From SPCTools
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r7671 | real_procopio | 2017-11-03 16:21:35 -0700 (Fri, 03 Nov 2017) | 1 line
[comet] Delete previous versions
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r7672 | real_procopio | 2017-11-06 15:02:29 -0800 (Mon, 06 Nov 2017) | 1 line
Removing obsolete/unused cgis and references to them (mostly old protXML viewer helpers)
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r7673 | real_procopio | 2017-11-06 15:53:29 -0800 (Mon, 06 Nov 2017) | 1 line
[pepXMLViewer] Freshen up the help page to reflect current state of viewer, and clean up grammar/spelling. More work needed...
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r7674 | real_procopio | 2017-11-07 17:40:03 -0800 (Tue, 07 Nov 2017) | 7 lines
[ProtXMLViewer]
- Attempt to guess organism from Uniprot annotations (OS=xxx yyy)
- Give breakdown of number of entries, single hits, spectra, etc by organism
- Update Gaggle format for export to Firegoose/Chrome Goose (if they ever work fully again...)
- Reduced size of font for entry id
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r7675 | mhoopmann | 2017-11-09 13:51:14 -0800 (Thu, 09 Nov 2017) | 3 lines
Changed how modifications are tracked and handled. No longer requires lookup table to reconcile differences in search parameters and pepXML output when representing peptide sequences. Some potential issues likely remain when reading pepXML from msgfplus with n-terminus modifications.
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r7676 | eng_jk | 2017-11-09 14:26:18 -0800 (Thu, 09 Nov 2017) | 2 lines
fix parsing non-matching strings into correct variable
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r7677 | dshteyn | 2017-11-15 11:11:44 -0800 (Wed, 15 Nov 2017) | 1 line
New features in PTMProphet
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r7678 | dshteyn | 2017-11-17 17:53:53 -0800 (Fri, 17 Nov 2017) | 1 line
PTMProphet: multi-threading
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r7679 | real_procopio | 2017-11-20 12:43:42 -0800 (Mon, 20 Nov 2017) | 1 line
[Prospector] Adding support for ProteinProspector
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r7680 | real_procopio | 2017-11-20 12:53:54 -0800 (Mon, 20 Nov 2017) | 1 line
[general] Removing old unused PeptideProphetMain (dates from we only supported SEQUEST and MASCOT); also remove similar old unused code from MixtureModel
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r7681 | real_procopio | 2017-11-21 10:44:55 -0800 (Tue, 21 Nov 2017) | 1 line
[XPRESS] Bugfixes: fix logic for actually reporting intensity-based ratios when using -H or -L options; fix typo in heavy_intensity_scan tag name
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r7682 | real_procopio | 2017-11-21 10:54:36 -0800 (Tue, 21 Nov 2017) | 1 line
[PepXMLViewer] Added (and fixed) support for XPRESS fields: light_area, heavy_area, light_intensity, heavy_intensity, intensity_ratio
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r7683 | real_procopio | 2017-11-21 11:00:00 -0800 (Tue, 21 Nov 2017) | 1 line
[Petunia] Added support for reporting intensity-based ratios in XPRESS
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r7684 | dshteyn | 2017-11-22 12:37:26 -0800 (Wed, 22 Nov 2017) | 1 line
ProteinProphet: compute exact error rates based on existing probabilities of all proteins, rather than applying artibtrary minimum probability thresholds, at request of Kristian for use with StPeter.
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r7685 | dshteyn | 2017-11-22 12:39:05 -0800 (Wed, 22 Nov 2017) | 1 line
PTMProphet: synchronize opening the file with cramp
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r7686 | dshteyn | 2017-11-23 10:19:25 -0800 (Thu, 23 Nov 2017) | 1 line
PTMProphet: improvements for faster execution for single and multi-threading.
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r7687 | dshteyn | 2017-11-24 09:10:43 -0800 (Fri, 24 Nov 2017) | 1 line
PTMProphet: fix compilation error ...
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r7688 | dshteyn | 2017-11-27 15:53:02 -0800 (Mon, 27 Nov 2017) | 1 line
mzParser: fix bug associated with reading scan headers using the scan index, for files that are filtered for a subset of scans. Throw error and revert to linear lookup when the index doesn't access the requested scan number.
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r7689 | dshteyn | 2017-11-27 15:55:48 -0800 (Mon, 27 Nov 2017) | 1 line
InteractParser: fix bug reported by Kristian on filtered mzML files. Append file extension to the data file path.
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r7690 | real_procopio | 2017-11-27 18:02:05 -0800 (Mon, 27 Nov 2017) | 1 line
[PepXMLViewer] Report number of *_UNMAPPED protein entries, when present, and disable links to sequence viewer from such entries; Display list of search engines when viewing iProphet results
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r7691 | real_procopio | 2017-11-29 12:58:08 -0800 (Wed, 29 Nov 2017) | 6 lines
[updatepaths]
- Ensure new directory is an absolute path
- Make sure we are updating the desired attribute's value (and not some other matching string within the tag)
- Perform extension-free check only if original file name is not found (fixes case when pepXML reference files within a protXML file got mismapped like so: interact.pep.xml --> interact.prot.xml)
- Remove duplicated documentation
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r7692 | real_procopio | 2017-11-29 13:21:08 -0800 (Wed, 29 Nov 2017) | 1 line
[RefreshParser] Report number of _UNMAPPED entries
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r7693 | real_procopio | 2017-11-29 18:22:04 -0800 (Wed, 29 Nov 2017) | 1 line
[InteractParser] Apply -C (correct charge states) automatically for OMSSA files (as per usage statement!); clean up usage statement and enzyme display, as well as some unused code
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r7694 | dshteyn | 2017-11-30 10:00:40 -0800 (Thu, 30 Nov 2017) | 1 line
PTMProphet: fix bug of skipping some pepXML tags in multithreaded execution.
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r7695 | real_procopio | 2017-11-30 16:04:20 -0800 (Thu, 30 Nov 2017) | 1 line
Delete old, corrupted (unreadable) file
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r7696 | real_procopio | 2017-11-30 18:18:11 -0800 (Thu, 30 Nov 2017) | 1 line
[subsetdb] Bump buffer to 500k bytes to accommodate super long PEFF description lines (longest so far observed is 210k chars!)
