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Merge branch 'bug/JAL-2865removeGC' into develop
[jalview.git]
/
src
/
jalview
/
ext
/
2018-03-14
gmungoc
JAL-2679 reinstating changes lost in VCF merge
tree
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commitdiff
2018-03-07
Jim Procter
Merge branch 'releases/Release_2_10_4_Branch' into...
tree
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commitdiff
2018-02-23
Jim Procter
Merge branch 'features/JAL-2885UniprotHttps' into relea...
tree
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commitdiff
2018-02-23
Jim Procter
JAL-2885 Ensembl* -> https
tree
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commitdiff
2018-02-23
Jim Procter
JAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL
tree
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commitdiff
2018-02-20
Jim Procter
Merge branch 'releases/Release_2_10_4_Branch' into...
tree
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commitdiff
2018-02-12
Jim Procter
JAL-2780 JAL-2781 ahem - add a semicolon if there isn...
tree
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commitdiff
2018-02-07
Jim Procter
JAL-2780 JAL-2781 don’t assume contiguous mapping to...
tree
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commitdiff
2018-01-30
gmungoc
JAL-1793 update spike build to latest incl stop and...
tree
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commitdiff
2018-01-29
gmungoc
JAL-2743 recoded EnsemblLookup without lambda expressio...
tree
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commitdiff
2018-01-26
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
tree
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commitdiff
2018-01-18
gmungoc
JAL-2679 update query id to actual case of retrieved...
tree
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commitdiff
2018-01-17
gmungoc
JAL-2679 case-insensitive comparison of query and retri...
tree
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commitdiff
2018-01-16
gmungoc
JAL-2679 use object_type=Transcript for lookup of Paren...
tree
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commitdiff
2018-01-16
gmungoc
JAL-2885 uniprot now https, uniprot/ensembl/pfam/xfam...
tree
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commitdiff
2017-12-04
gmungoc
JAL-2850 JAL-1766 option to load contig sequence refere...
tree
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commitdiff
2017-12-01
gmungoc
JAL-2835 spike updated to latest (use specific SO term...
tree
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commitdiff
2017-11-30
gmungoc
JAL-1766 additional tests for stub htsjdk wrapper
tree
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commitdiff
2017-11-15
gmungoc
JAL-2835 spike updated with latest
tree
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commitdiff
2017-11-13
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
tree
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commitdiff
2017-11-13
gmungoc
JAL-2679 example accession changed to CAD01290
tree
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commitdiff
2017-10-27
gmungoc
JAL-1793 spike branch updated to latest
tree
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commitdiff
2017-10-26
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
tree
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commitdiff
2017-10-25
gmungoc
JAL-2743 fall back to parsing description if chromosome...
tree
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commitdiff
2017-10-25
Jim Procter
Merge branch 'bug/JAL-2392_deadlockonpdbdisplay' into...
tree
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commitdiff
2017-10-24
gmungoc
JAL-2738 tidy Javadoc, remove debug logging
tree
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commitdiff
2017-10-24
gmungoc
JAL-2743 look up species and gene loci for Ensembl...
tree
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commitdiff
2017-10-24
gmungoc
JAL-1739 Javadoc updated for Lambda expression parser...
tree
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commitdiff
2017-10-24
gmungoc
JAL-2738 update spike branch with latest
tree
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commitdiff
2017-10-24
gmungoc
Merge branch 'develop' into features/JAL-1793VCF; lambd...
tree
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commitdiff
2017-10-23
Jim Procter
Merge branch 'bug/JAL-2253' into develop
tree
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commitdiff
2017-10-23
gmungoc
JAL-1854 keep fallthrough but with comment to suppress...
tree
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commitdiff
2017-10-23
gmungoc
JAL-1854 remove fallthrough of switch case (Checkstyle...
tree
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commitdiff
2017-10-20
gmungoc
Push 1793 latest to spike branch
tree
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commitdiff
2017-10-20
gmungoc
JAL-2253 pull up constant, additional unit test
bug/JAL-2253
tree
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commitdiff
2017-10-19
gmungoc
JAL-2755 add lookup of cds/cdna gene loci
tree
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commitdiff
2017-10-19
gmungoc
JAL-2755 add species lookup
tree
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commitdiff
2017-10-19
gmungoc
JAL-2755 rename EnsemblInfo as EnsemblData, add 'true...
tree
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commitdiff
2017-10-17
Jim Procter
JAL-2777 patch for whitespace chain
bugs/JAL-2777_whitespaceChain
tree
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commitdiff
2017-10-10
Jim Procter
Merge branch 'codereviews/JAL-1990_IProgressIndicator_j...
tree
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commitdiff
2017-10-09
gmungoc
JAL-2523 basic sleep and retry (3 times) on 429 respons...
features/JAL-2523httpRetries
tree
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commitdiff
2017-10-09
gmungoc
JAL-2523 convenience method to get model organisms
tree
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commitdiff
2017-10-04
gmungoc
JAL-2523 start of refactoring...
tree
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commitdiff
2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
tree
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commitdiff
2017-10-02
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
tree
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commitdiff
2017-10-02
gmungoc
JAL-2525 lookup transcript features by Ontology
tree
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commitdiff
2017-09-28
gmungoc
JAL-1796 GeneLociI as distinguished DBRefEntry
tree
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commitdiff
2017-09-26
gmungoc
JAL-2738 unit test for reverse strand gene
tree
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commitdiff
2017-09-25
gmungoc
JAL-2738 use complement base for a VCF variant on rever...
