Luis M committed [r9492] on Code

[AnalysisSummaryParser] Remove old, unused cgi

Luis M committed [r9491] on Code

[cometresult.cgi] Remove cgi viewer for pre-2012 Comet results

Luis M committed [r9490] on Code

[Pep3D] Remove long unsused cgis (disCidData_xml.cgi and getCidData_xml.cgi); verify that input file exists before running anything else; quell size warnings; clean up comments

Luis M committed [r9489] on Code

[version] Provisional version to help differentiate builds

Luis M committed [r9488] on Code

[Petunia] Fix detection of MSFragger on regis (broken by r9259); create new params files in tmp dir (again) before moving to user dir; capture success code from params file creation by Kojak and Magnum; minor cleanup

Luis M committed [r9487] on Code

[PepXMLViewer] Fix PTMPro filter fields which would display incorrectly when adding/removing any column (bad copy/paste job in original code); also add full list of fields to the undisplayed columns box (formerly all missing); simplified logic; minor code cleanup. ToDo: perhaps missing lability and massdiff fields? Meh. Bug reported by Rob M.

Luis M committed [r9486] on Code

[RefreshParser] New option DISCARD_UNMAPPED removes the parent <spectrum_query> tag and children from the output file whenever a <search_hit> peptide does not map to the specified database (which also means that it cannot be re-map later). Requested for PeptideAtlas. Use with care.

Luis M committed [r9485] on Code

[comet-fasta] properly size message buffer to avoid overruns; remove old code comments; re-tab

Luis M committed [r9484] on Code

[html] minor layout changes

Jimmy Eng committed [r9483] on Code

ProteinProphet: fix OOB/negative-index bugs, ~5-17x speedup on real data

Mike committed [r9482] on Code

[tpp2mzid] - fixed error caused by case where search to be converted had no PSMs to convert.

Luis M committed [r9481] on Code

[error handling] Improve error reporting and code cleanup

Luis M committed [r9480] on Code

[deprecation]

Luis M committed [r9479] on Code

[ProtXMLViewer] Make sure file exists before attempting to create models file

Luis M committed [r9478] on Code

[madcaps] Validate digestion parameters

Luis M committed [r9477] on Code

[ProteoMapper] v1.7.0: Ignore specified mass tolerance if not doing fuzzy matching; Accept U and O in input sequences; Correctly capture error code from system call to find number of cores; Some cleanup

Luis M committed [r9476] on Code

[cleanup] Re-tab RefreshParser.cpp for clarity

Luis M committed [r9475] on Code

[comet] v2026.01.0

Luis M committed [r9474] on Code

Latest Unimod data, up to id=2147

Jimmy Eng committed [r9473] on Code

modify DatabaseParser to account for Comet .idx extension

Luis M committed [r9472] on Code

[comet] v2025.03.0

Luis M committed [r9471] on Code

[Petunia] Updated path to Python in local UB24 (regis)

Jimmy Eng committed [r9470] on Code

Correct parsing of MS1 peaks for mzML files with ion mobility dimension.

Luis M committed [r9469] on Code

[showXIC] Display RT in minutes insetad of seconds (as per Lab request). Minor style adjustment to max ppm

Jimmy Eng committed [r9468] on Code

Add logic when finding correpsonding MS1 scan if scanHeader.precursorScanNum==0.

SASHIMI released /Trans-Proteomic Pipeline (TPP)/TPP v7.3 (Trade Wind) rev 0/TPP_Setup_7.3.0.exe

SASHIMI released /Trans-Proteomic Pipeline (TPP)/TPP v7.3 (Trade Wind) rev 0/TPP_7.3.0-src.tgz

SASHIMI released /TPP_7.3.0-src.tgz

Luis M committed [r9467] on Code

Tagging 7.3.0 release

Luis M committed [r9466] on Code

[qsir] Deal with Windoze paths...

