TPP:5.1.0 SVN Log

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[comet] Updating zip file structure, since distributed file for latest version is different than previous ones [comet] Updating zip file structure, since distributed file for latest version is different than previous ones
 +------------------------------------------------------------------------
 +r7596 | dshteyn | 2017-06-02 14:36:35 -0700 (Fri, 02 Jun 2017) | 1 line
 +
 +reSpect: fix problem with neutral losses ... also MININTMODE
 +------------------------------------------------------------------------
 +r7597 | dshteyn | 2017-06-02 14:38:52 -0700 (Fri, 02 Jun 2017) | 1 line
 +
 +ProteinProphet: set maxppmdiff default value to 1e6 to keep original behavior after adding this parameter.
 +------------------------------------------------------------------------
 +r7598 | eng_jk | 2017-06-13 14:39:10 -0700 (Tue, 13 Jun 2017) | 2 lines
 +
 +update packages required for centos TPP5 install
 +
 +------------------------------------------------------------------------
 +r7599 | eng_jk | 2017-06-14 14:09:28 -0700 (Wed, 14 Jun 2017) | 2 lines
 +
 +fix RAMPface.cpp so that mzML precursor m/z values aren't all reported as 0.0
 +
 +------------------------------------------------------------------------
 +r7600 | real_procopio | 2017-06-16 13:33:48 -0700 (Fri, 16 Jun 2017) | 1 line
 +
 +[tpp_hashmap] Store this with Linux line endings, not Windows!
 +------------------------------------------------------------------------
 +r7601 | real_procopio | 2017-06-16 13:36:22 -0700 (Fri, 16 Jun 2017) | 1 line
 +
 +[Enzymes] Delete elements properly to avoid potential memory issues
 +------------------------------------------------------------------------
 +r7602 | real_procopio | 2017-06-16 13:40:34 -0700 (Fri, 16 Jun 2017) | 1 line
 +
 +[mzParser] Only attempt to open a file if there is an actual filename, which avoids potential memory errors. Also, include file name in error when unable to open
 +------------------------------------------------------------------------
 +r7603 | real_procopio | 2017-06-16 13:46:36 -0700 (Fri, 16 Jun 2017) | 1 line
 +
 +[Tandem2XML] Fix some error leaks; some code reformatting and clean-up
 +------------------------------------------------------------------------
 +r7604 | real_procopio | 2017-06-19 15:04:30 -0700 (Mon, 19 Jun 2017) | 1 line
 +
 +[common] Strip leading and trailing spaces from user-specified build settings, as they may cause errors
 +------------------------------------------------------------------------
 +r7605 | dshteyn | 2017-06-23 16:07:32 -0700 (Fri, 23 Jun 2017) | 1 line
 +
 +DISCO: fix some crashes and use proper o: character in Hardklo:r
 +------------------------------------------------------------------------
 +r7606 | dshteyn | 2017-07-28 15:03:02 -0700 (Fri, 28 Jul 2017) | 1 line
 +
 +PTMProphet: fix bug associated with reporting peptides with a terminal mod. Change pepXML reporting of terminal probabilities to new scheme planned with Luis.
 +------------------------------------------------------------------------
 +r7607 | real_procopio | 2017-07-28 15:27:33 -0700 (Fri, 28 Jul 2017) | 1 line
 +
 +[PepXMLViewer] Handle and display terminal mods and probabilities from PTMProphet as per the updated schema
 +------------------------------------------------------------------------
 +r7608 | dshteyn | 2017-08-09 11:57:29 -0700 (Wed, 09 Aug 2017) | 1 line
 +
 +Spectrast: OpenMod search, allow the tolerance to be specified and passed to allow mass differences bigger than 300 amu.
 +------------------------------------------------------------------------
 +r7609 | dshteyn | 2017-08-09 11:59:06 -0700 (Wed, 09 Aug 2017) | 1 line
 +
 +Support for search engine SIPROS.
 +------------------------------------------------------------------------
 +r7610 | dshteyn | 2017-08-09 12:00:15 -0700 (Wed, 09 Aug 2017) | 1 line
 +
 +Support for search engine SIPROS.
 +------------------------------------------------------------------------
 +r7611 | dshteyn | 2017-08-09 12:02:49 -0700 (Wed, 09 Aug 2017) | 1 line
 +
 +Support for search engine SIPROS.
 +------------------------------------------------------------------------
 +r7612 | dshteyn | 2017-08-09 12:15:05 -0700 (Wed, 09 Aug 2017) | 1 line
 +
 +Support for search engine SIPROS.
 +------------------------------------------------------------------------
 +r7613 | dshteyn | 2017-08-09 12:31:23 -0700 (Wed, 09 Aug 2017) | 1 line
 +
 +PDLStats: perl interface to gsl for statistics.
 +------------------------------------------------------------------------
 +r7614 | dshteyn | 2017-08-10 08:43:46 -0700 (Thu, 10 Aug 2017) | 1 line
 +
 +Don't build pdlstats for now.
 +------------------------------------------------------------------------
 +r7615 | eng_jk | 2017-08-10 14:43:18 -0700 (Thu, 10 Aug 2017) | 2 lines
 +
 +Add long overdue support for isotope peaks to XPRESS cgi. When C13 isotope peaks are used in the quantitation, the cgi XPressPeptideUpdateParser.cgi is now aware of them and will display the same ratio,taking into account the data in the C13 isotope peaks.
 +
 +------------------------------------------------------------------------
 +r7616 | real_procopio | 2017-08-15 12:06:13 -0700 (Tue, 15 Aug 2017) | 1 line
 +
 +[PepXMLViewer] Added support for PEFF modifications and substitutions; also fixed modified peptide display (for n-terminus)
 +------------------------------------------------------------------------
 +r7617 | real_procopio | 2017-08-16 14:12:28 -0700 (Wed, 16 Aug 2017) | 1 line
 +
 +[PDLStats] Remove install directive breaking the nightly build
 +------------------------------------------------------------------------
 +r7618 | dshteyn | 2017-08-18 16:47:50 -0700 (Fri, 18 Aug 2017) | 1 line
 +
 +RTCalculator: correct header comment, don't print the peptide by peptide rt info in non-verbose mode.
 +------------------------------------------------------------------------
 +r7619 | dshteyn | 2017-08-18 16:54:00 -0700 (Fri, 18 Aug 2017) | 1 line
 +
 +PeptideProphet: correctly name RT Mixture Model...
 +------------------------------------------------------------------------
 +r7620 | dshteyn | 2017-08-18 16:57:17 -0700 (Fri, 18 Aug 2017) | 1 line
 +
 +DiscoFilter: change the way isolation windows are specified (now requires flag WINDOWS=<file>), use HardKlor to ID unfragged MS1 precursor features for DISCO extraction.
 +------------------------------------------------------------------------
 +r7621 | dshteyn | 2017-08-21 07:47:57 -0700 (Mon, 21 Aug 2017) | 1 line
 +
 +Hardklor Changes for DISCO MS1 and MS2 feature extraction.
 +------------------------------------------------------------------------
 +r7622 | dshteyn | 2017-08-21 07:49:03 -0700 (Mon, 21 Aug 2017) | 1 line
 +
 +MSToolkit Build: Turn on optimization when not being compiled for debugging...
 +------------------------------------------------------------------------
 +r7623 | real_procopio | 2017-08-21 14:18:10 -0700 (Mon, 21 Aug 2017) | 1 line
 +
 +[Petunia] Update for new Disco command invocation
 +------------------------------------------------------------------------
 +r7624 | real_procopio | 2017-08-24 15:03:58 -0700 (Thu, 24 Aug 2017) | 1 line
 +
 +Name release 5.1, release candidate 1
 +------------------------------------------------------------------------
 +r7625 | eng_jk | 2017-09-06 13:27:15 -0700 (Wed, 06 Sep 2017) | 2 lines
 +
 +Per bug report by Oded Kleifeld in spctools-discuss, terminal mods were not handled correctly. Turns out issue was a string comparison for 'n' and 'c' terminal specification being compared against 'N' and 'C' terminus attribute in the terminal_modification element. Correcting this case comparison issue seems to solve the reported problem.
 +
 +------------------------------------------------------------------------
 +r7626 | eng_jk | 2017-09-13 09:59:55 -0700 (Wed, 13 Sep 2017) | 2 lines
 +
 +Streamline XPRESS isotopic labeling support. XPRESS will now automatically determine if peptide is C13 or N15 light/heavy labeled based on modification state of peptide.
 +
 +------------------------------------------------------------------------
 +r7627 | dshteyn | 2017-09-17 17:30:13 -0700 (Sun, 17 Sep 2017) | 1 line
 +
 +PTMProphet: Fix tripping over windows full paths.
 +------------------------------------------------------------------------
 +r7628 | dshteyn | 2017-10-02 10:57:44 -0700 (Mon, 02 Oct 2017) | 1 line
 +
 +BUGFIX: correct issues with massdiffmode and unknown modifications (e.g. incorrectly reported n-terminal acetylation)
 +------------------------------------------------------------------------
 +r7629 | dshteyn | 2017-10-02 11:01:52 -0700 (Mon, 02 Oct 2017) | 1 line
 +
 +Update the User Specified Mod with new mass.
 +------------------------------------------------------------------------
 +r7630 | dshteyn | 2017-10-02 14:52:21 -0700 (Mon, 02 Oct 2017) | 1 line
 +
 +mzParser: use the byte offset index to access the header info more quickly...
 +------------------------------------------------------------------------
 +r7631 | dshteyn | 2017-10-02 14:53:10 -0700 (Mon, 02 Oct 2017) | 1 line
 +
 +InteractParser/mzParser: use the byte offset index to access the header info more quickly...
 +------------------------------------------------------------------------
 +r7632 | real_procopio | 2017-10-10 17:44:14 -0700 (Tue, 10 Oct 2017) | 1 line
 +
 +[fetchDataset] Add utility to download and unpack public proteomics datasets
 +------------------------------------------------------------------------
 +r7633 | real_procopio | 2017-10-10 17:46:52 -0700 (Tue, 10 Oct 2017) | 1 line
 +
 +[comet] Update to newest version: 2017-01-0
 +------------------------------------------------------------------------
 +r7634 | real_procopio | 2017-10-10 17:48:46 -0700 (Tue, 10 Oct 2017) | 1 line
 +
 +[xinteract] Update usage statement for XPRESS metabolic labeling
 +------------------------------------------------------------------------
 +r7635 | real_procopio | 2017-10-10 17:53:20 -0700 (Tue, 10 Oct 2017) | 1 line
 +
 +[fetchDataset] Add utility to download and unpack public proteomics datasets
 +------------------------------------------------------------------------
 +r7636 | real_procopio | 2017-10-10 18:07:07 -0700 (Tue, 10 Oct 2017) | 4 lines
 +
 +[Petunia]
 +- Added page for new fetchDataset tool; also added ability to query tool version and abilities, as well as link to auto-update
 +- Minor rearrangement of XPRESS interface: clarify metabolic options; add two more potential modified residues for a total of five
 +
 +------------------------------------------------------------------------
 +r7637 | real_procopio | 2017-10-17 13:39:00 -0700 (Tue, 17 Oct 2017) | 1 line
 +
 +[Petunia] Add link to show fetchDataset version and info after updating. Other minor text and loop changes
 +------------------------------------------------------------------------
 +r7638 | real_procopio | 2017-10-17 13:42:02 -0700 (Tue, 17 Oct 2017) | 1 line
 +
 +[fetchDataset] Update to v0.7.4: keep shebang line when updating; assume all zip files are bdbags; include MD5 module for expected hash check
 +------------------------------------------------------------------------
 +r7639 | real_procopio | 2017-10-17 13:43:11 -0700 (Tue, 17 Oct 2017) | 1 line
 +
 +[version] Spell Syzygy properly; increment to rc2
 +------------------------------------------------------------------------
 +r7640 | real_procopio | 2017-10-18 18:20:01 -0700 (Wed, 18 Oct 2017) | 1 line
 +
 +[Windows installer] Do not auto-install/run tpptray; add link to TPP log files from Programs menu
 +------------------------------------------------------------------------
 +r7641 | dshteyn | 2017-10-23 14:31:06 -0700 (Mon, 23 Oct 2017) | 1 line
 +
 +iProphet: fix a bug with small sized runs.
 +------------------------------------------------------------------------
 +r7642 | real_procopio | 2017-10-24 16:32:11 -0700 (Tue, 24 Oct 2017) | 1 line
 +
 +[madcaps] Add link to Uniprot for "sp|xxxx|" entries; Use correct specificity for chymotrypsin; Turn off CGI::LIST_CONTEXT_WARN
 +------------------------------------------------------------------------
 +r7643 | real_procopio | 2017-10-24 16:35:32 -0700 (Tue, 24 Oct 2017) | 1 line
 +
 +[enzymes] Fix chymotrypsin specificity (which was clobbered by commit r6497), and harmonize across various tools; Remove obsolete code
 +------------------------------------------------------------------------
 +r7644 | real_procopio | 2017-10-24 17:14:02 -0700 (Tue, 24 Oct 2017) | 1 line
 +
 +[comet] Update to 2017-01-1, which contains important bug fixes
------------------------------------------------------------------------ ------------------------------------------------------------------------

