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2018-05-28	gmungoc	JAL-2994 restrict search to \Program Files\Chimera*	commit \| commitdiff \| tree
2018-05-28	gmungoc	JAL-2994 use pattern matches to search for chimera.exe	commit \| commitdiff \| tree
2018-05-28	gmungoc	Merge branch 'develop' into features/mchmmer	commit \| commitdiff \| tree
2018-05-28	gmungoc	Merge branch 'bug/JAL-797' into develop	commit \| commitdiff \| tree
2018-05-28	gmungoc	Merge remote-tracking branch 'origin/releases/Release_2_10_4...	commit \| commitdiff \| tree
2018-05-25	gmungoc	JAL-2992 simpler heuristic for available height	commit \| commitdiff \| tree
2018-05-25	gmungoc	JAL-2995 tooltip on fields with double-click to browse...	commit \| commitdiff \| tree
2018-05-25	gmungoc	JAL-2994 temporary patch with paths to Chimera for...	commit \| commitdiff \| tree
2018-05-24	gmungoc	JAL-2997 additional tests	commit \| commitdiff \| tree
2018-05-23	gmungoc	JAL-2993 AlignFrame listen for keystrokes in OverviewPanel	commit \| commitdiff \| tree
2018-05-23	gmungoc	JAL-2997 unit test	commit \| commitdiff \| tree
2018-05-23	gmungoc	JAL-2997 handle tab-delimited trailing column number...	commit \| commitdiff \| tree
2018-05-22	gmungoc	JAL-2716 fix to reset choice parameter on Revert	commit \| commitdiff \| tree
2018-05-22	gmungoc	JAL-2716 fix broken checkIfModified behaviour	commit \| commitdiff \| tree
2018-05-22	gmungoc	JAL-2629 method refactor and menu tidying	commit \| commitdiff \| tree
2018-05-21	gmungoc	JAL-797 Cmd-W act WHEN_IN_FOCUSED_WINDOW	commit \| commitdiff \| tree
2018-05-15	gmungoc	JAL-2719 parse bit score annotation from search results	commit \| commitdiff \| tree
2018-05-15	gmungoc	JAL-1264 exclude score-only from 'Add Reference Annotations'	commit \| commitdiff \| tree
2018-05-15	gmungoc	JAL-2629 JAL-2937 respect 'align automatically' option...	commit \| commitdiff \| tree
2018-05-14	gmungoc	JAL-2989 refactoring to reduce code duplication	commit \| commitdiff \| tree
2018-05-14	gmungoc	JAL-2711 show short file names in search database combo box	commit \| commitdiff \| tree
2018-05-14	gmungoc	JAL-2989 support value display names for Option or...	commit \| commitdiff \| tree
2018-05-14	gmungoc	JAL-2711 removed unused and flaky utility method	commit \| commitdiff \| tree
2018-05-14	gmungoc	JAL-2939 check for hmm present when processing groups	commit \| commitdiff \| tree
2018-05-11	gmungoc	JAL-2985 show label instead of checkbox for a required...	commit \| commitdiff \| tree
2018-05-11	gmungoc	Merge branch 'develop' into features/mchmmer	commit \| commitdiff \| tree
2018-05-11	gmungoc	JAL-2986 corrected findIndex for out of range residue...	commit \| commitdiff \| tree
2018-05-11	gmungoc	JAL-2986 additional asserts for SequenceCursor updates	commit \| commitdiff \| tree
2018-05-11	gmungoc	JAL-2986 failing test added	commit \| commitdiff \| tree
2018-05-10	gmungoc	JAL-2629 revert to showing Profile parameter even if...	commit \| commitdiff \| tree
2018-05-10	gmungoc	JAL-2629 default HMMBuild to alignment if not specified...	commit \| commitdiff \| tree
2018-05-10	gmungoc	JAL-591 reduced updating by checking/setting 'updating...	commit \| commitdiff \| tree
2018-05-10	gmungoc	JAL-2629 handle decline 'Add Database'	commit \| commitdiff \| tree
