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[jalview.git] / test / jalview / analysis / AlignmentUtilsTests.java

2020-09-23	Jim Procter	JAL-3748 reusable assert to trace specific issues with...	blob \| commitdiff
2019-08-09	gmungoc	JAL-3187 removal of variant feature (non-virtual) trans...	blob \| commitdiff \| diff to current
2019-06-17	gmungoc	JAL-3187 update alignAs code and unit tests for 'shared...	blob \| commitdiff \| diff to current
2019-06-07	gmungoc	JAL-2738 use GeneLocus extends DBRefEntry to hold chrom...	blob \| commitdiff \| diff to current
2019-02-04	gmungoc	JAL-3143 update unit test for ID -> id change feature/JAL-3143ensemblJSON	blob \| commitdiff \| diff to current
2018-06-04	gmungoc	JAL-3019 correctly form toRange of 'traversed' MapList	blob \| commitdiff \| diff to current
2018-03-07	Jim Procter	Merge branch 'releases/Release_2_10_4_Branch' into...	blob \| commitdiff \| diff to current
2018-02-09	gmungoc	JAL-2789 avoid using transcript (with no UTR) as CDS... bug/JAL-2666	blob \| commitdiff \| diff to current
2018-02-05	gmungoc	JAL-2897 more informative description on synonymous...	blob \| commitdiff \| diff to current
2018-02-05	gmungoc	JAL-2897 more informative description on synonymous...	blob \| commitdiff \| diff to current
2018-02-05	gmungoc	Merge branch 'spikes/mungo' into trialMerge	blob \| commitdiff \| diff to current
2018-02-05	gmungoc	JAL-2897 more informative description on synonymous...	blob \| commitdiff \| diff to current
2018-01-30	gmungoc	JAL-1793 update spike build to latest incl stop and...	blob \| commitdiff \| diff to current
2018-01-30	gmungoc	JAL-2898 show 'stop_gained' variants on peptide sequences	blob \| commitdiff \| diff to current
2018-01-30	gmungoc	JAL-2897 generate peptide variants for synonymous codon...	blob \| commitdiff \| diff to current
2017-10-27	gmungoc	JAL-1793 spike branch updated to latest	blob \| commitdiff \| diff to current
2017-10-26	gmungoc	Merge branch 'develop' into features/JAL-1793VCF	blob \| commitdiff \| diff to current
2017-10-05	gmungoc	JAL-2738 update spikes/mungo	blob \| commitdiff \| diff to current
2017-10-05	gmungoc	JAL-2755 transfer chromosomal reference from transcript...	blob \| commitdiff \| diff to current
2017-10-03	gmungoc	JAL-2738 copy to spikes/mungo	blob \| commitdiff \| diff to current
2017-09-26	gmungoc	JAL-2738 JAL-2154 add DBRef from transcript to synthesi...	blob \| commitdiff \| diff to current
2017-09-04	gmungoc	JAL-2617 unit tests for CDS + stop codon, CDS with... bug/JAL-2617mappedStopCodon	blob \| commitdiff \| diff to current
2017-06-09	gmungoc	JAL-2446 merged to spike branch	blob \| commitdiff \| diff to current
2017-05-25	gmungoc	JAL-2557 removal of Sequence.sequenceFeatures	blob \| commitdiff \| diff to current
2016-11-28	gmungoc	Merge branch 'develop' into trialMerge	blob \| commitdiff \| diff to current
2016-11-25	gmungoc	Merge branch 'develop' into trialMerge	blob \| commitdiff \| diff to current
2016-11-24	tcofoegbu	JAL-2326 added setup method for JvOptionPane in all... features/JAL-2326_JOptionPane-refactoring	blob \| commitdiff \| diff to current
2016-10-28	Jim Procter	JAL-966 JAL-1738 JAL-345 interfaces for SearchResults...	blob \| commitdiff \| diff to current
2016-10-25	Jim Procter	JAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch	blob \| commitdiff \| diff to current
2016-10-06	Jim Procter	JAL-2089 Merge branch releases/Release_2_10_Branch...	blob \| commitdiff \| diff to current
2016-10-05	Jim Procter	JAL-2189 format tests	blob \| commitdiff \| diff to current
2016-09-27	gmungoc	JAL-2230 JAL-2049 added sequence feature transfer to	blob \| commitdiff \| diff to current
