JAL-3541 removed clover report generation debug flag (utf-8 encoding enforcement...
[jalview.git] / src / jalview / ext /
2017-09-25 gmungocJAL-2738 query unindexed file, unit test for VCFLoader
2017-09-25 gmungocJAL-2738 one constant in codebase for "alleles" attribu...
2017-09-22 gmungocJAL-2738 correct handling of reverse strand genes
2017-09-22 gmungocJAL-2738 lookup GRCh38/37 gene mapping
2017-09-21 gmungocJAL-2738 add chromosome coordinate mappings to transcripts
2017-09-21 gmungocJAL-2738 PoC of Load VCF file on to gene sequence
2017-09-19 gmungocJAL-1793 wrapper for plain or indexed VCF + simple...
2017-08-31 gmungocJAL-2105 REST versions updated to 6.1 (Ensembl) 6.0...
2017-08-31 gmungocJAL-2253 safer simpler resolution of identifiers using...
2017-08-25 gmungocJAL-2480 suppress debug timing output that got left in
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList
2017-08-16 Jim ProcterJAL-2418 add GPL to main sources
2017-08-16 Jim ProcterJAL-2418 source formatting
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the...
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-06-05 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-06-04 Jim ProcterJAL-2582 comment about IDs being lost if they resembl...
2017-06-04 Jim ProcterJAL-2582 recognise ENS…P peptide IDs and make two getPa...
2017-05-30 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-05-29 Jim ProcterMerge branch 'features/JAL-2465_No-mapping_Jmol-structu...
2017-05-25 gmungocJAL-2050 make SequenceFeature.score final, adjust const...
2017-05-24 gmungocJAL-2529 add object_type=cdna to EnsemblCdna parameters
2017-05-18 gmungocJAL-2490 retrieve visible features only
2017-05-16 gmungocJAL-2525 put in missing "transcript" feature type
2017-05-15 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-05-12 gmungocJAL-2525 get sequence features for Ontology term(s...
2017-05-12 gmungocJAL-2480 renamed java.util.RangeComparator to IntRangeC...
2017-05-09 gmungocJAL-2505 use constructors to set (what will be) final...
2017-05-08 tcofoegbuMerge branch 'develop' of https://source.jalview.org...
2017-05-05 kiramtMerge remote-tracking branch 'origin/develop' into
2017-05-03 gmungocJAL-2105 Ensembl REST now at 5.0
2017-05-01 tcofoegbuJAL-2465 bugfix and rerefactor renamed getPdbFile(...
2017-04-26 kiramtMerge remote-tracking branch 'origin/develop' into...
2017-04-26 kiramtMerge remote-tracking branch 'origin/develop' into...
2017-04-24 gmungocJAL-2487 remove redundant refreshGUI to minimise thread...
2017-04-24 kiramtJAL-2388 Hidden cols separated from column selection...
2017-03-31 gmungocJAL-2430 code tidy, unit test for Jmol hidden column...
2017-03-21 gmungocJAL-2438 check for null FeatureRenderer
2017-03-15 gmungocJAL-2443 push getResidueBoxColour inside getResidueColour
2017-03-13 gmungocJAL-2438 FeatureColourFinder refactored from FeatureRen...
2017-03-08 gmungocJAL-2430 colour columns hidden in alignment gray on...
2017-03-08 gmungocJAL-2295 avoid quotes breaking attribute value parsing
2017-03-07 gmungocJAL-2295 status messages for Chimera attributes set...
2017-03-01 gmungocMerge branch 'features/JAL-2295setChimeraAttributes...
2017-02-09 gmungocMerge branch 'develop' into features/JAL-2379pcaMemory features/JAL-2379pcaMemory
2017-01-23 gmungocJAL-2379 made SparseMatrix.divide() so as to exactly...
2017-01-17 gmungocMerge branch 'develop' into features/JAL-2295setChimera...
2017-01-17 gmungocJAL-2379 SparseDoubleArray added (for use by SparseMatrix)
2017-01-09 gmungocJAL-2371 remove ColourSchemeI.findColour(c), pure inter...
2016-12-22 gmungocJAL-2360 structure viewers now using ColourMenuHelper...
