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2016-01-23	gmungoc	JAL-1705 todo comment re writing DBRefEntry/SequenceFeature...	commit \| commitdiff \| tree
2016-01-23	gmungoc	JAL-1705 compute peptide variants from dna; add "consequence...	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-1705 transfer features to the dataset sequence...	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-1705 reworked Ensembl clients now fetching and...	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-653 refactor / tidy	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-653 JAL-1705 set strand for GFF sequence feature	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-1705 removed (only) usage of otherwise unused constant	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-653 comments/javadoc tidy only	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-1796 parse ensembl genomic coordinates to set start...	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-1705 AlignmentUtils method renamed	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-1705 ENSEMBL added, unused constants removed	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-1705 features transferred to CDS sequence; makeExon...	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-1705 redundant comment removed	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-1705 suppress jvsuffix (for sequence id matching...	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-1705 unused import removed	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-1705 include dummy sequences in returned alignment	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-1705 tidy and todo comment, no functional change	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-1705 tests for amended toString	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-1705 added isSequenceVariant(), commonly used SO...	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-1705 isFromForwardStrand added; toString (for debug...	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-1705 canonicalise ENSEMBL name; code tidy	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-1705 get xrefs only for dna/peptide; code tidy	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-1705 toString() added (for debugging)	commit \| commitdiff \| tree
2016-01-21	gmungoc	JAL-1705 isEmpty() and (debug) toString() methods added	commit \| commitdiff \| tree
2016-01-12	gmungoc	JAL-1191 cache isA (great-)grandparents as well for...	commit \| commitdiff \| tree
2016-01-08	gmungoc	JAL-1705 DbSourceProxy properties converted to methods...	commit \| commitdiff \| tree
2016-01-05	gmungoc	JAL-653 updating 'align as' tests to match latest tweaks...	commit \| commitdiff \| tree
2016-01-05	gmungoc	Merge remote-tracking branch 'origin/features/JAL-1705_ensem...	commit \| commitdiff \| tree
2016-01-05	gmungoc	JAL-653 typed map for feature colours in method signature	commit \| commitdiff \| tree
2016-01-05	gmungoc	JAL-1191 check for obsolete term when descriptions...	commit \| commitdiff \| tree
2015-12-23	gmungoc	JAL-1191 unzipped OBO file removed	commit \| commitdiff \| tree
2015-12-23	gmungoc	JAL-1191 zipped SO OBO file added to /resources, more...	commit \| commitdiff \| tree
2015-12-22	gmungoc	JAL-1191 more test cases	commit \| commitdiff \| tree
2015-12-22	gmungoc	JAL-1191 and provide the SO OBO file in /resources :-)	commit \| commitdiff \| tree
2015-12-22	gmungoc	JAL-1191 SequenceOntology wrapping/caching SO.OBO via...	commit \| commitdiff \| tree
2015-12-22	gmungoc	JAL-1191 stub class for a SequenceOntology wrapper	commit \| commitdiff \| tree
2015-12-22	gmungoc	JAL-1551 don't autoformat /* comments */	commit \| commitdiff \| tree
2015-12-22	gmungoc	JAL-1421 parameterised map constructor used	commit \| commitdiff \| tree
2015-12-22	gmungoc	JAL-653 encapsulate Strand, Attributes, Status of SequenceFe...	commit \| commitdiff \| tree
2015-12-22	gmungoc	JAL-653 realise virtual mappings and align when adding...	commit \| commitdiff \| tree
2015-12-22	gmungoc	JAL-391 new Calculate options to Reverse, Reverse Complement...	commit \| commitdiff \| tree
2015-12-22	gmungoc	JAL-653 AlignedCodonFrame collections changed from...	commit \| commitdiff \| tree
2015-12-22	gmungoc	JAL-653 set showSequenceFeatures=true on loading a...	commit \| commitdiff \| tree
2015-12-22	gmungoc	JAL-653 GFF new/refactored helper classes	commit \| commitdiff \| tree
2015-12-22	gmungoc	JAL-653 AlignedCodonFrame internal refactor, merge...	commit \| commitdiff \| tree
2015-12-22	gmungoc	JAL-653 hold AlignedCodonFrame collections as list...	commit \| commitdiff \| tree
2015-12-03	gmungoc	JAL-653 code tidy / tests for 'realise gff mappings'	commit \| commitdiff \| tree
2015-12-03	gmungoc	JAL-653 handle reverse strand mapping in SearchResults...	commit \| commitdiff \| tree