Luis M committed [r9465] on Code

[ProtXMLViewer] Make Windows path comparisons case-insensitive; add [ + ] to Legend link for clarity. [Quetzal] Point to main Quetzal for links from L-keet

Luis M committed [r9464] on Code

[Windows installer] Skip check for old ARCH type; minor text change. [Landing Page] Update link to Release Notes

Luis M committed [r9463] on Code

[Comet] Update to V.2025.01.1

Luis M committed [r9462] on Code

[PWiz] Revert VERSION string for successful compilation in Windows...

Luis M committed [r9461] on Code

[TPP files] Replace backslashes with forward ones. [Petunia] Point to updated Python in regis

Luis M committed [r9460] on Code

[version] The winds of change...

Luis M committed [r9459] on Code

[Cuva/ShowXIC] Configuration tweaks for Windows

Luis M committed [r9458] on Code

[Quetzal] Remove outdated code and related config; will re-add newer version at a later date

Jimmy Eng committed [r9457] on Code

Finally fix expect score filtering when small values previous end up as 0.0000, messing up subsequent page updates. Also changed the integer param values to show as integers instead of decimal numbers.

Luis M committed [r9456] on Code

[ProteoGrapher] Remove links to ProteoGrapher; consider reinstating when/if it can be made more performant, and with recent GO data. Remove old/obsolete custom GO definition files of unknown provenance

Luis M committed [r9455] on Code

[ShowXIC]

Luis M committed [r9454] on Code

[ShowXIC]

Luis M committed [r9453] on Code

[CUVALibRe]

Luis M committed [r9452] on Code

[Petunia]

Luis M committed [r9451] on Code

[comet] Generate two sample comet params files: basic (-p) and full (-q)

Luis M committed [r9450] on Code

[ASAP peptide] Overlay hit data only from relevant MS run; highlight same-sequence hits; silence compiler warnings

Luis M committed [r9449] on Code

[qsir] Require mzML path so as to retrieve hit data that corresponds only to that MS run; add RT to returned data

Luis M committed [r9448] on Code

[extern] Much-belated removal of unneeded files... part zwei

SASHIMI released /Trans-Proteomic Pipeline (TPP)/README

SASHIMI released /Trans-Proteomic Pipeline (TPP)/README_4sashimiSF.txt

Luis M committed [r9447] on Code

[ShowXIC]

Luis M committed [r9446] on Code

[kojak] Ignore error code thrown by Kojak when (successfully) generating conf file during build process

Luis M committed [r9445] on Code

[kojak] Place correct Kojak code back! And remove the unneeded one... Oops.

Luis M committed [r9444] on Code

[ShowXIC]

Luis M committed [r9443] on Code

[ASAPRatio] Fix long-dormant memory overflow bug only recently uncovered by new compilers

Luis M committed [r9442] on Code

[mzXML] Remove pre-Wiz mz[X]ML converters, long since last used or built

Luis M committed [r9441] on Code

[PSI-MOD.obo] Update to version 1.031.6 (latest)

Luis M committed [r9440] on Code

[extern] Much-belated removal of unneeded files... part eins

Luis M committed [r9439] on Code

[python] Add simple Makefile to install tpp-python executables (with more todo); display TPP version when running RumAndCoke

Luis M committed [r9438] on Code

[html] Add html5 DOCTYPE and link to TPP icon

Luis M committed [r9437] on Code

[ShowXIC]

Luis M committed [r9436] on Code

[ShowXIC]

Luis M committed [r9435] on Code

[version] Bump for clarity in dev builds

Luis M committed [r9434] on Code

[kojak magnum stpeter] Include <cstdint> in non-Win builds to avoid SIZE_MAX not declared error (surfaced in Ub24.04)

Luis M committed [r9433] on Code

[pwiz] Remove boost lib that crashed under Ubuntu 24.04; remove strangely-duplicated Makefile directive; update version file

Luis M committed [r9432] on Code

[XPressPeptide] New commandline switch -Z to look for a closing tag of </msms_run_summary> instead of the default </msms_pipeline_analysis>. For use when splitting files for (faster) parallel analysis. Some code cleanup

Luis M committed [r9431] on Code

[proteographer] Capture isoforms and neXtProt NX_ accessions

Luis M committed [r9430] on Code

[ShowXIC] Clean up messy code; add link to new viewer from PepXMLViewer; add PPM default to interface

Luis M committed [r9429] on Code

[css] New Spinner for white/light backgrounds

Luis M committed [r9428] on Code

[Petunia] Remove NIGMS image and add link to ISB Funding page; link to new XIC viewer; clean up some sloppy code

Luis M committed [r9427] on Code

[pwiz] Remove unnecessarily checked-in files...