Revision as of 00:54, 25 October 2017

r7425 | real_procopio | 2016-10-11 17:05:00 -0700 (Tue, 11 Oct 2016) | 1 line

[tpp] Make TPP 5.0 code the new TRUNK!

r7426 | real_procopio | 2016-10-12 18:19:28 -0700 (Wed, 12 Oct 2016) | 1 line

[comet-fastadb] Encode protein description as XML (and HTML) friendly

r7427 | real_procopio | 2016-10-13 15:08:15 -0700 (Thu, 13 Oct 2016) | 1 line

[Mascot2XML] Fix XML encoding of alternative protein descirptions; reported and contributed by J. Eckels. Also removed a couple of deprecated Cygwin-specific code blocks

r7428 | real_procopio | 2016-10-17 17:22:20 -0700 (Mon, 17 Oct 2016) | 6 lines

[ProtXMLViewer] - Added ability to sort and filter by Libra number of peptides - Added background color gradient to pvalue and libra values (text mode) - Removed heatmap display option from asap/xpress/stpeter - Fixed alignment/width of protein annotation span

r7429 | real_procopio | 2016-10-17 18:18:12 -0700 (Mon, 17 Oct 2016) | 6 lines

[PepXMLViewer] - Use database used by RefreshParser, if present; otherwise default to using db used in original search - Do not generate protein link for '_UNMAPPED' entries - Removed some old (commented out) debug code


r7430 | real_procopio | 2016-10-18 13:30:56 -0700 (Tue, 18 Oct 2016) | 1 line

[Petunia] Fix chdir when in Windows (one must also execute change drive!) - centralized code to do this in new sub "safe_chdir()"

r7431 | real_procopio | 2016-10-19 13:20:22 -0700 (Wed, 19 Oct 2016) | 8 lines

[PepXMLViewer] - show quantitation ratios with a gradient background color (blue->white->red) - generate required css on the fly when quant values exist in pepXML file - show normalized libra ratios by default (formerly: show absolute values) - changed alternate row color from light blue to light green - added css entry for red/white error messages div - minor code cleanup

r7432 | real_procopio | 2016-10-20 11:24:15 -0700 (Thu, 20 Oct 2016) | 5 lines

[PepXMLViewer] - align xl xlink peptides and show xl location with a bar connecting them - fix text/excel export of loop xlink peptides, Format is as: 

 K.FC[160.03]KFIKSMR.A(3+6)  <-- xlink loop positions

r7433 | real_procopio | 2016-10-21 14:25:24 -0700 (Fri, 21 Oct 2016) | 1 line

[apache conf] Need to add explicit grant access in case TPP_DATADIR is not under INSTALL_DIR

r7434 | mhoopmann | 2016-10-21 15:07:19 -0700 (Fri, 21 Oct 2016) | 3 lines

Added biotin as a modification mass.


