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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git]
/
src
/
jalview
/
ext
/ ensembl
2023-11-03
James Procter
JAL-4090 JAL-1551 spotlessApply
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commitdiff
2023-08-10
Ben Soares
JAL-629 Change all stdout and stderr output to use...
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commitdiff
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
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commitdiff
2022-03-08
Jim Procter
JAL-3108 updated Ensembl client and model species names
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commitdiff
2022-02-11
Jim Procter
JAL-3949 - refactor logging from jalview.bin.Cache...
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commitdiff
2022-02-11
Ben Soares
JAL-3949 Complete new abstracted logging framework...
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commitdiff
2021-09-21
Ben Soares
JAL-3691 automatic insertion of Locale.ROOT to toUpperC...
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commitdiff
2021-09-02
gmungoc
JAL-1842 adjust code to match changed semantics of...
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commitdiff
2020-08-31
gmungoc
JAL-3018 Ensembl reviewed REST version updated to 13.0
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commitdiff
2020-08-24
gmungoc
JAL-3018 updated reviewed REST version to 12.0
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commitdiff
2020-07-31
Ben Soares
Merge branch 'releases/Release_2_11_1_Branch' into...
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commitdiff
2020-05-18
gmungoc
Merge branch 'Jalview-JS/develop' into develop
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commitdiff
2020-04-21
Jim Procter
JAL-3407 add GPL license to Jalview source files
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commitdiff
2020-03-30
gmungoc
JAL-3210 debug logging commented out
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commitdiff
2020-03-30
gmungoc
Merge branch 'develop' into Jalview-JS/develop
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commitdiff
2020-02-06
gmungoc
JAL-1842 adjust code to match changed semantics of...
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commitdiff
2019-10-08
gmungoc
Merge branch 'develop' into Jalview-JS/develop
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commitdiff
2019-08-22
gmungoc
JAL-3121 round trip GFF attributes including map-valued...
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commitdiff
2019-07-16
gmungoc
JAL-3210 Merge branch 'develop' into trialMerge
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commitdiff
2019-06-11
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
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commitdiff
2019-06-11
gmungoc
JAL-3143 also parse "phase" from JSON response if present
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commitdiff
2019-06-07
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
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commitdiff
2019-06-07
gmungoc
JAL-2738 use GeneLocus extends DBRefEntry to hold chrom...
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commitdiff
2019-06-06
gmungoc
Merge branch 'develop' into trialMerge
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commitdiff
2019-04-26
gmungoc
JAL-2743 class Javadoc
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commitdiff
2019-04-18
gmungoc
Merge branch 'develop' into Jalview-JS/develop
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commitdiff
2019-04-18
gmungoc
JAL-3193 dbSource always "ENSEMBL"
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commitdiff
2019-04-15
gmungoc
Merge branch 'develop' into Jalview-JS/develop
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commitdiff
2019-04-10
gmungoc
JAL-3193 rest.ensemblgenomes.org merged to rest.ensembl.org
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commitdiff
2019-04-10
gmungoc
JAL-3018 REST version updated to 10.0
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commitdiff
2019-04-03
hansonr
replacing @j2sNative with @j2sIgnore where appropriate...
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commitdiff
2019-04-01
gmungoc
JAL-3032 use small example Ensembl gene for JalviewJS
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commitdiff
2019-04-01
hansonr
JSON refactoring of a few methods; fixing JavaScript...
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commitdiff
2019-03-19
gmungoc
JAL-3210 code formatting only
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commitdiff
2019-03-13
gmungoc
Merge branch 'develop' into trialMerge
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commitdiff
2019-03-08
gmungoc
JAL-3193 defensive trim of URL read from properties...
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commitdiff
2019-02-28
gmungoc
Merge branch 'feature/JAL-3143ensemblJSON' into merge...
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commitdiff
2019-02-20
gmungoc
Merge branch 'feature/JAL-3143ensemblJSON' into feature...
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commitdiff
2019-01-29
gmungoc
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of...
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commitdiff
2019-01-29
gmungoc
Merge branch 'feature/JAL-3143ensemblJSON' into trialMerge
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commitdiff
2019-01-29
gmungoc
JAL-3143 format alleles array for feature description
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commitdiff
2019-01-29
hansonr
time check, iterators
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commitdiff
2019-01-29
hansonr
more iterators out; some time checks
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commitdiff
2019-01-26
hansonr
Platform.timecheck calls removed or commented out.
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commitdiff
2019-01-26
hansonr
Jalview.isJS() --> Platform.isJS(), DBRefEntry[] -...
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commitdiff
2019-01-25
hansonr
JSON refactoring
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commitdiff
2019-01-25
gmungoc
JAL-3187 don't compute variant features on peptide...
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commitdiff
2019-01-24
gmungoc
JAL-3018 Ensembl version updated to 9.0
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commitdiff
2019-01-18
gmungoc
JAL-3143 'id' not 'ID' attribute drives generation...
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commitdiff
2018-11-19
gmungoc
JAL-3032 reinstate methods now available in SwingJS
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commitdiff
2018-11-12
gmungoc
JAL-3076 JalviewJS requires lower case content-type...
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commitdiff
2018-11-11
hansonr
adds explicit AJAX-allowed
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commitdiff
2018-11-01
gmungoc
Merge branch 'feature/JAL-3143ensemblJSON' into
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commitdiff
2018-11-01
gmungoc
Merge branch 'Jalview-BH/JAL-3026' into
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commitdiff
2018-10-31
gmungoc
Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' into...
feature/JAL-3144noJTree
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commitdiff
2018-10-31
gmungoc
JAL-3026 skip unsupported HttpURLConnection methods...
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commitdiff
2018-10-25
gmungoc
JAL-3143 comma-delimited feature attributes for alleles,
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commitdiff
2018-10-25
gmungoc
JAL-3143 fetch Ensembl(Genomes) features as JSON not GFF
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commitdiff
2018-09-03
gmungoc
JAL-3076 fetch Ensembl sequence as JSON instead of...
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commitdiff
2018-09-03
Jim Procter
JAL-3076 clarify javadoc handling single sequence respo...
bug/JAL-3076ensemblGeneId
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commitdiff
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
2018-06-07
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
2018-03-16
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
2018-01-30
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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commitdiff
2018-01-16
gmungoc
JAL-2885 uniprot now https, uniprot/ensembl/pfam/xfam...
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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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commitdiff
2017-10-27
gmungoc
JAL-1793 spike branch updated to latest
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commitdiff
2017-10-25
gmungoc
JAL-2743 fall back to parsing description if chromosome...
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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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commitdiff
2017-10-24
gmungoc
JAL-2738 update spike branch with latest
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commitdiff
2017-10-24
gmungoc
Merge branch 'develop' into features/JAL-1793VCF; lambd...
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commitdiff
2017-10-23
Jim Procter
Merge branch 'bug/JAL-2253' into develop
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commitdiff
2017-10-20
gmungoc
Push 1793 latest to spike branch
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commitdiff
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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commitdiff
2017-10-19
gmungoc
JAL-2755 add species lookup
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commitdiff
2017-10-19
gmungoc
JAL-2755 rename EnsemblInfo as EnsemblData, add 'true...
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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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commitdiff
2017-10-04
gmungoc
JAL-2523 start of refactoring...
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