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small tidy
2018-03-30 gmungocsmall tidy
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2018-03-30 gmungocJAL-2938 revisions to implementation details
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2018-03-30 gmungocJAL-2939 remove commented out code
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2018-03-30 gmungocJAL-2599 move utility method to MappingUtils
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2018-03-30 gmungocJAL-2939 simplified way of getting hmm consensus residue
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2018-03-30 gmungocJAL-2629 add title to output alignment window
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2018-03-30 gmungocJAL-2629 select HMM selects sequence under cursor
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2018-03-30 gmungocJAL-2599 corrected test file name in unit test
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2018-03-29 gmungocJAL-2907 test method renamed to match method name change
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2018-03-29 gmungocJAL-2907 bug fix redone on HMMER branch
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2018-03-28 gmungocJAL-1265 output all dbrefs in Stockholm (+tests) (...
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2018-03-26 gmungocJAL-2939 pull up set/IsNormalise[HMM]SequenceLogo
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2018-03-26 gmungocJAL-2939 unused action handler methods removed
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2018-03-26 gmungocJAL-2939 no need to recalc HMM annotation for show...
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2018-03-26 gmungocJAL-2939 always store Information profile
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2018-03-23 gmungocJAL-2629 pad gaps when exporting alignment as 'database...
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2018-03-23 gmungocJAL-2937 unused field removed
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2018-03-23 gmungocJAL-2938 update colour schemes enum for class name...
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2018-03-23 gmungocJAL-2938 extracted base class for Hmmer colour schems
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2018-03-21 gmungocJAL-2629 tweaks to Information annotation updating
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2018-03-20 gmungocJAL-2629 InformationThread.findOrCreateAnnotation and...
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2018-03-20 gmungocMerge branch 'develop' into features/mchmmer
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2018-03-16 gmungocJAL-2679 getGeneId() now uses the same pattern as getGeneLoc...
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2018-03-16 gmungocMerge remote-tracking branch 'origin/releases/Release_2_10_4...
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2018-03-16 gmungocJAL-2922 update FeatureRenderer and repaint feature...
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2018-03-16 gmungocMerge branch 'develop' into features/mchmmer
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2018-03-16 gmungocMerge branch 'bug/JAL-2865removeGC' into develop
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2018-03-16 gmungocMerge branch 'develop' into trialMerge
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2018-03-15 gmungocJAL-2893 enabling Get Crossreferences to ENSEMBLGENOMES
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2018-03-14 gmungocJAL-2893 include ENSEMBLGENOMES as a 'roundtrip db...
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2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge
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2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge
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2018-03-13 gmungocJAL-2913 use FIGURE_FIXEDIDWIDTH (not FIGURE_USERIDWIDTH)
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2018-03-08 gmungocMerge remote-tracking branch 'origin/releases/Release_2_10_4...
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2018-03-08 gmungocJAL-2885 tests updated for code changes
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2018-03-08 gmungocJAL-2930 use MouseWheelEvent.getPreciseWheelRotation...
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2018-03-07 gmungocMerge branch 'bugs/JAL-2922' into releases/Release_2_10_4_Branch
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2018-03-07 gmungocJAL-2922 [2] not [1] for Boolean column of table
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2018-03-07 gmungocMerge branch 'bugs/JAL-2922' into releases/Release_2_10_4_Branch
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2018-03-07 gmungocJAL-2922 i18n and bespoke handler for Invert Selection
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2018-03-07 gmungocMerge branch 'bug/JAL-2924nullTooltip' into releases...
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2018-03-07 gmungocJAL-2926 fix copy group consensus (and paste sequence...
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2018-03-07 gmungocJAL-2925 handle empty annotation when copying group...
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2018-03-07 gmungocJAL-2913 use FIGURE_USERIDWIDTH for fixed id width...
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2018-03-07 gmungocJAL-2629 storage and lifecycle of alignment/group HMM...
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2018-03-02 gmungocJAL-2729 draft help pages for HMMER menu
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2018-03-01 gmungocJAL-2629 revising hmmer annotation updating (wip)
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2018-02-28 gmungocJAL-2924 no tooltip over null annotation positions
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2018-02-28 gmungocJAL-2629 some tidying of Hmmer commands (wip)
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2018-02-27 gmungocJAL-2668 method name change for clarity
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2018-02-27 gmungocJAL-2668 fix broken factory method for colour scheme
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2018-02-27 gmungocJAL-2717 JAL-2668 fixes to HMMER colour scheme display...
