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Diff Rev Age Author Log Message
(edit) @4554   9 years Fredrik Levander Refs #776. Moving some settings to configuration file.
(edit) @4553   9 years Fredrik Levander Refs #805. Adding file associations to raw files from PRIDE XML files
(edit) @4552   9 years Fredrik Levander Refs #805. Reactivated writing of URL since this is now supported by …
(edit) @4551   9 years Fredrik Levander Refs #630. Added support for URIs with basic authentication. Refs …
(edit) @4550   9 years Fredrik Levander Added sulfo modification
(edit) @4549   9 years Fredrik Levander Avoiding export of multiple entries for modified peptides with delta scores
(edit) @4548   9 years Fredrik Levander Catching unexpected modifications in msp library export.
(edit) @4547   9 years Fredrik Levander Corrected formatting of peaks and added protein ids in msp library export.
(edit) @4546   9 years Fredrik Levander Writing theoretical m/z for matched ions in library export.
(edit) @4545   9 years Fredrik Levander Updates to Modification to give diff formula. Updates to contrib …
(edit) @4544   9 years Fredrik Levander Refs #823. Avoiding null pointer exception if connection properties …
(edit) @4543   9 years olle Refs #823. Loading of connection property values in class/file …
(edit) @4542   9 years olle Refs #823. First version of support for reading connection properties …
(edit) @4541   9 years Fredrik Levander Refs #822. Taking care of 'pm' and 'id' annotations for the aa …
(edit) @4540   9 years Fredrik Levander Refs #819, Refs #821. Clearing cluster IDs before matching. Fix when …
(edit) @4539   9 years Fredrik Levander Refs #821.
(edit) @4538   9 years Fredrik Levander Refs #820. Removed unused code.
(edit) @4537   9 years Fredrik Levander Fixes #820. Peptide level filtering
(edit) @4536   10 years Fredrik Levander Only reporting modified peptides once for updated Mascot XML export.
(edit) @4535   10 years Fredrik Levander Refs #819. Adding support for matching low-confidence identifications …
(edit) @4534   10 years Fredrik Levander Avoiding duplicate entries and infinte evalues in modified Mascot XML
(edit) @4533   10 years Fredrik Levander One more for the modified Mascot XML export
(edit) @4532   10 years Fredrik Levander One more fix for modified Mascot XML
(edit) @4531   10 years Fredrik Levander Fix for edited Mascot XML export
(edit) @4530   10 years Fredrik Levander Add-on to the Mascot file reader for modified XML files.
(edit) @4529   10 years olle Outermost Ant build file build.xml updated in version data to prepare …
(edit) @4528   10 years olle Tagging release 2.19.0
(edit) @4527   10 years olle Outermost Ant build file build.xml updated by setting property …
(edit) @4526   10 years olle Refs #805. Retraction of writing URL of files instead of local path …
(edit) @4525   10 years olle Refs #818. Refs #805. File selection updated to avoid creating extra …
(edit) @4524   10 years Fredrik Levander Refs #774. Avoiding null pointer exception
(edit) @4523   10 years Fredrik Levander Fix for merged spectrum titles with MGF input in X!tandem results …
(edit) @4522   10 years Fredrik Levander Fixes #817.
(edit) @4521   10 years Fredrik Levander Refs #816. Added symbols and new commands to project home view.
(edit) @4520   10 years Fredrik Levander Fixes #815. Incorporating msnumpress support.
(edit) @4519   10 years Fredrik Levander Updated tandem xsd to accomodate new act attribute.
(edit) @4518   10 years Fredrik Levander Refs #814. Added apache commons lang jar for escaping html.
(edit) @4517   10 years Fredrik Levander Fixes #814. Escaping the selected option list when matching.
(edit) @4516   10 years Fredrik Levander Refs #808. Refs #807. Changed writing of zero length data arrays to …
(edit) @4515   10 years Fredrik Levander Refs #805. Writing URL of files instead of local path for …
(edit) @4514   10 years Fredrik Levander Refs #807. Added some new required fields to the generated PRIDE XML. …
(edit) @4513   10 years Fredrik Levander Refs #808. Updated converter to display hostname in path to sourcefile.
(edit) @4512   10 years Fredrik Levander Fixes #809. Fixed reporting of static modifications when no variable …
(edit) @4511   10 years Fredrik Levander Refs #808. Refs #807. Updated converter to output as many digits as in …
(edit) @4510   10 years Fredrik Levander Refs #807. Exchanged ontology term for m/z in PRIDE output.
(edit) @4509   10 years Fredrik Levander Refs #813. Removed old versions of http client from previous …
(edit) @4508   10 years Fredrik Levander Refs #813. Removed old versions of http client
(edit) @4507   10 years Fredrik Levander Fixes #813. Updated mascot results retrieval to use new version of …
(edit) @4506   10 years Fredrik Levander Fixes #812. Querying only for distinct score types with at least one …
(edit) @4505   10 years Fredrik Levander Fixes #811. Restored functionality for protocol file selection. Now …
(edit) @4504   10 years Fredrik Levander Refs #809. Setting modification mass difference if absent.
