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JAL-2089 fix broken help link
[jalview.git]
/
src
/
jalview
/
datamodel
/
2016-09-22
gmungoc
JAL-1421 typed ResidueProperties.propHash; JAL-2176...
tree
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commitdiff
2016-09-22
gmungoc
JAL-2216 finalize() refactored so not called programmat...
tree
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commitdiff
2016-09-19
gmungoc
JAL-2172 test and code updates for readonly selection...
tree
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commitdiff
2016-09-16
gmungoc
JAL-2157 JAL-1803 refactored Sequence.updatePDBIds...
tree
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commitdiff
2016-09-13
gmungoc
JAL-1803 extracted class ChainId to jalview.util.CaseIn...
tree
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commitdiff
2016-09-07
Jim Procter
Merge branch 'develop' into bug/JAL-1803_JAL-2157
tree
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commitdiff
2016-09-07
Jim Procter
JAL-1803 first pass at updatePDBEntry
tree
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commitdiff
2016-09-06
gmungoc
JAL-2106 DBRefEntry.isPrimary() renamed isPrimaryCandid...
tree
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commitdiff
2016-09-05
gmungoc
JAL-2106 increased coverage for testGetPrimaryDbRefs
tree
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commitdiff
2016-09-05
gmungoc
JAL-2106 corrections to DBRefEntry.isPrimary code and...
tree
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commitdiff
2016-09-04
Jim Procter
JAL-1803 chainCode moved onto property hashtable as...
tree
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commitdiff
2016-08-31
Jim Procter
JAL-1926 JAL-2106 fix PDB primary DBRef semantics:...
tree
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commitdiff
2016-08-31
Jim Procter
JAL-2034 fix logic so recalcConservation(true) returns...
tree
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commitdiff
2016-08-30
Jim Procter
Merge branch 'develop' into merge/develop_bug/JAL-2154p...
tree
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commitdiff
2016-08-26
Jim Procter
JAL-2106 fix (last one!) remove the Sequence.sourceDBRe...
bug/JAL-2154projectMappings
tree
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commitdiff
2016-08-26
gmungoc
Merge branch 'develop' into bug/JAL-1841rnaSecStr
tree
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commitdiff
2016-08-26
Jim Procter
JAL-2154 drop PDB from Protein db list to remove from...
tree
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commitdiff
2016-08-25
Jim Procter
JAL-2106 tighten DBRefEntry primary seq test for PDB
tree
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commitdiff
2016-08-25
gmungoc
JAL-1854 missing case break statements added
tree
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commitdiff
2016-08-25
Jim Procter
Merge branch 'refactor/JAL-2106_sourceDbRef_revision...
tree
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commitdiff
2016-08-25
Jim Procter
Merge branch 'develop' into bug/JAL-2154projectMappings
tree
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commitdiff
2016-08-25
Jim Procter
Merge branch 'develop' into refactor/JAL-2106_sourceDbR...
tree
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commitdiff
2016-08-24
Jim Procter
JAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
tree
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commitdiff
2016-08-24
Jim Procter
JAL-2106 stricter check for 1:1 mapping (same numbering...
tree
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commitdiff
2016-08-24
Jim Procter
JAL-2106 rejig test to minimally verify patch that...
tree
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commitdiff
2016-08-24
Jim Procter
JAL-2106 formatting
tree
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commitdiff
2016-08-24
Jim Procter
JAL-2106 DBRefEntry.isPrimary() minimal test & implemen...
tree
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commitdiff
2016-08-24
Jim Procter
JAL-2106 convenience method to find all dbsource names...
tree
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commitdiff
2016-08-24
gmungoc
JAL-1424 removed unused and duplicated message keys
tree
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commitdiff
2016-08-23
Jim Procter
Merge branch 'develop' into bug/JAL-2154projectMappings
tree
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commitdiff
2016-08-23
gmungoc
JAL-2174 markColumns() refactored inside ColumnSelection
tree
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commitdiff
2016-08-22
Jim Procter
JAL-2154 always check dataset sequence for sequence...