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2018-02-26 gmungocJAL-2599 test coverage and bug fixes for 'minimal file...
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2018-02-23 gmungocJAL-2599 corrected case-insensitive symbol indexing
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2018-02-23 gmungocJAL-2599 parser and datamodel use primitive double...
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2018-02-22 gmungocJAL-2629 tidy tests, refactor hmmer node mapping slightly
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2018-02-22 gmungocJAL-2629 tidy unit tests, constants etc
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2018-02-21 gmungocJAL-2629 simplifying method signatures in Hmmer command...
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2018-02-20 gmungocJAL-2629 removed SequenceI.get/setLastPosition and...
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2018-02-20 gmungocMerge branch 'develop' into features/mchmmer
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2018-02-20 gmungocJAL-2897 updated unit test for code change
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2018-02-20 gmungocMerge branch 'develop' into features/JAL-1793VCF
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2018-02-19 gmungocJAL-2629 refactoring of Hmmer preferences
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2018-02-19 gmungocJAL-2629 partial refactoring of Hmmer command classes
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2018-02-19 gmungocJAL-2629 formatting only
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2018-02-09 gmungocJAL-2789 avoid using transcript (with no UTR) as CDS...
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2018-02-09 gmungocJAL-2789 code format changes only (before functional...
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2018-02-09 gmungocJAL-2666 fix failure to scroll split alignment of height 1
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2018-02-08 gmungocJAL-2666 basic initial fix for split screen scroll bug
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2018-02-07 gmungocJAL-2808 ensure pattern field re-enabled when needed...
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2018-02-05 gmungocJAL-2897 more informative description on synonymous...
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2018-02-05 gmungocJAL-2897 more informative description on synonymous...
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2018-02-05 gmungocMerge branch 'spikes/mungo' into trialMerge
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2018-02-05 gmungocJAL-2897 more informative description on synonymous...
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2018-02-02 gmungocJAL-984 merged to spikes-mungo
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2018-02-02 gmungocMerge branch 'feature/JAL-984splitAdjuster' into features...
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2018-02-02 gmungocJAL-984 use cursor for drag regions to adjust annotation...
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2018-02-02 gmungocJAL-984 better behaved panel height adjuster
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2018-01-31 gmungocJAL-2792 added tooltip to menu items in case of truncation
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2018-01-30 gmungocJAL-2069 menu item now "Variable colour..." to hint...
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2018-01-30 gmungocJAL-1793 update spike build to latest incl stop and...
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2018-01-30 gmungocJAL-2898 show 'stop_gained' variants on peptide sequences
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2018-01-30 gmungocJAL-2897 generate peptide variants for synonymous codon...
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2018-01-30 gmungocJAL-2897 formatting change only prior to functional...
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2018-01-29 gmungocMerge branch 'feature/JAL-2759' of https://source.jalview...
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2018-01-29 gmungocJAL-1270 testPadGaps() added
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2018-01-29 gmungocJAL-2743 recoded EnsemblLookup without lambda expressions...
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2018-01-26 gmungocMerge branch 'develop' into features/JAL-1793VCF
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2018-01-18 gmungocJAL-2810 JAL-2886 i18n
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2018-01-18 gmungocJAL-2679 update query id to actual case of retrieved...
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2018-01-17 gmungocJAL-2679 case-insensitive comparison of query and retrieved...
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2018-01-16 gmungocJAL-2679 use object_type=Transcript for lookup of Parent...
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2018-01-16 gmungocJAL-2885 uniprot now https, uniprot/ensembl/pfam/xfam...
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2018-01-16 gmungocJAL-1270 JAL-2885 clear properties before load
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2018-01-10 gmungocJAL-2865 unhelpful System.gc() calls removed
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2018-01-10 gmungocJAL-1793 update spike branch to latest
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2018-01-10 gmungocJAL-2791 ignore feature type visibility in getColor()
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2018-01-09 gmungocJAL-2843 test roundtrip of feature colours and filters...
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2018-01-09 gmungocJAL-2843 unit tests for writing filters to Jalview...
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2018-01-09 gmungocJAL-2843 unit tests for Save/Load colours and filters...
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