r7435 | mhoopmann | 2016-10-21 15:08:45 -0700 (Fri, 21 Oct 2016) | 3 lines

Update version number and date


r7436 | real_procopio | 2016-10-21 17:17:11 -0700 (Fri, 21 Oct 2016) | 8 lines

[PepXMLViewer] - Initial support for Novor search results - New novor_peptide field shows sequence with aaScore as a colored bar above each AA. (similar to ptm_peptide) - Implemented mouse-over description text for column headers - Removed deprecated Cygwin conditional code - Use correct spelling for "accessIble" - Some code formatting for consistency

r7437 | real_procopio | 2016-10-24 12:52:57 -0700 (Mon, 24 Oct 2016) | 5 lines

[PepXMLViewer] - Fixed index file bug: asapratio_mean was being duplicated which caused issues with sorting in certain cases - Fixed "require consistent xpress/asap ratios" filter - Some code clean-up

r7438 | dshteyn | 2016-11-02 09:49:31 -0700 (Wed, 02 Nov 2016) | 1 line

Unmodified Cys immonium

r7439 | dshteyn | 2016-11-02 11:14:42 -0700 (Wed, 02 Nov 2016) | 1 line

PTMProphet: use Gaussian to approx Poisson when mu is high to prevent some gsl crashes. Correct crashes when immonium table contains null for some amino acid tokens (e.g. 'Z').

r7440 | real_procopio | 2016-11-09 17:54:03 -0800 (Wed, 09 Nov 2016) | 1 line

[LibraPeptide] Print error and exit if scan has no peaks (instead of segfault). Also: code re-formatting!

r7441 | real_procopio | 2016-11-14 11:13:36 -0800 (Mon, 14 Nov 2016) | 1 line

[ProteinProphet] Use normal exit() instead of WEXITSTATUS which does NOT return anything other than '0' (no child process). This preserves the error exit codes.

r7442 | dshteyn | 2016-11-14 14:51:06 -0800 (Mon, 14 Nov 2016) | 1 line

PTMProphet: MASSDIFFMODE bug fixes.

r7443 | dshteyn | 2016-11-16 10:07:36 -0800 (Wed, 16 Nov 2016) | 1 line

InteractParser: place dataset_derivation tag AFTER the analysis_summaries ...

r7444 | dshteyn | 2016-11-16 23:35:02 -0800 (Wed, 16 Nov 2016) | 1 line

Remove old ProteoWizard

r7445 | dshteyn | 2016-11-17 11:08:20 -0800 (Thu, 17 Nov 2016) | 2 lines

New Proteowizard

r7446 | dshteyn | 2016-11-17 13:47:52 -0800 (Thu, 17 Nov 2016) | 1 line

New Proteowizard uses boost_chrono

r7447 | real_procopio | 2016-11-17 17:40:22 -0800 (Thu, 17 Nov 2016) | 1 line

[pepXML schema] Added 'type' attribute (for XL analysis); belated addition of decoy analysis tags; expanded list of possible aa- and term- modification symbols

r7448 | real_procopio | 2016-11-17 17:45:40 -0800 (Thu, 17 Nov 2016) | 1 line

[decoyModels] Removed non-compliant id attribute from analysis_summary; added an extra test for <dataset_derivation> tag when looking for place to insert <decoy> analysis tags, for robustness

r7449 | dshteyn | 2016-11-17 18:53:06 -0800 (Thu, 17 Nov 2016) | 1 line

Changes to make sure we can still compile under windows mingw64 using msys2

r7450 | dshteyn | 2016-11-17 20:55:23 -0800 (Thu, 17 Nov 2016) | 1 line

committing all new ProteoWizard stuff

r7451 | dshteyn | 2016-11-17 21:39:38 -0800 (Thu, 17 Nov 2016) | 1 line

ProteoWizard pieces missed on last checkin

r7452 | dshteyn | 2016-11-17 22:19:29 -0800 (Thu, 17 Nov 2016) | 1 line

ProteoWizard missing pieces

r7453 | dshteyn | 2016-11-17 22:25:33 -0800 (Thu, 17 Nov 2016) | 1 line

ProteoWizard missing pieces

r7454 | dshteyn | 2016-11-17 22:36:38 -0800 (Thu, 17 Nov 2016) | 1 line

ProteoWizard pieces

r7455 | dshteyn | 2016-11-17 22:50:28 -0800 (Thu, 17 Nov 2016) | 1 line

Older g++ versions may no implement -std=c++11 (only tested to work under 5.2.0)

r7456 | real_procopio | 2016-11-18 12:52:13 -0800 (Fri, 18 Nov 2016) | 1 line

[Kojak] Updating to v1.5.3

r7457 | dshteyn | 2016-11-18 15:56:58 -0800 (Fri, 18 Nov 2016) | 1 line

New d3 stuff for ProteoGrapher.

r7458 | dshteyn | 2016-11-18 15:57:44 -0800 (Fri, 18 Nov 2016) | 1 line

ProteoGrapher version 2.0

r7459 | dshteyn | 2016-11-18 15:59:15 -0800 (Fri, 18 Nov 2016) | 1 line

New option to specify cut / no cut sites when creating decoy peptides from target proteins.

r7460 | eng_jk | 2016-11-21 11:45:00 -0800 (Mon, 21 Nov 2016) | 2 lines

Char string set too small (buf[2]) to hold a string value greater than a single digit. This causes a buffer overflow when NMC is 10 or larger.

r7461 | real_procopio | 2016-11-21 14:07:21 -0800 (Mon, 21 Nov 2016) | 1 line

[PepXMLViewer] Fix web link to xml and models files that kept causing access problems mainly in Linux; also default to show 100 rows (old: 50)

r7462 | real_procopio | 2016-11-21 18:42:29 -0800 (Mon, 21 Nov 2016) | 1 line

[PepXMLViewer] Adding Novor score filter

r7463 | dshteyn | 2016-11-22 21:28:50 -0800 (Tue, 22 Nov 2016) | 1 line

this is from boost 1_61_0 because broken in 1_56_0

r7464 | dshteyn | 2016-11-22 21:29:38 -0800 (Tue, 22 Nov 2016) | 1 line

Fix boost compilation under mingw/gcc

r7465 | dshteyn | 2016-11-22 22:46:40 -0800 (Tue, 22 Nov 2016) | 1 line

remove bad patch

r7466 | dshteyn | 2016-11-23 09:58:26 -0800 (Wed, 23 Nov 2016) | 1 line

remove bad patch

r7467 | dshteyn | 2016-11-23 11:14:44 -0800 (Wed, 23 Nov 2016) | 29 lines

Increase accuracy of primary Immonium ion masses per Eric's Calculations:

Here are the primary ones (the "A" means the primary one). This is monoisotopic, high accuracy:

G A 30.03382547 A A 44.04947547 S A 60.04439007 P A 70.06512547 V A 72.08077547 T A 74.06004007 C A 76.02154727 I A 86.09642547 L A 86.09642547 N A 87.05528907 D A 88.03930467 Q A 101.07093907 K A 101.10732447 E A 102.05495467 M A 104.05284727 H A 110.07127347 F A 120.08077547 R A 129.11347247 Y A 136.07569007 W A 159.09167447 C[160] A 133.04301127 C[161] A 134.02702627 M[147] A 120.04776227 W[202] A 175.08658947

r7468 | dshteyn | 2016-11-28 15:16:31 -0800 (Mon, 28 Nov 2016) | 1 line

Install new d3 dependencies for ProteoGrapher

r7469 | dshteyn | 2016-11-29 11:44:39 -0800 (Tue, 29 Nov 2016) | 1 line

extern: update MSToolkit

r7470 | dshteyn | 2016-11-29 11:46:09 -0800 (Tue, 29 Nov 2016) | 1 line

extern: update HardKlor

r7471 | real_procopio | 2016-11-29 13:20:26 -0800 (Tue, 29 Nov 2016) | 1 line

[ProtXMLViewer] Display and export protein length

r7472 | dshteyn | 2016-11-29 15:46:29 -0800 (Tue, 29 Nov 2016) | 1 line

Finish updates to MSToolkit and HardKlor, make sure DiscoFilter can still function...\nNext up using MSToolkit to read isolation window parameters and report if not consistent with input SWATH windows

r7473 | dshteyn | 2016-11-29 15:48:43 -0800 (Tue, 29 Nov 2016) | 1 line

Undo personalizations in common.mk checked in by mistake

r7474 | dshteyn | 2016-12-02 10:33:14 -0800 (Fri, 02 Dec 2016) | 1 line

PTMProphet: Fix bug not allowing PTMProphet to run when only one modification was being specified for localization

r7475 | dshteyn | 2016-12-02 10:38:35 -0800 (Fri, 02 Dec 2016) | 1 line

Update immonium masses

r7476 | dshteyn | 2016-12-02 15:38:26 -0800 (Fri, 02 Dec 2016) | 1 line

Include missing library header...