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r7697 | real_procopio | 2017-11-30 19:46:32 -0800 (Thu, 30 Nov 2017) | 6 lines
[madcaps]
- Use case-sensitive option (-C) when calling subsetdb for faster performance (>100x faster with PEFF files!)
- Bolden keywords (KEY=) in protein annotations
- Provide direct link to neXtProt proteomics page for "nxp:NX_" entries
- Adjust width and alignment of sequence zoom window
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r7698 | dshteyn | 2017-12-01 16:33:13 -0800 (Fri, 01 Dec 2017) | 1 line
PTMProphet bug fixes associated with check in of newest features.
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r7699 | real_procopio | 2017-12-01 17:39:18 -0800 (Fri, 01 Dec 2017) | 1 line
[subsetdb] For case-insensitive searches, only apply toupper() to chars in the range a-z - this boosts performace by an order+ of magnitude when processing PEFF databases; remove unused SUBSET_SIZE define
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r7700 | real_procopio | 2017-12-01 18:47:47 -0800 (Fri, 01 Dec 2017) | 1 line
[PTMProphet] Report processing progress in one line (overwriting itself), instead of creating a new one each time, to save space on output. It can get funky with multiple threads, so a threadsafe cleanup might be desired
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r7701 | dshteyn | 2017-12-04 11:18:35 -0800 (Mon, 04 Dec 2017) | 1 line
ProteinProphet: expand isotopic offsets considered for mass diff to -1,0,1,2,3 per Alexey request for Open Mass Searching (e.g MSFragger).
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r7702 | real_procopio | 2017-12-14 11:45:25 -0800 (Thu, 14 Dec 2017) | 1 line
[ramp] Also delete scan headers cache when "closing" file
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r7703 | dshteyn | 2017-12-15 10:24:44 -0800 (Fri, 15 Dec 2017) | 1 line
PTMProphet: BUGFIX neutral losses were not being picked up from the commandline nor utilized correctly; FEATURE auto enable DIRECT mode under specific conditions.
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r7704 | dshteyn | 2017-12-15 11:13:42 -0800 (Fri, 15 Dec 2017) | 1 line
DISCO: report number of precursors being tracked. Improve code for tracking the precursors near their local peak maxima to improve efficiency.
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r7705 | real_procopio | 2017-12-15 13:43:12 -0800 (Fri, 15 Dec 2017) | 9 lines
[XPRESS]
- Implement calculation of protein ratios based on peptide peak intensities (new -i option in XPressProteinRatioParser)
- Added new "ratio_basis" attribute to protXML (possible values are "area" and "intensity")
- Added usage statement to XPressProteinRatioParser
- Establish a floor (0.001) and ceiling (999.0) for intensity-based peptide ratios (as is done for area-based ratios). Also report "-1" when no ratio can be calculated.
- Remove unsused -C option from XPressPeptideParser usage statement (and minor clean-up)
- Fix various memory leaks and minor code clean-up
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r7706 | real_procopio | 2017-12-15 14:05:00 -0800 (Fri, 15 Dec 2017) | 7 lines
[PepXMLViewer]
- Added support for XPRESS label-free analysis; new fields are:
peak_area (default), first_scan, last_scan, peak_intensity, peak_intensity_scan
- Implement background color gradient for intensity-based XPRESS ratios
- Minor code simplification for better performance
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r7707 | real_procopio | 2017-12-15 14:14:08 -0800 (Fri, 15 Dec 2017) | 1 line
[tpp_models] Added support for XPRESS label-free analysis parameters
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r7708 | real_procopio | 2017-12-15 14:20:05 -0800 (Fri, 15 Dec 2017) | 1 line
[Petunia] Added option to run XPRESS label-free analysis; re-arranged XPRESS options for more logical/visual flow
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r7709 | real_procopio | 2017-12-15 14:24:08 -0800 (Fri, 15 Dec 2017) | 1 line
[ProtXMLViewer] Added label when viewing intensity-based ratios from XPRESS
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r7710 | real_procopio | 2017-12-15 15:01:29 -0800 (Fri, 15 Dec 2017) | 6 lines
[ProteinProphet]
- Implement XPRESS_INT parameter to run XPressProteinRatioParser with new -i option
- Don't report raw_intensity when unavailable
- Partial fixes for memory leaks, some code clean-up
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r7711 | real_procopio | 2017-12-15 15:07:52 -0800 (Fri, 15 Dec 2017) | 1 line
[xinteract] Change meaning of -Ot option; it now will pass PLOTPNG option to ProteinProphet (replacing long-vacated NOPLOT option)
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r7712 | real_procopio | 2017-12-15 17:47:09 -0800 (Fri, 15 Dec 2017) | 1 line
[batchcoverage] Fix memory leaks, clean up code
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r7713 | eng_jk | 2017-12-19 15:50:20 -0800 (Tue, 19 Dec 2017) | 2 lines
set default number of isotope peaks (-p) to "1" as stated in xinteract usage statement
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r7714 | real_procopio | 2017-12-19 16:16:03 -0800 (Tue, 19 Dec 2017) | 1 line
[InteractParser] Fix bug that mangled spectrum names from files that contain a dot in their names; also fixed bad logic (from r6329) that prevented fallback capture of scans and charge from spectrum names; and while we're at it, plug various memory leaks
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r7715 | real_procopio | 2017-12-19 18:59:14 -0800 (Tue, 19 Dec 2017) | 1 line
[cygwin] Remove all references to cygpath -- the first of several steps to remove long-unmaintained and deprecated cygwin code
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r7716 | real_procopio | 2017-12-20 11:32:08 -0800 (Wed, 20 Dec 2017) | 1 line
[cygwin] Remove all references to WINDOWS_CYGWIN -- the second of several steps to remove long-unmaintained and deprecated cygwin code
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r7717 | mhoopmann | 2017-12-20 15:04:57 -0800 (Wed, 20 Dec 2017) | 2 lines
Cosmetic changes to verbage during use. Removed exporting of non-normalized results and removed unintended creation of text files used during testing.
