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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / test / jalview / analysis / AlignmentUtilsTests.java
2023-05-22 James ProcterJAL-1551 spotless commit | commitdiff
2023-05-19 James ProcterJAL-1551 spotlessApply commit | commitdiff
2023-05-19 James ProcterJAL-1551 spotlessApply commit | commitdiff
2023-05-15 James ProcterJAL-4182 failing test commit | commitdiff
2023-05-14 James ProcterJAL-2349 fix up tests for Java 11 compatibility and... commit | commitdiff
2023-03-20 James ProcterJAL-2349 fix off by one when resolving columns for... commit | commitdiff
2023-03-15 James ProcterJAL-4091 JAL-629 ‘Add Reference Annotations’ takes... commit | commitdiff
2022-10-17 Jim ProcterJAL-2349 JAL-3855 tests that probably should be part... commit | commitdiff
2022-10-17 Jim ProcterJAL-2349 JAL-3855 Integrate pAE retrieval in StructureF... commit | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 commit | commitdiff
2020-09-23 Jim ProcterJAL-3748 reusable assert to trace specific issues with... commit | commitdiff
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop commit | commitdiff
2019-08-09 gmungocJAL-3187 removal of variant feature (non-virtual) trans... commit | commitdiff
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge commit | commitdiff
2019-06-17 gmungocJAL-3187 update alignAs code and unit tests for 'shared... commit | commitdiff
2019-06-07 gmungocJAL-2738 use GeneLocus extends DBRefEntry to hold chrom... commit | commitdiff
2019-02-04 hansonrTest suite try/catch reverted commit | commitdiff
2019-02-04 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into Jalview... commit | commitdiff
2019-02-04 gmungocJAL-3143 update unit test for ID -> id change feature/JAL-3143ensemblJSON commit | commitdiff
2019-01-29 hansonrtest package fix for List<DBRefEntry> DBrefs (untested) commit | commitdiff
2018-06-04 gmungocJAL-3019 correctly form toRange of 'traversed' MapList commit | commitdiff
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... commit | commitdiff
2018-02-09 gmungocJAL-2789 avoid using transcript (with no UTR) as CDS... bug/JAL-2666 commit | commitdiff
2018-02-05 gmungocJAL-2897 more informative description on synonymous... commit | commitdiff
2018-02-05 gmungocJAL-2897 more informative description on synonymous... commit | commitdiff
2018-02-05 gmungocMerge branch 'spikes/mungo' into trialMerge commit | commitdiff
2018-02-05 gmungocJAL-2897 more informative description on synonymous... commit | commitdiff
2018-01-30 gmungocJAL-1793 update spike build to latest incl stop and... commit | commitdiff
2018-01-30 gmungocJAL-2898 show 'stop_gained' variants on peptide sequences commit | commitdiff
2018-01-30 gmungocJAL-2897 generate peptide variants for synonymous codon... commit | commitdiff
2017-10-27 gmungocJAL-1793 spike branch updated to latest commit | commitdiff
2017-10-26 gmungocMerge branch 'develop' into features/JAL-1793VCF commit | commitdiff
2017-10-05 gmungocJAL-2738 update spikes/mungo commit | commitdiff
2017-10-05 gmungocJAL-2755 transfer chromosomal reference from transcript... commit | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo commit | commitdiff
2017-09-26 gmungocJAL-2738 JAL-2154 add DBRef from transcript to synthesi... commit | commitdiff
2017-09-04 gmungocJAL-2617 unit tests for CDS + stop codon, CDS with... bug/JAL-2617mappedStopCodon commit | commitdiff
2017-06-09 gmungocJAL-2446 merged to spike branch commit | commitdiff
2017-05-25 gmungocJAL-2557 removal of Sequence.sequenceFeatures commit | commitdiff
2016-11-28 gmungocMerge branch 'develop' into trialMerge commit | commitdiff
2016-11-25 gmungocMerge branch 'develop' into trialMerge commit | commitdiff
2016-11-24 tcofoegbuJAL-2326 added setup method for JvOptionPane in all... features/JAL-2326_JOptionPane-refactoring commit | commitdiff
2016-10-28 Jim ProcterJAL-966 JAL-1738 JAL-345 interfaces for SearchResults... commit | commitdiff
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch commit | commitdiff
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch... commit | commitdiff
2016-10-05 Jim ProcterJAL-2189 format tests commit | commitdiff
2016-09-27 gmungocJAL-2230 JAL-2049 added sequence feature transfer to commit | commitdiff
2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p... commit | commitdiff
2016-08-30 gmungocMerge branch 'develop' into features/filetypeEnum commit | commitdiff
2016-08-26 gmungocJAL-2049 set Ensembl variant source to ENSEMBL if ... commit | commitdiff