r7477 | dshteyn | 2016-12-05 11:04:22 -0800 (Mon, 05 Dec 2016) | 1 line

include missing header

r7478 | real_procopio | 2016-12-29 17:32:11 -0800 (Thu, 29 Dec 2016) | 6 lines

[ProtXMLViewer] - Add color annotated color scale for libra and pvalue quant values - Fixed FF/Chrome vertical alignment quirks - Simplified css shadows - Other minor css tweaks

r7479 | dshteyn | 2017-01-03 15:18:21 -0800 (Tue, 03 Jan 2017) | 1 line

BUGFIX: iProphet NRS model edge condition corrected (missing '-' included)

r7480 | real_procopio | 2017-01-03 18:43:07 -0800 (Tue, 03 Jan 2017) | 5 lines

[PepXMLViewer] - Add color annotated color scale for quant values - Use <!DOCTYPE html> for html5 - Correctly display "unavailable" libra values

r7481 | real_procopio | 2017-01-06 15:35:41 -0800 (Fri, 06 Jan 2017) | 1 line

Fix names of variables for site.mk example in Linux build notes

r7482 | mhoopmann | 2017-01-09 11:57:16 -0800 (Mon, 09 Jan 2017) | 12 lines

mzIMLTools:

READ and WRITE mzIdentML like a BADASS!

Now you too can enjoy the magical world of proteomics standards initiatives! Stand out at conferences! Look and smell smarter! Stupify your cat! The possibilities are endless with these AMAZING tools!

Bring your software dreams to reality with the simple object interface! Just link the library and you're ready to go! These tools DEMYSTIFY the mzid format for you! You don't need to actually understand any of it! Fool your friends! Make your grandma love you more than Philip! The secret can be yours!

Disclaimer: These statements have not been evaluated. Makefile not included. Cat sold separately. Results may vary. mzIMLTools do not yet read mzid files. Intelligence is relative. In your case, possibly more relative. Follow all instructions and always wear safety goggles. Parental supervision recommended. All sales are final.


r7483 | mhoopmann | 2017-01-09 13:03:19 -0800 (Mon, 09 Jan 2017) | 3 lines

Updating makefiles for mzIMLTools


r7484 | mhoopmann | 2017-01-09 13:05:17 -0800 (Mon, 09 Jan 2017) | 3 lines

one last makefile to update.


r7485 | real_procopio | 2017-01-10 11:55:18 -0800 (Tue, 10 Jan 2017) | 1 line

[decoyFastaGenerator] Fix code so that the "new" (seemingly untested) options actually work; some code cleanup

r7486 | real_procopio | 2017-01-10 13:34:19 -0800 (Tue, 10 Jan 2017) | 1 line

[decoyFastaGenerator] Strip out Linux and Windows EOL chars lest they end up mid-sequence...

r7487 | dshteyn | 2017-01-10 15:06:27 -0800 (Tue, 10 Jan 2017) | 1 line

Correct problem causing options to be interpretted as input file.

r7488 | real_procopio | 2017-01-10 16:05:58 -0800 (Tue, 10 Jan 2017) | 1 line

[decoyFastaGenerator] Fix this code, yet again. (Fixing the "fix" that happened after the actual fix.) But heck, who wants to run a simple test, right?

r7489 | real_procopio | 2017-01-11 14:38:57 -0800 (Wed, 11 Jan 2017) | 1 line

Remove long-ago deprecated program pepxmlcheck.pl

r7490 | real_procopio | 2017-01-11 15:06:30 -0800 (Wed, 11 Jan 2017) | 1 line

[BUILD_LINUX] Updating incorrect reference to TPP_BASEURL

r7491 | real_procopio | 2017-01-12 12:24:00 -0800 (Thu, 12 Jan 2017) | 11 lines

[Petunia] - Add Database file chooser for Kojak; usage is optional, it will replace entry within selected Kojak.conf - Added new -c and -n options for randomized decoy generator - Directly link to SpectraST output file if only one input file was used (otherwise keep directory as job output) - Remove leading and trailing spaces in xtandem params (it chokes otherwise!); also ensure only one space after a comma - Dim/highlight refinement-related xtandem params when value of 'refine' is set to/not to 'yes' - Show smooth job status transition when udpating to a new status - Added 'no centroiding' option to Libra conditions and made it the default - Rearranged Libra normalization options so that 'not recommended' values are sorted/displayed last - Flag filenames that contain spaces when listing files; do not allow to select these for input

r7492 | real_procopio | 2017-01-17 17:25:59 -0800 (Tue, 17 Jan 2017) | 10 lines

[Novor] Adding basic integration of Novor de-novo engine into TPP - Added Novor to available engines in Petunia; moved Tandem up on the list - Added page to launch Novor; checks for novor.sh/.bat and warns user if not found - Added Novor "home" page with analysis steps currently supported in TPP - Novor params edit already supported by current code (!) - Added page to launch conversion to pepXML - Replaced "format used by xinteract" to "format used by TPP" - Added new converter from novor.csv to pepXML

r7493 | dshteyn | 2017-01-18 12:25:38 -0800 (Wed, 18 Jan 2017) | 1 line

tpp_model.pl: Exit and report error (as opposed to continuing and failing later) when an msms_run_summary open tag is found while inside another msms_run_summary...

r7494 | dshteyn | 2017-01-18 12:38:33 -0800 (Wed, 18 Jan 2017) | 1 line

ProteoGrapher: Classify the GO terms in all three categories: Biol.Proc., Mol.Func., Cel.Comp. - now works with Firefox

r7495 | dshteyn | 2017-01-18 12:41:54 -0800 (Wed, 18 Jan 2017) | 1 line

ProtXMLViewer.pl: remove terms.json from URL when calling ProteoGrapher.

r7496 | real_procopio | 2017-01-18 13:53:16 -0800 (Wed, 18 Jan 2017) | 1 line

[PepXMLViewer] Allow filtering by xlink_type if column is being displayed (or serach engine is Kojak|PLink

r7497 | real_procopio | 2017-01-18 14:09:22 -0800 (Wed, 18 Jan 2017) | 1 line

[novor2xml] Display consistent 'Warning:' messages

r7498 | real_procopio | 2017-01-18 16:52:31 -0800 (Wed, 18 Jan 2017) | 1 line

[tpp_models] Reverting latest UNTESTED code change that, once again, broke previous functionality

r7499 | dshteyn | 2017-01-18 20:34:58 -0800 (Wed, 18 Jan 2017) | 1 line

Recommitting reverted change that gave additional functionality. This change became neccessary because ProphetModels.pl functionality was changed when it was updated to use tpp_models.pl. Here is wishing development was always more forward driven.

r7500 | mhoopmann | 2017-01-19 12:46:40 -0800 (Thu, 19 Jan 2017) | 3 lines

Adding license statments and little feature additions. Made the demo program a little smarter, but it is still very stupid.


r7501 | real_procopio | 2017-01-19 16:30:30 -0800 (Thu, 19 Jan 2017) | 6 lines

[ProtXMLViewer] - Enable sorting and filtering by number of spectra used by Xpress, ASAPRatio - Avoid calling Wobniar (colors) repeatedly when displaying graphical peptide view - Provide legend when displaying graphical peptide view - Do not display protein length if not present in protXML - Tweak css for missing/empty protein annotations

r7502 | dshteyn | 2017-01-24 15:08:37 -0800 (Tue, 24 Jan 2017) | 1 line

ProteinPilot support

r7503 | real_procopio | 2017-01-30 17:37:32 -0800 (Mon, 30 Jan 2017) | 1 line

[ploTPP] New tool PloTPP for simple interactive visualization, including overplotting of values from different sources. HTML page and related cgi

r7504 | real_procopio | 2017-01-30 17:52:04 -0800 (Mon, 30 Jan 2017) | 5 lines

[ProtXMLViewer] - Enable export of single (histogram) or pairs (scatterplot) of columns for visualization in new PloTPP utility - Link to view results only opens in new window unless window already present; it auto-refreshes otherwise - Added min/max filtering for each Libra channel

r7505 | mhoopmann | 2017-01-31 13:15:07 -0800 (Tue, 31 Jan 2017) | 3 lines

Updating makefile for mzIMLTools


r7506 | mhoopmann | 2017-01-31 13:15:46 -0800 (Tue, 31 Jan 2017) | 4 lines

Added mzid reading functionality to mzIMLTools. Expanded the mzIMLDemo to now give examples of both reading and writing mzIdentML. 1) if given a pep.xml file, it is converted to mzid. 2) if given an mzid file, it is read and summary statistics provided. AND the first instance of a peptide shared by 20 database protein mappings is displayed. 'Cuz it's important, you know? Finally, after reading the mzid file, a file named "hopethisworks.mzid" is created, that hopefully exports the data identically to what was imported. So far, so good, 

but results are not guaranteed, otherwise it would be called "thisworks.mzid". Greatest demo ever, am I right?


