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2018-03-01	gmungoc	JAL-2629 revising hmmer annotation updating (wip)	commit \| commitdiff \| tree
2018-02-28	gmungoc	JAL-2629 some tidying of Hmmer commands (wip)	commit \| commitdiff \| tree
2018-02-27	gmungoc	JAL-2668 method name change for clarity	commit \| commitdiff \| tree
2018-02-27	gmungoc	JAL-2668 fix broken factory method for colour scheme	commit \| commitdiff \| tree
2018-02-27	gmungoc	JAL-2717 JAL-2668 fixes to HMMER colour scheme display...	commit \| commitdiff \| tree
2018-02-26	gmungoc	JAL-2599 test coverage and bug fixes for 'minimal file...	commit \| commitdiff \| tree
2018-02-23	gmungoc	JAL-2599 corrected case-insensitive symbol indexing	commit \| commitdiff \| tree
2018-02-23	gmungoc	JAL-2599 parser and datamodel use primitive double...	commit \| commitdiff \| tree
2018-02-22	gmungoc	JAL-2629 tidy tests, refactor hmmer node mapping slightly	commit \| commitdiff \| tree
2018-02-22	gmungoc	JAL-2629 tidy unit tests, constants etc	commit \| commitdiff \| tree
2018-02-21	gmungoc	JAL-2629 simplifying method signatures in Hmmer command...	commit \| commitdiff \| tree
2018-02-20	gmungoc	JAL-2629 removed SequenceI.get/setLastPosition and...	commit \| commitdiff \| tree
2018-02-20	gmungoc	Merge branch 'develop' into features/mchmmer	commit \| commitdiff \| tree
2018-02-20	gmungoc	JAL-2897 updated unit test for code change	commit \| commitdiff \| tree
2018-02-20	gmungoc	Merge branch 'develop' into features/JAL-1793VCF	commit \| commitdiff \| tree
2018-02-19	gmungoc	JAL-2629 refactoring of Hmmer preferences	commit \| commitdiff \| tree
2018-02-19	gmungoc	JAL-2629 partial refactoring of Hmmer command classes	commit \| commitdiff \| tree
2018-02-19	gmungoc	JAL-2629 formatting only	commit \| commitdiff \| tree
2018-02-07	gmungoc	JAL-2808 ensure pattern field re-enabled when needed...	commit \| commitdiff \| tree
2018-02-05	gmungoc	JAL-2897 more informative description on synonymous...	commit \| commitdiff \| tree
2018-02-05	gmungoc	JAL-2897 more informative description on synonymous...	commit \| commitdiff \| tree
2018-02-05	gmungoc	Merge branch 'spikes/mungo' into trialMerge	commit \| commitdiff \| tree
2018-02-05	gmungoc	JAL-2897 more informative description on synonymous...	commit \| commitdiff \| tree
2018-02-02	gmungoc	JAL-984 merged to spikes-mungo	commit \| commitdiff \| tree
2018-02-02	gmungoc	Merge branch 'feature/JAL-984splitAdjuster' into features...	commit \| commitdiff \| tree
2018-02-02	gmungoc	JAL-984 use cursor for drag regions to adjust annotation...	commit \| commitdiff \| tree
2018-02-02	gmungoc	JAL-984 better behaved panel height adjuster	commit \| commitdiff \| tree
2018-01-31	gmungoc	JAL-2792 added tooltip to menu items in case of truncation	commit \| commitdiff \| tree
2018-01-30	gmungoc	JAL-2069 menu item now "Variable colour..." to hint...	commit \| commitdiff \| tree
2018-01-30	gmungoc	JAL-1793 update spike build to latest incl stop and...	commit \| commitdiff \| tree
2018-01-30	gmungoc	JAL-2898 show 'stop_gained' variants on peptide sequences	commit \| commitdiff \| tree
2018-01-30	gmungoc	JAL-2897 generate peptide variants for synonymous codon...	commit \| commitdiff \| tree
2018-01-30	gmungoc	JAL-2897 formatting change only prior to functional...	commit \| commitdiff \| tree
