Merge remote-tracking branch 'origin/develop' into bug/JAL-2491
[jalview.git] / src / jalview / datamodel /
2016-10-28 Jim ProcterJAL-966 JAL-1738 JAL-345 interfaces for SearchResults...
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-24 Jim ProcterMerge branch 'releases/Release_2_10_0_Branch'
2016-10-24 gmungocMerge branch 'develop' into bug/JAL-98consensusMemory
2016-10-14 gmungocMerge branch 'releases/Release_2_10_Branch' into task... task/JAL-2196pdbeProperties
2016-10-06 gmungocJAL-2254 map error text in root node of EMBL XML response
2016-10-06 gmungocMerge branch 'develop' into bug/JAL-98consensusMemory
2016-10-06 gmungocMerge branch 'develop' into task/JAL-2196pdbeProperties
2016-10-06 gmungocJAL-2245 checks for null added (in case EMBL fetch...
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch...
2016-10-05 Jim ProcterJAL-2189 apply license
2016-10-05 Jim ProcterJAL-2189 source formatting
2016-10-05 gmungocMerge branch 'develop' into task/JAL-2196pdbeProperties
2016-10-05 Jim ProcterRevert "JAL-2245 Castor mapping and code changes for...
2016-10-05 gmungocJAL-2245 defence against NullPointer if no EMBL data...
2016-10-04 gmungocMerge branch 'bug/JAL-2245enaXmlChange' into develop
2016-10-04 gmungocJAL-2245 Castor mapping and code changes for change... bug/JAL-2245enaXmlChange
2016-10-04 gmungocJAL-2232 JAL-2154 update dbrefs to newly created datase...
2016-10-03 gmungocJAL-2110 additional tests for setDatasetSequence, javad...
2016-10-03 gmungocJAL-98 use Profile to store consensus, ResidueCount...
2016-10-03 Jim ProcterJAL-2210 need to add both transcript and product, and...
2016-10-02 Jim ProcterJAL-2210 remove ENSEMBL from protein DB list:
2016-09-28 Jim ProcterJAL-2235 raise exceptions if self reference or referenc...
2016-09-28 Jim ProcterJAL-2210 instrument setDBRefs to call ensurePrimaries
2016-09-27 Jim ProcterMerge branch 'develop' into bug/JAL-2210_ensembl_unipro...
2016-09-27 Jim ProcterJAL-2210 promote direct dbrefs from verified sources...
2016-09-27 Jim ProcterJAL-2210 resolve todo - addDBRef adds to dataset sequen...
2016-09-22 gmungocJAL-1421 typed ResidueProperties.propHash; JAL-2176...
2016-09-22 gmungocJAL-2216 finalize() refactored so not called programmat...
2016-09-19 gmungocJAL-2172 test and code updates for readonly selection...
2016-09-16 gmungocJAL-2157 JAL-1803 refactored Sequence.updatePDBIds...
2016-09-13 gmungocJAL-2196 refactor PDBEntry.getProperty,setProperty...
2016-09-13 gmungocJAL-1803 extracted class ChainId to jalview.util.CaseIn...
2016-09-07 Jim ProcterMerge branch 'develop' into bug/JAL-1803_JAL-2157
2016-09-07 Jim ProcterJAL-1803 first pass at updatePDBEntry
2016-09-06 gmungocJAL-2106 DBRefEntry.isPrimary() renamed isPrimaryCandid...
2016-09-05 gmungocJAL-2106 increased coverage for testGetPrimaryDbRefs
2016-09-05 gmungocJAL-2106 corrections to DBRefEntry.isPrimary code and...
2016-09-04 Jim ProcterJAL-1803 chainCode moved onto property hashtable as...
2016-08-31 Jim ProcterJAL-1926 JAL-2106 fix PDB primary DBRef semantics:...
2016-08-31 Jim ProcterJAL-2034 fix logic so recalcConservation(true) returns...
2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p...
2016-08-30 gmungocMerge branch 'develop' into features/filetypeEnum
2016-08-26 Jim ProcterJAL-2106 fix (last one!) remove the Sequence.sourceDBRe... bug/JAL-2154projectMappings
2016-08-26 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr
2016-08-26 Jim ProcterJAL-2154 drop PDB from Protein db list to remove from...
2016-08-25 Jim ProcterJAL-2106 tighten DBRefEntry primary seq test for PDB
2016-08-25 gmungocJAL-1854 missing case break statements added
2016-08-25 Jim ProcterMerge branch 'refactor/JAL-2106_sourceDbRef_revision...