r7507 | real_procopio | 2017-01-31 17:23:08 -0800 (Tue, 31 Jan 2017) | 6 lines

[PepXMLViewer] Minor L&F revamp to mimic recent changes to other TPP interfaces: - Establish fixed header, footer, and menus - New toolbar with menus to open/close sections for filtering, displaying , messages, etc. - Small color updates

r7508 | dshteyn | 2017-02-02 11:09:33 -0800 (Thu, 02 Feb 2017) | 1 line

iProphet: keep track of open analysis_summary tags and close all open ones, when they are nested...prevent iProphet from creating invalid pepXML due to unclosed analysis_summaries. Clean up unused code.

r7509 | dshteyn | 2017-02-02 11:11:16 -0800 (Thu, 02 Feb 2017) | 1 line

Remove unused variable

r7510 | real_procopio | 2017-02-02 17:30:03 -0800 (Thu, 02 Feb 2017) | 1 line

[Petunia] Add link to new ploTPP.html for relevant .dat files; allow choosing pepXML and protXML files as input to idConvert; add link to GPM/Tandem from tandem search page; remove "terms" from link to ProteoGrapher

r7511 | real_procopio | 2017-02-02 17:57:52 -0800 (Thu, 02 Feb 2017) | 7 lines

[ploTPP] - Better number handling (force digits+decimal point only until we implement string categories) - Handle Windows/Linux line endings, always - Add "PLOTPP" identifying string to file header - Make sure we return proper message if cannot find/open directory


r7512 | real_procopio | 2017-02-02 18:39:29 -0800 (Thu, 02 Feb 2017) | 11 lines

[PepXMLViewer] - Enable export of single (histogram) or pairs (scatterplot) of columns for visualization in new PloTPP utility - Link to view results only opens in new window unless window already present; it auto-refreshes otherwise - General cleanup of html template -- Moved Comet expect filter to top of section -- <bold> selected display options and filters in respective summary texts -- Add <label> tags to most radio and checkbox inputs for easier user interaction -- Compact several form fields -- Remove some comments - Remove unused TODO file

r7513 | real_procopio | 2017-02-02 18:45:19 -0800 (Thu, 02 Feb 2017) | 8 lines

[ploTPP] (missed on previous commit...) - Better number handling (force digits+decimal point only until we implement string categories) - Handle Windows/Linux line endings, always - Add "PLOTPP" identifying string to file header - Make sure we return proper message if cannot find/open directory


r7514 | real_procopio | 2017-02-07 16:36:08 -0800 (Tue, 07 Feb 2017) | 11 lines

[tpp_models] - Update L&F to match latest template (darker blue, similar tabs, footer, etc) - Place labels on x-axes for most models - Scale secondary models to +/- 100% for easier comparison - Clean up x-tickmarks Also: - Petunia: do not crash on non-existent directory; return empty file list instead - ploTPP: skip empty lines - ProtXMLViewer: add full file path to footer


r7515 | real_procopio | 2017-02-22 18:18:19 -0800 (Wed, 22 Feb 2017) | 6 lines

[PepXMLViewer] - Added tool name to background of menu for easier identification - Changed mouse-over color for filter/display options - Simplified row highlight mechanism: use css :hover; removed mouse-over/out code - Make sure footer stays in place when scrolling horizontally; close menu if clicked upon - Fixed glyc and ASAP labels

r7516 | eng_jk | 2017-02-28 11:40:20 -0800 (Tue, 28 Feb 2017) | 2 lines

add precursor charge to the "-h" text output file

r7517 | dshteyn | 2017-03-08 14:51:25 -0800 (Wed, 08 Mar 2017) | 1 line

Separate -g from -DDEBUG for compiling.

r7518 | real_procopio | 2017-03-09 15:42:08 -0800 (Thu, 09 Mar 2017) | 1 line

Bump version to distingish current dev work from official 5.0.0 release

r7519 | real_procopio | 2017-03-10 16:58:20 -0800 (Fri, 10 Mar 2017) | 5 lines

[PepXMLViewer] - Fix tab-delimited export of ptm_peptide field: get rid of leading comma that showed up in certain conditions - Slightly compress and simplify ASAPRatio and XPRESS filters - Add more html labels to ASAP/XPRESS filter options

r7520 | real_procopio | 2017-03-10 17:01:27 -0800 (Fri, 10 Mar 2017) | 1 line

[subsetdb] Add option to specify line length for sequences (default=80, as per previous behavior)

r7521 | real_procopio | 2017-03-10 17:18:29 -0800 (Fri, 10 Mar 2017) | 1 line

[tpp_models & ploTPP] Add tool name to top nav bar, as per new design

r7522 | real_procopio | 2017-03-10 17:24:17 -0800 (Fri, 10 Mar 2017) | 4 lines

[Petunia] - Add tool name to top nav bar, as per new design - Add 'X' link to remove current filter - Added js check for 'alljobs' element before operating on it

r7523 | real_procopio | 2017-03-10 17:34:25 -0800 (Fri, 10 Mar 2017) | 4 lines

[ProtXMLViewer] - Add link to new sequence alignment and digestion tool: madcaps. Starting with indistinguishable protein entries; will expand later. - Add tool name to top nav bar, as per new design

r7524 | real_procopio | 2017-03-10 17:38:21 -0800 (Fri, 10 Mar 2017) | 1 line

[madcaps] New viz tool MADCAPS: Multiple Alignment, Digestion, Coverage, and Annotations of Protein Sequences

r7525 | real_procopio | 2017-03-10 17:47:46 -0800 (Fri, 10 Mar 2017) | 1 line

[clustal omega] Adding external alignment tool Clustal Omega; used by new MADCAPS viz tool

r7526 | real_procopio | 2017-03-13 12:19:13 -0700 (Mon, 13 Mar 2017) | 1 line

[make] Revert Makefile default values; also remove reduntant -lpthread linking (already included in BOOST_LDFLAGS)

r7527 | real_procopio | 2017-03-13 16:07:22 -0700 (Mon, 13 Mar 2017) | 6 lines

[PepXMLViewer] - Changed menu background color to better differentiate from data table; also added thicker borders - Changed extension to ".data" for exported values - Do not export empty values


r7528 | real_procopio | 2017-03-13 16:09:26 -0700 (Mon, 13 Mar 2017) | 1 line

Changed extension to '.data' for exported values; deal with empty data sets

r7529 | real_procopio | 2017-03-13 19:12:35 -0700 (Mon, 13 Mar 2017) | 1 line

[Petunia] Implement simple visualization of tsv files

r7530 | mhoopmann | 2017-03-14 14:47:44 -0700 (Tue, 14 Mar 2017) | 10 lines

Many accumulated updates, my apologies if I forget to mention any: 1. Better handle precursors, especially multiple precursors (MSX mode) 2. Updated MSNumpress 3. Improved parsing of predicted vs selected precursor ion m/z 4. Added selected ion window parsing 5. Improved reading of chromatograms from mzML 6. Additional header information reading from mzML 7. Minor code visualization updates


r7531 | mhoopmann | 2017-03-14 15:14:18 -0700 (Tue, 14 Mar 2017) | 3 lines

restoring an unused buffer that is apparently used outside mzParser.


r7532 | mhoopmann | 2017-03-14 15:37:34 -0700 (Tue, 14 Mar 2017) | 3 lines

Adding back some legacy functions for Tandem support.


