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Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git]
/
test
/
jalview
/
analysis
/ AlignmentUtilsTests.java
2024-08-05
Jim Procter
JAL-1551 gradle spotlessApply and doc tweaks
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commitdiff
2024-05-15
Renia Correya
JAL-4386 - Implementation of retrieving secondary structure
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commitdiff
2024-05-13
Renia Correya
JAL-4386 - Implementation of substitution matrix and...
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commitdiff
2023-05-22
James Procter
JAL-1551 spotless
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commitdiff
2023-05-19
James Procter
JAL-1551 spotlessApply
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commitdiff
2023-05-19
James Procter
JAL-1551 spotlessApply
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commitdiff
2023-05-15
James Procter
JAL-4182 failing test
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commitdiff
2023-05-14
James Procter
JAL-2349 fix up tests for Java 11 compatibility and...
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commitdiff
2023-03-20
James Procter
JAL-2349 fix off by one when resolving columns for...
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commitdiff
2023-03-15
James Procter
JAL-4091 JAL-629 ‘Add Reference Annotations’ takes...
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commitdiff
2022-10-17
Jim Procter
JAL-2349 JAL-3855 tests that probably should be part...
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commitdiff
2022-10-17
Jim Procter
JAL-2349 JAL-3855 Integrate pAE retrieval in StructureF...
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commitdiff
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
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commitdiff
2020-09-23
Jim Procter
JAL-3748 reusable assert to trace specific issues with...
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commitdiff
2019-10-08
gmungoc
Merge branch 'develop' into Jalview-JS/develop
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commitdiff
2019-08-09
gmungoc
JAL-3187 removal of variant feature (non-virtual) trans...
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commitdiff
2019-07-16
gmungoc
JAL-3210 Merge branch 'develop' into trialMerge
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commitdiff
2019-06-17
gmungoc
JAL-3187 update alignAs code and unit tests for 'shared...
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commitdiff
2019-06-07
gmungoc
JAL-2738 use GeneLocus extends DBRefEntry to hold chrom...
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commitdiff
2019-02-04
hansonr
Test suite try/catch reverted
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commitdiff
2019-02-04
gmungoc
Merge branch 'feature/JAL-3143ensemblJSON' into Jalview...
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commitdiff
2019-02-04
gmungoc
JAL-3143 update unit test for ID -> id change
feature/JAL-3143ensemblJSON
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commitdiff
2019-01-29
hansonr
test package fix for List<DBRefEntry> DBrefs (untested)
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commitdiff
2018-06-04
gmungoc
JAL-3019 correctly form toRange of 'traversed' MapList
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commitdiff
2018-03-07
Jim Procter
Merge branch 'releases/Release_2_10_4_Branch' into...
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commitdiff
2018-02-09
gmungoc
JAL-2789 avoid using transcript (with no UTR) as CDS...
bug/JAL-2666
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commitdiff
2018-02-05
gmungoc
JAL-2897 more informative description on synonymous...
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commitdiff
2018-02-05
gmungoc
JAL-2897 more informative description on synonymous...
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commitdiff
2018-02-05
gmungoc
Merge branch 'spikes/mungo' into trialMerge
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commitdiff
2018-02-05
gmungoc
JAL-2897 more informative description on synonymous...
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commitdiff
2018-01-30
gmungoc
JAL-1793 update spike build to latest incl stop and...
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commitdiff
2018-01-30
gmungoc
JAL-2898 show 'stop_gained' variants on peptide sequences
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commitdiff
2018-01-30
gmungoc
JAL-2897 generate peptide variants for synonymous codon...
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commitdiff
2017-10-27
gmungoc
JAL-1793 spike branch updated to latest
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commitdiff
2017-10-26
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
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2017-10-05
gmungoc
JAL-2738 update spikes/mungo
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2017-10-05
gmungoc
JAL-2755 transfer chromosomal reference from transcript...
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commitdiff
2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
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commitdiff
2017-09-26
gmungoc
JAL-2738 JAL-2154 add DBRef from transcript to synthesi...
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commitdiff
2017-09-04
gmungoc
JAL-2617 unit tests for CDS + stop codon, CDS with...
bug/JAL-2617mappedStopCodon
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commitdiff
2017-06-09
gmungoc
JAL-2446 merged to spike branch
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commitdiff
2017-05-25
gmungoc
JAL-2557 removal of Sequence.sequenceFeatures
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commitdiff
2016-11-28
gmungoc
Merge branch 'develop' into trialMerge
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2016-11-25
gmungoc
Merge branch 'develop' into trialMerge
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commitdiff
2016-11-24
tcofoegbu
JAL-2326 added setup method for JvOptionPane in all...
features/JAL-2326_JOptionPane-refactoring
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commitdiff
2016-10-28
Jim Procter
JAL-966 JAL-1738 JAL-345 interfaces for SearchResults...
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commitdiff
2016-10-25
Jim Procter
JAL-2089 patch broken merge to master for Release 2...
releases/Release_2_10_0_Branch
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commitdiff
2016-10-06
Jim Procter
JAL-2089 Merge branch releases/Release_2_10_Branch...
