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Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git]
/
src
/
jalview
/
ext
/
ensembl
/ EnsemblGene.java
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
2021-09-02
gmungoc
JAL-1842 adjust code to match changed semantics of...
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commitdiff
2020-02-06
gmungoc
JAL-1842 adjust code to match changed semantics of...
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commitdiff
2019-07-16
gmungoc
JAL-3210 Merge branch 'develop' into trialMerge
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commitdiff
2019-06-07
gmungoc
JAL-2738 use GeneLocus extends DBRefEntry to hold chrom...
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commitdiff
2019-04-01
gmungoc
JAL-3032 use small example Ensembl gene for JalviewJS
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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
2018-10-25
gmungoc
JAL-3143 fetch Ensembl(Genomes) features as JSON not GFF
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commitdiff
2018-08-10
gmungoc
JAL-3076 refactor for more efficient scan of 'gene...
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commitdiff
2018-01-30
gmungoc
JAL-1793 update spike build to latest incl stop and...
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commitdiff
2018-01-26
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
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-2743 look up species and gene loci for Ensembl...
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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
2017-10-03
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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commitdiff
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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commitdiff
2017-09-25
gmungoc
JAL-2738 use complement base for a VCF variant on rever...
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commitdiff
2017-09-22
gmungoc
JAL-2738 correct handling of reverse strand genes
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commitdiff
2017-09-21
gmungoc
JAL-2738 add chromosome coordinate mappings to transcripts
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commitdiff
2017-08-31
gmungoc
JAL-2253 safer simpler resolution of identifiers using...
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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 source formatting
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commitdiff
2017-06-09
gmungoc
JAL-2446 merged to spike branch
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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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commitdiff
2017-05-16
gmungoc
JAL-2525 put in missing "transcript" feature type
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commitdiff
2017-05-12
gmungoc
JAL-2525 get sequence features for Ontology term(s...
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commitdiff
2016-10-05
Jim Procter
JAL-2189 apply license
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commitdiff
2016-10-05
Jim Procter
JAL-2189 source formatting
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commitdiff
2016-09-18
Jim Procter
JAL-1795 JAL-2206 prevent NPE when no data returned...
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commitdiff
2016-08-25
Jim Procter
JAL-2106 JAL-2154 cross-refs from Ensembl should verify...
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commitdiff
2016-05-10
gmungoc
Merge branch 'develop' into features/JAL-1956_featureStyles
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commitdiff
2016-04-29
gmungoc
JAL-2051 better checking of retrieved / duplicated...
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commitdiff
2016-04-11
gmungoc
JAL-2051 fetch Ensembl Gene accessions one at a time
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commitdiff
2016-04-01
gmungoc
JAL-1705 fetch all Ensembl xrefs (except GO terms)
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commitdiff
2016-03-15
gmungoc
JAL-2016 FeatureSettingsI now FeatureSettingsModelI
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commitdiff
2016-03-15
gmungoc
JAL-1705 code tidy/comment only
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commitdiff
2016-03-11
gmungoc
JAL-1705 refactoring etc for fetching Ensembl --> Uniprot
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commitdiff
2016-03-04
gmungoc
JAL-1705 parse 'description' from GFF as sequence descr...
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commitdiff
2016-03-03
gmungoc
JAL-1705 include stop codons in derived CDS; support...
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commitdiff
2016-03-01
gmungoc
JAL-1705 align CDS and peptide products to transcripts
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commitdiff
2016-02-22
gmungoc
JAL-1705 first pass at applying preset feature colourin...
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2016-02-19
gmungoc
JAL-1705 return Ensembl genes for model species for...
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commitdiff
2016-02-12
gmungoc
JAL-1705 various refactoring towards Uniprot-to-Ensembl...
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commitdiff
2016-02-04
gmungoc
JAL-1705 additional tests, validation regexp tweaks...
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commitdiff
2016-02-01
gmungoc
JAL-1705 JAL-1191 SequenceOntologyLite added as hard...
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2016-01-30
gmungoc
JAL-1705 refactored cross-reference fetching (CCDS...
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commitdiff
2016-01-27
gmungoc
JAL-1705 use GET for single queries; set gene name...
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commitdiff
2016-01-26
gmungoc
JAL-1705 derive transcript sequences from gene sequence...
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commitdiff
2016-01-25
gmungoc
JAL-1705 EnsemblGene added, and related refactoring
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