r7533 | real_procopio | 2017-03-15 15:30:11 -0700 (Wed, 15 Mar 2017) | 5 lines

[Lorikeet] - Display the precursor isolation window (if available) - Updated to new TPP L&F


r7534 | real_procopio | 2017-03-20 13:21:12 -0700 (Mon, 20 Mar 2017) | 1 line

[Pep3D] Break down CIDs by charge state; updated to new L&F

r7535 | mhoopmann | 2017-03-22 15:42:41 -0700 (Wed, 22 Mar 2017) | 3 lines

Added ability to read and write protXML to mzid.


r7536 | mhoopmann | 2017-03-22 15:43:13 -0700 (Wed, 22 Mar 2017) | 3 lines

updating makefile for mzIMLTools


r7537 | mhoopmann | 2017-03-22 15:43:53 -0700 (Wed, 22 Mar 2017) | 3 lines

updating libraries make for mzIMLTools


r7538 | mhoopmann | 2017-03-23 17:18:15 -0700 (Thu, 23 Mar 2017) | 2 lines

Improved ProtXML parsing to handle differences between modified peptide sequence representation from iProphet and PeptideProphet.

r7539 | real_procopio | 2017-03-24 17:24:12 -0700 (Fri, 24 Mar 2017) | 13 lines

[madcaps] - Add c-terminal cutting enzymes to available digestion list - Make sure we grab only the wanted protein and not all that are superstrings of the accession - List up to 4 other proteins that non-unique peptides map to, with mouse-over highlighting - Move differentiable peptides column - Sort proteins and peptides within expanded input text area - Accept space-separated items in input - Clean up spaces before processing input options - Calculate masses of unmapped observed peptides - Minor style updates [ProtXMLViewer] - Add full group link from ProtXMLViewer to MADCAPS

r7540 | mhoopmann | 2017-03-27 16:11:24 -0700 (Mon, 27 Mar 2017) | 3 lines

making it F-F-F-FASTER!!!!!


r7541 | real_procopio | 2017-03-28 16:03:02 -0700 (Tue, 28 Mar 2017) | 1 line

[PepXMLViewer] Add link from MASSDIFF column to Unimod search with +/- 1 mass window; enable ions link to Lorikeet for SpectraST results

r7542 | real_procopio | 2017-03-28 16:07:35 -0700 (Tue, 28 Mar 2017) | 1 line

[ProtXMLViewer] Keep showing Protein Group headers when filtering only by probability

r7543 | real_procopio | 2017-03-28 16:09:02 -0700 (Tue, 28 Mar 2017) | 1 line

[MADCAPS] Re-work error handling so as to silence perl warnings when bad input is given

r7544 | dshteyn | 2017-04-03 10:07:06 -0700 (Mon, 03 Apr 2017) | 1 line

DISCO: Multi-thread hardklor, external hardklor parameters, clean-up code, run at blindingly fast speeds with multiple threads.

r7545 | dshteyn | 2017-04-03 10:20:59 -0700 (Mon, 03 Apr 2017) | 1 line

[DISCO]: DIAUmpire support improved with native format reading

r7546 | dshteyn | 2017-04-03 10:22:28 -0700 (Mon, 03 Apr 2017) | 1 line

[DISCO]: DIAUmpire support improved with native format reading

r7547 | dshteyn | 2017-04-03 15:00:35 -0700 (Mon, 03 Apr 2017) | 1 line

[DISCO] squash small bug

r7548 | real_procopio | 2017-04-04 16:07:11 -0700 (Tue, 04 Apr 2017) | 1 line

[html] Perform path replacement using sed instead of perl due to Windows build oddities

r7549 | real_procopio | 2017-04-04 18:04:32 -0700 (Tue, 04 Apr 2017) | 1 line

[Petunia] Add new Disco input: select Hardklor params; add support for editing said params; minor code clean-up

r7550 | real_procopio | 2017-04-05 17:49:08 -0700 (Wed, 05 Apr 2017) | 1 line

[plotspectrast] Fix path issue that resulted in a broken image link

r7551 | real_procopio | 2017-04-06 11:26:40 -0700 (Thu, 06 Apr 2017) | 1 line

[Pep3D & Lorikeet] Properly escape percent % within fprintf!

r7552 | real_procopio | 2017-04-06 12:51:28 -0700 (Thu, 06 Apr 2017) | 1 line

[Lib2HTML] Pass correct cgi url from Petunia; Remove unneeded text/html declaration; open spectra in separate window

r7553 | dshteyn | 2017-04-06 19:50:04 -0700 (Thu, 06 Apr 2017) | 1 line

[DISCO]: MS1 Peak integration for quantitation ... fix some memory issues for DIAUmp targets.

r7554 | real_procopio | 2017-04-06 20:18:10 -0700 (Thu, 06 Apr 2017) | 1 line

[PepXMLViewer] Support for new speclib search engine Calibr; also provide better error report when encountering bad modified peptide; clean-up html template

r7555 | real_procopio | 2017-04-06 20:22:05 -0700 (Thu, 06 Apr 2017) | 1 line

[PepXMLViewer] Fixing previous commit: provide better error report when encountering bad modified peptide

r7556 | real_procopio | 2017-04-07 17:47:41 -0700 (Fri, 07 Apr 2017) | 1 line

[make html] Break out text and image files -- the latter of which should not go through sed, as it potentially corrupts these files

r7557 | real_procopio | 2017-04-11 15:04:13 -0700 (Tue, 11 Apr 2017) | 1 line

[InteractParser] Do not attempt to correct start/end scan numbers and charge if already present in file (fixes instances where the index=NN within spectrumNativeID was being used, sometimes incorrectly, causing bad files to be produced); Only show "success" message if file and/or extension were actually corrected; Re-tabbed and some grammar corrections

r7558 | real_procopio | 2017-04-17 17:58:11 -0700 (Mon, 17 Apr 2017) | 9 lines

[madcaps] - Added "pre-aligned" option; skips clustalo step - Avoid repeated peptide sequences - Report error if any of the called executables fails - Clean up subsetdb output, since it may pick up extra proteins due to substring matching - Provide digestible sequence stats in coverage info - Hightlight label when checkbox is selected


r7559 | real_procopio | 2017-04-18 13:32:54 -0700 (Tue, 18 Apr 2017) | 9 lines

[MADCAPS] - Fixed word-wrapping for long protein accessions - Sort _UNMAPPED entries last [digestdb] - Allow long protein accessions (100 chars vs previous 50) [ProtXMLViewer] - Shorten link to MADCAPS by including each peptide sequence only once - Do not inlcude proteins filtered out by probability in Group link to MADCAPS

r7560 | real_procopio | 2017-04-18 19:48:02 -0700 (Tue, 18 Apr 2017) | 1 line

[ProtXMLViewer] Implemented command-line invocation, mostly suited for exporting .tsv and .data files. See usage statement for more info and instructions.

r7561 | dshteyn | 2017-04-19 10:16:52 -0700 (Wed, 19 Apr 2017) | 1 line

ProteoGrapher: Fix incorrect paths...add godef.json file

r7562 | dshteyn | 2017-04-19 12:11:30 -0700 (Wed, 19 Apr 2017) | 1 line

ProteoGrapher: fix JSON object loading error.

r7563 | eng_jk | 2017-04-19 13:38:00 -0700 (Wed, 19 Apr 2017) | 2 lines

make a couple of variables global otherwise crashes immediately under Windows

r7564 | real_procopio | 2017-04-20 15:58:08 -0700 (Thu, 20 Apr 2017) | 1 line

[ProtXMLViewer] Fix link to XPress CGI; clarify in headings that ratios are Heavy/Light

r7565 | real_procopio | 2017-04-20 16:04:22 -0700 (Thu, 20 Apr 2017) | 1 line

[tpplib_perl] When looking for tpp_hostname executable, first try under TPP_HOME/bin; Minor message text change

r7566 | real_procopio | 2017-04-24 18:23:28 -0700 (Mon, 24 Apr 2017) | 1 line

[MADCAPS] Use double quotes for protein match strings (single quotes were failing in Windows)

r7567 | dshteyn | 2017-04-27 12:08:44 -0700 (Thu, 27 Apr 2017) | 1 line

NEW FEATURE: Allow to compare proteins based on precursor intensities

r7568 | dshteyn | 2017-04-27 12:10:58 -0700 (Thu, 27 Apr 2017) | 1 line

NEW FEATURE: Allow to compare proteins based on precursor intensities

r7569 | dshteyn | 2017-04-27 12:13:31 -0700 (Thu, 27 Apr 2017) | 1 line

DISCO: BUGFIX issues preventing DISCO from running to completion in certain edge cases...