2016-08-25 Jim ProcterJAL-2106 JAL-2154 fix test for additional reference... commit | commitdiff
2016-08-25 Jim ProcterMerge branch 'trailm' into trial_fixMakeCDSDBRefPropagation commit | commitdiff
2016-08-25 Jim ProcterMerge branch 'develop' into refactor/JAL-2106_sourceDbR... commit | commitdiff
2016-08-24 Jim ProcterJAL-2106 FIXME for test failure commit | commitdiff
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe... commit | commitdiff
2016-08-23 Jim ProcterJAL-2154 updated testMakeCDSAlignment for expected... commit | commitdiff
2016-08-22 gmungocJAL-2011 adjust method to fix failing unit test commit | commitdiff
2016-08-04 Jim ProcterJAL-2110 comment on failing test (consider skipping... commit | commitdiff
2016-07-12 Jim ProcterJAL-2110 note about use case for when alignAsSameSequen... commit | commitdiff
2016-07-12 Jim ProcterJAL-2110 test demonstrating limitation of current imple... commit | commitdiff
2016-07-11 gmungocfile format enum wip changes commit | commitdiff
2016-07-07 gmungocJAL-2110 added alignAsSameSequences to handle 'direct... commit | commitdiff
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds commit | commitdiff
2016-07-04 gmungocRevert "JAL-2110 use shared alignment dataset when... commit | commitdiff
2016-07-04 gmungocJAL-2110 use shared alignment dataset when copying... commit | commitdiff
2016-07-01 gmungocJAL-2110 add 'products' parameter to filter results... commit | commitdiff
2016-06-21 gmungocJAL-2110 updated unit test to match code changes commit | commitdiff
2016-06-20 Jim ProcterJAL-2110 pass dataset to makeCDSalignment commit | commitdiff
2016-06-16 Jim ProcterJAL-2110 change test for desired behaviour of getCodonF... commit | commitdiff
2016-06-16 Jim ProcterJAL-2110 throw implementation error if not given a... commit | commitdiff
2016-06-14 gmungocJAL-2110 fixes to dbref resolution and mappings, use... commit | commitdiff
2016-05-20 gmungocJAL-2049 unit test updated for HGVS syntax, feature... commit | commitdiff
2016-04-14 gmungocJAL-2041 add ID,clinical_significance to feature attrib... commit | commitdiff
2016-04-14 gmungocJAL-2049 revised computePeptideVariants to transfer... commit | commitdiff
2016-04-12 gmungocJAL-2049 separate protein variant per dna variant ... commit | commitdiff
2016-04-01 gmungocJAL-1705 ensure the right mapping is used to align... commit | commitdiff
2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and... commit | commitdiff
2016-03-11 gmungocJAL-1705 refactoring etc for fetching Ensembl --> Uniprot commit | commitdiff
2016-03-07 gmungocJAL-2023 CDS sequences added to / share alignment dataset commit | commitdiff
2016-03-03 gmungocJAL-1705 unit test for aligning with incomplete start... commit | commitdiff
2016-03-01 gmungocJAL-1705 align CDS and peptide products to transcripts commit | commitdiff
2016-01-28 gmungocJAL-1705 refine feature copying to including 5' and... commit | commitdiff
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge commit | commitdiff
2016-01-21 gmungocJAL-1705 features transferred to CDS sequence; makeExon... commit | commitdiff
2016-01-05 gmungocJAL-653 updating 'align as' tests to match latest tweak... commit | commitdiff
2015-12-22 gmungocJAL-653 AlignedCodonFrame collections changed from... commit | commitdiff
2015-11-05 tcofoegbuJAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc... commit | commitdiff
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2 commit | commitdiff
2015-10-15 tcofoegbuJAL-1479 refactored SequenceI interface - changed getDB... commit | commitdiff
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright commit | commitdiff
2015-09-22 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch commit | commitdiff
2015-09-14 gmungocJAL-1880 handle sequence offsets properly when mapping... commit | commitdiff
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin... commit | commitdiff
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports commit | commitdiff
2015-09-09 gmungocJAL-1619 'align protein as cDNA' now leaves unmapped... commit | commitdiff
2015-09-07 gmungocJAL-1636 translate stop codon as '*', mouseover * as... commit | commitdiff
2015-08-17 gmungocJAL-1270 testIsMappable added commit | commitdiff
2015-07-08 gmungocJAL-1759 merge from develop commit | commitdiff
2015-07-07 tcofoegbuJAL-1805 test envirionment separation commit | commitdiff
2015-06-23 Jim ProcterJAL-1782 JAL-1780 JAL-653 JAL-1892 update patched refac... commit | commitdiff
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