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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / analysis / AlignmentUtils.java
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply commit | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... commit | commitdiff
2023-06-22 James ProcterJAL-4213 - document the addReferenceAnnotations method... commit | commitdiff
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 patch - map selection group onto sequence... commit | commitdiff
2023-05-13 James ProcterJAL-2349 JAL-3855 helper method to make it easy to... commit | commitdiff
2023-03-15 James ProcterJAL-4091 JAL-629 ‘Add Reference Annotations’ takes... commit | commitdiff
2022-12-05 Ben SoaresJAL-629 implementation of --tempfac options 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
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache... commit | commitdiff
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework... commit | commitdiff
2022-01-26 Jim ProcterMerge branch 'task/JAL-3763_newDatasetForCds' into... commit | commitdiff
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... commit | commitdiff
2020-10-27 Jim ProcterJAL-3700 JAL-3748 JAL-3763 don’t add stop codon via... commit | commitdiff
2020-10-22 gmungocJAL-3763 always make a new dataset sequence for CDS... commit | commitdiff
2020-10-08 gmungocJAL-3763 always make a new dataset sequence for CDS... commit | commitdiff
2020-09-16 Jim ProcterJAL-3748 pass a list to findAlignedSequence to return... commit | commitdiff
2020-03-30 gmungocMerge branch 'develop' into Jalview-JS/develop commit | commitdiff
2020-02-18 Mungo CarstairsJAL-3536 JAL-3187 don't create duplicate CDS-to-protein... bug/JAL-3536getCrossrefTwice commit | commitdiff
2020-01-28 gmungocJAL-3187 one more obsolete method removed commit | commitdiff
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop commit | commitdiff
2019-08-22 gmungocJAL-3187 one more obsolete method removed 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
2019-06-11 gmungocJAL-3187 CDS has same dataset sequence as transcript commit | commitdiff
2019-06-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures commit | commitdiff
2019-06-07 gmungocJAL-2738 use GeneLocus extends DBRefEntry to hold chrom... commit | commitdiff
2019-02-20 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into feature... commit | commitdiff
2019-02-19 gmungocJAL-3187 hacks to get peptide variant in to Jmol hover... commit | commitdiff
2019-01-29 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into trialMerge commit | commitdiff
2019-01-26 hansonrJalview.isJS() --> Platform.isJS(), DBRefEntry[] -... commit | commitdiff
2019-01-25 hansonrJSON refactoring commit | commitdiff
2019-01-21 gmungocJAL-3187 (hacked up) show complement features on struct... commit | commitdiff
2019-01-18 gmungocJAL-3143 'id' not 'ID' attribute drives generation... commit | commitdiff
2018-06-20 hansonrJAL-3032 for (var var 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
2018-02-09 gmungocJAL-2789 code format changes only (before functional... 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
2018-01-30 gmungocJAL-2897 formatting change only prior to functional... 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
2017-10-04 gmungocJAL-2738 match consequence "Allele" to VCF allele;... 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
2017-09-25 gmungocJAL-2738 one constant in codebase for "alleles" attribu... commit | commitdiff
2017-09-21 gmungocJAL-2738 compute VCF on peptide, extract AF (allele... commit | commitdiff
2017-09-04 gmungocJAL-2617 unit tests for CDS + stop codon, CDS with... bug/JAL-2617mappedStopCodon commit | commitdiff
2017-09-01 gmungocJAL-2617 omit stop codon from synthesized CDS sequence commit | commitdiff
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList commit | commitdiff
2017-08-16 Jim ProcterJAL-2418 source formatting commit | commitdiff
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the... commit | commitdiff
2017-06-09 gmungocJAL-2446 merged to spike branch commit | commitdiff
2017-05-25 gmungocJAL-2050 make SequenceFeature.score final, adjust const... commit | commitdiff
2017-05-15 gmungocJAL-2480 redundant code removed commit | commitdiff
2017-05-12 gmungocJAL-2525 get sequence features for Ontology term(s... commit | commitdiff
2017-05-09 gmungocJAL-2505 use constructors to set (what will be) final... commit | commitdiff
2017-03-01 gmungocMerge branch 'features/JAL-2295setChimeraAttributes... commit | commitdiff
2016-12-16 gmungocJAL-1705 JAL-98 use SortedMap as more accurate type... commit | commitdiff
2016-11-08 gmungocJAL-2295 make RangeComparator a top level class for... 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 source formatting commit | commitdiff
2016-09-27 gmungocJAL-2230 use correct mapping to transfer features to... commit | commitdiff
2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p... commit | commitdiff
2016-08-29 Jim ProcterJAL-2154 don’t synthesise multiple CDS|<Acc> sequences... commit | commitdiff
2016-08-26 Jim ProcterJAL-2154 don’t add any remaining xrefed sequences of... commit | commitdiff
2016-08-26 gmungocJAL-2049 set Ensembl variant source to ENSEMBL if ... commit | commitdiff
2016-08-25 Jim ProcterJAL-2154 JAL-2106 transfer primary refs to CDS for... 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 removed setSourceDBRef, refactor getSourceDBRe... commit | commitdiff
2016-08-23 Jim ProcterJAL-2154 propagate from contig to CDS after constructin... commit | commitdiff
2016-08-23 Jim ProcterJAL-2154 should only add mappings between dataset sequences commit | commitdiff
2016-08-23 Jim ProcterJAL-2154 - only copy DBRef from contig to new CDS seque... commit | commitdiff
2016-08-22 gmungocJAL-2011 adjust method to fix failing unit test commit | commitdiff
2016-07-14 Jim ProcterJAL-2110 JAL-2147 JAL-2145 - pad CDS alignment reconstr... commit | commitdiff
2016-07-12 Jim ProcterJAL-2110 test demonstrating limitation of current imple... commit | commitdiff
2016-07-12 Jim ProcterJAL-2110 javadoc commit | commitdiff
2016-07-12 Jim ProcterJAL-2110 scalability todo commit | commitdiff
2016-07-12 Jim ProcterJAL-1381 JAL-2110 efficiency TODO commit | commitdiff
2016-07-07 gmungocJAL-2110 added alignAsSameSequences to handle 'direct... commit | commitdiff
2016-07-06 gmungocJAL-2110 AlignmentUtils.alignCdsAsProtein implemented commit | commitdiff
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds commit | commitdiff
2016-07-04 gmungocJAL-2110 use shared dataset when copying alignment... 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 bug fixing and tidying for get cross-refs commit | commitdiff
2016-07-01 gmungocJAL-2110 add 'products' parameter to filter results... commit | commitdiff
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