JAL-2416 order score models by order of addition rather than name
[jalview.git] / src / jalview / datamodel /
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...
2016-06-21 gmungocJAL-2113 tidy up canonicalisation of Uniprot xrefs...
2016-06-21 gmungocJAL-2113 tidy up canonicalisation of Uniprot xrefs...
2016-06-20 Jim ProcterJAL-1551 tidy
2016-06-20 Jim ProcterJAL-2068 avoid ArrayIndexOutOfBounds when consensus...
2016-06-20 Jim ProcterJAL-2110 catch case when updateDBRef argument has null...
2016-06-20 Jim ProcterJAL-2110 copy alcodonframes only if copy constructor...
2016-06-19 Jim ProcterJAL-2110 JAL-2131 JAL-1765 remove reference to jalview...
2016-06-16 Jim ProcterJAL-2110 todo - select mappings involving sequences...
2016-06-16 Jim ProcterJAL-2110 equals and hashcode should check fromSeq
2016-06-16 Jim ProcterJAL-2110 typo caused infinite loop
2016-06-16 gmungocJAL-2112 optimisation of EMBL CDS parsing
2016-06-15 Jim ProcterMerge branch 'develop' into features/JAL-2110_crossRefD...
2016-06-14 gmungocJAL-2114 more helpful reporting of parse failures
2016-06-14 gmungocJAL-2110 ensure "UniProtKB/Swiss-Prot" dbrefs canonical...
2016-06-14 gmungocJAL-1686 JAL-2110 equals and/or hashCode method added
2016-06-09 gmungocJAL-2110 work in progress
2016-06-01 Jim Procterfix build
2016-05-31 gmungocJAL-2023 adjustments to mappings added for split frame...
2016-05-31 gmungocJAL-2110 refactor + tests to allow a dbref version...
2016-05-31 Jim ProcterMerge branch 'develop' into features/JAL-2113_emblXml1.2
2016-05-30 gmungocJAL-1989 equals method strengthened to fully match...
2016-05-30 Jim ProcterMerge branch 'develop' into efficiency/JAL-2034_JAL...
2016-05-27 gmungocJAL-1989 added hashCode and equals, renamed field to...
2016-05-26 gmungocJAL-2113 additions to embl_mapping.xml / data models... features/JAL-2113_emblXml1.2
2016-05-23 gmungocJAL-2113 remove spaces in sequence from unmarshalling...
2016-05-23 gmungocJAL-2114 save 'raw' ENA location as a sequence feature...
2016-05-20 gmungocJAL-2113 embl_mapping.xml and code updated for EMBL...
2016-05-17 tcofoegbuJAL-2106 JAL-1926 updated source doc for set/getSourceDBRef
2016-05-13 gmungocJAL-2105 capture Ensembl data version, check REST versi...
2016-05-05 Jim ProcterJAL-192 patch for off-by one and pathological case...
2016-04-29 Jim ProcterJAL-192 need visible and actual sequence limits for...
2016-04-29 Jim ProcterJAL-192 fix bounds when no hidden regions, and when...
2016-04-29 Jim ProcterJAL-966 JAL-1553
 todo: remove UI components from Colum...
2016-04-29 Jim ProcterJAL-1551 formatting

2016-04-29 Jim ProcterJAL-192 ‘efficiently’ locate visible bounds for a seque...
2016-04-29 Jim ProcterJAL-1551 formatting
2016-04-23 Jim ProcterJAL-2075 findPosition for SeqCigar (with test)
2016-04-23 Jim ProcterJAL-2075 formatting
2016-04-14 gmungocJAL-2041 add ID,clinical_significance to feature attrib...
2016-04-14 gmungocJAL-2049 small refactor of constructors to avoid code...
2016-04-13 Jim ProcterMerge branch 'bug/JAL-2046_ds_sharing_features_broken...
2016-04-11 tcofoegbuJAL-2054 Renamed getStartEnd in AlignFrame to getVisibl...
2016-04-11 Jim ProcterMerge branch 'develop' into efficiency/JAL-2034_JAL...
2016-04-08 Jim ProcterJAL-2050 JAL-1722 new getSelectedRange() method to...
2016-04-08 Jim ProcterJAL-2053 JAL-1551 javadoc and simpler code
2016-04-05 Jim ProcterJAL-2046 add/delete SequenceFeature operate on dataset...
2016-04-05 Jim ProcterJAL-2046 setSequenceFeature contract implementation...
2016-04-05 Jim ProcterJAL-2046 explicit contract for get/set SequenceFeatures...
2016-04-05 Jim ProcterJAL-2046 remove javadoc
2016-04-05 Jim ProcterJAL-2046 simpler deriveSequence - promote to dataset...
2016-04-05 Jim ProcterJAL-2046 clarify contract for copy constructor and...
2016-04-05 Jim ProcterJAL-2046 explicitly copy char[] when cloning sequence...
2016-04-05 Jim ProcterJAL-2046 safer createDatasetSequence manipulates privat...
2016-04-04 Jim ProcterJAL-2001 drop isSelected(int) in favour of original...
2016-04-04 Jim ProcterJAL-2001 catch -ve column values
2016-04-04 Jim ProcterJAL-2001 faster check for a column being selected
2016-04-04 Jim ProcterJAL-2001 javadoc
2016-04-04 Jim ProcterJAL-2001 faster getMax/getMin selected column, with...
2016-04-04 Jim ProcterJAL-2001 JAL-1722 - store selection as ArrayList and...
2016-04-01 gmungocJAL-1705 ensure the right mapping is used to align...
2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and...
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