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r7718 | real_procopio | 2017-12-20 15:48:17 -0800 (Wed, 20 Dec 2017) | 1 line
[Petunia] Remove StPeter option for exporting non-normalized results
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r7719 | dshteyn | 2017-12-25 23:40:00 -0800 (Mon, 25 Dec 2017) | 1 line
Correcting windows compilation problems...
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r7720 | dshteyn | 2017-12-26 10:18:38 -0800 (Tue, 26 Dec 2017) | 1 line
Fix mingw compilation issue of tandem.
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r7721 | dshteyn | 2017-12-26 11:14:04 -0800 (Tue, 26 Dec 2017) | 1 line
Enable SIMD in tandem code to compile under MINGW gcc
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r7722 | mhoopmann | 2017-12-27 11:02:11 -0800 (Wed, 27 Dec 2017) | 3 lines
Fixed bug that skipped n-terminally modified peptides. And very minor other bits of code cleaning.
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r7723 | mhoopmann | 2017-12-27 11:28:50 -0800 (Wed, 27 Dec 2017) | 2 lines
Adding alternative enzyme names and fixing incorrect expression for TrypChymo
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r7724 | mhoopmann | 2018-01-16 15:34:39 -0800 (Tue, 16 Jan 2018) | 3 lines
[STPETER]: Use natural log fragment ion peak values.
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r7725 | dshteyn | 2018-02-27 11:24:45 -0800 (Tue, 27 Feb 2018) | 1 line
DISCO: streamline parallel execution, fix file output of intermediate results on Windows, remove RT in secs correction factor, upgrade threading to use c++11 standard library
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r7726 | dshteyn | 2018-02-27 14:33:33 -0800 (Tue, 27 Feb 2018) | 1 line
Makefile: enable -std=c++11 for sufficiently high versions of gcc
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r7727 | dshteyn | 2018-02-27 15:32:05 -0800 (Tue, 27 Feb 2018) | 1 line
MzXML2Search: take advantage of the index to faster read spectrum headers with mzParser.
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r7728 | dshteyn | 2018-02-27 15:36:11 -0800 (Tue, 27 Feb 2018) | 1 line
RTCatalog: Allow for negative RT values as some iRTs can be negative, use unsigned long instead of ints for larger datasets.
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r7729 | dshteyn | 2018-02-27 15:38:55 -0800 (Tue, 27 Feb 2018) | 1 line
Mascot2XML: more descriptive warning messages for poorly formatted Mascot results, and allow conversion to proceed after reporting the issues.
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r7730 | dshteyn | 2018-02-27 15:45:36 -0800 (Tue, 27 Feb 2018) | 1 line
Tandem2XML: new options in Tandem2XML to allow it to work with newer versions of tandem and format spectrum names for TPP according t TPP conventions.
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r7731 | dshteyn | 2018-02-27 15:50:44 -0800 (Tue, 27 Feb 2018) | 1 line
RTCatalog: prevent overwriting existing files.
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r7732 | dshteyn | 2018-02-27 17:49:58 -0800 (Tue, 27 Feb 2018) | 1 line
Tag.h: including system types header.
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r7733 | dshteyn | 2018-02-27 18:42:00 -0800 (Tue, 27 Feb 2018) | 1 line
ShowXIC.cgi: user settable MAXPPM error tolerance.
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r7734 | dshteyn | 2018-02-27 18:46:52 -0800 (Tue, 27 Feb 2018) | 1 line
InteractParser: report TIC and S2N in pepXML
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r7735 | dshteyn | 2018-02-27 18:48:19 -0800 (Tue, 27 Feb 2018) | 1 line
Spectrum Viewer: faster reading of spectra by use of index
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r7736 | dshteyn | 2018-02-27 18:49:58 -0800 (Tue, 27 Feb 2018) | 1 line
PepXMLViewer: plot histograms with 1000 bins by default.
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r7737 | dshteyn | 2018-02-27 18:53:27 -0800 (Tue, 27 Feb 2018) | 1 line
InteractParser: compile with gsl for stats.
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r7738 | dshteyn | 2018-02-27 18:55:50 -0800 (Tue, 27 Feb 2018) | 1 line
SpectraST: New function for returning the nearest peak to a given mz value in a spectrum; default constructor for Peptide
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r7739 | dshteyn | 2018-02-27 19:04:10 -0800 (Tue, 27 Feb 2018) | 1 line
PTMProphet: use the max of user set mz tolerance and PSM massdiff to localize
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r7740 | dshteyn | 2018-02-27 19:07:31 -0800 (Tue, 27 Feb 2018) | 1 line
PeptideProphet: tell Mascot user which scores are missing
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r7741 | dshteyn | 2018-02-27 19:15:19 -0800 (Tue, 27 Feb 2018) | 1 line
PeptideProphet: SpectraST modeling correct errors in initial settings.
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r7742 | dshteyn | 2018-02-27 19:19:41 -0800 (Tue, 27 Feb 2018) | 1 line
iProphet: make use of spectrum_label when available.
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r7743 | dshteyn | 2018-02-27 19:22:47 -0800 (Tue, 27 Feb 2018) | 1 line
reSpect: when multiple spectra of the same scan number are in the same analysis, only process the highest probability PSM
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r7744 | dshteyn | 2018-02-27 19:36:28 -0800 (Tue, 27 Feb 2018) | 1 line
HardKlor: allow modeling of intesities less than 1
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r7745 | dshteyn | 2018-02-27 19:40:20 -0800 (Tue, 27 Feb 2018) | 1 line
ProteoWizard: set centroid CV term
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r7746 | dshteyn | 2018-02-28 17:07:41 -0800 (Wed, 28 Feb 2018) | 1 line
changes to compile on RedHat OS7 gcc 4.8.2
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r7747 | dshteyn | 2018-02-28 17:36:16 -0800 (Wed, 28 Feb 2018) | 1 line
changes to compile on RedHat OS7 gcc 4.8.2
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r7748 | dshteyn | 2018-02-28 17:38:11 -0800 (Wed, 28 Feb 2018) | 1 line
changes to compile on RedHat OS7 gcc 4.8.2
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r7749 | dshteyn | 2018-03-01 09:01:35 -0800 (Thu, 01 Mar 2018) | 1 line
changes to compile on RedHat OS7 gcc 4.8.2
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r7750 | dshteyn | 2018-03-05 10:00:34 -0800 (Mon, 05 Mar 2018) | 1 line
Use std::isnan to allow pwiz to compile.