2016-08-30	Jim Procter	Merge branch 'develop' into merge/develop_bug/JAL-2154p...	blob \| commitdiff \| diff to current
2016-08-30	gmungoc	Merge branch 'develop' into features/filetypeEnum	blob \| commitdiff \| diff to current
2016-08-26	gmungoc	JAL-2049 set Ensembl variant source to ENSEMBL if ...	blob \| commitdiff \| diff to current
2016-08-25	Jim Procter	JAL-2106 JAL-2154 fix test for additional reference...	blob \| commitdiff \| diff to current
2016-08-25	Jim Procter	Merge branch 'trailm' into trial_fixMakeCDSDBRefPropagation	blob \| commitdiff \| diff to current
2016-08-25	Jim Procter	Merge branch 'develop' into refactor/JAL-2106_sourceDbR...	blob \| commitdiff \| diff to current
2016-08-24	Jim Procter	JAL-2106 FIXME for test failure	blob \| commitdiff \| diff to current
2016-08-24	Jim Procter	JAL-2106 removed setSourceDBRef, refactor getSourceDBRe...	blob \| commitdiff \| diff to current
2016-08-23	Jim Procter	JAL-2154 updated testMakeCDSAlignment for expected...	blob \| commitdiff \| diff to current
2016-08-22	gmungoc	JAL-2011 adjust method to fix failing unit test	blob \| commitdiff \| diff to current
2016-08-04	Jim Procter	JAL-2110 comment on failing test (consider skipping...	blob \| commitdiff \| diff to current
2016-07-12	Jim Procter	JAL-2110 note about use case for when alignAsSameSequen...	blob \| commitdiff \| diff to current
2016-07-12	Jim Procter	JAL-2110 test demonstrating limitation of current imple...	blob \| commitdiff \| diff to current
2016-07-11	gmungoc	file format enum wip changes	blob \| commitdiff \| diff to current
2016-07-07	gmungoc	JAL-2110 added alignAsSameSequences to handle 'direct...	blob \| commitdiff \| diff to current
2016-07-06	gmungoc	JAL-2110 ensuring mapped dbrefs between protein and cds	blob \| commitdiff \| diff to current
2016-07-04	gmungoc	Revert "JAL-2110 use shared alignment dataset when...	blob \| commitdiff \| diff to current
2016-07-04	gmungoc	JAL-2110 use shared alignment dataset when copying...	blob \| commitdiff \| diff to current
2016-07-01	gmungoc	JAL-2110 add 'products' parameter to filter results...	blob \| commitdiff \| diff to current
2016-06-21	gmungoc	JAL-2110 updated unit test to match code changes	blob \| commitdiff \| diff to current
2016-06-20	Jim Procter	JAL-2110 pass dataset to makeCDSalignment	blob \| commitdiff \| diff to current
2016-06-16	Jim Procter	JAL-2110 change test for desired behaviour of getCodonF...	blob \| commitdiff \| diff to current
2016-06-16	Jim Procter	JAL-2110 throw implementation error if not given a...	blob \| commitdiff \| diff to current
2016-06-14	gmungoc	JAL-2110 fixes to dbref resolution and mappings, use...	blob \| commitdiff \| diff to current
2016-05-20	gmungoc	JAL-2049 unit test updated for HGVS syntax, feature...	blob \| commitdiff \| diff to current
2016-04-14	gmungoc	JAL-2041 add ID,clinical_significance to feature attrib...	blob \| commitdiff \| diff to current
2016-04-14	gmungoc	JAL-2049 revised computePeptideVariants to transfer...	blob \| commitdiff \| diff to current
2016-04-12	gmungoc	JAL-2049 separate protein variant per dna variant ...	blob \| commitdiff \| diff to current
2016-04-01	gmungoc	JAL-1705 ensure the right mapping is used to align...	blob \| commitdiff \| diff to current
2016-04-01	gmungoc	JAL-1705 reworked AlignmentUtils.makeCdsAlignment and...	blob \| commitdiff \| diff to current
2016-03-11	gmungoc	JAL-1705 refactoring etc for fetching Ensembl --> Uniprot	blob \| commitdiff \| diff to current
2016-03-07	gmungoc	JAL-2023 CDS sequences added to / share alignment dataset	blob \| commitdiff \| diff to current
2016-03-03	gmungoc	JAL-1705 unit test for aligning with incomplete start...	blob \| commitdiff \| diff to current