2018-01-29	gmungoc	JAL-2743 recoded EnsemblLookup without lambda expressions...	commit \| commitdiff \| tree
2018-01-26	gmungoc	Merge branch 'develop' into features/JAL-1793VCF	commit \| commitdiff \| tree
2018-01-18	gmungoc	JAL-2810 JAL-2886 i18n	commit \| commitdiff \| tree
2018-01-18	gmungoc	JAL-2679 update query id to actual case of retrieved...	commit \| commitdiff \| tree
2018-01-17	gmungoc	JAL-2679 case-insensitive comparison of query and retrieved...	commit \| commitdiff \| tree
2018-01-16	gmungoc	JAL-2679 use object_type=Transcript for lookup of Parent...	commit \| commitdiff \| tree
2018-01-10	gmungoc	JAL-1793 update spike branch to latest	commit \| commitdiff \| tree
2018-01-10	gmungoc	JAL-2791 ignore feature type visibility in getColor()	commit \| commitdiff \| tree
2018-01-09	gmungoc	JAL-2843 test roundtrip of feature colours and filters...	commit \| commitdiff \| tree
2018-01-09	gmungoc	JAL-2843 unit tests for writing filters to Jalview...	commit \| commitdiff \| tree
2018-01-09	gmungoc	JAL-2843 unit tests for Save/Load colours and filters...	commit \| commitdiff \| tree
2018-01-09	gmungoc	JAL-2808 small tweaks to api / Javadoc	commit \| commitdiff \| tree
2018-01-08	gmungoc	JAL-2069 fix setting initial value of slider from threshold	commit \| commitdiff \| tree
2017-12-14	gmungoc	JAL-2843 missed Castor class	commit \| commitdiff \| tree
2017-12-14	gmungoc	JAL-2843 save/restore colour feature by attribute,...	commit \| commitdiff \| tree
2017-12-14	gmungoc	JAL-2879 save/restore feature sub-attributes in Jalview...	commit \| commitdiff \| tree
2017-12-14	gmungoc	JAL-2843 missed Castor class	commit \| commitdiff \| tree
2017-12-14	gmungoc	JAL-2843 and Castor metadata file for latest changes	commit \| commitdiff \| tree
2017-12-14	gmungoc	JAL-2843 schema and code changes to save colour by...	commit \| commitdiff \| tree
2017-12-13	gmungoc	JAL-2843 add isByAttribute to interface for convenience	commit \| commitdiff \| tree
2017-12-11	gmungoc	JAL-2843 add colour by attribute, and no value colour...	commit \| commitdiff \| tree
2017-12-08	gmungoc	JAL-2843 example filters added	commit \| commitdiff \| tree
2017-12-08	gmungoc	JAL-2843 read/write feature filters from/to Jalview...	commit \| commitdiff \| tree
2017-12-08	gmungoc	JAL-2843 refactor / tidy for feature filter input/output	commit \| commitdiff \| tree
2017-12-08	gmungoc	JAL-2843 methods relocated	commit \| commitdiff \| tree
2017-12-08	gmungoc	JAL-2843 toStableString, fromString for Jalview features...	commit \| commitdiff \| tree
2017-12-08	gmungoc	JAL-2843 FeatureRenderer.getFeatureFilters returns...	commit \| commitdiff \| tree
2017-12-05	gmungoc	Merge branch 'develop' into features/JAL-1793VCF	commit \| commitdiff \| tree
2017-12-04	gmungoc	JAL-2808 JAL-2850 update spike build to latest	commit \| commitdiff \| tree
2017-12-04	gmungoc	Merge branch 'spikes/mungo' into features/JAL-1793VCF	commit \| commitdiff \| tree
2017-12-04	gmungoc	JAL-2850 JAL-1766 option to load contig sequence referenced...	commit \| commitdiff \| tree
2017-12-04	gmungoc	JAL-2845 locate reverse strand insertion as complement...	commit \| commitdiff \| tree
2017-12-04	gmungoc	JAL-2835 small refactor to only extract transcript...	commit \| commitdiff \| tree
2017-12-01	gmungoc	JAL-2835 spike updated to latest (use specific SO term...	commit \| commitdiff \| tree