tree
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commitdiff
2016-08-19
Jim Procter
JAL-2154 refactor setSequenceAt to replaceSequenceAt...
tree
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commitdiff
2016-08-18
gmungoc
Merge branch 'develop' into bug/JAL-1841rnaSecStr
tree
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commitdiff
2016-08-18
gmungoc
JAL-1855 fail gracefully if XML has no <sequence> element
tree
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commitdiff
2016-08-18
gmungoc
JAL-2001 return copy of selection in getSelected()
tree
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commitdiff
2016-08-16
gmungoc
JAL-2171 matching bracket default character for rna...
tree
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commitdiff
2016-08-12
gmungoc
JAL-1841 bug fixes / code tidy for rna SS rendering...
tree
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commitdiff
2016-08-07
Jim Procter
JAL-2154 add in missing class for createDatasetAlignmen...
tree
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commitdiff
2016-08-04
Jim Procter
JAL-2154 make sure all sequences referenced via DBRefEn...
tree
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commitdiff
2016-08-04
Jim Procter
JAL-2046 stack trace for implementation warning
tree
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commitdiff
2016-08-02
Jim Procter
JAL-2046 additional logic to suppress spurious implemen...
tree
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commitdiff
2016-08-02
Jim Procter
Merge branch 'develop' into efficiency/JAL-2034_JAL...
tree
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commitdiff
2016-07-21
Jim Procter
Merge branch 'apifix/JAL-1926_JAL-2106' into develop
tree
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commitdiff
2016-07-20
Jim Procter
JAL-1926 JAL-2106 remove startRes/endRes fields - not...
tree
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commitdiff
2016-07-19
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-07-19
tcofoegbu
JAL-1919 set default structure file format to mmCIF...
tree
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commitdiff
2016-07-19
Jim Procter
Merge branch 'develop' into efficiency/JAL-2034_JAL...
tree
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commitdiff
2016-07-18
Jim Procter
JAL-2121 cleanup TODO
tree
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commitdiff
2016-07-18
Jim Procter
JAL-2145 documentation of getWidth()
tree
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commitdiff
2016-07-14
Jim Procter
JAL-1115 change implementation to avoid possibility...
tree
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commitdiff
2016-07-14
Jim Procter
JAL-1270 test coverage TODO Alignment.append(AlignmentI)
tree
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commitdiff
2016-07-12
Jim Procter
JAL-2144 TODO - new methods for canonicalisation and...
tree
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commitdiff
2016-07-12
Jim Procter
JAL-2110 javadoc and TODO re shortcomings of implementation
tree
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commitdiff
2016-07-12
Jim Procter
JAL-2110 javadoc
tree
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commitdiff
2016-07-06
gmungoc
JAL-2110 generic rather than specific check for gap...
tree
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commitdiff
2016-07-06
gmungoc
JAL-2110 ensuring mapped dbrefs between protein and cds
tree
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commitdiff
2016-07-06
gmungoc
JAL-2110 add 'mapFromId' to Mapping (for e.g. EMBL...
tree
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commitdiff
2016-07-06
gmungoc
JAL-2110 fixes and tests for adding dbrefs to EMBL...
tree
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commitdiff
2016-07-04
gmungoc
JAL-2110 unused method removed
tree
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commitdiff
2016-07-04
gmungoc
JAL-2110 defensive check in code
tree
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commitdiff
2016-07-01
gmungoc
JAL-2110 bug fixing and tidying for get cross-refs
tree
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commitdiff
2016-07-01
gmungoc
JAL-2110 code/comment tidy
tree
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commitdiff
2016-06-30
gmungoc
JAL-2110 fixes and tests for synthesized EMBLCDSPROTEIN...
tree
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commitdiff
2016-06-29
gmungoc
Merge branch 'develop' into features/JAL-2110_crossRefD...
tree
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commitdiff
2016-06-27
gmungoc
JAL-1270 unit tests for HiddenSequences
tree
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commitdiff
2016-06-23
Jim Procter
JAL-2110 SequenceI.isProtein method
tree
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commitdiff
2016-06-21
Jim Procter
Merge branch 'features/JAL-2110_crossRefDuplications...
