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JAL-2939 exit calc thread if no HMM in alignment
2018-04-24 gmungocJAL-2939 exit calc thread if no HMM in alignment
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2018-04-24 gmungocJAL-591 use constant for Preferences key
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2018-04-24 gmungocJAL-2616 unused field removed
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2018-04-24 gmungocJAL-2956 unit test
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2018-04-23 gmungocJAL-2956 save/restore HMMER profile to/from Jalview...
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2018-04-23 gmungocJAL-2957 don't validate input on arrow keys
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2018-04-23 gmungocJAL-591 ensure slider hidden if text input field only
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2018-04-20 gmungocJAL-591 slider scale factor now derived from min-max...
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2018-04-20 gmungocJAL-591 tidy and comment code
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2018-04-20 gmungocJAL-2629 tweaks to text
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2018-04-20 gmungocJAL-591 OptionBox FlowLayout, tweaks to wrapping of...
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2018-04-19 gmungocJAL-591 utility method renamed and slightly generalised
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2018-04-18 gmungocMerge branch 'develop' into features/mchmmer
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2018-04-18 gmungocMerge branch 'releases/Release_2_10_4_Branch' into...
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2018-04-18 gmungocJAL-2593 render 'duplicate' features if transparency...
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2018-04-18 gmungocJAL-2629 corrected cutoff parameter passing to hmmsearch
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2018-04-17 gmungocMerge branch 'features/mchmmer' of https://source.jalview...
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2018-04-17 gmungocJAL-2629 choice of hmm profile now a parameter not...
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2018-04-16 gmungocJAL-2629 JAL-2937 remove redundant is/setHMMConsensusSequence
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2018-04-16 gmungocJAL-2937 use preferences for presets, simplify some...
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2018-03-30 gmungocJAL-2599 MapList from HMM nodes to consensus dataset...
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2018-03-30 gmungocJAL-2629 tidy code, factory methods for param sets
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2018-03-30 gmungocJAL-2629 use correct gap character, revised deletion...
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2018-03-30 gmungocJAL-2629 Javadoc updates
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2018-03-30 gmungocJAL-2629 combine with/without defaults in one method...
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2018-03-30 gmungocJAL-2939 field/method naming more consistent
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2018-03-30 gmungocJAL-2629 ensure hmm consensus sequence set on alignment...
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2018-03-30 gmungocJAL-2941 'map hmm to RF' removed pending clarifications
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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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2018-03-22 gmungocJAL-2929 unit test, tidy unused/unneeded fields/parameters
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2018-03-21 gmungocJAL-2929 use configure Overview gap colour instead...
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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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