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JAL-2154 test for CDS->protein map
[jalview.git] / src / jalview / datamodel /
2016-08-02 Jim ProcterJAL-2046 additional logic to suppress spurious implemen... tree | commitdiff
2016-08-02 Jim ProcterMerge branch 'develop' into efficiency/JAL-2034_JAL... tree | commitdiff
2016-07-21 Jim ProcterMerge branch 'apifix/JAL-1926_JAL-2106' into develop tree | commitdiff
2016-07-20 Jim ProcterJAL-1926 JAL-2106 remove startRes/endRes fields - not... tree | commitdiff
2016-07-19 tcofoegbuMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-07-19 tcofoegbuJAL-1919 set default structure file format to mmCIF... tree | commitdiff
2016-07-19 Jim ProcterMerge branch 'develop' into efficiency/JAL-2034_JAL... tree | commitdiff
2016-07-18 Jim ProcterJAL-2121 cleanup TODO tree | commitdiff
2016-07-18 Jim ProcterJAL-2145 documentation of getWidth() tree | commitdiff
2016-07-14 Jim ProcterJAL-1115 change implementation to avoid possibility... tree | commitdiff
2016-07-14 Jim ProcterJAL-1270 test coverage TODO Alignment.append(AlignmentI) tree | commitdiff
2016-07-12 Jim ProcterJAL-2144 TODO - new methods for canonicalisation and... tree | commitdiff
2016-07-12 Jim ProcterJAL-2110 javadoc and TODO re shortcomings of implementation tree | commitdiff
2016-07-12 Jim ProcterJAL-2110 javadoc tree | commitdiff
2016-07-06 gmungocJAL-2110 generic rather than specific check for gap... tree | commitdiff
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds tree | commitdiff
2016-07-06 gmungocJAL-2110 add 'mapFromId' to Mapping (for e.g. EMBL... tree | commitdiff
2016-07-06 gmungocJAL-2110 fixes and tests for adding dbrefs to EMBL... tree | commitdiff
2016-07-04 gmungocJAL-2110 unused method removed tree | commitdiff
2016-07-04 gmungocJAL-2110 defensive check in code tree | commitdiff
2016-07-01 gmungocJAL-2110 bug fixing and tidying for get cross-refs tree | commitdiff
2016-07-01 gmungocJAL-2110 code/comment tidy tree | commitdiff
2016-06-30 gmungocJAL-2110 fixes and tests for synthesized EMBLCDSPROTEIN... tree | commitdiff
2016-06-29 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD... tree | commitdiff
2016-06-27 gmungocJAL-1270 unit tests for HiddenSequences tree | commitdiff
2016-06-23 Jim ProcterJAL-2110 SequenceI.isProtein method tree | commitdiff
2016-06-21 Jim ProcterMerge branch 'features/JAL-2110_crossRefDuplications... tree | commitdiff
2016-06-21 Jim ProcterJAL-1369 make sure the fake AlignmentI produced by... tree | commitdiff
2016-06-21 Jim ProcterJAL-1369 HUGE WARNING: datamodel.HiddenSequences is... tree | commitdiff
2016-06-21 gmungocJAL-2113 tidy up canonicalisation of Uniprot xrefs... tree | commitdiff
2016-06-21 gmungocJAL-2113 tidy up canonicalisation of Uniprot xrefs... tree | commitdiff
2016-06-20 Jim ProcterJAL-1551 tidy tree | commitdiff
2016-06-20 Jim ProcterJAL-2068 avoid ArrayIndexOutOfBounds when consensus... tree | commitdiff
2016-06-20 Jim ProcterJAL-2110 catch case when updateDBRef argument has null... tree | commitdiff
2016-06-20 Jim ProcterJAL-2110 copy alcodonframes only if copy constructor... tree | commitdiff
2016-06-19 Jim ProcterJAL-2110 JAL-2131 JAL-1765 remove reference to jalview... tree | commitdiff
2016-06-16 Jim ProcterJAL-2110 todo - select mappings involving sequences... tree | commitdiff
2016-06-16 Jim ProcterJAL-2110 equals and hashcode should check fromSeq tree | commitdiff
2016-06-16 Jim ProcterJAL-2110 typo caused infinite loop tree | commitdiff
2016-06-16 gmungocJAL-2112 optimisation of EMBL CDS parsing tree | commitdiff
2016-06-15 Jim ProcterMerge branch 'develop' into features/JAL-2110_crossRefD... tree | commitdiff
2016-06-14 gmungocJAL-2114 more helpful reporting of parse failures tree | commitdiff
2016-06-14 gmungocJAL-2110 ensure "UniProtKB/Swiss-Prot" dbrefs canonical... tree | commitdiff
2016-06-14 gmungocJAL-1686 JAL-2110 equals and/or hashCode method added tree | commitdiff
2016-06-09 gmungocJAL-2110 work in progress tree | commitdiff
2016-06-01 Jim Procterfix build tree | commitdiff
2016-05-31 gmungocJAL-2023 adjustments to mappings added for split frame... tree | commitdiff
2016-05-31 gmungocJAL-2110 refactor + tests to allow a dbref version... tree | commitdiff
2016-05-31 Jim ProcterMerge branch 'develop' into features/JAL-2113_emblXml1.2 tree | commitdiff
2016-05-30 gmungocJAL-1989 equals method strengthened to fully match... tree | commitdiff
2016-05-30 Jim ProcterMerge branch 'develop' into efficiency/JAL-2034_JAL... tree | commitdiff