tree
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commitdiff
2016-06-21
Jim Procter
JAL-1369 make sure the fake AlignmentI produced by...
tree
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commitdiff
2016-06-21
Jim Procter
JAL-1369 HUGE WARNING: datamodel.HiddenSequences is...
tree
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commitdiff
2016-06-21
gmungoc
JAL-2113 tidy up canonicalisation of Uniprot xrefs...
tree
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commitdiff
2016-06-21
gmungoc
JAL-2113 tidy up canonicalisation of Uniprot xrefs...
tree
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commitdiff
2016-06-20
Jim Procter
JAL-1551 tidy
tree
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commitdiff
2016-06-20
Jim Procter
JAL-2068 avoid ArrayIndexOutOfBounds when consensus...
tree
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commitdiff
2016-06-20
Jim Procter
JAL-2110 catch case when updateDBRef argument has null...
tree
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commitdiff
2016-06-20
Jim Procter
JAL-2110 copy alcodonframes only if copy constructor...
tree
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commitdiff
2016-06-19
Jim Procter
JAL-2110 JAL-2131 JAL-1765 remove reference to jalview...
tree
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commitdiff
2016-06-16
Jim Procter
JAL-2110 todo - select mappings involving sequences...
tree
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commitdiff
2016-06-16
Jim Procter
JAL-2110 equals and hashcode should check fromSeq
tree
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commitdiff
2016-06-16
Jim Procter
JAL-2110 typo caused infinite loop
tree
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commitdiff
2016-06-16
gmungoc
JAL-2112 optimisation of EMBL CDS parsing
tree
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commitdiff
2016-06-15
Jim Procter
Merge branch 'develop' into features/JAL-2110_crossRefD...
tree
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commitdiff
2016-06-14
gmungoc
JAL-2114 more helpful reporting of parse failures
tree
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commitdiff
2016-06-14
gmungoc
JAL-2110 ensure "UniProtKB/Swiss-Prot" dbrefs canonical...
tree
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commitdiff
2016-06-14
gmungoc
JAL-1686 JAL-2110 equals and/or hashCode method added
tree
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commitdiff
2016-06-09
gmungoc
JAL-2110 work in progress
tree
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commitdiff
2016-06-01
Jim Procter
fix build
tree
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commitdiff
2016-05-31
gmungoc
JAL-2023 adjustments to mappings added for split frame...
tree
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commitdiff
2016-05-31
gmungoc
JAL-2110 refactor + tests to allow a dbref version...
tree
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commitdiff
2016-05-31
Jim Procter
Merge branch 'develop' into features/JAL-2113_emblXml1.2
tree
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commitdiff
2016-05-30
gmungoc
JAL-1989 equals method strengthened to fully match...
tree
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commitdiff
2016-05-30
Jim Procter
Merge branch 'develop' into efficiency/JAL-2034_JAL...
tree
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commitdiff
2016-05-27
gmungoc
JAL-1989 added hashCode and equals, renamed field to...
tree
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commitdiff
2016-05-26
gmungoc
JAL-2113 additions to embl_mapping.xml / data models...
features/JAL-2113_emblXml1.2
tree
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commitdiff
2016-05-23
gmungoc
JAL-2113 remove spaces in sequence from unmarshalling...
tree
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commitdiff
2016-05-23
gmungoc
JAL-2114 save 'raw' ENA location as a sequence feature...
tree
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commitdiff
2016-05-20
gmungoc
JAL-2113 embl_mapping.xml and code updated for EMBL...
tree
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commitdiff
2016-05-17
tcofoegbu
JAL-2106 JAL-1926 updated source doc for set/getSourceDBRef
tree
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commitdiff
2016-05-13
gmungoc
JAL-2105 capture Ensembl data version, check REST versi...
tree
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commitdiff
2016-05-05
Jim Procter
JAL-192 patch for off-by one and pathological case...
tree
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commitdiff
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