JAL-2994 put ‘\’ first in character class clause of regex - otherwise doesn’t compile...
[jalview.git] / src / jalview / ext / ensembl /
2018-06-07 gmungocJAL-2755 correct Javadoc and error handling
2018-06-04 gmungocJAL-3018 updated REST versions to 6.3
2018-03-16 gmungocJAL-2679 getGeneId() now uses the same pattern as getGe...
2018-03-16 gmungocMerge remote-tracking branch 'origin/releases/Release_2...
2018-03-15 gmungocJAL-2893 enabling Get Crossreferences to ENSEMBLGENOMES
2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge
2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2018-02-23 Jim ProcterMerge branch 'features/JAL-2885UniprotHttps' into relea...
2018-02-23 Jim ProcterJAL-2885 Ensembl* -> https
2018-02-23 Jim ProcterJAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL
2018-01-30 gmungocJAL-1793 update spike build to latest incl stop and...
2018-01-29 gmungocJAL-2743 recoded EnsemblLookup without lambda expressio...
2018-01-26 gmungocMerge branch 'develop' into features/JAL-1793VCF
2018-01-18 gmungocJAL-2679 update query id to actual case of retrieved...
2018-01-17 gmungocJAL-2679 case-insensitive comparison of query and retri...
2018-01-16 gmungocJAL-2679 use object_type=Transcript for lookup of Paren...
2018-01-16 gmungocJAL-2885 uniprot now https, uniprot/ensembl/pfam/xfam...
2017-11-15 gmungocJAL-2835 spike updated with latest
2017-11-13 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-11-13 gmungocJAL-2679 example accession changed to CAD01290
2017-10-27 gmungocJAL-1793 spike branch updated to latest
2017-10-25 gmungocJAL-2743 fall back to parsing description if chromosome...
2017-10-24 gmungocJAL-2738 tidy Javadoc, remove debug logging
2017-10-24 gmungocJAL-2743 look up species and gene loci for Ensembl...
2017-10-24 gmungocJAL-1739 Javadoc updated for Lambda expression parser...
2017-10-24 gmungocJAL-2738 update spike branch with latest
2017-10-24 gmungocMerge branch 'develop' into features/JAL-1793VCF; lambd...
2017-10-23 Jim ProcterMerge branch 'bug/JAL-2253' into develop
2017-10-20 gmungocPush 1793 latest to spike branch
2017-10-20 gmungocJAL-2253 pull up constant, additional unit test bug/JAL-2253
2017-10-19 gmungocJAL-2755 add lookup of cds/cdna gene loci
2017-10-19 gmungocJAL-2755 add species lookup
2017-10-19 gmungocJAL-2755 rename EnsemblInfo as EnsemblData, add 'true...
2017-10-09 gmungocJAL-2523 basic sleep and retry (3 times) on 429 respons... features/JAL-2523httpRetries
2017-10-09 gmungocJAL-2523 convenience method to get model organisms
2017-10-04 gmungocJAL-2523 start of refactoring...
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-10-02 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-10-02 gmungocJAL-2525 lookup transcript features by Ontology
2017-09-28 gmungocJAL-1796 GeneLociI as distinguished DBRefEntry
2017-09-26 gmungocJAL-2738 unit test for reverse strand gene
2017-09-25 gmungocJAL-2738 use complement base for a VCF variant on rever...
2017-09-25 gmungocJAL-2738 one constant in codebase for "alleles" attribu...
2017-09-22 gmungocJAL-2738 correct handling of reverse strand genes
2017-09-22 gmungocJAL-2738 lookup GRCh38/37 gene mapping
2017-09-21 gmungocJAL-2738 add chromosome coordinate mappings to transcripts
2017-08-31 gmungocJAL-2105 REST versions updated to 6.1 (Ensembl) 6.0...
2017-08-31 gmungocJAL-2253 safer simpler resolution of identifiers using...