Luis M committed [r9426] on Code

[pwiz] Update to actual version used since previous update

Luis M committed [r9425] on Code

[usage] Attempt to make several usage statements somewhat more legible

Luis M committed [r9424] on Code

[conf] Remove deprecated settings

Luis M committed [r9423] on Code

[ShowXIC] Overhaul to a far clearer, cleaner, and responsive interface, with ability to load files and directly set input parameters

Luis M committed [r9422] on Code

[js] Add Chart.js

Luis M committed [r9421] on Code

[ShowXIC] Add JSON output option to CGI so as to avoid outdated HTML output; functionality via previous links unaffected

Luis M committed [r9420] on Code

[tpp_models] New option -R to stop parsing file after main models and header info have been retrieved; skips individual MS Run info. Very useful for HUGE files that take a long time to parse

Luis M committed [r9419] on Code

[MADCAPS] Place css in its own file

Luis M committed [r9418] on Code

[ShowXIC] Make code more readable (mostly re-tabbing) to facilitate future decoupling; no functional changes

Luis M committed [r9417] on Code

[CUVALibRe] Remove outdated (and unnecessarily duplicated) code; minor improvements for eventual GO integration

SASHIMI released /Trans-Proteomic Pipeline (TPP)/Seq2MS Models/README

SASHIMI released /Trans-Proteomic Pipeline (TPP)/TPP v7.2 (Bombogenesis) rev 0/TPP_7-2-0-src.tgz

David Shteynberg committed [r9416] on Code

[Release 7.2.0 Bombogenesis:] Tag applied

SASHIMI released /Trans-Proteomic Pipeline (TPP)/TPP v7.2 (Bombogenesis) rev 0/TPP_Setup_7.2.0.exe

David Shteynberg committed [r9415] on Code

[Seq2MS:] configure to use /usr/bin/python3 on systems not windows

David Shteynberg committed [r9414] on Code

[extern:] Makefile seq2ms targets updated so they don't rebuild and reconfigure unnecessarily

SASHIMI released /Trans-Proteomic Pipeline (TPP)/Seq2MS Models/Seq2MS-default_model.tar.xz

SASHIMI released /Trans-Proteomic Pipeline (TPP)/TPP v7.2 Release Candidates/TPP_Setup_7.2.x_rc5.exe

SASHIMI released /Trans-Proteomic Pipeline (TPP)/Seq2MS Models/Seq2MS-default_model.zip

David Shteynberg committed [r9413] on Code

[Seq2MS:] disable autostart of serve.bat

David Shteynberg committed [r9412] on Code

[VERSION:] bump version prepare for release

David Shteynberg committed [r9411] on Code

[Seq2MS:] clean up system calls and exit codes...

David Shteynberg committed [r9410] on Code

[Seq2MS:] clean up system calls and exit codes...

David Shteynberg committed [r9409] on Code

[Windows Installer:] update keys to prevent unneccessary reinstalls

David Shteynberg committed [r9408] on Code

[QUETZAL:] match window origin

David Shteynberg committed [r9407] on Code

[Seq2MS:] process without the server when it is off

David Shteynberg committed [r9406] on Code

[QUETZAL:] configure for site

SASHIMI released /Trans-Proteomic Pipeline (TPP)/TPP v7.2 Release Candidates/TPP_Setup_7.2.x_rc4.exe

David Shteynberg committed [r9405] on Code

[windows installer:] BUGFIX new dependecies required for apache 2.4