2016-05-27 gmungocJAL-1989 added hashCode and equals, renamed field to... tree | commitdiff
2016-05-26 gmungocJAL-2113 additions to embl_mapping.xml / data models... features/JAL-2113_emblXml1.2 tree | commitdiff
2016-05-23 gmungocJAL-2113 remove spaces in sequence from unmarshalling... tree | commitdiff
2016-05-23 gmungocJAL-2114 save 'raw' ENA location as a sequence feature... tree | commitdiff
2016-05-20 gmungocJAL-2113 embl_mapping.xml and code updated for EMBL... tree | commitdiff
2016-05-17 tcofoegbuJAL-2106 JAL-1926 updated source doc for set/getSourceDBRef tree | commitdiff
2016-05-13 gmungocJAL-2105 capture Ensembl data version, check REST versi... tree | commitdiff
2016-05-05 Jim ProcterJAL-192 patch for off-by one and pathological case... tree | commitdiff
2016-04-29 Jim ProcterJAL-192 need visible and actual sequence limits for... tree | commitdiff
2016-04-29 Jim ProcterJAL-192 fix bounds when no hidden regions, and when... tree | commitdiff
2016-04-29 Jim ProcterJAL-966 JAL-1553
 todo: remove UI components from Colum... tree | commitdiff
2016-04-29 Jim ProcterJAL-1551 formatting
 tree | commitdiff
2016-04-29 Jim ProcterJAL-192 ‘efficiently’ locate visible bounds for a seque... tree | commitdiff
2016-04-29 Jim ProcterJAL-1551 formatting tree | commitdiff
2016-04-23 Jim ProcterJAL-2075 findPosition for SeqCigar (with test) tree | commitdiff
2016-04-23 Jim ProcterJAL-2075 formatting tree | commitdiff
2016-04-14 gmungocJAL-2041 add ID,clinical_significance to feature attrib... tree | commitdiff
2016-04-14 gmungocJAL-2049 small refactor of constructors to avoid code... tree | commitdiff
2016-04-13 Jim ProcterMerge branch 'bug/JAL-2046_ds_sharing_features_broken... tree | commitdiff
2016-04-11 tcofoegbuJAL-2054 Renamed getStartEnd in AlignFrame to getVisibl... tree | commitdiff
2016-04-11 Jim ProcterMerge branch 'develop' into efficiency/JAL-2034_JAL... tree | commitdiff
2016-04-08 Jim ProcterJAL-2050 JAL-1722 new getSelectedRange() method to... tree | commitdiff
2016-04-08 Jim ProcterJAL-2053 JAL-1551 javadoc and simpler code tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 add/delete SequenceFeature operate on dataset... tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 setSequenceFeature contract implementation... tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 explicit contract for get/set SequenceFeatures... tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 remove javadoc tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 simpler deriveSequence - promote to dataset... tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 clarify contract for copy constructor and... tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 explicitly copy char[] when cloning sequence... tree | commitdiff
2016-04-05 Jim ProcterJAL-2046 safer createDatasetSequence manipulates privat... tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 drop isSelected(int) in favour of original... tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 catch -ve column values tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 faster check for a column being selected tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 javadoc tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 faster getMax/getMin selected column, with... tree | commitdiff
2016-04-04 Jim ProcterJAL-2001 JAL-1722 - store selection as ArrayList and... tree | commitdiff
2016-04-01 gmungocJAL-1705 ensure the right mapping is used to align... tree | commitdiff
2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and... tree | commitdiff
2016-04-01 gmungocJAL-1705 include stop codon in mapped CDS range so... tree | commitdiff
2016-04-01 gmungocJAL-2037 set DBRefEntry.version to "0" not "" in EMBL... tree | commitdiff
2016-03-28 gmungocJAL-1705 Javadoc / debug output tweaks tree | commitdiff
2016-03-25 Jim ProcterJAL-2034 JAL-1421 use ArrayLists, and make ‘selection... tree | commitdiff
2016-03-25 Jim ProcterJAL-2034 make colour scheme update optional when group... tree | commitdiff
2016-03-25 Jim ProcterJAL-1551 tree | commitdiff
2016-03-21 gmungocMerge branch 'features/JAL-653_JAL-1766_htslib_refseqsu... tree | commitdiff
2016-03-21 gmungocMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-03-21 gmungocJAL-2029 further fixes to get correct xrefs and xrefs... tree | commitdiff
2016-03-21 gmungocJAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings tree | commitdiff
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