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r7751 | dshteyn | 2018-03-05 11:02:07 -0800 (Mon, 05 Mar 2018) | 1 line
including <cmath> to address isnan compiling issues
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r7752 | real_procopio | 2018-03-09 16:12:42 -0800 (Fri, 09 Mar 2018) | 1 line
[tpp_models] Capture and display Phospho models, when available
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r7753 | dshteyn | 2018-03-14 09:17:30 -0700 (Wed, 14 Mar 2018) | 1 line
Adding back protovis which is utilized in RTCatalog for drawing RT gradient corrections page...
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r7754 | dshteyn | 2018-03-14 10:19:25 -0700 (Wed, 14 Mar 2018) | 1 line
RTCatalog: new option DISCO to allow building catalog from DISCO/DIAUmpire results.
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r7755 | dshteyn | 2018-03-14 17:15:38 -0700 (Wed, 14 Mar 2018) | 1 line
Upgrading PWIZ ...
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r7756 | dshteyn | 2018-03-14 23:30:00 -0700 (Wed, 14 Mar 2018) | 1 line
Upgrading PWIZ ...
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r7757 | dshteyn | 2018-03-15 09:39:39 -0700 (Thu, 15 Mar 2018) | 1 line
Upgrading PWIZ ...
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r7758 | dshteyn | 2018-03-15 10:16:42 -0700 (Thu, 15 Mar 2018) | 1 line
Upgrading PWIZ ...
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r7759 | dshteyn | 2018-03-15 14:02:47 -0700 (Thu, 15 Mar 2018) | 1 line
Updating PWIZ ...
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r7760 | mhoopmann | 2018-03-15 14:10:28 -0700 (Thu, 15 Mar 2018) | 3 lines
[mzIMLTools]: fixed bug when copying a string. (old commit finally let through now that sourceforge is working again).
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r7761 | dshteyn | 2018-03-19 09:55:29 -0700 (Mon, 19 Mar 2018) | 1 line
Fix problem with windows build not copying the pwiz msi to the staging area ...
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r7762 | real_procopio | 2018-03-21 12:22:41 -0700 (Wed, 21 Mar 2018) | 1 line
[indexmzXML] New wrapper to run indexer, which renames .new file (if generated). Have Petunia call this instead of running the executable directly to avoid mis-communication to user when no .new file is created (i.e. index was good)
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r7763 | dshteyn | 2018-03-26 15:17:33 -0700 (Mon, 26 Mar 2018) | 1 line
Fix runtime bug with using boost regex match extra flag ... was crashing PepXMLViewer.
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r7764 | dshteyn | 2018-03-26 15:49:07 -0700 (Mon, 26 Mar 2018) | 1 line
Fix runtime bug with using boost regex match extra flag ... was crashing PepXMLViewer.
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r7765 | dshteyn | 2018-04-26 10:04:51 -0700 (Thu, 26 Apr 2018) | 1 line
cramp: use the index for faster lookups.
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r7766 | dshteyn | 2018-04-30 12:01:10 -0700 (Mon, 30 Apr 2018) | 1 line
cramp: use index for speed in reading peakLists...
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r7767 | dshteyn | 2018-05-10 14:12:37 -0700 (Thu, 10 May 2018) | 1 line
Lorikeet: Display Annotated Ion Current
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r7768 | dshteyn | 2018-05-10 14:20:36 -0700 (Thu, 10 May 2018) | 1 line
Lorikeet: Display Annotated Ion Current
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r7769 | dshteyn | 2018-05-14 15:53:32 -0700 (Mon, 14 May 2018) | 1 line
PTMProphet: make options to set N-term and C-term fragment ions for PTMProphet to consider.
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r7770 | dshteyn | 2018-05-14 16:39:58 -0700 (Mon, 14 May 2018) | 1 line
compute_p: simple utility to compute p-values for some common distributions using GSL.
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r7771 | dshteyn | 2018-05-16 16:11:05 -0700 (Wed, 16 May 2018) | 1 line
PTMProphet: use ppm fragment tolerance.
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r7772 | dshteyn | 2018-05-16 16:19:43 -0700 (Wed, 16 May 2018) | 1 line
PTMProphet: merging copies ...
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r7773 | dshteyn | 2018-05-16 16:34:23 -0700 (Wed, 16 May 2018) | 1 line
PTMProphet: use PPM for auto tolerance selection ...
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r7774 | dshteyn | 2018-05-16 22:19:51 -0700 (Wed, 16 May 2018) | 1 line
PTMProphet: correct problem in previous checkin...
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r7775 | dshteyn | 2018-05-18 10:03:36 -0700 (Fri, 18 May 2018) | 1 line
PTMProphet: test for NULL pointer to prevent crashes ...
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r7776 | dshteyn | 2018-05-21 08:51:49 -0700 (Mon, 21 May 2018) | 1 line
DiscoFilter: Test for spectrum list bounds overruns as QE DIA data may not have complete cycles...
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r7777 | real_procopio | 2018-05-31 17:36:38 -0700 (Thu, 31 May 2018) | 1 line
Bump version as we prepare for a pre-release candidate
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r7778 | dshteyn | 2018-07-09 10:25:49 -0700 (Mon, 09 Jul 2018) | 1 line
Mascot2XML: updates to allow handling of newer mascot results ...
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r7779 | dshteyn | 2018-07-09 10:29:05 -0700 (Mon, 09 Jul 2018) | 1 line
RTCalculator: function to read coefficients from a user specified file
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r7780 | dshteyn | 2018-07-09 10:32:54 -0700 (Mon, 09 Jul 2018) | 1 line
RTCatalog: when reading catalog ignore the header line. Report RT in minutes.
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r7781 | dshteyn | 2018-07-09 10:33:57 -0700 (Mon, 09 Jul 2018) | 1 line
Objects for handling Magnum and Morpheus results...