tree
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commitdiff
2017-09-25
gmungoc
JAL-2738 query unindexed file, unit test for VCFLoader
tree
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commitdiff
2017-09-25
gmungoc
JAL-2738 one constant in codebase for "alleles" attribu...
tree
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commitdiff
2017-09-22
gmungoc
JAL-2738 correct handling of reverse strand genes
tree
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commitdiff
2017-09-22
gmungoc
JAL-2738 lookup GRCh38/37 gene mapping
tree
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commitdiff
2017-09-21
gmungoc
JAL-2738 add chromosome coordinate mappings to transcripts
tree
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commitdiff
2017-09-21
gmungoc
JAL-2738 PoC of Load VCF file on to gene sequence
tree
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commitdiff
2017-09-19
gmungoc
JAL-1793 wrapper for plain or indexed VCF + simple...
tree
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commitdiff
2017-08-31
gmungoc
JAL-2105 REST versions updated to 6.1 (Ensembl) 6.0...
tree
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commitdiff
2017-08-31
gmungoc
JAL-2253 safer simpler resolution of identifiers using...
tree
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commitdiff
2017-08-25
gmungoc
JAL-2480 suppress debug timing output that got left in
tree
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commitdiff
2017-08-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-2446NCList
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 add GPL to main sources
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 source formatting
tree
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commitdiff
2017-06-14
gmungoc
JAL-2598 Sequence.getSequence return a copy of the...
tree
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commitdiff
2017-06-09
gmungoc
JAL-2446 merged to spike branch
tree
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commitdiff
2017-06-05
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-06-04
Jim Procter
JAL-2582 comment about IDs being lost if they resembl...
tree
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commitdiff
2017-06-04
Jim Procter
JAL-2582 recognise ENS…P peptide IDs and make two getPa...
tree
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commitdiff
2017-05-30
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-05-29
Jim Procter
Merge branch 'features/JAL-2465_No-mapping_Jmol-structu...
tree
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commitdiff
2017-05-25
gmungoc
JAL-2050 make SequenceFeature.score final, adjust const...
tree
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commitdiff
2017-05-24
gmungoc
JAL-2529 add object_type=cdna to EnsemblCdna parameters
tree
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commitdiff
2017-05-18
gmungoc
JAL-2490 retrieve visible features only
tree
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commitdiff
2017-05-16
gmungoc
JAL-2525 put in missing "transcript" feature type
tree
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commitdiff
2017-05-15
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-05-12
gmungoc
JAL-2525 get sequence features for Ontology term(s...
tree
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commitdiff
2017-05-12
gmungoc
JAL-2480 renamed java.util.RangeComparator to IntRangeC...
tree
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commitdiff
2017-05-09
gmungoc
JAL-2505 use constructors to set (what will be) final...
tree
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commitdiff
2017-05-08
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2017-05-05
kiramt
Merge remote-tracking branch 'origin/develop' into
tree
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commitdiff
2017-05-03
gmungoc
JAL-2105 Ensembl REST now at 5.0
tree
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commitdiff
2017-05-01
tcofoegbu
JAL-2465 bugfix and rerefactor renamed getPdbFile(...
tree
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commitdiff
2017-04-26
kiramt
Merge remote-tracking branch 'origin/develop' into...
tree
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commitdiff
2017-04-26
kiramt
Merge remote-tracking branch 'origin/develop' into...
tree
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commitdiff
2017-04-24
gmungoc
JAL-2487 remove redundant refreshGUI to minimise thread...
tree
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commitdiff
2017-04-24
kiramt
JAL-2388 Hidden cols separated from column selection...
tree
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commitdiff
2017-03-31
gmungoc
JAL-2430 code tidy, unit test for Jmol hidden column...
tree
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commitdiff
2017-03-21
gmungoc
JAL-2438 check for null FeatureRenderer
tree
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commitdiff
2017-03-15
gmungoc
JAL-2443 push getResidueBoxColour inside getResidueColour
tree
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commitdiff
2017-03-13
gmungoc
JAL-2438 FeatureColourFinder refactored from FeatureRen...
tree
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commitdiff
2017-03-08
gmungoc
JAL-2430 colour columns hidden in alignment gray on...
tree
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commitdiff
2017-03-08
gmungoc
JAL-2295 avoid quotes breaking attribute value parsing
tree
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commitdiff
2017-03-07
gmungoc
JAL-2295 status messages for Chimera attributes set...
tree
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commitdiff
2017-03-01
gmungoc
Merge branch 'features/JAL-2295setChimeraAttributes...
tree
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commitdiff
2017-02-09
gmungoc
Merge branch 'develop' into features/JAL-2379pcaMemory
features/JAL-2379pcaMemory
tree
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commitdiff
2017-01-23
gmungoc
JAL-2379 made SparseMatrix.divide() so as to exactly...
tree
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commitdiff
2017-01-17
gmungoc
Merge branch 'develop' into features/JAL-2295setChimera...
tree
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commitdiff
2017-01-17
gmungoc
JAL-2379 SparseDoubleArray added (for use by SparseMatrix)
tree
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commitdiff
2017-01-09
gmungoc
JAL-2371 remove ColourSchemeI.findColour(c), pure inter...
tree
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commitdiff
2016-12-22
gmungoc
JAL-2360 structure viewers now using ColourMenuHelper...
tree
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commitdiff
2016-12-16
gmungoc
JAL-2360 refactoring for JalviewColourScheme enum,
tree
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commitdiff
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