2016-12-16 gmungocJAL-2360 refactoring for JalviewColourScheme enum,
2016-12-12 gmungocJAL-2632 corrected lookup of residue colour
2016-12-09 gmungocJAL-2105 updated for reviewed REST version 4.8
2016-12-08 gmungocMerge branch 'develop' into features/JAL-2295setChimera...
2016-12-07 gmungocJAL-2354 handle error response when fetching features
2016-12-02 gmungocMerge branch 'develop' into features/JAL-2295setChimera...
2016-11-30 Jim ProcterMerge branch 'features/JAL-2320_closeChimeraAction...
2016-11-29 gmungocMerge branch 'develop' into features/JAL-2295setChimera...
2016-11-25 gmungocMerge branch 'develop' into trialMerge
2016-11-23 gmungocMerge branch 'develop' into features/JAL-2295setChimera...
2016-11-22 Jim ProcterMerge branch 'features/JAL-2177_update_jmol_to_14.6...
2016-11-17 gmungocJAL-98 javadoc, third party acknowledgements (and very...
2016-11-16 gmungocJAL-2296 unit test for reading Chimera attributes to...
2016-11-16 gmungocMerge branch 'develop' into features/JAL-2295setChimera...
2016-11-16 gmungocJAL-2296 don't copy attribute with value False
2016-11-16 gmungocJAL-2295 don't exclude RESNUM from transfer to Chimera
2016-11-14 gmungocJAL-2296 new code and refactoring for 'copy Chimera...
2016-11-14 gmungocJAL-2295 don't copy 'Chimera' features back to Chimera
2016-11-14 gmungocJAL-2295 JAL-2296 skeleton 'attributes to features...
2016-11-11 gmungocJAL-2295 (optionally) return Chimera command reply
2016-11-11 gmungocJAL-2295 correct test for Float.isNaN(score) !
2016-11-10 tcofoegbuJAL-2317 Fixed Chimera command for hiding/showing disti... bug/JAL-2317_jmol_chimera-chain-factorisation
2016-11-10 gmungocJAL-2295 additional tests, stronger sanitisation of...
2016-11-10 tcofoegbuBugfix to enable accurate chain extraction/association...
2016-11-10 gmungocJAL-2320 thread to close Chimera viewer panel if Chimer... features/JAL-2320_closeChimeraAction
2016-11-09 gmungocJAL-2295 set attributes commands include feature value...
2016-11-08 gmungocJAL-2295 JAL-1596 method to pass a command script file...
2016-11-08 gmungocJAL-2295 feature and colour commands refactored to...
2016-11-08 gmungocJAL-2295 extracted AtomSpecModel for reuse in Chimera...
2016-11-08 gmungocJAL-2295 make RangeComparator a top level class for...
2016-11-07 gmungocJAL-2295 small tidy of javadoc only
2016-11-07 gmungocJAL-2295 (unoptimised) write Jalview features as Chimer...
2016-10-27 tcofoegbuJAL-2177 Jmol update from: Jmol-14.2.14_2015.06.11...
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-24 Jim ProcterMerge branch 'releases/Release_2_10_0_Branch'
2016-10-24 gmungocMerge branch 'develop' into bug/JAL-98consensusMemory
2016-10-17 tcofoegbuJAL-2262 JAL-2195 Improvement to set PDBId availability...
2016-10-13 gmungocJAL-2253 2 second timeout on ping URL, default 5 minute... feature/JAL-2553ensemblGenomes
2016-10-13 gmungocMerge branch 'releases/Release_2_10_Branch' into develop
2016-10-13 gmungocJAL-2044 ensure AAStructureBindingModel.pdbEntry has...
2016-10-11 gmungocMerge branch 'releases/Release_2_10_Branch' into develop
2016-10-11 gmungocJAL-2233 reverted changes to Jmol logging levels
2016-10-10 tcofoegbuJAL-2262 JAL-2195 bug fix for mapping local structure...
2016-10-06 gmungocMerge branch 'develop' into bug/JAL-98consensusMemory
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch...
2016-10-05 Jim ProcterJAL-2189 apply license
2016-10-05 Jim ProcterJAL-2189 source formatting
2016-10-05 gmungocJAL-1191 use full SO in desktop application
2016-10-05 gmungocJAL-2105 update Ensembl REST version to 4.7
2016-10-03 gmungocJAL-2110 JAL-1705 handle not found (400) better
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