source: trunk/client/servlet

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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) @4551   9 years Fredrik Levander Refs #630. Added support for URIs with basic authentication. Refs …
(edit) @4542   9 years olle Refs #823. First version of support for reading connection properties …
(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) @4537   9 years Fredrik Levander Fixes #820. Peptide level filtering
(edit) @4535   9 years Fredrik Levander Refs #819. Adding support for matching low-confidence identifications …
(edit) @4525   9 years olle Refs #818. Refs #805. File selection updated to avoid creating extra …
(edit) @4522   9 years Fredrik Levander Fixes #817.
(edit) @4521   9 years Fredrik Levander Refs #816. Added symbols and new commands to project home view.
(edit) @4517   9 years Fredrik Levander Fixes #814. Escaping the selected option list when matching.
(edit) @4505   9 years Fredrik Levander Fixes #811. Restored functionality for protocol file selection. Now …
(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) @4496   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) @4479   10 years olle Refs #807. PRIDE XML export is updated to support automatic conversion …
(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) @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) @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) @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 …
(edit) @4454   10 years olle Refs #800. Removal of files from biomaterial implemented for extracts …
(edit) @4453   10 years olle #800. Added client class for removing files from biomaterial.
(edit) @4439   10 years olle Refs #799. Proteios SE spectrum viewer updated to indicate the zoom …
(edit) @4438   10 years olle Refs #799. JavaScript www/static/js/script.js in client/servlet/
(edit) @4437   10 years olle Refs #799. JavaScript www/static/js/script.js in client/servlet/
(edit) @4436   10 years olle Refs #799. Proteios SE mass spectrum viewer updated to allow a zoom …
(edit) @4435   10 years olle Refs #799. Class/files action/peakList/PeakAnnotationUtil.java, …
(edit) @4434   10 years olle Refs #799. Proteios SE updated to allow id, ondragstart, …
(edit) @4433   10 years Fredrik Levander Refs #800. Added client class for removing biomaterials from file.
(edit) @4431   10 years Fredrik Levander Refs #283. Fixed display of file type when not set.
(edit) @4430   10 years olle Refs #793. Unix/Linux shell script www/WEB-INF/init.sh in …
(edit) @4422   10 years olle Refs #797. JavaScript www/static/js/script.js in client/servlet/
(edit) @4421   10 years olle Refs #797. Regular update of the job table via Ajax updated to prevent …
(edit) @4420   10 years olle Refs #797. Class/file action/job/ListJobsAjax.java in …
(edit) @4419   10 years olle Refs #797. Regular update of the job table via Ajax updated to not …
(edit) @4417   10 years olle Refs #327. Refs #797. Compiler warning for unchecked calls in …
(edit) @4412   10 years olle Refs #798. Refs #620. Refs #46. Classes/files …
(edit) @4410   10 years olle Refs #797. First version of regular updates of job table contents: …
(edit) @4398   10 years olle Refs #796. Refs #795. Refs #783. Update of table preferences …
(edit) @4397   10 years olle Refs #795. Class/file action/job/ListJobs.java in client/servlet/
(edit) @4396   10 years olle Refs #795. Class/file action/job/ListJobs.java in client/servlet/
(edit) @4392   10 years olle Refs #794. Class/file gui/web/GUIConverter.java in client/servlet/
(edit) @4391   10 years olle Refs #793. Ant build.xml files updated to refer to environment …
(edit) @4387   10 years olle Refs #793. Unix shell script www/WEB-INF/init.sh in …
(edit) @4386   10 years olle Refs #793. Configuration Unix shell script www/WEB-INF/config in …
(edit) @4384   10 years olle Refs #789. Bug fixed in class/file gui/form/ImportFileForm.java in …
(edit) @4383   10 years olle Refs #610. Proteios web service basic authentication updated to send a …
(edit) @4381   10 years olle Refs #610. Proteios SE web service updated to support basic …
(edit) @4375   10 years Fredrik Levander Refs #744. Refs #781. Fix for another bug with multiple files when …
(edit) @4374   10 years Fredrik Levander Refs #744. Refs #781. Fix for bug with multiple files when running …
(edit) @4371   10 years olle Refs #788. Unix/Linux *.sh shell scripts have the shebang line …
(edit) @4370   10 years olle Refs #788. Changes the default dialect to …
(edit) @4368   10 years olle Refs #787. Refs #471. When a new OMSSA search parameter set is …
(edit) @4367   10 years olle Refs #787. Refs. #534. When a new Mascot search parameter set is …
(edit) @4366   10 years olle Refs #787. Refs #362. Refs #363. When a new X!Tandem search parameter …
(edit) @4359   10 years Fredrik Levander Fixes #770. Added label for PQPQ export option.
(edit) @4339   11 years Fredrik Levander Refs #754. Added hit FDR cutoff when matching features and hits.
(edit) @4329   11 years marianne Refs #774. FeatureSequencePropagator?: Checking previous hits speed up, …
(edit) @4311   11 years Fredrik Levander
(edit) @4305   11 years Fredrik Levander Removed unused import.
(edit) @4303   11 years Fredrik Levander Fixes #779.
(edit) @4302   11 years Fredrik Levander Updated BILS file publisher
(edit) @4281   11 years Fredrik Levander Refs #777. First version of report for all features in project.
(edit) @4278   11 years Fredrik Levander Refs #776. First version of BILS file publisher.
(edit) @4276   11 years Fredrik Levander Refs #774. Added GUI classes for feature sequence propagation.
(edit) @4275   11 years Fredrik Levander Refs #772. Updated dictionary with new option.
(edit) @4274   11 years Fredrik Levander Refs #772. Updated protein assembly for optional per replicate assembly.
(edit) @4269   11 years Fredrik Levander Refs #772. Updated info reader and hits import.
(edit) @4258   11 years Fredrik Levander Refs #770. Added isotope correction and peptide report export for PQPQ
(edit) @4253   11 years Fredrik Levander Fixes #768.
(edit) @4247   12 years olle Refs #766. Proteios SE "About" HTML page content/about.html in …
(edit) @4245   12 years olle Refs #766. Proteios SE "About" HTML page content/about.html in …
(edit) @4239   12 years olle Refs #763. Refs #471. Refs #287. Refs #290. Support of running OMSSA …
(edit) @4238   12 years olle Refs #763. Refs #362. Refs #287. Refs #290. Support of running …
(edit) @4236   12 years olle Refs #763. Refs #534. Support of running Mascot searches from Proteios …
(edit) @4234   12 years olle Refs #763. Refs #534. Refs #287. Refs #290. Support of running Mascot …
(edit) @4232   12 years olle Refs #763. Refs #534. Class/file …
(edit) @4231   12 years olle Refs #763. Refs #534. Class/file gui/form/MascotStorageForm.java in …
(edit) @4230   12 years olle Refs #763. Refs #534. Class/file …
(edit) @4229   12 years olle Refs #764. MIME type set for output files when exporting table data to …
(edit) @4222   12 years olle Refs #517. Refs #760. Class/file …
(edit) @4221   12 years olle Refs #517. Refs #760. Class/file …
(edit) @4220   12 years olle Refs #517. Refs #760. Moving a selected job to the High Priority Queue …
(edit) @4217   12 years olle Refs #517. Refs #760. Several JobQueueManager methods reverted to …
(edit) @4216   12 years olle Refs #517. Refs #760. Message shown after requesting jobs to be moved …
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