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r7782 | dshteyn | 2018-07-09 10:36:02 -0700 (Mon, 09 Jul 2018) | 1 line
Add option to store the RTCatalog coefficients file when using it in PeptideProphet modeling.
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r7783 | dshteyn | 2018-07-09 10:38:11 -0700 (Mon, 09 Jul 2018) | 1 line
QUANTIC: first commit ...
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r7784 | dshteyn | 2018-07-09 10:38:29 -0700 (Mon, 09 Jul 2018) | 1 line
QUANTIC: first commit ...
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r7785 | dshteyn | 2018-07-09 10:44:54 -0700 (Mon, 09 Jul 2018) | 1 line
DISCO: updates and implement support for analysis of simply formated RT mz tables files...
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r7786 | dshteyn | 2018-07-09 10:46:47 -0700 (Mon, 09 Jul 2018) | 1 line
PeptideProphet: support for Magnum ...
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r7787 | dshteyn | 2018-07-09 10:47:10 -0700 (Mon, 09 Jul 2018) | 1 line
PeptideProphet: support for Morpheus ...
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r7788 | dshteyn | 2018-07-09 10:48:33 -0700 (Mon, 09 Jul 2018) | 1 line
Makefile support for Magnum, Morpheus and new DISCO functionality ...
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r7789 | dshteyn | 2018-07-09 10:51:09 -0700 (Mon, 09 Jul 2018) | 1 line
Support for Magnum, Morpheus and new RT model functionality in PeptideProphet
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r7790 | dshteyn | 2018-07-09 10:52:18 -0700 (Mon, 09 Jul 2018) | 1 line
Support for new RT model functionality in PeptideProphet ...
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r7791 | dshteyn | 2018-07-09 10:56:29 -0700 (Mon, 09 Jul 2018) | 1 line
PTMProphet: Use bootstrapped fragment PPM tolerance when left unspecified ...
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r7792 | dshteyn | 2018-07-09 10:58:49 -0700 (Mon, 09 Jul 2018) | 1 line
Support for Magnum and new RT model functionality in PeptideProphet
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r7793 | dshteyn | 2018-07-09 11:00:38 -0700 (Mon, 09 Jul 2018) | 1 line
InteractParser: record base peak intensity in pepXML.
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r7794 | dshteyn | 2018-07-09 11:03:27 -0700 (Mon, 09 Jul 2018) | 1 line
PepXMLViewer: change to allow export of PTMProphet features and Quantic results ...
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r7795 | dshteyn | 2018-07-09 11:05:15 -0700 (Mon, 09 Jul 2018) | 1 line
Xinteract: support for new RT model functionality in PeptideProphet
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r7796 | dshteyn | 2018-07-09 11:06:14 -0700 (Mon, 09 Jul 2018) | 1 line
Makefile: support for Magnum and Morpheus
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r7797 | dshteyn | 2018-07-09 11:22:31 -0700 (Mon, 09 Jul 2018) | 1 line
Tools to generate quantitative volcano plots on Proteins and Peptides ...
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r7799 | henryhlam | 2018-07-24 22:34:00 -0700 (Tue, 24 Jul 2018) | 1 line
[SpectraST] Fix MSP import of latest NIST HCD libraries.
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r7801 | henryhlam | 2018-07-25 00:29:10 -0700 (Wed, 25 Jul 2018) | 1 line
[SpectraST] PepXML import allows modification specified as SpectraST-recognized mod names (in place of "mass" in mod_aminoacid_mass). This is a temporary fix until we have better ways of specifying mods in PepXML.
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r7802 | dshteyn | 2018-08-06 17:20:04 -0700 (Mon, 06 Aug 2018) | 1 line
PepXMLViewer: report new stats norm_entropy and mean_best_prob.
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r7803 | real_procopio | 2018-08-07 18:39:37 -0700 (Tue, 07 Aug 2018) | 1 line
[comet] New version 2018012
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r7804 | real_procopio | 2018-08-07 18:48:07 -0700 (Tue, 07 Aug 2018) | 1 line
[version] 5.2.0(beta)0 pre-release
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r7805 | real_procopio | 2018-08-08 11:05:30 -0700 (Wed, 08 Aug 2018) | 1 line
[comet] Fix Makefile target for unpacking comet sources
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r7806 | real_procopio | 2018-08-09 10:26:18 -0700 (Thu, 09 Aug 2018) | 1 line
[version] WE HAVE FOUND THE NAME!
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r7807 | dshteyn | 2018-08-10 12:37:40 -0700 (Fri, 10 Aug 2018) | 1 line
boost patch for copy_file linking error
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r7808 | dshteyn | 2018-08-10 18:04:14 -0700 (Fri, 10 Aug 2018) | 1 line
Build updates for newer compilers. Tested on Mingw64 with gcc 7.3.0 and RedHat 7.4 with gcc 4.8.5.
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r7809 | dshteyn | 2018-08-21 16:51:53 -0700 (Tue, 21 Aug 2018) | 1 line
PepXMLViewer: report PTMProphet stats for different mod types in different columns.
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r7810 | real_procopio | 2018-09-12 19:27:47 -0700 (Wed, 12 Sep 2018) | 1 line
[petunia] Remove unnecessary tags from stylesheet
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r7811 | real_procopio | 2018-09-12 19:29:15 -0700 (Wed, 12 Sep 2018) | 1 line
[updatepaths] Updating svn keywords
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r7812 | real_procopio | 2018-09-12 19:30:44 -0700 (Wed, 12 Sep 2018) | 1 line
[tpptray] Updating svn keywords
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r7813 | real_procopio | 2018-09-12 19:32:08 -0700 (Wed, 12 Sep 2018) | 1 line
[runMzIndex] Updating svn keywords; minor code cleanup
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r7814 | real_procopio | 2018-09-12 19:37:52 -0700 (Wed, 12 Sep 2018) | 1 line
[ProteoMapper] Adding clips and promast
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r7815 | real_procopio | 2018-09-13 19:39:23 -0700 (Thu, 13 Sep 2018) | 1 line
[perl] Fix make install rules for new ProteoMapper components; also add Id keyword to track version
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r7816 | dshteyn | 2018-09-14 12:53:17 -0700 (Fri, 14 Sep 2018) | 1 line
Mascot2XML: bug fixes for Alastair and c++11 infinite template recursion crash
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r7817 | dshteyn | 2018-09-24 16:30:14 -0700 (Mon, 24 Sep 2018) | 1 line
BUGFIX: fix subsetdb memory issue
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r7818 | dshteyn | 2018-09-24 16:32:42 -0700 (Mon, 24 Sep 2018) | 1 line
BUGFIX: address long standing LibraPeptideParser memory issues causing crashes on new build
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r7819 | dshteyn | 2018-09-25 22:40:18 -0700 (Tue, 25 Sep 2018) | 1 line
BUGFIX: Tandem2XML had issues with blank spectrum names and scan numbers inconsistent with comet under default conditions using INDEXOFF1, switching Tandem2XML to using INDEXOFF0 as the default.