2018-05-10	gmungoc	JAL-2629 adjust placement and optionality of arguments...	commit \| commitdiff \| tree
2018-05-10	gmungoc	JAL-591 show choice list with a single option	commit \| commitdiff \| tree
2018-05-09	gmungoc	JAL-2714 HMMSearch cutoff by E-Value, Score or None	commit \| commitdiff \| tree
2018-05-09	gmungoc	JAL-2984 add pdb as sequence(s) if associate structure...	commit \| commitdiff \| tree
2018-05-08	gmungoc	Merge branch 'develop' into features/mchmmer	commit \| commitdiff \| tree
2018-05-07	gmungoc	JAL-2808 ensure test setUp/tearDown alwaysRun	commit \| commitdiff \| tree
2018-05-07	gmungoc	Merge branch 'releases/Release_2_10_4_Branch' into...	commit \| commitdiff \| tree
2018-05-04	gmungoc	JAL-2906 small tweaks to release notes	commit \| commitdiff \| tree
2018-04-24	gmungoc	JAL-2959 no Print dialog shown if Page Format is Cancelled	commit \| commitdiff \| tree
2018-04-24	gmungoc	JAL-2939 exit calc thread if no HMM in alignment	commit \| commitdiff \| tree
2018-04-24	gmungoc	JAL-591 use constant for Preferences key	commit \| commitdiff \| tree
2018-04-24	gmungoc	JAL-2616 unused field removed	commit \| commitdiff \| tree
2018-04-24	gmungoc	JAL-2956 unit test	commit \| commitdiff \| tree
2018-04-23	gmungoc	JAL-2956 save/restore HMMER profile to/from Jalview...	commit \| commitdiff \| tree
2018-04-23	gmungoc	JAL-2954 more efficient SearchResults.markColumns	commit \| commitdiff \| tree
2018-04-23	gmungoc	JAL-2952 set negative TempFactor values as AlignmentAnnotati...	commit \| commitdiff \| tree
2018-04-23	gmungoc	JAL-2957 don't validate input on arrow keys	commit \| commitdiff \| tree
2018-04-23	gmungoc	JAL-591 ensure slider hidden if text input field only	commit \| commitdiff \| tree
2018-04-20	gmungoc	JAL-591 slider scale factor now derived from min-max...	commit \| commitdiff \| tree
2018-04-20	gmungoc	JAL-591 tidy and comment code	commit \| commitdiff \| tree
2018-04-20	gmungoc	JAL-2629 tweaks to text	commit \| commitdiff \| tree
2018-04-20	gmungoc	JAL-591 OptionBox FlowLayout, tweaks to wrapping of...	commit \| commitdiff \| tree
2018-04-19	gmungoc	JAL-591 utility method renamed and slightly generalised	commit \| commitdiff \| tree
2018-04-18	gmungoc	Merge branch 'develop' into features/mchmmer	commit \| commitdiff \| tree
2018-04-18	gmungoc	Merge branch 'releases/Release_2_10_4_Branch' into...	commit \| commitdiff \| tree
2018-04-18	gmungoc	JAL-2593 render 'duplicate' features if transparency...	commit \| commitdiff \| tree
2018-04-18	gmungoc	JAL-2629 corrected cutoff parameter passing to hmmsearch	commit \| commitdiff \| tree
2018-04-17	gmungoc	Merge branch 'features/mchmmer' of https://source.jalview...	commit \| commitdiff \| tree
2018-04-17	gmungoc	JAL-2629 choice of hmm profile now a parameter not...	commit \| commitdiff \| tree
2018-04-17	Mungo Carstairs	JAL-2937 working Cygwin bash execution of hmmbuild...	commit \| commitdiff \| tree
2018-04-16	gmungoc	JAL-2629 JAL-2937 remove redundant is/setHMMConsensusSequence	commit \| commitdiff \| tree
2018-04-16	gmungoc	JAL-2937 use preferences for presets, simplify some...	commit \| commitdiff \| tree
2018-04-13	gmungoc	Merge branch 'features/JAL-2944_openStructuresInSelectedView...	commit \| commitdiff \| tree
