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JAL-3011 JAL-2719 JAL-1958 add posterior probability scores to score and value annota...
[jalview.git] / src /
2018-04-16 gmungocJAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe... tree | commitdiff
2018-04-16 gmungocJAL-2937 use preferences for presets, simplify some... tree | commitdiff
2018-04-13 gmungocMerge branch 'features/JAL-2944_openStructuresInSelecte... features/JAL-2944_openStructuresInSelectedView tree | commitdiff
2018-04-12 gmungocJAL-2223 don't add duplicate mappings to StructureSelec... tree | commitdiff
2018-04-12 gmungocJAL-1847 minor post-review updates tree | commitdiff
2018-04-12 gmungocJAL-2944 tidies for review comments tree | commitdiff
2018-04-11 Jim ProcterJAL-2946 catch unexpected SIFTS mapping exceptions... tree | commitdiff
2018-04-09 Mungo CarstairsJAL-2937 Cygwin path preference, method refactoring tree | commitdiff
2018-04-09 Mungo CarstairsJAL-2629 more error checking tree | commitdiff
2018-04-09 Mungo CarstairsJAL-2937 extract reusable utility method tree | commitdiff
2018-04-09 Mungo CarstairsJAL-2069 typo tree | commitdiff
2018-04-09 Jim ProcterJAL-2944 ’new view’ and ‘add to view’ button rather... tree | commitdiff
2018-04-09 Jim ProcterJAL-1847 superpose checkbox in structure chooser tree | commitdiff
2018-04-09 Jim ProcterJAL-1847 JAL-2944 make superposition step a configurabl... tree | commitdiff
2018-04-05 Jim ProcterJAL-2945 resolve model as PDB file. Need to verify... tree | commitdiff
2018-04-05 Jim ProcterJAL-2945 provide access to last highlighted results tree | commitdiff
2018-04-05 Jim ProcterJAL-2944 open selected structures in existing or a... tree | commitdiff
2018-04-05 Jim ProcterJAL-2944 combo box to pick which viewer to load structu... tree | commitdiff
2018-04-05 Jim ProcterJAL-2944 methods to check existence and get a title... tree | commitdiff
2018-04-05 Jim ProcterJAL-2944 allow StructureViewer proxy to be created... tree | commitdiff
2018-04-05 Jim ProcterJAL-2944 get viewer’s title via toString() tree | commitdiff
2018-04-05 Jim ProcterJAL-2944 expose UI update methods in api tree | commitdiff
2018-04-05 Jim ProcterJAL-2944 remove modal prompt logic and expose methods... tree | commitdiff
2018-04-05 Jim ProcterJAL-2944 pull up structure viewer discovery routine... tree | commitdiff
2018-03-30 gmungocJAL-2599 MapList from HMM nodes to consensus dataset... tree | commitdiff
2018-03-30 gmungocJAL-2629 tidy code, factory methods for param sets tree | commitdiff
2018-03-30 gmungocJAL-2629 use correct gap character, revised deletion... tree | commitdiff
2018-03-30 gmungocJAL-2629 Javadoc updates tree | commitdiff
2018-03-30 gmungocJAL-2629 combine with/without defaults in one method... tree | commitdiff
2018-03-30 gmungocJAL-2939 field/method naming more consistent tree | commitdiff
2018-03-30 gmungocJAL-2629 ensure hmm consensus sequence set on alignment... tree | commitdiff
2018-03-30 gmungocJAL-2941 'map hmm to RF' removed pending clarifications tree | commitdiff
2018-03-30 gmungocJAL-2938 revisions to implementation details tree | commitdiff
2018-03-30 gmungocJAL-2939 remove commented out code tree | commitdiff
2018-03-30 gmungocJAL-2599 move utility method to MappingUtils tree | commitdiff
2018-03-30 gmungocJAL-2939 simplified way of getting hmm consensus residue tree | commitdiff
2018-03-30 gmungocJAL-2629 add title to output alignment window tree | commitdiff
2018-03-30 gmungocJAL-2629 select HMM selects sequence under cursor tree | commitdiff
2018-03-29 gmungocJAL-2907 bug fix redone on HMMER branch tree | commitdiff
2018-03-28 gmungocJAL-1265 output all dbrefs in Stockholm (+tests) (... tree | commitdiff
2018-03-26 gmungocJAL-2939 pull up set/IsNormalise[HMM]SequenceLogo tree | commitdiff
2018-03-26 gmungocJAL-2939 unused action handler methods removed tree | commitdiff
2018-03-26 gmungocJAL-2939 no need to recalc HMM annotation for show... tree | commitdiff
2018-03-26 gmungocJAL-2939 always store Information profile tree | commitdiff
2018-03-23 gmungocJAL-2629 pad gaps when exporting alignment as 'database... tree | commitdiff
2018-03-23 gmungocJAL-2937 unused field removed tree | commitdiff
2018-03-23 gmungocJAL-2938 update colour schemes enum for class name... tree | commitdiff
2018-03-23 gmungocJAL-2938 extracted base class for Hmmer colour schems tree | commitdiff
2018-03-22 gmungocJAL-2929 unit test, tidy unused/unneeded fields/parameters tree | commitdiff
2018-03-21 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... tree | commitdiff
