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jalview.git
2016-01-21 gmungocJAL-1705 tests for amended toString commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 added isSequenceVariant(), commonly used SO... commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 isFromForwardStrand added; toString (for debug... commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 canonicalise ENSEMBL name; code tidy commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 get xrefs only for dna/peptide; code tidy commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 toString() added (for debugging) commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 isEmpty() and (debug) toString() methods added commit | commitdiff | tree | snapshot
2016-01-12 gmungocJAL-1191 cache isA (great-)grandparents as well for... commit | commitdiff | tree | snapshot
2016-01-08 gmungocJAL-1705 DbSourceProxy properties converted to methods... commit | commitdiff | tree | snapshot
2016-01-05 gmungocJAL-653 updating 'align as' tests to match latest tweak... commit | commitdiff | tree | snapshot
2016-01-05 gmungocMerge remote-tracking branch 'origin/features/JAL-1705_... commit | commitdiff | tree | snapshot
2016-01-05 gmungocJAL-653 typed map for feature colours in method signature commit | commitdiff | tree | snapshot
2016-01-05 gmungocJAL-1191 check for obsolete term when descriptions... commit | commitdiff | tree | snapshot
2015-12-23 gmungocJAL-1191 unzipped OBO file removed commit | commitdiff | tree | snapshot
2015-12-23 gmungocJAL-1191 zipped SO OBO file added to /resources, more... commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-1191 more test cases commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-1191 and provide the SO OBO file in /resources :-) commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-1191 SequenceOntology wrapping/caching SO.OBO via... commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-1191 stub class for a SequenceOntology wrapper commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-1551 don't autoformat /* comments */ commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-1421 parameterised map constructor used commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-653 encapsulate Strand, Attributes, Status of Seque... commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-653 realise virtual mappings and align when adding... commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-391 new Calculate options to Reverse, Reverse Compl... commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-653 AlignedCodonFrame collections changed from... commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-653 set showSequenceFeatures=true on loading a... commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-653 GFF new/refactored helper classes commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-653 AlignedCodonFrame internal refactor, merge... commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-653 hold AlignedCodonFrame collections as list... commit | commitdiff | tree | snapshot
2015-12-03 gmungocJAL-653 code tidy / tests for 'realise gff mappings' commit | commitdiff | tree | snapshot
2015-12-03 gmungocJAL-653 handle reverse strand mapping in SearchResults... commit | commitdiff | tree | snapshot
2015-12-03 gmungocJAL-653 mappings always reside on the dataset alignment... commit | commitdiff | tree | snapshot
2015-12-03 gmungocJAL-653 handle reverse strand mappings also commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-1421 generics loop syntax; 'bug?' comment added commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-653 test for 'resolving GFF mappings to sequences... commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-653 small comment change only commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-652 refactored to remove one method commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-653 (experimental) 'realise' dummy sequences in... commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-1980 check for null alignment; JAL-1551 @Override... commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-653 (experimental) methods to resolve dummy to... commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-1270 constructor test added commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-653 getStrand javadoc/refactor/test commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-1421 use generics JAL-1551 @Override annotations... commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-1270 constructor tests added, compiler warnings... commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-652 further refactoring / tests commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-652 correct case for test file name commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-653 MapList constructor merges any contiguous ranges commit | commitdiff | tree | snapshot
2015-11-23 gmungocJAL-653 Gff tests moved back in to FeaturesFileTest commit | commitdiff | tree | snapshot
2015-11-22 gmungocJAL-653 test for 'groups file' and mixed Jalview/GFF commit | commitdiff | tree | snapshot
2015-11-21 gmungocJAL-1968 remove feature links commit | commitdiff | tree | snapshot
