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jalview.git
2018-04-17 gmungocMerge branch 'features/mchmmer' of https://source.jalvi... commit | commitdiff | tree | snapshot
2018-04-17 gmungocJAL-2629 choice of hmm profile now a parameter not... commit | commitdiff | tree | snapshot
2018-04-17 Mungo CarstairsJAL-2937 working Cygwin bash execution of hmmbuild... commit | commitdiff | tree | snapshot
2018-04-16 gmungocJAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe... commit | commitdiff | tree | snapshot
2018-04-16 gmungocJAL-2937 use preferences for presets, simplify some... commit | commitdiff | tree | snapshot
2018-04-09 Mungo CarstairsJAL-2937 Cygwin path preference, method refactoring commit | commitdiff | tree | snapshot
2018-04-09 Mungo CarstairsJAL-2629 more error checking commit | commitdiff | tree | snapshot
2018-04-09 Mungo CarstairsJAL-2937 extract reusable utility method commit | commitdiff | tree | snapshot
2018-04-09 Mungo CarstairsJAL-2069 typo commit | commitdiff | tree | snapshot
2018-03-30 gmungocJAL-2599 MapList from HMM nodes to consensus dataset... commit | commitdiff | tree | snapshot
2018-03-30 gmungocJAL-2629 tidy code, factory methods for param sets commit | commitdiff | tree | snapshot
2018-03-30 gmungocJAL-2629 use correct gap character, revised deletion... commit | commitdiff | tree | snapshot
2018-03-30 gmungocJAL-2629 Javadoc updates commit | commitdiff | tree | snapshot
2018-03-30 gmungocJAL-2629 combine with/without defaults in one method... commit | commitdiff | tree | snapshot
2018-03-30 gmungocJAL-2939 field/method naming more consistent commit | commitdiff | tree | snapshot
2018-03-30 gmungocJAL-2629 ensure hmm consensus sequence set on alignment... commit | commitdiff | tree | snapshot
2018-03-30 gmungocJAL-2941 'map hmm to RF' removed pending clarifications commit | commitdiff | tree | snapshot
2018-03-30 gmungocsmall tidy commit | commitdiff | tree | snapshot
2018-03-30 gmungocJAL-2938 revisions to implementation details commit | commitdiff | tree | snapshot
2018-03-30 gmungocJAL-2939 remove commented out code commit | commitdiff | tree | snapshot
2018-03-30 gmungocJAL-2599 move utility method to MappingUtils commit | commitdiff | tree | snapshot
2018-03-30 gmungocJAL-2939 simplified way of getting hmm consensus residue commit | commitdiff | tree | snapshot
2018-03-30 gmungocJAL-2629 add title to output alignment window commit | commitdiff | tree | snapshot
2018-03-30 gmungocJAL-2629 select HMM selects sequence under cursor commit | commitdiff | tree | snapshot
2018-03-30 gmungocJAL-2599 corrected test file name in unit test commit | commitdiff | tree | snapshot
2018-03-29 gmungocJAL-2907 test method renamed to match method name change commit | commitdiff | tree | snapshot
2018-03-29 gmungocJAL-2907 bug fix redone on HMMER branch commit | commitdiff | tree | snapshot
2018-03-28 gmungocJAL-1265 output all dbrefs in Stockholm (+tests) (... commit | commitdiff | tree | snapshot
2018-03-26 gmungocJAL-2939 pull up set/IsNormalise[HMM]SequenceLogo commit | commitdiff | tree | snapshot
2018-03-26 gmungocJAL-2939 unused action handler methods removed commit | commitdiff | tree | snapshot
2018-03-26 gmungocJAL-2939 no need to recalc HMM annotation for show... commit | commitdiff | tree | snapshot
2018-03-26 gmungocJAL-2939 always store Information profile commit | commitdiff | tree | snapshot
2018-03-23 gmungocJAL-2629 pad gaps when exporting alignment as 'database... commit | commitdiff | tree | snapshot
2018-03-23 gmungocJAL-2937 unused field removed commit | commitdiff | tree | snapshot