r7570 | dshteyn | 2017-04-27 12:16:39 -0700 (Thu, 27 Apr 2017) | 1 line

NEW FEATURES: RTCatalog PEPSBYRUN= file to match peptide to appropriate run for reporting in RTCatalog. MINPTMPROB= use minimum PTMProphet probability for reporting peptides.

r7571 | dshteyn | 2017-04-27 12:18:16 -0700 (Thu, 27 Apr 2017) | 1 line

define another hashmap type

r7572 | dshteyn | 2017-04-27 12:19:06 -0700 (Thu, 27 Apr 2017) | 1 line

typo fix

r7573 | real_procopio | 2017-04-28 09:30:36 -0700 (Fri, 28 Apr 2017) | 1 line

[PepXMLViewer] Plug memory leaks

r7574 | dshteyn | 2017-05-01 11:27:46 -0700 (Mon, 01 May 2017) | 1 line

PeptideProphetParser: MASSWIDTH= option for open mass searches, ProteinProphet: MAXPPMDIFF option for open mass searches. PTMProphetParser: EM iteration convergence testing was flawed. DiscoFilter: tuning parameters.

r7575 | real_procopio | 2017-05-01 14:31:00 -0700 (Mon, 01 May 2017) | 4 lines

[ASAPRatioPValue] - Fix numerous memory leaks and other errors - Remove unused variables and code - Remove obsolete Cygwin-specific code

r7576 | dshteyn | 2017-05-02 07:44:08 -0700 (Tue, 02 May 2017) | 1 line

New member variable for setting masswidth of mass model.

r7577 | dshteyn | 2017-05-02 16:18:33 -0700 (Tue, 02 May 2017) | 1 line

PepXMLViewer.cgi: allow to filter based on massdiff

r7578 | dshteyn | 2017-05-02 19:59:22 -0700 (Tue, 02 May 2017) | 1 line

plotpp.pl: flexible binning in the histogram controlled by url variable.

r7579 | dshteyn | 2017-05-02 19:59:49 -0700 (Tue, 02 May 2017) | 1 line

plotpp.pl: flexible binning in the histogram controlled by url variable.

r7580 | dshteyn | 2017-05-02 20:00:29 -0700 (Tue, 02 May 2017) | 1 line

Adjust Makefile rules...

r7581 | dshteyn | 2017-05-04 14:26:31 -0700 (Thu, 04 May 2017) | 1 line

Fix uninitialized variable....was creating a major memory issue when compiled with optimization under gcc 4.4.7

r7582 | real_procopio | 2017-05-08 12:50:49 -0700 (Mon, 08 May 2017) | 4 lines

[ASAPRatioProteinRatio] - Fix numerous memory leaks and other errors - Remove unused variables and code

r7583 | real_procopio | 2017-05-08 12:56:19 -0700 (Mon, 08 May 2017) | 1 line

Taking back unintended commit of Makefile

r7584 | dshteyn | 2017-05-12 11:26:10 -0700 (Fri, 12 May 2017) | 1 line

DISCO: relax requirements for having isolation window offset parameters whihich are absent if current ABSciex mzML files.

r7585 | real_procopio | 2017-05-15 15:58:48 -0700 (Mon, 15 May 2017) | 1 line

[LibraProtein] Fix numerous memory leaks and other errors, including one that consistently reported incorrect results in the exported tsv file

r7586 | dshteyn | 2017-05-16 14:58:43 -0700 (Tue, 16 May 2017) | 1 line

ProteinProphet: Don't report pct_intensity when unavailable...

r7587 | real_procopio | 2017-05-16 15:34:19 -0700 (Tue, 16 May 2017) | 12 lines

[plot-msms / Lorikeet] - New optional feature: shade precursor selection window in MS1 scan - New feature to label neutral losses of the (unfragmented) precursor peak - Added C-linked hexose as a detectable custom neutral loss - New feature to allow and label more than one neutral loss on any fragment (still working on making this work for the precursor) Miscellaneous code enhancements: - free pointer instead of deleting it - Added ";" to the end of a few lines that were missing it (specview.js) - Fixed calculation of PhosphoLossMass_avg (ion.js) - Unix line endings - Commented out console debugging string (jquery.flot.js)

r7588 | real_procopio | 2017-05-17 13:50:23 -0700 (Wed, 17 May 2017) | 1 line

[ploTPP] Remove unnecessary json attribute that introduced a bug when displaying scatterplots. Clean up previous check-in.

r7589 | real_procopio | 2017-05-19 17:34:07 -0700 (Fri, 19 May 2017) | 1 line

[ProphetModels/Petunia] It was decided to call it a "decoy rate" instead of a ratio. Pre-check NEGGAMMA when Pipeline=XTandem. Clean up messy code that mangled form labels from previous check-in...

r7590 | real_procopio | 2017-05-19 18:00:55 -0700 (Fri, 19 May 2017) | 1 line

[Kojak] Updating to v1.5.5

r7591 | real_procopio | 2017-05-23 19:05:53 -0700 (Tue, 23 May 2017) | 1 line

[mzParser] Initialize scanHeader.scanType

r7592 | real_procopio | 2017-05-23 19:11:55 -0700 (Tue, 23 May 2017) | 5 lines

[Pep3D] - Tweaks to match current TPP L&F (html title and header) - Fixed memory leaks and related code errors - Code clean-up

r7593 | real_procopio | 2017-05-26 16:37:07 -0700 (Fri, 26 May 2017) | 1 line

[plot-msms] Added CH3SOH loss from Met[ox]; Make error messages match current L&F

r7594 | real_procopio | 2017-05-30 16:12:05 -0700 (Tue, 30 May 2017) | 1 line

[comet] New version 2016.01.3

r7595 | real_procopio | 2017-05-31 11:53:12 -0700 (Wed, 31 May 2017) | 1 line

[comet] Updating zip file structure, since distributed file for latest version is different than previous ones

r7596 | dshteyn | 2017-06-02 14:36:35 -0700 (Fri, 02 Jun 2017) | 1 line

reSpect: fix problem with neutral losses ... also MININTMODE

r7597 | dshteyn | 2017-06-02 14:38:52 -0700 (Fri, 02 Jun 2017) | 1 line

ProteinProphet: set maxppmdiff default value to 1e6 to keep original behavior after adding this parameter.

r7598 | eng_jk | 2017-06-13 14:39:10 -0700 (Tue, 13 Jun 2017) | 2 lines

update packages required for centos TPP5 install

r7599 | eng_jk | 2017-06-14 14:09:28 -0700 (Wed, 14 Jun 2017) | 2 lines

fix RAMPface.cpp so that mzML precursor m/z values aren't all reported as 0.0

r7600 | real_procopio | 2017-06-16 13:33:48 -0700 (Fri, 16 Jun 2017) | 1 line

[tpp_hashmap] Store this with Linux line endings, not Windows!

r7601 | real_procopio | 2017-06-16 13:36:22 -0700 (Fri, 16 Jun 2017) | 1 line

[Enzymes] Delete elements properly to avoid potential memory issues

r7602 | real_procopio | 2017-06-16 13:40:34 -0700 (Fri, 16 Jun 2017) | 1 line

[mzParser] Only attempt to open a file if there is an actual filename, which avoids potential memory errors. Also, include file name in error when unable to open

r7603 | real_procopio | 2017-06-16 13:46:36 -0700 (Fri, 16 Jun 2017) | 1 line

[Tandem2XML] Fix some error leaks; some code reformatting and clean-up

r7604 | real_procopio | 2017-06-19 15:04:30 -0700 (Mon, 19 Jun 2017) | 1 line

[common] Strip leading and trailing spaces from user-specified build settings, as they may cause errors

r7605 | dshteyn | 2017-06-23 16:07:32 -0700 (Fri, 23 Jun 2017) | 1 line

DISCO: fix some crashes and use proper o: character in Hardklo:r

r7606 | dshteyn | 2017-07-28 15:03:02 -0700 (Fri, 28 Jul 2017) | 1 line

PTMProphet: fix bug associated with reporting peptides with a terminal mod. Change pepXML reporting of terminal probabilities to new scheme planned with Luis.