2017-08-25 gmungocJAL-2480 suppress debug timing output that got left in
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList
2017-08-16 Jim ProcterJAL-2418 source formatting
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-06-05 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-06-04 Jim ProcterJAL-2582 comment about IDs being lost if they resembl...
2017-06-04 Jim ProcterJAL-2582 recognise ENS…P peptide IDs and make two getPa...
2017-05-25 gmungocJAL-2050 make SequenceFeature.score final, adjust const...
2017-05-24 gmungocJAL-2529 add object_type=cdna to EnsemblCdna parameters
2017-05-16 gmungocJAL-2525 put in missing "transcript" feature type
2017-05-12 gmungocJAL-2525 get sequence features for Ontology term(s...
2017-05-12 gmungocJAL-2480 renamed java.util.RangeComparator to IntRangeC...
2017-05-09 gmungocJAL-2505 use constructors to set (what will be) final...
2017-05-03 gmungocJAL-2105 Ensembl REST now at 5.0
2017-01-17 gmungocMerge branch 'develop' into features/JAL-2295setChimera...
2016-12-09 gmungocJAL-2105 updated for reviewed REST version 4.8
2016-12-08 gmungocMerge branch 'develop' into features/JAL-2295setChimera...
2016-12-07 gmungocJAL-2354 handle error response when fetching features
2016-11-29 gmungocMerge branch 'develop' into features/JAL-2295setChimera...
2016-11-25 gmungocMerge branch 'develop' into trialMerge
2016-11-08 gmungocJAL-2295 make RangeComparator a top level class for...
2016-10-13 gmungocJAL-2253 2 second timeout on ping URL, default 5 minute... feature/JAL-2553ensemblGenomes
2016-10-05 Jim ProcterJAL-2189 apply license
2016-10-05 Jim ProcterJAL-2189 source formatting
2016-10-05 gmungocJAL-2105 update Ensembl REST version to 4.7
2016-10-03 gmungocJAL-2110 JAL-1705 handle not found (400) better
2016-09-30 Jim ProcterJAL-2210 add uniprot+mapping between ENST and ENSP...
2016-09-28 Jim ProcterJAL-2210 JAL-2232 check response code before attempting...
2016-09-27 Jim ProcterJAL-2210 report stack trace for unexpected exceptions
2016-09-18 Jim ProcterJAL-1795 JAL-2206 prevent NPE when no data returned...
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 gmungocJAL-2049 set Ensembl variant source to ENSEMBL if ...
2016-08-25 Jim ProcterJAL-2106 JAL-2154 cross-refs from Ensembl should verify...
2016-08-25 Jim ProcterMerge branch 'develop' into refactor/JAL-2106_sourceDbR...
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
2016-08-17 gmungocJAL-2105 rest versions updated to 4.6, change log link...
2016-07-18 gmungocJAL-2105 check content of Ensembl REST ping response
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds
2016-06-21 Jim ProcterMerge branch 'features/JAL-1956_featureStyles' into...
2016-05-13 gmungocJAL-2105 capture Ensembl data version, check REST versi...
2016-05-10 gmungocMerge branch 'develop' into features/JAL-1956_featureStyles
2016-04-29 gmungocJAL-2051 better checking of retrieved / duplicated...
2016-04-14 gmungocJAL-1705 refactored/utility methods to detect e.g....
2016-04-11 gmungocJAL-1705 code/comment tidy only
2016-04-11 gmungocJAL-2051 fetch Ensembl Gene accessions one at a time
2016-04-01 gmungocJAL-1705 fetch all Ensembl xrefs (except GO terms)
2016-03-23 gmungocJAL-1705 add DBRefEntry for 'self' to retrieved transcr...
2016-03-16 gmungocJAL-1705 xref ENST to correct (ENSP) accession id
2016-03-15 gmungocJAL-2016 FeatureSettingsI now FeatureSettingsModelI
2016-03-15 gmungocJAL-1705 code tidy/comment only
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