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r7820 | dshteyn | 2018-09-28 15:51:57 -0700 (Fri, 28 Sep 2018) | 1 line
For windows include winsock2.h BEFORE windows.h to stop gcc from complaining
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r7821 | mhoopmann | 2018-10-10 16:24:03 -0700 (Wed, 10 Oct 2018) | 9 lines
Adding two new parsing libraries that will form the basis of several upcoming tool additions to the TPP.
[LIBPEPXML] is a library for parsing PepXML files (stored under Parsers/PepXMLParser).
[LIBPROTXML] is a library for parsing ProtXML files (stored under Parsers/ProtXMLParser).
Both libraries are honed to my needs, but are easily extensible. The interface can be changed with a single object as needs arise.
The makefiles have been updated to automatically compile the new libraries.
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r7822 | mhoopmann | 2018-10-11 13:30:36 -0700 (Thu, 11 Oct 2018) | 3 lines
[mzIMLTools] Added a new object, removed the forced std namespace, and performed minor bug fixes.
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r7823 | mhoopmann | 2018-10-11 13:34:12 -0700 (Thu, 11 Oct 2018) | 14 lines
[tpp2mzid]: created new tool for converting PepXML and ProtXML to mzIdentML.
This is actually an updated version of the now deprecated mzIMLTools demo program.
The new version adds cross-linking and PTMProphet support, and fixes minor bugs.
Command line statement shown here:
tpp2mzid v0.5.1 (Oct 10 2018), copyright Mike Hoopmann, Institute for Systems Biology.
This program converts pepXML and protXML to mzIdentML (mzid).
When given a pepXML or protXML file, it will convert it to mzIdentML.
When given an mzIdentML file, it will output a fairly useless summary, and make a copy to annoy you.
USAGE: tpp2mzid <pepXML|protXML|mzid>
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r7824 | mhoopmann | 2018-10-11 13:37:03 -0700 (Thu, 11 Oct 2018) | 3 lines
[mzIMLTools]: removing deprecated mzIMLDemo. It has been replaced with tpp2mzid found in
/src/Parsers/Algorithm2XML/tpp2mzid
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r7825 | mhoopmann | 2018-10-11 13:41:29 -0700 (Thu, 11 Oct 2018) | 3 lines
Updating makefiles to compile new parsing libraries and tools.
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r7826 | mhoopmann | 2018-10-11 13:50:23 -0700 (Thu, 11 Oct 2018) | 3 lines
Further makefile cleanup
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r7827 | mhoopmann | 2018-10-11 16:00:49 -0700 (Thu, 11 Oct 2018) | 3 lines
[mzIMLTools]:fixed a bug that occurred during the purely academic scenario of reading an mzIdentML file and converting it to mzIdentML. Very useful, this fix.
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r7828 | dshteyn | 2018-10-12 14:08:44 -0700 (Fri, 12 Oct 2018) | 1 line
PepXMLViewer: PTMProphet filters
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r7829 | dshteyn | 2018-10-12 15:14:25 -0700 (Fri, 12 Oct 2018) | 1 line
Mascot2XML: updates for Alastair
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r7830 | dshteyn | 2018-10-16 14:50:44 -0700 (Tue, 16 Oct 2018) | 1 line
tpp_gui.pl: Updates for PTMProphet
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r7831 | real_procopio | 2018-10-16 17:45:05 -0700 (Tue, 16 Oct 2018) | 1 line
[fetchDataset] version 0.8.1 : adds support for downloading http/ftp * .gz datasets
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r7832 | real_procopio | 2018-10-16 17:46:31 -0700 (Tue, 16 Oct 2018) | 1 line
[tpp install] added basic check for required perl modules
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r7833 | real_procopio | 2018-10-16 17:48:57 -0700 (Tue, 16 Oct 2018) | 1 line
[version] RC1!
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r7834 | dshteyn | 2018-10-16 21:24:08 -0700 (Tue, 16 Oct 2018) | 1 line
PTMProphet
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r7835 | dshteyn | 2018-10-16 21:24:57 -0700 (Tue, 16 Oct 2018) | 1 line
PepXMLViewer.cgi: the link is a file
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r7836 | dshteyn | 2018-10-17 07:11:21 -0700 (Wed, 17 Oct 2018) | 1 line
helper function for cRamp getFileName()
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r7837 | mhoopmann | 2018-10-17 16:46:25 -0700 (Wed, 17 Oct 2018) | 3 lines
Fixed a buffer overrun.
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r7838 | dshteyn | 2018-10-17 17:50:54 -0700 (Wed, 17 Oct 2018) | 1 line
Petunia: tpp2mzid support for PTMProphet
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r7839 | real_procopio | 2018-10-17 18:21:59 -0700 (Wed, 17 Oct 2018) | 1 line
[comet] fixes minor annoying warning regarding deprecated update_check parameter
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r7840 | real_procopio | 2018-10-17 18:55:11 -0700 (Wed, 17 Oct 2018) | 1 line
[petunia] make sure it can find local config settings
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r7841 | real_procopio | 2018-10-18 10:26:48 -0700 (Thu, 18 Oct 2018) | 1 line
[apache] Add Apache 2.4 directives for TPP (new file which can be used instead of default for 2.2)
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r7842 | dshteyn | 2018-10-18 17:17:17 -0700 (Thu, 18 Oct 2018) | 1 line
(petunia): oxydation -> oxidation
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r7843 | real_procopio | 2018-10-18 17:19:07 -0700 (Thu, 18 Oct 2018) | 6 lines
[Petunia]
General code clean-up:
- Remove unnecessary validation option ("float_blank")
- For PTMProphet, do not set FRAGPPMTOL option if no value is passed by user
- Clean up new TPP2MzID and PTMProphet pages and menu layout
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r7844 | real_procopio | 2018-10-19 16:17:04 -0700 (Fri, 19 Oct 2018) | 1 line
[comet] Fix invalid conversion error in old MSToolkit within Comet
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r7845 | real_procopio | 2018-10-19 16:37:26 -0700 (Fri, 19 Oct 2018) | 1 line
[version] rc2!
