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JAL-2147 additional test coverage for findMappingsForSequenceAndOthers
[jalview.git] / src / jalview / datamodel /
2016-09-05 gmungocJAL-2106 increased coverage for testGetPrimaryDbRefs tree | commitdiff
2016-09-05 gmungocJAL-2106 corrections to DBRefEntry.isPrimary code and... tree | commitdiff
2016-09-04 Jim ProcterJAL-1803 chainCode moved onto property hashtable as... tree | commitdiff
2016-08-31 Jim ProcterJAL-1926 JAL-2106 fix PDB primary DBRef semantics:... tree | commitdiff
2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p... tree | commitdiff
2016-08-26 Jim ProcterJAL-2106 fix (last one!) remove the Sequence.sourceDBRe... bug/JAL-2154projectMappings tree | commitdiff
2016-08-26 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr tree | commitdiff
2016-08-26 Jim ProcterJAL-2154 drop PDB from Protein db list to remove from... tree | commitdiff
2016-08-25 Jim ProcterJAL-2106 tighten DBRefEntry primary seq test for PDB tree | commitdiff
2016-08-25 gmungocJAL-1854 missing case break statements added tree | commitdiff
2016-08-25 Jim ProcterMerge branch 'refactor/JAL-2106_sourceDbRef_revision... tree | commitdiff
2016-08-25 Jim ProcterMerge branch 'develop' into bug/JAL-2154projectMappings tree | commitdiff
2016-08-25 Jim ProcterMerge branch 'develop' into refactor/JAL-2106_sourceDbR... tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe... tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 stricter check for 1:1 mapping (same numbering... tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 rejig test to minimally verify patch that... tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 formatting tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 DBRefEntry.isPrimary() minimal test & implemen... tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 convenience method to find all dbsource names... tree | commitdiff
2016-08-24 gmungocJAL-1424 removed unused and duplicated message keys tree | commitdiff
2016-08-23 Jim ProcterMerge branch 'develop' into bug/JAL-2154projectMappings tree | commitdiff
2016-08-23 gmungocJAL-2174 markColumns() refactored inside ColumnSelection tree | commitdiff
2016-08-22 Jim ProcterJAL-2154 always check dataset sequence for sequence... tree | commitdiff
2016-08-19 Jim ProcterJAL-2154 refactor setSequenceAt to replaceSequenceAt... tree | commitdiff
2016-08-18 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr tree | commitdiff
2016-08-18 gmungocJAL-1855 fail gracefully if XML has no <sequence> element tree | commitdiff
2016-08-18 gmungocJAL-2001 return copy of selection in getSelected() tree | commitdiff
2016-08-16 gmungocJAL-2171 matching bracket default character for rna... tree | commitdiff
2016-08-12 gmungocJAL-1841 bug fixes / code tidy for rna SS rendering... tree | commitdiff
2016-08-07 Jim ProcterJAL-2154 add in missing class for createDatasetAlignmen... tree | commitdiff
2016-08-04 Jim ProcterJAL-2154 make sure all sequences referenced via DBRefEn... tree | commitdiff
2016-08-04 Jim ProcterJAL-2046 stack trace for implementation warning tree | commitdiff
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
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