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Merge branch 'develop' into releases/Release_2_11_2_Branch
[jalview.git] / src / jalview / ext / ensembl /
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... tree | commitdiff
2021-09-02 gmungocJAL-1842 adjust code to match changed semantics of... tree | commitdiff
2020-08-31 gmungocJAL-3018 Ensembl reviewed REST version updated to 13.0 tree | commitdiff
2020-08-24 gmungocJAL-3018 updated reviewed REST version to 12.0 tree | commitdiff
2020-05-18 gmungocMerge branch 'Jalview-JS/develop' into develop tree | commitdiff
2020-04-21 Jim ProcterJAL-3407 add GPL license to Jalview source files tree | commitdiff
2020-03-30 gmungocJAL-3210 debug logging commented out tree | commitdiff
2020-03-30 gmungocMerge branch 'develop' into Jalview-JS/develop tree | commitdiff
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop tree | commitdiff
2019-08-22 gmungocJAL-3121 round trip GFF attributes including map-valued... tree | commitdiff
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge tree | commitdiff
2019-06-11 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures tree | commitdiff
2019-06-11 gmungocJAL-3143 also parse "phase" from JSON response if present tree | commitdiff
2019-06-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures tree | commitdiff
2019-06-07 gmungocJAL-2738 use GeneLocus extends DBRefEntry to hold chrom... tree | commitdiff
2019-06-06 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2019-04-26 gmungocJAL-2743 class Javadoc tree | commitdiff
2019-04-18 gmungocMerge branch 'develop' into Jalview-JS/develop tree | commitdiff
2019-04-18 gmungocJAL-3193 dbSource always "ENSEMBL" tree | commitdiff
2019-04-15 gmungocMerge branch 'develop' into Jalview-JS/develop tree | commitdiff
2019-04-10 gmungocJAL-3193 rest.ensemblgenomes.org merged to rest.ensembl.org tree | commitdiff
2019-04-10 gmungocJAL-3018 REST version updated to 10.0 tree | commitdiff
2019-04-03 hansonrreplacing @j2sNative with @j2sIgnore where appropriate... tree | commitdiff
2019-04-01 gmungocJAL-3032 use small example Ensembl gene for JalviewJS tree | commitdiff
2019-04-01 hansonrJSON refactoring of a few methods; fixing JavaScript... tree | commitdiff
2019-03-19 gmungocJAL-3210 code formatting only tree | commitdiff
2019-03-13 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2019-03-08 gmungocJAL-3193 defensive trim of URL read from properties... tree | commitdiff
2019-02-28 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into merge... tree | commitdiff
2019-02-20 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into feature... tree | commitdiff
2019-01-29 gmungocMerge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of... tree | commitdiff
2019-01-29 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into trialMerge tree | commitdiff
2019-01-29 gmungocJAL-3143 format alleles array for feature description tree | commitdiff
2019-01-29 hansonrtime check, iterators tree | commitdiff
2019-01-29 hansonrmore iterators out; some time checks tree | commitdiff
2019-01-26 hansonrPlatform.timecheck calls removed or commented out. tree | commitdiff
2019-01-26 hansonrJalview.isJS() --> Platform.isJS(), DBRefEntry[] -... tree | commitdiff
2019-01-25 hansonrJSON refactoring tree | commitdiff
2019-01-25 gmungocJAL-3187 don't compute variant features on peptide... tree | commitdiff
2019-01-24 gmungocJAL-3018 Ensembl version updated to 9.0 tree | commitdiff
2019-01-18 gmungocJAL-3143 'id' not 'ID' attribute drives generation... tree | commitdiff
2018-11-19 gmungocJAL-3032 reinstate methods now available in SwingJS tree | commitdiff
2018-11-12 gmungocJAL-3076 JalviewJS requires lower case content-type... tree | commitdiff
2018-11-11 hansonradds explicit AJAX-allowed tree | commitdiff
2018-11-01 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into tree | commitdiff
2018-11-01 gmungocMerge branch 'Jalview-BH/JAL-3026' into tree | commitdiff
2018-10-31 gmungocMerge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' into... feature/JAL-3144noJTree tree | commitdiff
2018-10-31 gmungocJAL-3026 skip unsupported HttpURLConnection methods... tree | commitdiff
2018-10-25 gmungocJAL-3143 comma-delimited feature attributes for alleles, tree | commitdiff
2018-10-25 gmungocJAL-3143 fetch Ensembl(Genomes) features as JSON not GFF tree | commitdiff
