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Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
[jalview.git]
/
src
/
jalview
/
io
/
gff
/
2023-11-03
James Procter
JAL-4090 JAL-1551 spotlessApply
tree
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commitdiff
2023-08-10
Ben Soares
JAL-629 Change all stdout and stderr output to use...
tree
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commitdiff
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
tree
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commitdiff
2021-09-21
Ben Soares
JAL-3691 automatic insertion of Locale.ROOT to toUpperC...
tree
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commitdiff
2020-01-24
gmungoc
JAL=3121 more data format validation/tests, help text...
feature/JAL-3121gffAttributeMap
tree
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commitdiff
2020-01-23
gmungoc
JAL-3121 'attributes map' in GFF3 without special ...
tree
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commitdiff
2019-08-22
gmungoc
JAL-3121 slightly cleaner parsing of, and unit test...
tree
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commitdiff
2019-08-22
gmungoc
JAL-3121 round trip GFF attributes including map-valued...
tree
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commitdiff
2019-06-13
gmungoc
JAL-3143 recognise lnc_RNA as transcript
tree
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commitdiff
2018-01-30
gmungoc
JAL-1793 update spike build to latest incl stop and...
tree
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commitdiff
2018-01-30
gmungoc
JAL-2898 show 'stop_gained' variants on peptide sequences
tree
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commitdiff
2018-01-30
gmungoc
JAL-2897 generate peptide variants for synonymous codon...
tree
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commitdiff
2017-12-01
gmungoc
JAL-2835 spike updated to latest (use specific SO term...
tree
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commitdiff
2017-12-01
gmungoc
JAL-2835 additional sub-terms of sequence_variant added
tree
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commitdiff
2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
tree
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commitdiff
2017-09-25
gmungoc
JAL-2738 one constant in codebase for "alleles" attribu...
tree
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commitdiff
2017-08-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-2446NCList
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 source formatting
tree
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commitdiff
2017-06-09
gmungoc
JAL-2446 merged to spike branch
tree
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commitdiff
2017-05-25
gmungoc
JAL-2050 make SequenceFeature.score final, adjust const...
tree
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commitdiff
2017-05-16
gmungoc
JAL-2505 refactor to set type and group in SequenceFeat...
tree
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commitdiff
2017-05-09
gmungoc
JAL-2505 use constructors to set (what will be) final...
tree
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commitdiff
2016-10-05
Jim Procter
JAL-2189 apply license
tree
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commitdiff
2016-10-05
Jim Procter
JAL-2189 source formatting
tree
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commitdiff
2016-10-05
gmungoc
JAL-1191 revert to using SequenceOntologyLite due to...
tree
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commitdiff
2016-10-05
gmungoc
JAL-1191 configure full SO for desktop, SOLite for...
tree
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commitdiff
2016-10-05
gmungoc
JAL-1191 use full SO in desktop application
tree
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commitdiff
2016-10-05
gmungoc
JAL-1191 refined warning message
tree
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commitdiff
2016-10-05
gmungoc
JAL-1191 added mRNA isA transcript to SequenceOntologyL...
tree
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commitdiff
2016-04-14
gmungoc
JAL-2041 add ID,clinical_significance to feature attrib...
tree
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commitdiff
2016-03-22
gmungoc
JAL-1191 isolated SequenceOntology (BioJava wrapper...
tree
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commitdiff
2016-02-19
gmungoc
JAL-1705 JAL-1191 more terms added to hard-coded version
tree
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commitdiff
2016-02-12
gmungoc
JAL-1191 additions to SOLite, tweak to test
tree
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commitdiff
2016-02-12
gmungoc
JAL-1705 take feature ID for description if nothing...
tree
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commitdiff
2016-02-01
gmungoc
JAL-1705 further unit tests
tree
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commitdiff
2016-02-01
gmungoc
JAL-1191 more terms added to SequenceOntologyLite
tree
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commitdiff
2016-02-01
gmungoc
JAL-1705 JAL-1191 SequenceOntologyLite added as hard...
tree
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commitdiff
2016-01-27
gmungoc
JAL-1705 add exon name to features and render on peptid...
tree
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commitdiff
2016-01-26
gmungoc
JAL-1705 derive transcript sequences from gene sequence...
tree
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commitdiff
2016-01-25
gmungoc
JAL-1705 EnsemblGene added, and related refactoring
tree
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commitdiff
2016-01-23
gmungoc
JAL-1705 compute peptide variants from dna; add "conseq...
tree
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commitdiff
2016-01-21
gmungoc
JAL-653 refactor / tidy
tree
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commitdiff
2016-01-21
gmungoc
JAL-653 JAL-1705 set strand for GFF sequence feature
tree
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commitdiff
2016-01-21
gmungoc
JAL-653 comments/javadoc tidy only
tree
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commitdiff
2016-01-21
gmungoc
JAL-1705 added isSequenceVariant(), commonly used SO...
tree
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commitdiff
2016-01-12
gmungoc
JAL-1191 cache isA (great-)grandparents as well for...
tree
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commitdiff
2016-01-05
gmungoc
JAL-1191 check for obsolete term when descriptions...
tree
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commitdiff
2015-12-23
gmungoc
JAL-1191 zipped SO OBO file added to /resources, more...
tree
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commitdiff
2015-12-22
gmungoc
JAL-1191 and provide the SO OBO file in /resources :-)
tree
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commitdiff
2015-12-22
gmungoc
JAL-1191 SequenceOntology wrapping/caching SO.OBO via...
tree
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commitdiff
2015-12-22
gmungoc
JAL-1191 stub class for a SequenceOntology wrapper
tree
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commitdiff
2015-12-22
gmungoc
JAL-653 GFF new/refactored helper classes
tree
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commitdiff