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r7846 | real_procopio | 2018-10-19 19:17:27 -0700 (Fri, 19 Oct 2018) | 7 lines
[Petunia]
- Default minProb = 0.0 for xinteract
- Always show File Output options for xinteract, iProphet, PTMProphet, and ProteinProphet pages
- Try to get correct .ipro* output filename in PTMProphet form
- Remove old references to pepXML default pre-2008
- Minor grammar corrections
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r7847 | real_procopio | 2018-10-19 19:18:41 -0700 (Fri, 19 Oct 2018) | 1 line
[make] add libgd and libpng to Linux targets
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r7848 | real_procopio | 2018-10-19 19:20:07 -0700 (Fri, 19 Oct 2018) | 1 line
[version] rc3...
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r7849 | real_procopio | 2018-10-20 13:10:10 -0700 (Sat, 20 Oct 2018) | 1 line
[petunia] Fix typo; update TPP URL
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r7850 | real_procopio | 2018-10-20 13:11:14 -0700 (Sat, 20 Oct 2018) | 1 line
[make] remove libpng to Linux targets...
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r7851 | real_procopio | 2018-10-20 13:14:51 -0700 (Sat, 20 Oct 2018) | 1 line
[PepXMLViewer] Bring it to the future...
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r7852 | real_procopio | 2018-10-20 13:15:22 -0700 (Sat, 20 Oct 2018) | 1 line
[version] rc4
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r7853 | real_procopio | 2018-10-25 12:34:51 -0700 (Thu, 25 Oct 2018) | 1 line
[make] Configure _PORT_ and tandem_params on Linux installations
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r7854 | real_procopio | 2018-10-25 19:40:34 -0700 (Thu, 25 Oct 2018) | 1 line
[ProteinProphet] Skip PEFF-style comments (which start with "#")
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r7855 | real_procopio | 2018-10-25 20:19:07 -0700 (Thu, 25 Oct 2018) | 1 line
[PepXMLViewer] Comment out noisy debugging line
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r7856 | real_procopio | 2018-10-26 18:14:20 -0700 (Fri, 26 Oct 2018) | 1 line
[PepXMLViewer] Do not clog command-line output with unnecessary noise (it was not the debug line after all...)
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r7857 | dshteyn | 2018-10-29 13:44:34 -0700 (Mon, 29 Oct 2018) | 1 line
xinteract: BUGFIX commandline parsing for PTMProphet that includes "...THREADS=..."
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r7858 | mhoopmann | 2018-11-06 14:12:54 -0800 (Tue, 06 Nov 2018) | 3 lines
[mzIMLTools] Updated some userParams to export as generalized cvParams.
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r7859 | dshteyn | 2018-11-16 15:28:33 -0800 (Fri, 16 Nov 2018) | 1 line
PTMProphet: changes for 5.2
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r7860 | dshteyn | 2018-11-19 11:18:06 -0800 (Mon, 19 Nov 2018) | 1 line
SpectraST: added library function flexibility and PTMProphet support.
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r7861 | dshteyn | 2018-11-19 11:19:33 -0800 (Mon, 19 Nov 2018) | 1 line
KDModel library changes to support added PTMProphet functionality.
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r7862 | dshteyn | 2018-11-21 12:46:51 -0800 (Wed, 21 Nov 2018) | 1 line
BUGFIX: compiling problem exposed by Ubuntu 18. Fixed by including math.h in the header, implementing a templated function has to be defined in the header and uses fabs from math.h.
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r7863 | dshteyn | 2018-11-27 14:53:26 -0800 (Tue, 27 Nov 2018) | 1 line
PTMProphet: updates, switching ROC curve to use MBPr ...
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r7864 | dshteyn | 2018-11-27 15:00:08 -0800 (Tue, 27 Nov 2018) | 1 line
PTMProphet: only fit the pos observations and neg observations once when learning the model
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r7865 | dshteyn | 2018-11-27 15:01:02 -0800 (Tue, 27 Nov 2018) | 1 line
KDModel: add a flag to allow fiting the observations or not ...
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r7866 | dshteyn | 2018-11-27 16:37:58 -0800 (Tue, 27 Nov 2018) | 1 line
Quantic: update function call, function is now templated
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r7867 | dshteyn | 2018-11-27 16:39:04 -0800 (Tue, 27 Nov 2018) | 1 line
reSpect: update function call, function is now templated
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r7868 | dshteyn | 2018-11-27 16:40:53 -0800 (Tue, 27 Nov 2018) | 1 line
reserve seemed to not be reserving on windows so switched to push_back
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r7869 | dshteyn | 2018-11-28 11:47:54 -0800 (Wed, 28 Nov 2018) | 1 line
Flush the stream to avoid issues with multithreaded writers...
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r7870 | dshteyn | 2018-11-29 13:47:11 -0800 (Thu, 29 Nov 2018) | 1 line
PTMProphet: rename was failing when run through apache on linux, replaced with copy_file ...
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r7871 | dshteyn | 2018-11-29 14:11:52 -0800 (Thu, 29 Nov 2018) | 1 line
PTMProphet: improve progress report ...
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r7872 | real_procopio | 2018-11-30 19:31:15 -0800 (Fri, 30 Nov 2018) | 10 lines
[Petunia]
- Added Quantic page
- Centralized PTMProphet options form:
- remove ms1 ppm tolerance option
- set default minprob=0.5
- add drop-down to help choose ms2 ppm tolerance
- Move Mayu to External Tools menu
- Removed page for idConvert (use TPP2MzId)
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r7873 | mhoopmann | 2018-12-03 13:33:58 -0800 (Mon, 03 Dec 2018) | 3 lines
[mzIMLTools]: Cosmetic fixes when exporting negative values.