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commitdiff
2016-10-05
Jim Procter
JAL-2189 format tests
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2016-09-27
gmungoc
JAL-2230 JAL-2049 added sequence feature transfer to
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commitdiff
2016-08-30
Jim Procter
Merge branch 'develop' into merge/develop_bug/JAL-2154p...
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commitdiff
2016-08-30
gmungoc
Merge branch 'develop' into features/filetypeEnum
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commitdiff
2016-08-26
gmungoc
JAL-2049 set Ensembl variant source to ENSEMBL if ...
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commitdiff
2016-08-25
Jim Procter
JAL-2106 JAL-2154 fix test for additional reference...
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2016-08-25
Jim Procter
Merge branch 'trailm' into trial_fixMakeCDSDBRefPropagation
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2016-08-25
Jim Procter
Merge branch 'develop' into refactor/JAL-2106_sourceDbR...
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2016-08-24
Jim Procter
JAL-2106 FIXME for test failure
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commitdiff
2016-08-24
Jim Procter
JAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
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commitdiff
2016-08-23
Jim Procter
JAL-2154 updated testMakeCDSAlignment for expected...
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commitdiff
2016-08-22
gmungoc
JAL-2011 adjust method to fix failing unit test
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commitdiff
2016-08-04
Jim Procter
JAL-2110 comment on failing test (consider skipping...
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commitdiff
2016-07-12
Jim Procter
JAL-2110 note about use case for when alignAsSameSequen...
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commitdiff
2016-07-12
Jim Procter
JAL-2110 test demonstrating limitation of current imple...
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commitdiff
2016-07-11
gmungoc
file format enum wip changes
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commitdiff
2016-07-07
gmungoc
JAL-2110 added alignAsSameSequences to handle 'direct...
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commitdiff
2016-07-06
gmungoc
JAL-2110 ensuring mapped dbrefs between protein and cds
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commitdiff
2016-07-04
gmungoc
Revert "JAL-2110 use shared alignment dataset when...
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commitdiff
2016-07-04
gmungoc
JAL-2110 use shared alignment dataset when copying...
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commitdiff
2016-07-01
gmungoc
JAL-2110 add 'products' parameter to filter results...
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commitdiff
2016-06-21
gmungoc
JAL-2110 updated unit test to match code changes
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commitdiff
2016-06-20
Jim Procter
JAL-2110 pass dataset to makeCDSalignment
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commitdiff
2016-06-16
Jim Procter
JAL-2110 change test for desired behaviour of getCodonF...
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commitdiff
2016-06-16
Jim Procter
JAL-2110 throw implementation error if not given a...
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commitdiff
2016-06-14
gmungoc
JAL-2110 fixes to dbref resolution and mappings, use...
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commitdiff
2016-05-20
gmungoc
JAL-2049 unit test updated for HGVS syntax, feature...
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commitdiff
2016-04-14
gmungoc
JAL-2041 add ID,clinical_significance to feature attrib...
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commitdiff
2016-04-14
gmungoc
JAL-2049 revised computePeptideVariants to transfer...
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2016-04-12
gmungoc
JAL-2049 separate protein variant per dna variant ...
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commitdiff
2016-04-01
gmungoc
JAL-1705 ensure the right mapping is used to align...
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commitdiff
2016-04-01
gmungoc
JAL-1705 reworked AlignmentUtils.makeCdsAlignment and...
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commitdiff
2016-03-11
gmungoc
JAL-1705 refactoring etc for fetching Ensembl --> Uniprot
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commitdiff
2016-03-07
gmungoc
JAL-2023 CDS sequences added to / share alignment dataset
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commitdiff
2016-03-03
gmungoc
JAL-1705 unit test for aligning with incomplete start...
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commitdiff
2016-03-01
gmungoc
JAL-1705 align CDS and peptide products to transcripts
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commitdiff
2016-01-28
gmungoc
JAL-1705 refine feature copying to including 5' and...
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commitdiff
2016-01-28
gmungoc
Merge branch 'develop' into JAL-1705_trialMerge
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2016-01-21
gmungoc
JAL-1705 features transferred to CDS sequence; makeExon...
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commitdiff
2016-01-05
gmungoc
JAL-653 updating 'align as' tests to match latest tweak...
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commitdiff
2015-12-22
gmungoc
JAL-653 AlignedCodonFrame collections changed from...
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2015-11-05
tcofoegbu
JAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc...
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commitdiff
2015-10-16
Jim Procter
JAL-1925 update source version in license
Release_2_9_0b2
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commitdiff
2015-10-15
tcofoegbu
JAL-1479 refactored SequenceI interface - changed getDB...
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commitdiff
2015-10-08
Jim Procter
JAL-1894 update year/version in copyright
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commitdiff
2015-09-22
Jim Procter
Merge branch 'develop' into Release_2_9_0b1_Branch
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commitdiff
2015-09-14
gmungoc
JAL-1880 handle sequence offsets properly when mapping...
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commitdiff
2015-09-10
Jim Procter
JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
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commitdiff
2015-09-10
Jim Procter
JAL-1645 source formatting and organise imports
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commitdiff
2015-09-09
gmungoc
JAL-1619 'align protein as cDNA' now leaves unmapped...
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2015-09-07
gmungoc
JAL-1636 translate stop codon as '*', mouseover * as...
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2015-08-17
gmungoc
JAL-1270 testIsMappable added
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