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JAL-3763 always make a new dataset sequence for CDS sequence
[jalview.git] / src / jalview / analysis / AlignmentUtils.java
2020-10-22 gmungocJAL-3763 always make a new dataset sequence for CDS... blob | commitdiff
2020-09-16 Jim ProcterJAL-3748 pass a list to findAlignedSequence to return... blob | commitdiff | diff to current
2020-02-18 Mungo CarstairsJAL-3536 JAL-3187 don't create duplicate CDS-to-protein... bug/JAL-3536getCrossrefTwice blob | commitdiff | diff to current
2020-01-28 gmungocJAL-3187 one more obsolete method removed blob | commitdiff | diff to current
2019-08-22 gmungocJAL-3187 one more obsolete method removed blob | commitdiff | diff to current
2019-08-09 gmungocJAL-3187 removal of variant feature (non-virtual) trans... blob | commitdiff | diff to current
2019-06-17 gmungocJAL-3187 update alignAs code and unit tests for 'shared... blob | commitdiff | diff to current
2019-06-11 gmungocJAL-3187 CDS has same dataset sequence as transcript blob | commitdiff | diff to current
2019-06-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures blob | commitdiff | diff to current
2019-06-07 gmungocJAL-2738 use GeneLocus extends DBRefEntry to hold chrom... blob | commitdiff | diff to current
2019-02-20 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into feature... blob | commitdiff | diff to current
2019-02-19 gmungocJAL-3187 hacks to get peptide variant in to Jmol hover... blob | commitdiff | diff to current
2019-01-21 gmungocJAL-3187 (hacked up) show complement features on struct... blob | commitdiff | diff to current
2019-01-18 gmungocJAL-3143 'id' not 'ID' attribute drives generation... blob | commitdiff | diff to current
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... blob | commitdiff | diff to current
2018-02-09 gmungocJAL-2789 avoid using transcript (with no UTR) as CDS... bug/JAL-2666 blob | commitdiff | diff to current
2018-02-09 gmungocJAL-2789 code format changes only (before functional... blob | commitdiff | diff to current
2018-02-05 gmungocJAL-2897 more informative description on synonymous... blob | commitdiff | diff to current
2018-02-05 gmungocMerge branch 'spikes/mungo' into trialMerge blob | commitdiff | diff to current
2018-02-05 gmungocJAL-2897 more informative description on synonymous... blob | commitdiff | diff to current
2018-01-30 gmungocJAL-1793 update spike build to latest incl stop and... blob | commitdiff | diff to current
2018-01-30 gmungocJAL-2898 show 'stop_gained' variants on peptide sequences blob | commitdiff | diff to current
2018-01-30 gmungocJAL-2897 generate peptide variants for synonymous codon... blob | commitdiff | diff to current
2018-01-30 gmungocJAL-2897 formatting change only prior to functional... blob | commitdiff | diff to current
2017-10-27 gmungocJAL-1793 spike branch updated to latest blob | commitdiff | diff to current
2017-10-26 gmungocMerge branch 'develop' into features/JAL-1793VCF blob | commitdiff | diff to current
2017-10-05 gmungocJAL-2738 update spikes/mungo blob | commitdiff | diff to current
2017-10-05 gmungocJAL-2755 transfer chromosomal reference from transcript... blob | commitdiff | diff to current
2017-10-04 gmungocJAL-2738 match consequence "Allele" to VCF allele;... blob | commitdiff | diff to current
2017-10-03 gmungocJAL-2738 copy to spikes/mungo blob | commitdiff | diff to current
2017-09-26 gmungocJAL-2738 JAL-2154 add DBRef from transcript to synthesi... blob | commitdiff | diff to current
2017-09-25 gmungocJAL-2738 one constant in codebase for "alleles" attribu... blob | commitdiff | diff to current
2017-09-21 gmungocJAL-2738 compute VCF on peptide, extract AF (allele... blob | commitdiff | diff to current