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r7874 | mhoopmann | 2018-12-03 13:35:35 -0800 (Mon, 03 Dec 2018) | 3 lines
[LIBPEPXML]: Adding new parameter reading features for PTMProphet XML files.
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r7875 | mhoopmann | 2018-12-03 13:36:53 -0800 (Mon, 03 Dec 2018) | 3 lines
[tpp2mzid]: Updating parser to recognize changes in PTMProphet-generated pepXML files.
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r7876 | dshteyn | 2018-12-03 14:12:49 -0800 (Mon, 03 Dec 2018) | 1 line
PepXMLViewer: changes for quantic
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r7877 | dshteyn | 2018-12-03 14:43:53 -0800 (Mon, 03 Dec 2018) | 1 line
Quantic: changes for running through Petunia and closing pepXML tags ...
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r7878 | dshteyn | 2018-12-13 11:22:34 -0800 (Thu, 13 Dec 2018) | 1 line
PTMProphet: plug memory leaks caught by valgrind
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r7879 | real_procopio | 2018-12-28 19:27:38 -0800 (Fri, 28 Dec 2018) | 1 line
[Petunia] Add support for 12 channels when generating Libra condition file; added default values for TMT-11
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r7880 | real_procopio | 2019-01-03 20:04:35 -0800 (Thu, 03 Jan 2019) | 1 line
[pwiz msi] Updating to Windows MSI 3.0.1903.e3b352005 -- should install without checking for .NET 3.5
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r7881 | real_procopio | 2019-01-04 18:07:05 -0800 (Fri, 04 Jan 2019) | 1 line
[PepXMLViewer] Recreate models file if it is older than pepXML file
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r7882 | real_procopio | 2019-01-08 17:20:54 -0800 (Tue, 08 Jan 2019) | 1 line
[pwiz msi] Updating to Windows MSI 3.0.1908.43e675997 -- **THIS ONE** should install without checking for .NET 3.5
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r7883 | real_procopio | 2019-01-08 17:23:40 -0800 (Tue, 08 Jan 2019) | 1 line
[version] Bump RC --> 5
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r7884 | dshteyn | 2019-01-15 11:49:51 -0800 (Tue, 15 Jan 2019) | 1 line
PTMProphet: prior probabilities ...
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r7885 | dshteyn | 2019-01-24 10:45:12 -0800 (Thu, 24 Jan 2019) | 1 line
mzParser: ascertain indexes are sorted and the peaks are being read properly using the index .. bug exposed by PTMProphet on filtered mzML files.
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r7886 | mhoopmann | 2019-01-24 14:40:19 -0800 (Thu, 24 Jan 2019) | 3 lines
[tpp2mzid] removed pval from PTMProphet results, as it is no longer used.
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r7887 | dshteyn | 2019-01-25 11:38:47 -0800 (Fri, 25 Jan 2019) | 1 line
RefreshParser: now using case insensitive matching to compare sample_enzyme to enzymatic_search_constraint enzyme information ... so that matched proteins will be returned if the peptide has NTT consistent with search paramerters as detected by RefreshParser based on this case insensitive matching. Bug reported by Andy Keller.
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r7888 | real_procopio | 2019-02-21 12:58:52 -0800 (Thu, 21 Feb 2019) | 1 line
[Lorikeet] updating to latest (#84 - Aug 2018). Includes enhacements to precursor neutral losses (LM) and display of Quantic values (DDS)
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r7889 | real_procopio | 2019-02-21 13:08:25 -0800 (Thu, 21 Feb 2019) | 1 line
[Comet] updating to 2018.01.4
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r7890 | real_procopio | 2019-02-21 15:54:19 -0800 (Thu, 21 Feb 2019) | 1 line
[Lorikeet] Support for TMT-11 reporter ions
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r7891 | real_procopio | 2019-02-21 18:40:11 -0800 (Thu, 21 Feb 2019) | 1 line
[xinteract] minor cleanup; no change in execution
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r7892 | real_procopio | 2019-02-21 18:46:06 -0800 (Thu, 21 Feb 2019) | 1 line
[pwiz] Update README to more proper English; added svn tag to Makefile
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r7893 | real_procopio | 2019-02-21 19:19:14 -0800 (Thu, 21 Feb 2019) | 8 lines
[Petunia]
- Added ability to specify location of PWiz installation via separate variable
- Set this to the appropriate location for current TPP release (ProteoWizard 3.0.1903)
- Removed rarely used $doMzXMLGzip (auto select gzip when converting)
- Removing references to mzXML in favor of mzML
- Minor changes in menu wording
- Increased size of text box in msconvert user params, from 50 (max 500) to 90 (900)
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r7894 | real_procopio | 2019-02-21 19:20:05 -0800 (Thu, 21 Feb 2019) | 1 line
[version] bump rc
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r7895 | real_procopio | 2019-02-25 19:12:05 -0800 (Mon, 25 Feb 2019) | 1 line
[Pep3D] Display instrument and ms run info; add flush to display messages on screen more quickly
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r7896 | dshteyn | 2019-03-01 10:22:34 -0800 (Fri, 01 Mar 2019) | 1 line
all shouldn't rebuild things that shouldn't have to be rebuilt
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r7897 | real_procopio | 2019-03-01 19:53:37 -0800 (Fri, 01 Mar 2019) | 1 line
[Petunia] Use correct version of Windows PWiz that is included with TPP
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r7898 | real_procopio | 2019-03-01 19:55:27 -0800 (Fri, 01 Mar 2019) | 1 line
[version] bump tp rc7
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r7899 | dshteyn | 2019-03-11 14:38:57 -0700 (Mon, 11 Mar 2019) | 1 line
DiscoFilter: bug fix to allow processing of partial files
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r7900 | real_procopio | 2019-03-12 18:04:10 -0700 (Tue, 12 Mar 2019) | 1 line
[version] Final 5.2.0 release
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