2018-03-21 Jim ProcterMerge branch 'patch/JAL-2754_patch2104forJava8' into... tree | commitdiff
2018-03-21 Jim ProcterJAL-2754 fix eclipse compilation error about referencin... tree | commitdiff
2018-03-21 gmungocJAL-2929 use configure Overview gap colour instead... tree | commitdiff
2018-03-21 gmungocJAL-2629 tweaks to Information annotation updating tree | commitdiff
2018-03-20 gmungocJAL-2629 InformationThread.findOrCreateAnnotation and... tree | commitdiff
2018-03-20 gmungocMerge branch 'develop' into features/mchmmer tree | commitdiff
2018-03-16 gmungocJAL-2679 getGeneId() now uses the same pattern as getGe... tree | commitdiff
2018-03-16 gmungocMerge remote-tracking branch 'origin/releases/Release_2... tree | commitdiff
2018-03-16 gmungocJAL-2922 update FeatureRenderer and repaint feature... tree | commitdiff
2018-03-16 gmungocMerge branch 'develop' into features/mchmmer tree | commitdiff
2018-03-16 gmungocMerge branch 'bug/JAL-2865removeGC' into develop tree | commitdiff
2018-03-16 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2018-03-15 gmungocJAL-2893 enabling Get Crossreferences to ENSEMBLGENOMES tree | commitdiff
2018-03-14 gmungocJAL-2893 include ENSEMBLGENOMES as a 'roundtrip db... tree | commitdiff
2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge tree | commitdiff
2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge tree | commitdiff
2018-03-13 gmungocJAL-2913 use FIGURE_FIXEDIDWIDTH (not FIGURE_USERIDWIDTH) tree | commitdiff
2018-03-08 gmungocMerge remote-tracking branch 'origin/releases/Release_2... merges/JAL-2906_update2_11_from_2_10_4 tree | commitdiff
2018-03-08 gmungocJAL-2885 tests updated for code changes tree | commitdiff
2018-03-08 gmungocJAL-2930 use MouseWheelEvent.getPreciseWheelRotation... tree | commitdiff
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... tree | commitdiff
2018-03-07 gmungocMerge branch 'bugs/JAL-2922' into releases/Release_2_10... tree | commitdiff
2018-03-07 gmungocJAL-2922 [2] not [1] for Boolean column of table bugs/JAL-2922 tree | commitdiff
2018-03-07 gmungocMerge branch 'bugs/JAL-2922' into releases/Release_2_10... tree | commitdiff
2018-03-07 gmungocJAL-2922 i18n and bespoke handler for Invert Selection tree | commitdiff
2018-03-07 gmungocMerge branch 'bug/JAL-2924nullTooltip' into releases... tree | commitdiff
2018-03-07 gmungocJAL-2926 fix copy group consensus (and paste sequence... tree | commitdiff
2018-03-07 gmungocJAL-2925 handle empty annotation when copying group... tree | commitdiff
2018-03-07 gmungocJAL-2913 use FIGURE_USERIDWIDTH for fixed id width... tree | commitdiff
2018-03-07 gmungocJAL-2629 storage and lifecycle of alignment/group HMM... tree | commitdiff
2018-03-01 gmungocJAL-2629 revising hmmer annotation updating (wip) tree | commitdiff
2018-02-28 gmungocJAL-2924 no tooltip over null annotation positions bug/JAL-2924nullTooltip tree | commitdiff
2018-02-28 gmungocJAL-2629 some tidying of Hmmer commands (wip) tree | commitdiff
2018-02-27 gmungocJAL-2668 method name change for clarity tree | commitdiff
2018-02-27 gmungocJAL-2668 fix broken factory method for colour scheme tree | commitdiff
2018-02-27 gmungocJAL-2717 JAL-2668 fixes to HMMER colour scheme display... tree | commitdiff
2018-02-27 Jim ProcterMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104 tree | commitdiff
2018-02-27 Jim Procterfix for JAL-2922 - update states all at once and then... tree | commitdiff
2018-02-26 Jim ProcterJAL-2920 parse variation and original elements of the... tree | commitdiff
2018-02-26 gmungocJAL-2599 test coverage and bug fixes for 'minimal file... tree | commitdiff
2018-02-23 gmungocJAL-2599 corrected case-insensitive symbol indexing tree | commitdiff
2018-02-23 Jim ProcterMerge branch 'features/JAL-2885UniprotHttps' into relea... tree | commitdiff
2018-02-23 gmungocJAL-2599 parser and datamodel use primitive double... tree | commitdiff
2018-02-23 Jim ProcterJAL-2885 xfam https features/JAL-2885UniprotHttps tree | commitdiff
2018-02-23 Jim ProcterJAL-2885 XFAM_DOMAIN->XFAM_BASEURL tree | commitdiff
2018-02-23 Jim ProcterJAL-2885 Ensembl* -> https tree | commitdiff
2018-02-23 Jim ProcterJAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL tree | commitdiff
2018-02-23 Jim ProcterJAL-2885 renamed base URL getter from getDomain.. tree | commitdiff
2018-02-22 gmungocJAL-2629 tidy tests, refactor hmmer node mapping slightly tree | commitdiff
2018-02-22 Jim ProcterMerge branch 'feature/JAL-984splitAdjuster' into releas... tree | commitdiff
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