwa | 2012-07-03 15:11:09 -0700 (Tue, 03 Jul 2012) | 2 lines

Merging Mike r5913 change into branch

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