(edit) @4503   10 years Fredrik Levander Refs #809. Phosphorylation name fixed.
(edit) @4502   10 years Fredrik Levander Refs #809. Bug fix.
(edit) @4501   10 years Fredrik Levander Fixes #810. Changed to multiple selection of samples, and generation …
(edit) @4500   10 years olle Refs #807. PRIDE XML export updated to show link to NEWT ontology …
(edit) @4499   10 years olle Refs #808. Refs #807. MGF to mzData converter in class/file …
(edit) @4498   10 years olle Refs #808. Refs #807. MGF to mzData converter in class/file …
(edit) @4497   10 years olle Refs #807. PRIDE XML export updated to search for an alternative mzML …
(edit) @4496   10 years olle Refs #807. PRIDE XML export updated to exclude Hit table entries with …
(edit) @4495   10 years Fredrik Levander Refs #807. Fix to not retrieve instrument serial number instead of …
(edit) @4494   10 years Fredrik Levander Refs #807. Throwing exception when no mzData file to use for export of …
(edit) @4493   10 years Fredrik Levander Refs #809. Refs #807. Update of PRIDE xml peptide modification writing …
(edit) @4492   10 years olle Refs #515. Refs #807. Classes/files io/XMLCrudeWriterImpl.java and …
(edit) @4491   10 years olle Refs #807. PRIDE XML export updated to exclude Hit table entries with …
(edit) @4490   10 years olle Refs #807. Class/file action/hit/CreatePrideExportJob.java in …
(edit) @4489   10 years olle Refs #807. PRIDE XML export updated to allow addition of species …
(edit) @4488   10 years olle Refs #807. Class/file plugins/MgfToMzDataPlugin.java in plugin/ …
(edit) @4487   10 years olle Refs #807. PRIDE XML export is updated for adding sample and contact …
(edit) @4486   10 years olle Refs #807. PRIDE XML export is updated to retrieve instrument part in …
(edit) @4485   10 years Fredrik Levander Refs #809. Initial refactoring to make functions for retrieval of …
(edit) @4484   10 years olle Refs #808. Refs #807. MGF to mzData converter in class/file …
(edit) @4483   10 years olle Refs #808. MGF to mzData converter in class/file …
(edit) @4482   10 years olle Refs #808. Refs #807. MGF to mzData converter in class/file …
(edit) @4481   10 years olle Refs #807. PRIDE XML export is updated to convert selected cvParam …
(edit) @4480   10 years olle Refs #808. Refs #807. MGF to mzData converter in class/file …
(edit) @4479   10 years olle Refs #807. PRIDE XML export is updated to support automatic conversion …
(edit) @4478   10 years olle Refs #808. Refs #807. MGF to mzData converter in class/file …
(edit) @4477   10 years olle Refs #808. MGF to mzData converter in class/file …
(edit) @4476   10 years olle Refs #808. Added MGF to mzData plug-in class/file …
(edit) @4475   10 years olle Refs #805. Support for simplifying ProteomeXchange submission by …
(edit) @4474   10 years Fredrik Levander Refs #776. Added possibility for alternate tomcat paths, and some …
(edit) @4473   10 years Fredrik Levander Fixes #806. Update svnant library files, and build files to use …
(edit) @4472   10 years olle Refs #805. Refs #406. Support for simplifying ProteomeXchange …
(edit) @4471   10 years olle Refs #805. Active project menu updated with new cascade item …
(edit) @4470   10 years olle Refs #805. ProteomeXchange submission changed to a hit context …
(edit) @4469   10 years olle Refs #805. Class/file action/file/ProteomeXchangeExport.java in …
(edit) @4468   10 years olle Refs #805. Support for simplifying ProteomeXchange submission by …
(edit) @4467   10 years olle Refs #805. Support for simplifying ProteomeXchange submission by …
(edit) @4466   10 years olle Refs #805. Default icon settings file icons/default in …
(edit) @4465   10 years olle Refs #805. First version of support for simplifying ProteomeXchange …
(edit) @4464   10 years olle Refs #804. First version of support for allowing the administrator to …
(edit) @4463   10 years olle Refs #804. Refactoring of some files/classes in client/servlet/ …
(edit) @4462   10 years olle Refs #792. First version of support for comparison of technical …
(edit) @4461   10 years olle Refs #802. Non-gel hits import updated to support replicate ID input …
(edit) @4460   10 years olle Refs #802. Refs #772. Class/file core/Hit.java in api/core/ …
(edit) @4459   10 years olle Refs #803. Class/file action/sample/AddSample.java in …
(edit) @4458   10 years olle Refs #803. Refs #283. Biomaterial - file associations can now be …
(edit) @4457   10 years olle Refs #283. Refs #339. Classes/files …
(edit) @4456   10 years olle Refs #327. Refs #339. Classes/files …
(edit) @4455   10 years olle Refs #803. New class ViewItemTable introduced for displaying a table …
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