Merge branch 'patch/JAL-4298_synchronize_consoledoc' into bug/JAL-4298_java_console_c...
[jalview.git] / src / jalview / ext / ensembl /
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use...
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0
2022-03-08 Jim ProcterJAL-3108 updated Ensembl client and model species names
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache...
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework...
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC...
2021-09-02 gmungocJAL-1842 adjust code to match changed semantics of...
2020-08-31 gmungocJAL-3018 Ensembl reviewed REST version updated to 13.0
2020-08-24 gmungocJAL-3018 updated reviewed REST version to 12.0
2020-07-31 Ben SoaresMerge branch 'releases/Release_2_11_1_Branch' into...
2020-05-18 gmungocMerge branch 'Jalview-JS/develop' into develop
2020-04-21 Jim ProcterJAL-3407 add GPL license to Jalview source files
2020-03-30 gmungocJAL-3210 debug logging commented out
2020-03-30 gmungocMerge branch 'develop' into Jalview-JS/develop
2020-02-06 gmungocJAL-1842 adjust code to match changed semantics of...
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop
2019-08-22 gmungocJAL-3121 round trip GFF attributes including map-valued...
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge
2019-06-11 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures
2019-06-11 gmungocJAL-3143 also parse "phase" from JSON response if present
2019-06-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures
2019-06-07 gmungocJAL-2738 use GeneLocus extends DBRefEntry to hold chrom...
2019-06-06 gmungocMerge branch 'develop' into trialMerge
2019-04-26 gmungocJAL-2743 class Javadoc
2019-04-18 gmungocMerge branch 'develop' into Jalview-JS/develop
2019-04-18 gmungocJAL-3193 dbSource always "ENSEMBL"
2019-04-15 gmungocMerge branch 'develop' into Jalview-JS/develop
2019-04-10 gmungocJAL-3193 rest.ensemblgenomes.org merged to rest.ensembl.org
2019-04-10 gmungocJAL-3018 REST version updated to 10.0
2019-04-03 hansonrreplacing @j2sNative with @j2sIgnore where appropriate...
2019-04-01 gmungocJAL-3032 use small example Ensembl gene for JalviewJS
2019-04-01 hansonrJSON refactoring of a few methods; fixing JavaScript...
2019-03-19 gmungocJAL-3210 code formatting only
2019-03-13 gmungocMerge branch 'develop' into trialMerge
2019-03-08 gmungocJAL-3193 defensive trim of URL read from properties...
2019-02-28 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into merge...
2019-02-20 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into feature...
2019-01-29 gmungocMerge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of...
2019-01-29 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into trialMerge
2019-01-29 gmungocJAL-3143 format alleles array for feature description
2019-01-29 hansonrtime check, iterators
2019-01-29 hansonrmore iterators out; some time checks
2019-01-26 hansonrPlatform.timecheck calls removed or commented out.
2019-01-26 hansonrJalview.isJS() --> Platform.isJS(), DBRefEntry[] -...
2019-01-25 hansonrJSON refactoring
2019-01-25 gmungocJAL-3187 don't compute variant features on peptide...
2019-01-24 gmungocJAL-3018 Ensembl version updated to 9.0
2019-01-18 gmungocJAL-3143 'id' not 'ID' attribute drives generation...
2018-11-19 gmungocJAL-3032 reinstate methods now available in SwingJS
2018-11-12 gmungocJAL-3076 JalviewJS requires lower case content-type...
2018-11-11 hansonradds explicit AJAX-allowed
2018-11-01 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into
2018-11-01 gmungocMerge branch 'Jalview-BH/JAL-3026' into
2018-10-31 gmungocMerge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' into... feature/JAL-3144noJTree
2018-10-31 gmungocJAL-3026 skip unsupported HttpURLConnection methods...
2018-10-25 gmungocJAL-3143 comma-delimited feature attributes for alleles,
2018-10-25 gmungocJAL-3143 fetch Ensembl(Genomes) features as JSON not GFF
2018-09-03 gmungocJAL-3076 fetch Ensembl sequence as JSON instead of...
2018-09-03 Jim ProcterJAL-3076 clarify javadoc handling single sequence respo... bug/JAL-3076ensemblGeneId
2018-08-10 gmungocJAL-3018 updated to Ensembl REST 7.0
2018-08-10 gmungocJAL-3076 refactor for more efficient scan of 'gene...
2018-08-10 gmungocJAL-3076 fetch Ensembl sequence as JSON instead of...
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
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