2018-03-23 gmungocJAL-2938 update colour schemes enum for class name... commit | commitdiff | tree | snapshot
2018-03-23 gmungocJAL-2938 extracted base class for Hmmer colour schems commit | commitdiff | tree | snapshot
2018-03-21 gmungocJAL-2629 tweaks to Information annotation updating commit | commitdiff | tree | snapshot
2018-03-20 gmungocJAL-2629 InformationThread.findOrCreateAnnotation and... commit | commitdiff | tree | snapshot
2018-03-20 gmungocMerge branch 'develop' into features/mchmmer commit | commitdiff | tree | snapshot
2018-03-16 gmungocJAL-2679 getGeneId() now uses the same pattern as getGe... commit | commitdiff | tree | snapshot
2018-03-16 gmungocMerge remote-tracking branch 'origin/releases/Release_2... commit | commitdiff | tree | snapshot
2018-03-16 gmungocJAL-2922 update FeatureRenderer and repaint feature... commit | commitdiff | tree | snapshot
2018-03-16 gmungocMerge branch 'develop' into features/mchmmer commit | commitdiff | tree | snapshot
2018-03-16 gmungocMerge branch 'bug/JAL-2865removeGC' into develop commit | commitdiff | tree | snapshot
2018-03-16 gmungocMerge branch 'develop' into trialMerge commit | commitdiff | tree | snapshot
2018-03-15 gmungocJAL-2893 enabling Get Crossreferences to ENSEMBLGENOMES commit | commitdiff | tree | snapshot
2018-03-14 gmungocJAL-2893 include ENSEMBLGENOMES as a 'roundtrip db... commit | commitdiff | tree | snapshot
2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge commit | commitdiff | tree | snapshot
2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge commit | commitdiff | tree | snapshot
2018-03-14 Jim ProcterJAL-2930 JAL-2924 JAL-2913 JAL-2926 JAL-2906 2.10.4... commit | commitdiff | tree | snapshot
2018-03-13 gmungocJAL-2913 use FIGURE_FIXEDIDWIDTH (not FIGURE_USERIDWIDTH) commit | commitdiff | tree | snapshot
2018-03-08 gmungocMerge remote-tracking branch 'origin/releases/Release_2... merges/JAL-2906_update2_11_from_2_10_4 commit | commitdiff | tree | snapshot
2018-03-08 gmungocJAL-2885 tests updated for code changes commit | commitdiff | tree | snapshot
2018-03-08 gmungocJAL-2930 use MouseWheelEvent.getPreciseWheelRotation... commit | commitdiff | tree | snapshot
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... commit | commitdiff | tree | snapshot
2018-03-07 gmungocMerge branch 'bugs/JAL-2922' into releases/Release_2_10... commit | commitdiff | tree | snapshot
2018-03-07 gmungocJAL-2922 [2] not [1] for Boolean column of table bugs/JAL-2922 commit | commitdiff | tree | snapshot
2018-03-07 gmungocMerge branch 'bugs/JAL-2922' into releases/Release_2_10... commit | commitdiff | tree | snapshot
2018-03-07 gmungocJAL-2922 i18n and bespoke handler for Invert Selection commit | commitdiff | tree | snapshot
2018-03-07 gmungocMerge branch 'bug/JAL-2924nullTooltip' into releases... commit | commitdiff | tree | snapshot
2018-03-07 gmungocJAL-2926 fix copy group consensus (and paste sequence... commit | commitdiff | tree | snapshot
2018-03-07 gmungocJAL-2925 handle empty annotation when copying group... commit | commitdiff | tree | snapshot
2018-03-07 gmungocJAL-2913 use FIGURE_USERIDWIDTH for fixed id width... commit | commitdiff | tree | snapshot
2018-03-07 gmungocJAL-2629 storage and lifecycle of alignment/group HMM... commit | commitdiff | tree | snapshot
2018-03-02 gmungocJAL-2729 draft help pages for HMMER menu commit | commitdiff | tree | snapshot
2018-03-01 gmungocJAL-2629 revising hmmer annotation updating (wip) commit | commitdiff | tree | snapshot
2018-02-28 gmungocJAL-2924 no tooltip over null annotation positions bug/JAL-2924nullTooltip commit | commitdiff | tree | snapshot
