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JAL-2994 use pattern matches to search for chimera.exe
2018-05-28 gmungocJAL-2994 use pattern matches to search for chimera.exe
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2018-05-28 gmungocMerge branch 'develop' into features/mchmmer
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2018-05-28 gmungocMerge branch 'bug/JAL-797' into develop
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2018-05-28 gmungocMerge remote-tracking branch 'origin/releases/Release_2_10_4...
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2018-05-25 gmungocJAL-2992 simpler heuristic for available height
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2018-05-25 gmungocJAL-2995 tooltip on fields with double-click to browse...
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2018-05-25 gmungocJAL-2994 temporary patch with paths to Chimera for...
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2018-05-24 gmungocJAL-2997 additional tests
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2018-05-23 gmungocJAL-2993 AlignFrame listen for keystrokes in OverviewPanel
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2018-05-23 gmungocJAL-2997 unit test
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2018-05-23 gmungocJAL-2997 handle tab-delimited trailing column number...
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2018-05-22 gmungocJAL-2716 fix to reset choice parameter on Revert
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2018-05-22 gmungocJAL-2716 fix broken checkIfModified behaviour
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2018-05-22 gmungocJAL-2629 method refactor and menu tidying
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2018-05-21 gmungocJAL-797 Cmd-W act WHEN_IN_FOCUSED_WINDOW
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2018-05-15 gmungocJAL-2719 parse bit score annotation from search results
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2018-05-15 gmungocJAL-1264 exclude score-only from 'Add Reference Annotations'
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2018-05-15 gmungocJAL-2629 JAL-2937 respect 'align automatically' option...
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2018-05-14 gmungocJAL-2989 refactoring to reduce code duplication
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2018-05-14 gmungocJAL-2711 show short file names in search database combo box
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2018-05-14 gmungocJAL-2989 support value display names for Option or...
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2018-05-14 gmungocJAL-2711 removed unused and flaky utility method
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2018-05-14 gmungocJAL-2939 check for hmm present when processing groups
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2018-05-11 gmungocJAL-2985 show label instead of checkbox for a required...
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2018-05-11 gmungocMerge branch 'develop' into features/mchmmer
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2018-05-11 gmungocJAL-2986 corrected findIndex for out of range residue...
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2018-05-11 gmungocJAL-2986 additional asserts for SequenceCursor updates
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2018-05-11 gmungocJAL-2986 failing test added
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2018-05-10 gmungocJAL-2629 revert to showing Profile parameter even if...
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2018-05-10 gmungocJAL-2629 default HMMBuild to alignment if not specified...
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2018-05-10 gmungocJAL-591 reduced updating by checking/setting 'updating...
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2018-05-10 gmungocJAL-2629 handle decline 'Add Database'
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2018-05-10 gmungocJAL-2629 adjust placement and optionality of arguments...
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2018-05-10 gmungocJAL-591 show choice list with a single option
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2018-05-09 gmungocJAL-2714 HMMSearch cutoff by E-Value, Score or None
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2018-05-09 gmungocJAL-2984 add pdb as sequence(s) if associate structure...
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2018-05-08 gmungocMerge branch 'develop' into features/mchmmer
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2018-05-07 gmungocJAL-2808 ensure test setUp/tearDown alwaysRun
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2018-05-07 gmungocMerge branch 'releases/Release_2_10_4_Branch' into...
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2018-05-04 gmungocJAL-2906 small tweaks to release notes
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2018-04-24 gmungocJAL-2959 no Print dialog shown if Page Format is Cancelled
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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-2954 more efficient SearchResults.markColumns
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2018-04-23 gmungocJAL-2952 set negative TempFactor values as AlignmentAnnotati...
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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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2018-04-13 gmungocMerge branch 'features/JAL-2944_openStructuresInSelectedView...
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2018-04-12 gmungocJAL-2223 don't add duplicate mappings to StructureSelectionM...
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2018-04-12 gmungocJAL-1847 minor post-review updates
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2018-04-12 gmungocJAL-2944 tidies for review comments
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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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2018-03-21 gmungocJAL-2754 renamed proguard.jar to include version number
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2018-03-21 gmungocJAL-2754 5.3.3 update of proguard.jar
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2018-03-21 gmungocJAL-2754 update to specify Java 1.8(+)
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