2016-03-01	gmungoc	JAL-1705 align CDS and peptide products to transcripts	blob \| commitdiff \| diff to current
2016-01-28	gmungoc	JAL-1705 refine feature copying to including 5' and...	blob \| commitdiff \| diff to current
2016-01-28	gmungoc	Merge branch 'develop' into JAL-1705_trialMerge	blob \| commitdiff \| diff to current
2016-01-21	gmungoc	JAL-1705 features transferred to CDS sequence; makeExon...	blob \| commitdiff \| diff to current
2016-01-05	gmungoc	JAL-653 updating 'align as' tests to match latest tweak...	blob \| commitdiff \| diff to current
2015-12-22	gmungoc	JAL-653 AlignedCodonFrame collections changed from...	blob \| commitdiff \| diff to current
2015-11-05	tcofoegbu	JAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc...	blob \| commitdiff \| diff to current
2015-10-16	Jim Procter	JAL-1925 update source version in license Release_2_9_0b2	blob \| commitdiff \| diff to current
2015-10-15	tcofoegbu	JAL-1479 refactored SequenceI interface - changed getDB...	blob \| commitdiff \| diff to current
2015-10-08	Jim Procter	JAL-1894 update year/version in copyright	blob \| commitdiff \| diff to current
2015-09-22	Jim Procter	Merge branch 'develop' into Release_2_9_0b1_Branch	blob \| commitdiff \| diff to current
2015-09-14	gmungoc	JAL-1880 handle sequence offsets properly when mapping...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 source formatting and organise imports	blob \| commitdiff \| diff to current
2015-09-09	gmungoc	JAL-1619 'align protein as cDNA' now leaves unmapped...	blob \| commitdiff \| diff to current
2015-09-07	gmungoc	JAL-1636 translate stop codon as '', mouseover as...	blob \| commitdiff \| diff to current
2015-08-17	gmungoc	JAL-1270 testIsMappable added	blob \| commitdiff \| diff to current
2015-07-08	gmungoc	JAL-1759 merge from develop	blob \| commitdiff \| diff to current
2015-07-07	tcofoegbu	JAL-1805 test envirionment separation	blob \| commitdiff \| diff to current
2015-06-23	Jim Procter	JAL-1782 JAL-1780 JAL-653 JAL-1892 update patched refac...	blob \| commitdiff \| diff to current
2015-06-22	Jim Procter	JAL-1780 JAL-653 Format/AppletFormat import and export...	blob \| commitdiff \| diff to current
2015-06-22	Jim Procter	JAL-653 JAL-1780 reorder imports	blob \| commitdiff \| diff to current
2015-06-19	tcofoegbu	JAL-1270 test suits import order refactor features/JAL-1270_JUnit-to-TestNG features/JAL-1782_JUnit-to-TestNG	blob \| commitdiff \| diff to current
2015-06-19	tcofoegbu	JAL-1270 JUnit to TestNG refactoring	blob \| commitdiff \| diff to current
2015-05-13	gmungoc	JAL-1712 fixes/tests for Castor binding of EMBL XML...	blob \| commitdiff \| diff to current
2015-05-12	gmungoc	JAL-1712 fixes/tests for Castor binding and 'show flank...	blob \| commitdiff \| diff to current
2015-04-21	gmungoc	JAL-1693 mappings added back to the original alignment	blob \| commitdiff \| diff to current
2015-04-14	gmungoc	JAL-1693 generate multiple exon sequences for 1-many...	blob \| commitdiff \| diff to current
2015-04-13	gmungoc	JAL-1693 make exon alignment for get-xref splitframe...	blob \| commitdiff \| diff to current
2015-03-30	gmungoc	JAL-1264 remove broken applet build dependencies	blob \| commitdiff \| diff to current
2015-03-26	gmungoc	Merge develop to Release_2_8_3_Branch	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	JAL-1683 replace year/version strings with tokens in...	blob \| commitdiff \| diff to current
2014-12-15	Jim Procter	JAL-1620 version bump and release notes	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 fix copyright for 2.8.2	blob \| commitdiff \| diff to current
2014-04-21	Jim Procter	JAL-1466 improved test and patched off by one that...	blob \| commitdiff \| diff to current
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