2018-09-03 gmungocJAL-3076 fetch Ensembl sequence as JSON instead of... tree | commitdiff
2018-09-03 Jim ProcterJAL-3076 clarify javadoc handling single sequence respo... bug/JAL-3076ensemblGeneId tree | commitdiff
2018-08-10 gmungocJAL-3018 updated to Ensembl REST 7.0 tree | commitdiff
2018-08-10 gmungocJAL-3076 refactor for more efficient scan of 'gene... tree | commitdiff
2018-08-10 gmungocJAL-3076 fetch Ensembl sequence as JSON instead of... tree | commitdiff
2018-06-07 gmungocJAL-2755 correct Javadoc and error handling tree | commitdiff
2018-06-04 gmungocJAL-3018 updated REST versions to 6.3 tree | commitdiff
2018-03-16 gmungocJAL-2679 getGeneId() now uses the same pattern as getGe... tree | commitdiff
2018-03-16 gmungocMerge remote-tracking branch 'origin/releases/Release_2... tree | commitdiff
2018-03-15 gmungocJAL-2893 enabling Get Crossreferences to ENSEMBLGENOMES tree | commitdiff
2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge tree | commitdiff
2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge tree | commitdiff
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... tree | commitdiff
2018-02-23 Jim ProcterMerge branch 'features/JAL-2885UniprotHttps' into relea... tree | commitdiff
2018-02-23 Jim ProcterJAL-2885 Ensembl* -> https tree | commitdiff
2018-02-23 Jim ProcterJAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL tree | commitdiff
2018-01-30 gmungocJAL-1793 update spike build to latest incl stop and... tree | commitdiff
2018-01-29 gmungocJAL-2743 recoded EnsemblLookup without lambda expressio... tree | commitdiff
2018-01-26 gmungocMerge branch 'develop' into features/JAL-1793VCF tree | commitdiff
2018-01-18 gmungocJAL-2679 update query id to actual case of retrieved... tree | commitdiff
2018-01-17 gmungocJAL-2679 case-insensitive comparison of query and retri... tree | commitdiff
2018-01-16 gmungocJAL-2679 use object_type=Transcript for lookup of Paren... tree | commitdiff
2018-01-16 gmungocJAL-2885 uniprot now https, uniprot/ensembl/pfam/xfam... tree | commitdiff
2017-11-15 gmungocJAL-2835 spike updated with latest tree | commitdiff
2017-11-13 gmungocMerge branch 'develop' into features/JAL-1793VCF tree | commitdiff
2017-11-13 gmungocJAL-2679 example accession changed to CAD01290 tree | commitdiff
2017-10-27 gmungocJAL-1793 spike branch updated to latest tree | commitdiff
2017-10-25 gmungocJAL-2743 fall back to parsing description if chromosome... tree | commitdiff
2017-10-24 gmungocJAL-2738 tidy Javadoc, remove debug logging tree | commitdiff
2017-10-24 gmungocJAL-2743 look up species and gene loci for Ensembl... tree | commitdiff
2017-10-24 gmungocJAL-1739 Javadoc updated for Lambda expression parser... tree | commitdiff
2017-10-24 gmungocJAL-2738 update spike branch with latest tree | commitdiff
2017-10-24 gmungocMerge branch 'develop' into features/JAL-1793VCF; lambd... tree | commitdiff
2017-10-23 Jim ProcterMerge branch 'bug/JAL-2253' into develop tree | commitdiff
2017-10-20 gmungocPush 1793 latest to spike branch tree | commitdiff
2017-10-20 gmungocJAL-2253 pull up constant, additional unit test bug/JAL-2253 tree | commitdiff
2017-10-19 gmungocJAL-2755 add lookup of cds/cdna gene loci tree | commitdiff
2017-10-19 gmungocJAL-2755 add species lookup tree | commitdiff
2017-10-19 gmungocJAL-2755 rename EnsemblInfo as EnsemblData, add 'true... tree | commitdiff
2017-10-09 gmungocJAL-2523 basic sleep and retry (3 times) on 429 respons... features/JAL-2523httpRetries tree | commitdiff
2017-10-09 gmungocJAL-2523 convenience method to get model organisms tree | commitdiff
2017-10-04 gmungocJAL-2523 start of refactoring... tree | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo tree | commitdiff
2017-10-02 gmungocMerge branch 'develop' into features/JAL-1793VCF tree | commitdiff
2017-10-02 gmungocJAL-2525 lookup transcript features by Ontology tree | commitdiff
2017-09-28 gmungocJAL-1796 GeneLociI as distinguished DBRefEntry tree | commitdiff
2017-09-26 gmungocJAL-2738 unit test for reverse strand gene tree | commitdiff
2017-09-25 gmungocJAL-2738 use complement base for a VCF variant on rever... tree | commitdiff
2017-09-25 gmungocJAL-2738 one constant in codebase for "alleles" attribu... tree | commitdiff
2017-09-22 gmungocJAL-2738 correct handling of reverse strand genes tree | commitdiff
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