jalview.git
2018-03-30 gmungocJAL-2599 MapList from HMM nodes to consensus dataset...
2018-03-30 gmungocJAL-2629 tidy code, factory methods for param sets
2018-03-30 gmungocJAL-2629 use correct gap character, revised deletion...
2018-03-30 gmungocJAL-2629 Javadoc updates
2018-03-30 gmungocJAL-2629 combine with/without defaults in one method...
2018-03-30 gmungocJAL-2939 field/method naming more consistent
2018-03-30 gmungocJAL-2629 ensure hmm consensus sequence set on alignment...
2018-03-30 gmungocJAL-2941 'map hmm to RF' removed pending clarifications
2018-03-30 gmungocsmall tidy
2018-03-30 gmungocJAL-2938 revisions to implementation details
2018-03-30 gmungocJAL-2939 remove commented out code
2018-03-30 gmungocJAL-2599 move utility method to MappingUtils
2018-03-30 gmungocJAL-2939 simplified way of getting hmm consensus residue
2018-03-30 gmungocJAL-2629 add title to output alignment window
2018-03-30 gmungocJAL-2629 select HMM selects sequence under cursor
2018-03-30 gmungocJAL-2599 corrected test file name in unit test
2018-03-29 gmungocJAL-2907 test method renamed to match method name change
2018-03-29 gmungocJAL-2907 bug fix redone on HMMER branch
2018-03-28 gmungocJAL-1265 output all dbrefs in Stockholm (+tests) (...
2018-03-26 gmungocJAL-2939 pull up set/IsNormalise[HMM]SequenceLogo
2018-03-26 gmungocJAL-2939 unused action handler methods removed
2018-03-26 gmungocJAL-2939 no need to recalc HMM annotation for show...
2018-03-26 gmungocJAL-2939 always store Information profile
2018-03-23 gmungocJAL-2629 pad gaps when exporting alignment as 'database...
2018-03-23 gmungocJAL-2937 unused field removed
2018-03-23 gmungocJAL-2938 update colour schemes enum for class name...
2018-03-23 gmungocJAL-2938 extracted base class for Hmmer colour schems
2018-03-21 gmungocJAL-2629 tweaks to Information annotation updating
2018-03-20 gmungocJAL-2629 InformationThread.findOrCreateAnnotation and...
2018-03-20 gmungocMerge branch 'develop' into features/mchmmer
2018-03-16 gmungocJAL-2679 getGeneId() now uses the same pattern as getGe...
2018-03-16 gmungocMerge remote-tracking branch 'origin/releases/Release_2...
2018-03-16 gmungocJAL-2922 update FeatureRenderer and repaint feature...
2018-03-16 gmungocMerge branch 'develop' into features/mchmmer
2018-03-16 gmungocMerge branch 'bug/JAL-2865removeGC' into develop
2018-03-16 gmungocMerge branch 'develop' into trialMerge
2018-03-15 gmungocJAL-2893 enabling Get Crossreferences to ENSEMBLGENOMES
2018-03-14 gmungocJAL-2893 include ENSEMBLGENOMES as a 'roundtrip db...
2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge
2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge
2018-03-14 Jim ProcterJAL-2930 JAL-2924 JAL-2913 JAL-2926 JAL-2906 2.10.4...
2018-03-13 gmungocJAL-2913 use FIGURE_FIXEDIDWIDTH (not FIGURE_USERIDWIDTH)
2018-03-08 gmungocMerge remote-tracking branch 'origin/releases/Release_2... merges/JAL-2906_update2_11_from_2_10_4
2018-03-08 gmungocJAL-2885 tests updated for code changes
2018-03-08 gmungocJAL-2930 use MouseWheelEvent.getPreciseWheelRotation...
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2018-03-07 gmungocMerge branch 'bugs/JAL-2922' into releases/Release_2_10...
2018-03-07 gmungocJAL-2922 [2] not [1] for Boolean column of table bugs/JAL-2922
2018-03-07 gmungocMerge branch 'bugs/JAL-2922' into releases/Release_2_10...
2018-03-07 gmungocJAL-2922 i18n and bespoke handler for Invert Selection
2018-03-07 gmungocMerge branch 'bug/JAL-2924nullTooltip' into releases...