2017-12-01	gmungoc	JAL-2835 refactored to extract specific consequence...	commit \| commitdiff \| tree
2017-12-01	gmungoc	JAL-2792 sort feature attributes for output, not for...	commit \| commitdiff \| tree
2017-12-01	gmungoc	JAL-2835 additional sub-terms of sequence_variant added	commit \| commitdiff \| tree
2017-11-30	gmungoc	JAL-2850 improved use of htsjdk api to read contig...	commit \| commitdiff \| tree
2017-11-30	gmungoc	JAL-1766 additional tests for stub htsjdk wrapper	commit \| commitdiff \| tree
2017-11-28	gmungoc	Merge branch 'develop' into features/JAL-1793VCF	commit \| commitdiff \| tree
2017-11-28	gmungoc	JAL-2850 MapList.isToForwardStrand added	commit \| commitdiff \| tree
2017-11-27	gmungoc	JAL-2850 VCFLoader refactored to load VCF to contig...	commit \| commitdiff \| tree
2017-11-24	gmungoc	JAL-2808 update spike to latest	commit \| commitdiff \| tree
2017-11-24	gmungoc	JAL-2808 refactoring to better handler filter by Score...	commit \| commitdiff \| tree
2017-11-24	gmungoc	JAL-2808 relocate constants for compiler, add COLUMN_COUNT...	commit \| commitdiff \| tree
2017-11-24	gmungoc	JAL-2808 refine FeatureMatcher interface and matcher...	commit \| commitdiff \| tree
2017-11-24	gmungoc	JAL-2808 don't cache i18n - MessageManager already...	commit \| commitdiff \| tree
2017-11-23	gmungoc	JAL-2808 update spike to latest (filter range tooltip...	commit \| commitdiff \| tree
2017-11-23	gmungoc	JAL-2808 refactor KeyedMatcher as FeatureMatcher with...	commit \| commitdiff \| tree
2017-11-23	gmungoc	JAL-2808 update spike to latest (filter range, Present...	commit \| commitdiff \| tree
2017-11-23	gmungoc	JAL-2808 removed field filters; sort CSQ data by key	commit \| commitdiff \| tree
2017-11-23	gmungoc	JAL-2808 added conditions Present, NotPresent as options	commit \| commitdiff \| tree
2017-11-23	gmungoc	JAL-2808 refactor conversion of table data to beans...	commit \| commitdiff \| tree
2017-11-23	gmungoc	JAL-2808 pass FeatureSettings to controller as array...	commit \| commitdiff \| tree
2017-11-22	gmungoc	JAL-2808 update conditions list on change of attribute...	commit \| commitdiff \| tree
2017-11-22	gmungoc	JAL-2069 spike updated with latest (FeatureTypeSettings)	commit \| commitdiff \| tree
2017-11-22	gmungoc	Merge branch 'develop' into features/JAL-1793VCF	commit \| commitdiff \| tree
2017-11-22	gmungoc	JAL-2808 JAL-2069 FeatureTypeSettings (with new Filters...	commit \| commitdiff \| tree
2017-11-22	gmungoc	JAL-2069 renamed helper method better	commit \| commitdiff \| tree
2017-11-22	gmungoc	JAL-2808 defer dispose to allow screen location to...	commit \| commitdiff \| tree
2017-11-22	gmungoc	JAL-2069 Javadoc added only	commit \| commitdiff \| tree
2017-11-22	gmungoc	JAL-1424 enhanced to report dynamic keys separately	commit \| commitdiff \| tree
2017-11-22	gmungoc	JAL-2808 capture feature attributes datatype (Character...	commit \| commitdiff \| tree
2017-11-17	gmungoc	JAL-2808 set (read-only) condition text field as disabled	commit \| commitdiff \| tree
2017-11-16	gmungoc	JAL-2069 fix minor bugs in variable setting	commit \| commitdiff \| tree
2017-11-16	gmungoc	Merge branch 'develop' into features/JAL-1793VCF	commit \| commitdiff \| tree
2017-11-16	gmungoc	JAL-2069 removed unused and redundant thresholdIsMinMax	commit \| commitdiff \| tree
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