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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git]
/
src
/
jalview
/ ext
2018-08-10
gmungoc
JAL-3018 updated to Ensembl REST 7.0
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commitdiff
2018-08-10
gmungoc
JAL-3076 refactor for more efficient scan of 'gene...
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commitdiff
2018-08-10
gmungoc
JAL-3076 fetch Ensembl sequence as JSON instead of...
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commitdiff
2018-07-22
hansonr
allows for null Jmol viewer
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commitdiff
2018-06-28
hansonr
JAL-3032 DND enabled; additional io changes for File...
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commitdiff
2018-06-07
gmungoc
JAL-2755 correct Javadoc and error handling
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commitdiff
2018-06-04
gmungoc
JAL-3018 updated REST versions to 6.3
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commitdiff
2018-05-28
gmungoc
Merge remote-tracking branch 'origin/releases/Release_2...
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commitdiff
2018-05-07
Jim Procter
JAL-2321 use StructureImportSettings singleton settings...
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commitdiff
2018-05-07
Jim Procter
JAL-2321 allow JmolParser to be configured before parsi...
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commitdiff
2018-05-07
gmungoc
Merge branch 'releases/Release_2_10_4_Branch' into...
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commitdiff
2018-05-04
Jim Procter
Merge branch 'bug/JAL-2899' into releases/Release_2_10_...
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commitdiff
2018-05-01
Jim Procter
JAL-2899 colouring moved from SwingWorker to a backgrou...
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commitdiff
2018-04-30
Jim Procter
Merge branch 'bug/JAL-2899' into releases/Release_2_10_...
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commitdiff
2018-04-05
Jim Procter
JAL-2945 resolve model as PDB file. Need to verify...
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commitdiff
2018-03-16
gmungoc
JAL-2679 getGeneId() now uses the same pattern as getGe...
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commitdiff
2018-03-16
gmungoc
Merge remote-tracking branch 'origin/releases/Release_2...
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commitdiff
2018-03-15
gmungoc
JAL-2893 enabling Get Crossreferences to ENSEMBLGENOMES
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commitdiff
2018-03-14
gmungoc
JAL-2679 reinstating changes lost in VCF merge
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commitdiff
2018-03-14
gmungoc
JAL-2679 reinstating changes lost in VCF merge
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commitdiff
2018-03-07
Jim Procter
Merge branch 'releases/Release_2_10_4_Branch' into...
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commitdiff
2018-02-23
Jim Procter
Merge branch 'features/JAL-2885UniprotHttps' into relea...
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commitdiff
2018-02-23
Jim Procter
JAL-2885 Ensembl* -> https
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commitdiff
2018-02-23
Jim Procter
JAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL
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commitdiff
2018-02-20
Jim Procter
Merge branch 'releases/Release_2_10_4_Branch' into...
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commitdiff
2018-02-12
Jim Procter
JAL-2780 JAL-2781 ahem - add a semicolon if there isn...
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commitdiff
2018-02-07
Jim Procter
JAL-2780 JAL-2781 don’t assume contiguous mapping to...
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commitdiff
2018-02-02
gmungoc
JAL-2899 asynchronous Jmol colour updates
bug/JAL-2899
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commitdiff
2018-01-30
gmungoc
JAL-1793 update spike build to latest incl stop and...
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commitdiff
2018-01-29
gmungoc
JAL-2743 recoded EnsemblLookup without lambda expressio...
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commitdiff
2018-01-26
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
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commitdiff
2018-01-18
gmungoc
JAL-2679 update query id to actual case of retrieved...
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commitdiff
2018-01-17
gmungoc
JAL-2679 case-insensitive comparison of query and retri...
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commitdiff
2018-01-16
gmungoc
JAL-2679 use object_type=Transcript for lookup of Paren...
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2018-01-16
gmungoc
JAL-2885 uniprot now https, uniprot/ensembl/pfam/xfam...
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2017-12-04
gmungoc
JAL-2850 JAL-1766 option to load contig sequence refere...
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commitdiff
2017-12-01
gmungoc
JAL-2835 spike updated to latest (use specific SO term...
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commitdiff
2017-11-30
gmungoc
JAL-1766 additional tests for stub htsjdk wrapper
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commitdiff
2017-11-15
gmungoc
JAL-2835 spike updated with latest
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commitdiff
2017-11-13
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
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commitdiff
2017-11-13
gmungoc
JAL-2679 example accession changed to CAD01290
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2017-10-27
gmungoc
JAL-1793 spike branch updated to latest
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commitdiff
2017-10-26
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
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commitdiff
2017-10-25
gmungoc
JAL-2743 fall back to parsing description if chromosome...
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2017-10-25
Jim Procter
Merge branch 'bug/JAL-2392_deadlockonpdbdisplay' into...
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commitdiff
2017-10-24
gmungoc
JAL-2738 tidy Javadoc, remove debug logging
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commitdiff
2017-10-24
gmungoc
JAL-2743 look up species and gene loci for Ensembl...