2018-03-07 gmungocJAL-2926 fix copy group consensus (and paste sequence...
2018-03-07 gmungocJAL-2925 handle empty annotation when copying group...
2018-03-07 gmungocJAL-2913 use FIGURE_USERIDWIDTH for fixed id width...
2018-03-07 gmungocJAL-2629 storage and lifecycle of alignment/group HMM...
2018-03-02 gmungocJAL-2729 draft help pages for HMMER menu
2018-03-01 gmungocJAL-2629 revising hmmer annotation updating (wip)
2018-02-28 gmungocJAL-2924 no tooltip over null annotation positions bug/JAL-2924nullTooltip
2018-02-28 gmungocJAL-2629 some tidying of Hmmer commands (wip)
2018-02-28 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch_merged_JAL...
2018-02-27 Jim ProcterJAL-2759 release notes for 2.10.4
2018-02-27 gmungocJAL-2668 method name change for clarity
2018-02-27 gmungocJAL-2668 fix broken factory method for colour scheme
2018-02-27 gmungocJAL-2717 JAL-2668 fixes to HMMER colour scheme display...
2018-02-27 Jim ProcterMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104
2018-02-27 Jim Procterfix for JAL-2922 - update states all at once and then...
2018-02-26 gmungocJAL-2599 test coverage and bug fixes for 'minimal file...
2018-02-26 Jim ProcterMerge branch 'feature/JAL-984splitAdjuster' into releas...
2018-02-26 Jim ProcterJAL-984 remove all references to idwidth.gif - in build... feature/JAL-984splitAdjuster
2018-02-23 Jim ProcterJAL-2885 release notes
2018-02-23 gmungocJAL-2599 corrected case-insensitive symbol indexing
2018-02-23 Jim ProcterMerge branch 'features/JAL-2885UniprotHttps' into relea...
2018-02-23 gmungocJAL-2599 parser and datamodel use primitive double...
2018-02-23 Jim ProcterJAL-2885 xfam https features/JAL-2885UniprotHttps
2018-02-23 Jim ProcterJAL-2885 XFAM_DOMAIN->XFAM_BASEURL
2018-02-23 Jim ProcterJAL-2885 Ensembl* -> https
2018-02-23 Jim ProcterJAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL
2018-02-23 Jim ProcterJAL-2885 renamed base URL getter from getDomain..
2018-02-22 gmungocJAL-2629 tidy tests, refactor hmmer node mapping slightly
2018-02-22 Jim ProcterMerge branch 'feature/JAL-984splitAdjuster' into releas...
2018-02-22 Jim ProcterJAL-984 ID width adjuster needs to be white !
2018-02-22 Jim ProcterJAL-2666 release notes
2018-02-22 Jim ProcterMerge branch 'bug/JAL-2666' into releases/Release_2_10_...
2018-02-22 Jim ProcterMerge branch 'feature/JAL-984splitAdjuster' into releas...
2018-02-22 Jim ProcterJAL-984 remove all references to idwidth.gif and use...
2018-02-22 Jim ProcterJAL-2906 typo fixes
2018-02-22 Jim ProcterJAL-984 release notes
2018-02-22 Jim ProcterMerge branch 'feature/JAL-984splitAdjuster' into releas...
2018-02-22 Jim ProcterJAL-294 remove unneeded paint() method
2018-02-22 Jim ProcterJAL-984 remove commented/unnecessary if clause
2018-02-22 gmungocJAL-2629 tidy unit tests, constants etc
2018-02-21 Jim ProcterJAL-2906 release notes for 2.10.4
2018-02-21 Jim ProcterMerge branch 'bug/JAL-2778again' into releases/Release_...
2018-02-21 Jim ProcterJAL-2778 reinstate transparent windows to avoid ugly... bug/JAL-2778again
2018-02-21 gmungocJAL-2629 simplifying method signatures in Hmmer command...
2018-02-21 kiramtJAL-2778 Adjust cursor changes in overview panel
2018-02-21 kiramtJAL-2778 Revert back to old synchronisation
2018-02-20 gmungocJAL-2629 removed SequenceI.get/setLastPosition and...
2018-02-20 gmungocMerge branch 'develop' into features/mchmmer
2018-02-20 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
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