2015-12-03	gmungoc	JAL-653 mappings always reside on the dataset alignment...	commit \| commitdiff \| tree
2015-12-03	gmungoc	JAL-653 handle reverse strand mappings also	commit \| commitdiff \| tree
2015-11-30	gmungoc	JAL-1421 generics loop syntax; 'bug?' comment added	commit \| commitdiff \| tree
2015-11-30	gmungoc	JAL-653 test for 'resolving GFF mappings to sequences...	commit \| commitdiff \| tree
2015-11-30	gmungoc	JAL-653 small comment change only	commit \| commitdiff \| tree
2015-11-30	gmungoc	JAL-652 refactored to remove one method	commit \| commitdiff \| tree
2015-11-30	gmungoc	JAL-653 (experimental) 'realise' dummy sequences in...	commit \| commitdiff \| tree
2015-11-30	gmungoc	JAL-1980 check for null alignment; JAL-1551 @Override...	commit \| commitdiff \| tree
2015-11-30	gmungoc	JAL-653 (experimental) methods to resolve dummy to...	commit \| commitdiff \| tree
2015-11-30	gmungoc	JAL-1270 constructor test added	commit \| commitdiff \| tree
2015-11-30	gmungoc	JAL-653 getStrand javadoc/refactor/test	commit \| commitdiff \| tree
2015-11-30	gmungoc	JAL-1421 use generics JAL-1551 @Override annotations...	commit \| commitdiff \| tree
2015-11-30	gmungoc	JAL-1270 constructor tests added, compiler warnings...	commit \| commitdiff \| tree
2015-11-30	gmungoc	JAL-652 further refactoring / tests	commit \| commitdiff \| tree
2015-11-30	gmungoc	JAL-652 correct case for test file name	commit \| commitdiff \| tree
2015-11-30	gmungoc	JAL-653 MapList constructor merges any contiguous ranges	commit \| commitdiff \| tree
2015-11-23	gmungoc	JAL-653 Gff tests moved back in to FeaturesFileTest	commit \| commitdiff \| tree
2015-11-22	gmungoc	JAL-653 test for 'groups file' and mixed Jalview/GFF	commit \| commitdiff \| tree
2015-11-21	gmungoc	JAL-1968 remove feature links	commit \| commitdiff \| tree
2015-11-21	gmungoc	JAL-653 JAL-1968 FeaturesFile now handles Jalview or...	commit \| commitdiff \| tree
2015-11-17	gmungoc	JAL-1961 update link to GFF2 spec	commit \| commitdiff \| tree
2015-11-09	gmungoc	JAL-1705 type enum can encapsulate the corresponding...	commit \| commitdiff \| tree
2015-10-08	gmungoc	JAL-1544 typo fix	commit \| commitdiff \| tree
2015-10-05	gmungoc	JAL-1812 set/return currentAlFrame for Groovy in headless...	commit \| commitdiff \| tree
2015-10-05	gmungoc	JAL-1684 JAL-1452 new applet parameters defaultColourNuc	commit \| commitdiff \| tree
2015-10-02	gmungoc	JAL-1815 restore split frame geometry including horizontal...	commit \| commitdiff \| tree
2015-09-28	gmungoc	JAL-1909 repaint complementary alignment panel after...	commit \| commitdiff \| tree
2015-09-25	gmungoc	JAL-1859 try hoverDelay of 0.1s in Jmol for more responsive...	commit \| commitdiff \| tree
2015-09-25	gmungoc	JAL-1815 restore split frame geometry correctly including...	commit \| commitdiff \| tree
2015-09-24	gmungoc	JAL-1905 parse url including & correctly	commit \| commitdiff \| tree
2015-09-24	gmungoc	JAL-1904 parse feature file colours on to alignment...	commit \| commitdiff \| tree
2015-09-22	gmungoc	JAL-1894 release notes updated	commit \| commitdiff \| tree
2015-09-22	gmungoc	JAL-1424 tidied output	commit \| commitdiff \| tree
2015-09-22	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2015-09-22	gmungoc	JAL-1859 adding "set hoverDelay 0.001;" to Jmol startup...	commit \| commitdiff \| tree
2015-09-21	gmungoc	JAL-1892 duplicate entry removed	commit \| commitdiff \| tree
2015-09-21	gmungoc	JAL-1799 update height of annotation labels to match...	commit \| commitdiff \| tree
2015-09-21	gmungoc	JAL-1892 Spanish additions for Jalview 2.9	commit \| commitdiff \| tree
2015-09-21	gmungoc	JAL-1152 set initial state of show alignment/sequence...	commit \| commitdiff \| tree
2015-09-21	gmungoc	JAL-1152 small change to match revised annotation sorting...	commit \| commitdiff \| tree
2015-09-21	gmungoc	JAL-1619 obsolete help removed	commit \| commitdiff \| tree
2015-09-18	gmungoc	JAL-1270 disable test as not really a test and goes...	commit \| commitdiff \| tree
2015-09-18	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2015-09-18	gmungoc	JAL-1805 typo corrected	commit \| commitdiff \| tree
2015-09-18	gmungoc	JAL-1788 typos corrected	commit \| commitdiff \| tree
2015-09-18	gmungoc	JAL-1788 broken href fixed	commit \| commitdiff \| tree
2015-09-18	gmungoc	JAL-1859 reinstated full path to file option (for local...	commit \| commitdiff \| tree
2015-09-18	gmungoc	JAL-1424 Ant task to report missing language bundle...	commit \| commitdiff \| tree
2015-09-16	gmungoc	JAL-1882 variable renamed to avoid confusion with member...	commit \| commitdiff \| tree
2015-09-16	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2015-09-16	gmungoc	JAL-1885 small fix to isVersionStringLaterThan plus...	commit \| commitdiff \| tree
2015-09-16	gmungoc	JAL-1684 typo correction	commit \| commitdiff \| tree
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