r7607 | real_procopio | 2017-07-28 15:27:33 -0700 (Fri, 28 Jul 2017) | 1 line

[PepXMLViewer] Handle and display terminal mods and probabilities from PTMProphet as per the updated schema

r7608 | dshteyn | 2017-08-09 11:57:29 -0700 (Wed, 09 Aug 2017) | 1 line

Spectrast: OpenMod search, allow the tolerance to be specified and passed to allow mass differences bigger than 300 amu.

r7609 | dshteyn | 2017-08-09 11:59:06 -0700 (Wed, 09 Aug 2017) | 1 line

Support for search engine SIPROS.

r7610 | dshteyn | 2017-08-09 12:00:15 -0700 (Wed, 09 Aug 2017) | 1 line

Support for search engine SIPROS.

r7611 | dshteyn | 2017-08-09 12:02:49 -0700 (Wed, 09 Aug 2017) | 1 line

Support for search engine SIPROS.

r7612 | dshteyn | 2017-08-09 12:15:05 -0700 (Wed, 09 Aug 2017) | 1 line

Support for search engine SIPROS.

r7613 | dshteyn | 2017-08-09 12:31:23 -0700 (Wed, 09 Aug 2017) | 1 line

PDLStats: perl interface to gsl for statistics.

r7614 | dshteyn | 2017-08-10 08:43:46 -0700 (Thu, 10 Aug 2017) | 1 line

Don't build pdlstats for now.

r7615 | eng_jk | 2017-08-10 14:43:18 -0700 (Thu, 10 Aug 2017) | 2 lines

Add long overdue support for isotope peaks to XPRESS cgi. When C13 isotope peaks are used in the quantitation, the cgi XPressPeptideUpdateParser.cgi is now aware of them and will display the same ratio,taking into account the data in the C13 isotope peaks.

r7616 | real_procopio | 2017-08-15 12:06:13 -0700 (Tue, 15 Aug 2017) | 1 line

[PepXMLViewer] Added support for PEFF modifications and substitutions; also fixed modified peptide display (for n-terminus)

r7617 | real_procopio | 2017-08-16 14:12:28 -0700 (Wed, 16 Aug 2017) | 1 line

[PDLStats] Remove install directive breaking the nightly build

r7618 | dshteyn | 2017-08-18 16:47:50 -0700 (Fri, 18 Aug 2017) | 1 line

RTCalculator: correct header comment, don't print the peptide by peptide rt info in non-verbose mode.

r7619 | dshteyn | 2017-08-18 16:54:00 -0700 (Fri, 18 Aug 2017) | 1 line

PeptideProphet: correctly name RT Mixture Model...

r7620 | dshteyn | 2017-08-18 16:57:17 -0700 (Fri, 18 Aug 2017) | 1 line

DiscoFilter: change the way isolation windows are specified (now requires flag WINDOWS=<file>), use HardKlor to ID unfragged MS1 precursor features for DISCO extraction.

r7621 | dshteyn | 2017-08-21 07:47:57 -0700 (Mon, 21 Aug 2017) | 1 line

Hardklor Changes for DISCO MS1 and MS2 feature extraction.

r7622 | dshteyn | 2017-08-21 07:49:03 -0700 (Mon, 21 Aug 2017) | 1 line

MSToolkit Build: Turn on optimization when not being compiled for debugging...

r7623 | real_procopio | 2017-08-21 14:18:10 -0700 (Mon, 21 Aug 2017) | 1 line

[Petunia] Update for new Disco command invocation

r7624 | real_procopio | 2017-08-24 15:03:58 -0700 (Thu, 24 Aug 2017) | 1 line

Name release 5.1, release candidate 1

r7625 | eng_jk | 2017-09-06 13:27:15 -0700 (Wed, 06 Sep 2017) | 2 lines

Per bug report by Oded Kleifeld in spctools-discuss, terminal mods were not handled correctly. Turns out issue was a string comparison for 'n' and 'c' terminal specification being compared against 'N' and 'C' terminus attribute in the terminal_modification element. Correcting this case comparison issue seems to solve the reported problem.

r7626 | eng_jk | 2017-09-13 09:59:55 -0700 (Wed, 13 Sep 2017) | 2 lines

Streamline XPRESS isotopic labeling support. XPRESS will now automatically determine if peptide is C13 or N15 light/heavy labeled based on modification state of peptide.

r7627 | dshteyn | 2017-09-17 17:30:13 -0700 (Sun, 17 Sep 2017) | 1 line

PTMProphet: Fix tripping over windows full paths.

r7628 | dshteyn | 2017-10-02 10:57:44 -0700 (Mon, 02 Oct 2017) | 1 line

BUGFIX: correct issues with massdiffmode and unknown modifications (e.g. incorrectly reported n-terminal acetylation)

r7629 | dshteyn | 2017-10-02 11:01:52 -0700 (Mon, 02 Oct 2017) | 1 line

Update the User Specified Mod with new mass.

r7630 | dshteyn | 2017-10-02 14:52:21 -0700 (Mon, 02 Oct 2017) | 1 line

mzParser: use the byte offset index to access the header info more quickly...

r7631 | dshteyn | 2017-10-02 14:53:10 -0700 (Mon, 02 Oct 2017) | 1 line

InteractParser/mzParser: use the byte offset index to access the header info more quickly...

r7632 | real_procopio | 2017-10-10 17:44:14 -0700 (Tue, 10 Oct 2017) | 1 line

[fetchDataset] Add utility to download and unpack public proteomics datasets

r7633 | real_procopio | 2017-10-10 17:46:52 -0700 (Tue, 10 Oct 2017) | 1 line

[comet] Update to newest version: 2017-01-0

r7634 | real_procopio | 2017-10-10 17:48:46 -0700 (Tue, 10 Oct 2017) | 1 line

[xinteract] Update usage statement for XPRESS metabolic labeling

r7635 | real_procopio | 2017-10-10 17:53:20 -0700 (Tue, 10 Oct 2017) | 1 line

[fetchDataset] Add utility to download and unpack public proteomics datasets

r7636 | real_procopio | 2017-10-10 18:07:07 -0700 (Tue, 10 Oct 2017) | 4 lines

[Petunia] - Added page for new fetchDataset tool; also added ability to query tool version and abilities, as well as link to auto-update - Minor rearrangement of XPRESS interface: clarify metabolic options; add two more potential modified residues for a total of five

r7637 | real_procopio | 2017-10-17 13:39:00 -0700 (Tue, 17 Oct 2017) | 1 line

[Petunia] Add link to show fetchDataset version and info after updating. Other minor text and loop changes

r7638 | real_procopio | 2017-10-17 13:42:02 -0700 (Tue, 17 Oct 2017) | 1 line

[fetchDataset] Update to v0.7.4: keep shebang line when updating; assume all zip files are bdbags; include MD5 module for expected hash check

r7639 | real_procopio | 2017-10-17 13:43:11 -0700 (Tue, 17 Oct 2017) | 1 line

[version] Spell Syzygy properly; increment to rc2

r7640 | real_procopio | 2017-10-18 18:20:01 -0700 (Wed, 18 Oct 2017) | 1 line

[Windows installer] Do not auto-install/run tpptray; add link to TPP log files from Programs menu

r7641 | dshteyn | 2017-10-23 14:31:06 -0700 (Mon, 23 Oct 2017) | 1 line

iProphet: fix a bug with small sized runs.

r7642 | real_procopio | 2017-10-24 16:32:11 -0700 (Tue, 24 Oct 2017) | 1 line

[madcaps] Add link to Uniprot for "sp|xxxx|" entries; Use correct specificity for chymotrypsin; Turn off CGI::LIST_CONTEXT_WARN

r7643 | real_procopio | 2017-10-24 16:35:32 -0700 (Tue, 24 Oct 2017) | 1 line

[enzymes] Fix chymotrypsin specificity (which was clobbered by commit r6497), and harmonize across various tools; Remove obsolete code

r7644 | real_procopio | 2017-10-24 17:14:02 -0700 (Tue, 24 Oct 2017) | 1 line

[comet] Update to 2017-01-1, which contains important bug fixes

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