2018-04-12	gmungoc	JAL-2223 don't add duplicate mappings to StructureSelectionM...	commit \| commitdiff \| tree
2018-04-12	gmungoc	JAL-1847 minor post-review updates	commit \| commitdiff \| tree
2018-04-12	gmungoc	JAL-2944 tidies for review comments	commit \| commitdiff \| tree
2018-04-09	Mungo Carstairs	JAL-2937 Cygwin path preference, method refactoring	commit \| commitdiff \| tree
2018-04-09	Mungo Carstairs	JAL-2629 more error checking	commit \| commitdiff \| tree
2018-04-09	Mungo Carstairs	JAL-2937 extract reusable utility method	commit \| commitdiff \| tree
2018-04-09	Mungo Carstairs	JAL-2069 typo	commit \| commitdiff \| tree
2018-03-30	gmungoc	JAL-2599 MapList from HMM nodes to consensus dataset...	commit \| commitdiff \| tree
2018-03-30	gmungoc	JAL-2629 tidy code, factory methods for param sets	commit \| commitdiff \| tree
2018-03-30	gmungoc	JAL-2629 use correct gap character, revised deletion...	commit \| commitdiff \| tree
2018-03-30	gmungoc	JAL-2629 Javadoc updates	commit \| commitdiff \| tree
2018-03-30	gmungoc	JAL-2629 combine with/without defaults in one method...	commit \| commitdiff \| tree
2018-03-30	gmungoc	JAL-2939 field/method naming more consistent	commit \| commitdiff \| tree
2018-03-30	gmungoc	JAL-2629 ensure hmm consensus sequence set on alignment...	commit \| commitdiff \| tree
2018-03-30	gmungoc	JAL-2941 'map hmm to RF' removed pending clarifications	commit \| commitdiff \| tree
2018-03-30	gmungoc	small tidy	commit \| commitdiff \| tree
2018-03-30	gmungoc	JAL-2938 revisions to implementation details	commit \| commitdiff \| tree
2018-03-30	gmungoc	JAL-2939 remove commented out code	commit \| commitdiff \| tree
2018-03-30	gmungoc	JAL-2599 move utility method to MappingUtils	commit \| commitdiff \| tree
2018-03-30	gmungoc	JAL-2939 simplified way of getting hmm consensus residue	commit \| commitdiff \| tree
2018-03-30	gmungoc	JAL-2629 add title to output alignment window	commit \| commitdiff \| tree
2018-03-30	gmungoc	JAL-2629 select HMM selects sequence under cursor	commit \| commitdiff \| tree
2018-03-30	gmungoc	JAL-2599 corrected test file name in unit test	commit \| commitdiff \| tree
2018-03-29	gmungoc	JAL-2907 test method renamed to match method name change	commit \| commitdiff \| tree
2018-03-29	gmungoc	JAL-2907 bug fix redone on HMMER branch	commit \| commitdiff \| tree
2018-03-28	gmungoc	JAL-1265 output all dbrefs in Stockholm (+tests) (...	commit \| commitdiff \| tree
2018-03-26	gmungoc	JAL-2939 pull up set/IsNormalise[HMM]SequenceLogo	commit \| commitdiff \| tree
2018-03-26	gmungoc	JAL-2939 unused action handler methods removed	commit \| commitdiff \| tree
2018-03-26	gmungoc	JAL-2939 no need to recalc HMM annotation for show...	commit \| commitdiff \| tree
2018-03-26	gmungoc	JAL-2939 always store Information profile	commit \| commitdiff \| tree
2018-03-23	gmungoc	JAL-2629 pad gaps when exporting alignment as 'database...	commit \| commitdiff \| tree
2018-03-23	gmungoc	JAL-2937 unused field removed	commit \| commitdiff \| tree
2018-03-23	gmungoc	JAL-2938 update colour schemes enum for class name...	commit \| commitdiff \| tree
2018-03-23	gmungoc	JAL-2938 extracted base class for Hmmer colour schems	commit \| commitdiff \| tree
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