2015-11-21 gmungocJAL-653 JAL-1968 FeaturesFile now handles Jalview or... commit | commitdiff | tree | snapshot
2015-11-17 gmungocJAL-1961 update link to GFF2 spec commit | commitdiff | tree | snapshot
2015-11-10 Jim ProcterJAL-653 added missing pragma string to processing filter commit | commitdiff | tree | snapshot
2015-11-10 Jim ProcterMerge branch 'features/JAL-1705_ensembl' of source... features/JAL-1705_ensembl commit | commitdiff | tree | snapshot
2015-11-09 gmungocJAL-1705 type enum can encapsulate the corresponding... commit | commitdiff | tree | snapshot
2015-10-15 Jim ProcterJAL-653 JAL-1766 merge 290b1 - fix erroneous conflicts... commit | commitdiff | tree | snapshot
2015-10-15 Jim ProcterMerge branch 'develop' into features/JAL-653_JAL-1766_h... commit | commitdiff | tree | snapshot
2015-10-15 Jim ProcterMerge branch 'develop' into features/JAL-1705_ensembl commit | commitdiff | tree | snapshot
2015-10-15 Jim ProcterJAL-1791 remove blanket sign of examples/*.jar commit | commitdiff | tree | snapshot
2015-10-15 Jim ProcterJAL-1791 id rather than name attrib commit | commitdiff | tree | snapshot
2015-10-15 Jim ProcterJAL-1791 sign the applet with/out timestamps commit | commitdiff | tree | snapshot
2015-10-15 Jim ProcterJAL-1791 add explicit proxy for benefit of jalview... commit | commitdiff | tree | snapshot
2015-10-15 Jim ProcterJAL-1791 fix ant target dependencies commit | commitdiff | tree | snapshot
2015-10-15 Jim ProcterJAL-1791 make timestamping optional using -Dtimestamp commit | commitdiff | tree | snapshot
2015-10-15 Jim ProcterJAL-1791 add jalview.tsaurl for specifying timestamp... commit | commitdiff | tree | snapshot
2015-10-15 Jim ProcterJAL-1791 add jalview.tsaurl for specifying timestamp... commit | commitdiff | tree | snapshot
2015-10-15 Jim ProcterMerge branch 'bug/JAL-1923_290b2_group_annots' into... commit | commitdiff | tree | snapshot
2015-10-15 Jim ProcterJAL-1923 formatting commit | commitdiff | tree | snapshot
2015-10-15 Jim ProcterJAL-1923 add groups to codon-complement and notify... commit | commitdiff | tree | snapshot
2015-10-15 Jim ProcterJAL-1923 fix: don’t add group twice commit | commitdiff | tree | snapshot
2015-10-08 Jim ProcterJAL-1684 updated fragment alignment for example and... commit | commitdiff | tree | snapshot
2015-10-08 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie... commit | commitdiff | tree | snapshot
2015-10-08 Jim ProcterJAL-1894 add licensing commit | commitdiff | tree | snapshot
2015-10-08 tcofoegbuJAL-1912 JAL-1896 release notes updated commit | commitdiff | tree | snapshot
2015-10-08 Jim ProcterJAL-1894 update what's new commit | commitdiff | tree | snapshot
2015-10-08 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie... commit | commitdiff | tree | snapshot
2015-10-08 tcofoegbuJAL-1912 JAL-1896 release notes updated commit | commitdiff | tree | snapshot
2015-10-08 gmungocJAL-1544 typo fix commit | commitdiff | tree | snapshot
2015-10-08 Jim ProcterJAL-1894 formatting commit | commitdiff | tree | snapshot
2015-10-08 Jim ProcterJAL-1894 organise imports commit | commitdiff | tree | snapshot
2015-10-08 tcofoegbumerge commit | commitdiff | tree | snapshot
2015-10-07 Jim ProcterJAL-1894 source formatting commit | commitdiff | tree | snapshot
2015-10-07 Jim ProcterJAL-1894 organise imports commit | commitdiff | tree | snapshot
2015-10-07 Jim ProcterJAL-1894 update release date commit | commitdiff | tree | snapshot
2015-10-07 tcofoegbuJAL-1912 added documentation features/JAL-1912_biojson-per-sequence-annotation commit | commitdiff | tree | snapshot
2015-10-07 Jim ProcterJAL-1912 formatting commit | commitdiff | tree | snapshot
2015-10-07 Jim ProcterJAL-1912 javadoc for adjustForAlignment stating current... commit | commitdiff | tree | snapshot
2015-10-07 Jim ProcterJAL-1912 efficiency: look up sequenceMapping once per... commit | commitdiff | tree | snapshot
2015-10-07 Jim ProcterMerge branch 'features/JAL-1912_biojson-per-sequence... commit | commitdiff | tree | snapshot
2015-10-05 tcofoegbuJAL-1912 house keeping commit | commitdiff | tree | snapshot
2015-10-05 tcofoegbuJAL-1912 added null check for SequenceMapping variable... commit | commitdiff | tree | snapshot
2015-10-05 gmungocJAL-1812 set/return currentAlFrame for Groovy in headle... commit | commitdiff | tree | snapshot
2015-10-05 Jim ProcterMerge branch 'develop' into features/JAL-1912_biojson... commit | commitdiff | tree | snapshot
2015-10-05 Jim ProcterJAL-1894 note about menu option bugfix JAL-1865 JAL... commit | commitdiff | tree | snapshot
2015-10-05 Jim ProcterJAL-1894 update release notes for JAL-1815 JAL-1860 commit | commitdiff | tree | snapshot
2015-10-05 gmungocJAL-1684 JAL-1452 new applet parameters defaultColourNuc commit | commitdiff | tree | snapshot
2015-10-05 tcofoegbumerge commit | commitdiff | tree | snapshot
2015-10-05 tcofoegbuJAL-1908 bugfix commit | commitdiff | tree | snapshot
2015-10-05 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie... commit | commitdiff | tree | snapshot
2015-10-05 Jim ProcterJAL-1684 trimmed proteins to just those sequences that... commit | commitdiff | tree | snapshot
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