2018-02-28 gmungocJAL-2629 some tidying of Hmmer commands (wip) commit | commitdiff | tree | snapshot
2018-02-28 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch_merged_JAL... commit | commitdiff | tree | snapshot
2018-02-27 Jim ProcterJAL-2759 release notes for 2.10.4 commit | commitdiff | tree | snapshot
2018-02-27 gmungocJAL-2668 method name change for clarity commit | commitdiff | tree | snapshot
2018-02-27 gmungocJAL-2668 fix broken factory method for colour scheme commit | commitdiff | tree | snapshot
2018-02-27 gmungocJAL-2717 JAL-2668 fixes to HMMER colour scheme display... commit | commitdiff | tree | snapshot
2018-02-27 Jim ProcterMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104 commit | commitdiff | tree | snapshot
2018-02-27 Jim Procterfix for JAL-2922 - update states all at once and then... commit | commitdiff | tree | snapshot
2018-02-26 gmungocJAL-2599 test coverage and bug fixes for 'minimal file... commit | commitdiff | tree | snapshot
2018-02-26 Jim ProcterMerge branch 'feature/JAL-984splitAdjuster' into releas... commit | commitdiff | tree | snapshot
2018-02-26 Jim ProcterJAL-984 remove all references to idwidth.gif - in build... feature/JAL-984splitAdjuster commit | commitdiff | tree | snapshot
2018-02-23 Jim ProcterJAL-2885 release notes commit | commitdiff | tree | snapshot
2018-02-23 gmungocJAL-2599 corrected case-insensitive symbol indexing commit | commitdiff | tree | snapshot
2018-02-23 Jim ProcterMerge branch 'features/JAL-2885UniprotHttps' into relea... commit | commitdiff | tree | snapshot
2018-02-23 gmungocJAL-2599 parser and datamodel use primitive double... commit | commitdiff | tree | snapshot
2018-02-23 Jim ProcterJAL-2885 xfam https features/JAL-2885UniprotHttps commit | commitdiff | tree | snapshot
2018-02-23 Jim ProcterJAL-2885 XFAM_DOMAIN->XFAM_BASEURL commit | commitdiff | tree | snapshot
2018-02-23 Jim ProcterJAL-2885 Ensembl* -> https commit | commitdiff | tree | snapshot
2018-02-23 Jim ProcterJAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL commit | commitdiff | tree | snapshot
2018-02-23 Jim ProcterJAL-2885 renamed base URL getter from getDomain.. commit | commitdiff | tree | snapshot
2018-02-22 gmungocJAL-2629 tidy tests, refactor hmmer node mapping slightly commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterMerge branch 'feature/JAL-984splitAdjuster' into releas... commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterJAL-984 ID width adjuster needs to be white ! commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterJAL-2666 release notes commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterMerge branch 'bug/JAL-2666' into releases/Release_2_10_... commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterMerge branch 'feature/JAL-984splitAdjuster' into releas... commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterJAL-984 remove all references to idwidth.gif and use... commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterJAL-2906 typo fixes commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterJAL-984 release notes commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterMerge branch 'feature/JAL-984splitAdjuster' into releas... commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterJAL-294 remove unneeded paint() method commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterJAL-984 remove commented/unnecessary if clause commit | commitdiff | tree | snapshot
2018-02-22 gmungocJAL-2629 tidy unit tests, constants etc commit | commitdiff | tree | snapshot
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