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commitdiff
2017-10-24
gmungoc
JAL-1739 Javadoc updated for Lambda expression parser...
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2017-10-24
gmungoc
JAL-2738 update spike branch with latest
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2017-10-24
gmungoc
Merge branch 'develop' into features/JAL-1793VCF; lambd...
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2017-10-23
Jim Procter
Merge branch 'bug/JAL-2253' into develop
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2017-10-23
gmungoc
JAL-1854 keep fallthrough but with comment to suppress...
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commitdiff
2017-10-23
gmungoc
JAL-1854 remove fallthrough of switch case (Checkstyle...
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commitdiff
2017-10-20
gmungoc
Push 1793 latest to spike branch
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2017-10-20
gmungoc
JAL-2253 pull up constant, additional unit test
bug/JAL-2253
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commitdiff
2017-10-19
gmungoc
JAL-2755 add lookup of cds/cdna gene loci
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2017-10-19
gmungoc
JAL-2755 add species lookup
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2017-10-19
gmungoc
JAL-2755 rename EnsemblInfo as EnsemblData, add 'true...
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commitdiff
2017-10-17
Jim Procter
JAL-2777 patch for whitespace chain
bugs/JAL-2777_whitespaceChain
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commitdiff
2017-10-10
Jim Procter
Merge branch 'codereviews/JAL-1990_IProgressIndicator_j...
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commitdiff
2017-10-09
gmungoc
JAL-2523 basic sleep and retry (3 times) on 429 respons...
features/JAL-2523httpRetries
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commitdiff
2017-10-09
gmungoc
JAL-2523 convenience method to get model organisms
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2017-10-04
gmungoc
JAL-2523 start of refactoring...
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2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
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commitdiff
2017-10-02
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
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commitdiff
2017-10-02
gmungoc
JAL-2525 lookup transcript features by Ontology
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2017-09-28
gmungoc
JAL-1796 GeneLociI as distinguished DBRefEntry
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commitdiff
2017-09-26
gmungoc
JAL-2738 unit test for reverse strand gene
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2017-09-25
gmungoc
JAL-2738 use complement base for a VCF variant on rever...
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commitdiff
2017-09-25
gmungoc
JAL-2738 query unindexed file, unit test for VCFLoader
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commitdiff
2017-09-25
gmungoc
JAL-2738 one constant in codebase for "alleles" attribu...
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2017-09-22
gmungoc
JAL-2738 correct handling of reverse strand genes
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commitdiff
2017-09-22
gmungoc
JAL-2738 lookup GRCh38/37 gene mapping
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2017-09-21
gmungoc
JAL-2738 add chromosome coordinate mappings to transcripts
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commitdiff
2017-09-21
gmungoc
JAL-2738 PoC of Load VCF file on to gene sequence
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2017-09-19
gmungoc
JAL-1793 wrapper for plain or indexed VCF + simple...
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commitdiff
2017-08-31
gmungoc
JAL-2105 REST versions updated to 6.1 (Ensembl) 6.0...
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commitdiff
2017-08-31
gmungoc
JAL-2253 safer simpler resolution of identifiers using...
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commitdiff
2017-08-25
gmungoc
JAL-2480 suppress debug timing output that got left in
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commitdiff
2017-08-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-2446NCList
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commitdiff
2017-08-16
Jim Procter
JAL-2418 add GPL to main sources
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commitdiff
2017-08-16
Jim Procter
JAL-2418 source formatting
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2017-06-14
gmungoc
JAL-2598 Sequence.getSequence return a copy of the...
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2017-06-09
gmungoc
JAL-2446 merged to spike branch
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commitdiff
2017-06-09
Jim Procter
Merge branch 'develop' into features/JAL-2349_matrixvis
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commitdiff
2017-06-05
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
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commitdiff
2017-06-04
Jim Procter
JAL-2582 comment about IDs being lost if they resembl...
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commitdiff
2017-06-04
Jim Procter
JAL-2582 recognise ENS…P peptide IDs and make two getPa...
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2017-05-30
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
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2017-05-29
Jim Procter
Merge branch 'features/JAL-2465_No-mapping_Jmol-structu...
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commitdiff
2017-05-25
gmungoc
JAL-2050 make SequenceFeature.score final, adjust const...
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2017-05-24
gmungoc
JAL-2529 add object_type=cdna to EnsemblCdna parameters
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2017-05-18
gmungoc
JAL-2490 retrieve visible features only
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commitdiff
2017-05-16
gmungoc
JAL-2525 put in missing "transcript" feature type
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commitdiff
2017-05-15
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
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2017-05-12
gmungoc
JAL-2525 get sequence features for Ontology term(s...
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commitdiff
2017-05-12
gmungoc
JAL-2480 renamed java.util.RangeComparator to IntRangeC...
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2017-05-09
gmungoc
JAL-2505 use constructors to set (what will be) final...
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2017-05-08
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
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2017-05-05
kiramt
Merge remote-tracking branch 'origin/develop' into
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