2016-08-25 Jim ProcterMerge branch 'develop' into bug/JAL-2154projectMappings
2016-08-25 Jim ProcterMerge branch 'develop' into refactor/JAL-2106_sourceDbR...
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
2016-08-24 Jim ProcterJAL-2106 stricter check for 1:1 mapping (same numbering...
2016-08-24 Jim ProcterJAL-2106 rejig test to minimally verify patch that...
2016-08-24 Jim ProcterJAL-2106 formatting
2016-08-24 Jim ProcterJAL-2106 DBRefEntry.isPrimary() minimal test & implemen...
2016-08-24 Jim ProcterJAL-2106 convenience method to find all dbsource names...
2016-08-24 gmungocJAL-1424 removed unused and duplicated message keys
2016-08-23 Jim ProcterMerge branch 'develop' into bug/JAL-2154projectMappings
2016-08-23 gmungocJAL-2174 markColumns() refactored inside ColumnSelection
2016-08-22 Jim ProcterJAL-2154 always check dataset sequence for sequence...
2016-08-19 Jim ProcterJAL-2154 refactor setSequenceAt to replaceSequenceAt...
2016-08-18 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr
2016-08-18 gmungocJAL-1855 fail gracefully if XML has no <sequence> element
2016-08-18 gmungocJAL-2001 return copy of selection in getSelected()
2016-08-16 gmungocJAL-2171 matching bracket default character for rna...
2016-08-12 gmungocJAL-1841 bug fixes / code tidy for rna SS rendering...
2016-08-07 Jim ProcterJAL-2154 add in missing class for createDatasetAlignmen...
2016-08-04 Jim ProcterJAL-2154 make sure all sequences referenced via DBRefEn...
2016-08-04 Jim ProcterJAL-2046 stack trace for implementation warning
2016-08-02 Jim ProcterJAL-2046 additional logic to suppress spurious implemen...
2016-08-02 Jim ProcterMerge branch 'develop' into efficiency/JAL-2034_JAL...
2016-07-21 Jim ProcterMerge branch 'apifix/JAL-1926_JAL-2106' into develop
2016-07-20 Jim ProcterJAL-1926 JAL-2106 remove startRes/endRes fields - not...
2016-07-19 tcofoegbuMerge branch 'develop' of https://source.jalview.org...
2016-07-19 tcofoegbuJAL-1919 set default structure file format to mmCIF...
2016-07-19 Jim ProcterMerge branch 'develop' into efficiency/JAL-2034_JAL...
2016-07-18 Jim ProcterJAL-2121 cleanup TODO
2016-07-18 Jim ProcterJAL-2145 documentation of getWidth()
2016-07-14 Jim ProcterJAL-1115 change implementation to avoid possibility...
2016-07-14 Jim ProcterJAL-1270 test coverage TODO Alignment.append(AlignmentI)
2016-07-12 Jim ProcterJAL-2144 TODO - new methods for canonicalisation and...
2016-07-12 Jim ProcterJAL-2110 javadoc and TODO re shortcomings of implementation
2016-07-12 Jim ProcterJAL-2110 javadoc
2016-07-11 gmungocfile format enum wip changes
2016-07-06 gmungocJAL-2110 generic rather than specific check for gap...
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds
2016-07-06 gmungocJAL-2110 add 'mapFromId' to Mapping (for e.g. EMBL...
2016-07-06 gmungocJAL-2110 fixes and tests for adding dbrefs to EMBL...
2016-07-04 gmungocJAL-2110 unused method removed
2016-07-04 gmungocJAL-2110 defensive check in code
2016-07-01 gmungocJAL-2110 bug fixing and tidying for get cross-refs
2016-07-01 gmungocJAL-2110 code/comment tidy
2016-06-30 gmungocJAL-2110 fixes and tests for synthesized EMBLCDSPROTEIN...
2016-06-29 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD...
2016-06-27 gmungocJAL-1270 unit tests for HiddenSequences
2016-06-23 Jim ProcterJAL-2110 SequenceI.isProtein method
2016-06-21 Jim ProcterMerge branch 'features/JAL-2110_crossRefDuplications...
2016-06-21 Jim ProcterJAL-1369 make sure the fake AlignmentI produced by...
2016-06-21 Jim ProcterJAL-1369 HUGE WARNING: datamodel.HiddenSequences is...
next