2017-09-04 gmungocJAL-2617 unit tests for CDS + stop codon, CDS with... bug/JAL-2617mappedStopCodon blob | commitdiff | diff to current
2017-09-01 gmungocJAL-2617 omit stop codon from synthesized CDS sequence blob | commitdiff | diff to current
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList blob | commitdiff | diff to current
2017-08-16 Jim ProcterJAL-2418 source formatting blob | commitdiff | diff to current
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the... blob | commitdiff | diff to current
2017-06-09 gmungocJAL-2446 merged to spike branch blob | commitdiff | diff to current
2017-05-25 gmungocJAL-2050 make SequenceFeature.score final, adjust const... blob | commitdiff | diff to current
2017-05-15 gmungocJAL-2480 redundant code removed blob | commitdiff | diff to current
2017-05-12 gmungocJAL-2525 get sequence features for Ontology term(s... blob | commitdiff | diff to current
2017-05-09 gmungocJAL-2505 use constructors to set (what will be) final... blob | commitdiff | diff to current
2017-03-01 gmungocMerge branch 'features/JAL-2295setChimeraAttributes... blob | commitdiff | diff to current
2016-12-16 gmungocJAL-1705 JAL-98 use SortedMap as more accurate type... blob | commitdiff | diff to current
2016-11-08 gmungocJAL-2295 make RangeComparator a top level class for... blob | commitdiff | diff to current
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch blob | commitdiff | diff to current
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch... blob | commitdiff | diff to current
2016-10-05 Jim ProcterJAL-2189 source formatting blob | commitdiff | diff to current
2016-09-27 gmungocJAL-2230 use correct mapping to transfer features to... blob | commitdiff | diff to current
2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p... blob | commitdiff | diff to current
2016-08-29 Jim ProcterJAL-2154 don’t synthesise multiple CDS|<Acc> sequences... blob | commitdiff | diff to current
2016-08-26 Jim ProcterJAL-2154 don’t add any remaining xrefed sequences of... blob | commitdiff | diff to current
2016-08-26 gmungocJAL-2049 set Ensembl variant source to ENSEMBL if ... blob | commitdiff | diff to current
2016-08-25 Jim ProcterJAL-2154 JAL-2106 transfer primary refs to CDS for... blob | commitdiff | diff to current
2016-08-25 Jim ProcterMerge branch 'trailm' into trial_fixMakeCDSDBRefPropagation blob | commitdiff | diff to current
2016-08-25 Jim ProcterMerge branch 'develop' into refactor/JAL-2106_sourceDbR... blob | commitdiff | diff to current
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe... blob | commitdiff | diff to current
2016-08-23 Jim ProcterJAL-2154 propagate from contig to CDS after constructin... blob | commitdiff | diff to current
2016-08-23 Jim ProcterJAL-2154 should only add mappings between dataset sequences blob | commitdiff | diff to current
2016-08-23 Jim ProcterJAL-2154 - only copy DBRef from contig to new CDS seque... blob | commitdiff | diff to current
2016-08-22 gmungocJAL-2011 adjust method to fix failing unit test blob | commitdiff | diff to current
2016-07-14 Jim ProcterJAL-2110 JAL-2147 JAL-2145 - pad CDS alignment reconstr... blob | commitdiff | diff to current
2016-07-12 Jim ProcterJAL-2110 test demonstrating limitation of current imple... blob | commitdiff | diff to current
2016-07-12 Jim ProcterJAL-2110 javadoc blob | commitdiff | diff to current
2016-07-12 Jim ProcterJAL-2110 scalability todo blob | commitdiff | diff to current
2016-07-12 Jim ProcterJAL-1381 JAL-2110 efficiency TODO blob | commitdiff | diff to current
2016-07-07 gmungocJAL-2110 added alignAsSameSequences to handle 'direct... blob | commitdiff | diff to current
2016-07-06 gmungocJAL-2110 AlignmentUtils.alignCdsAsProtein implemented blob | commitdiff | diff to current
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds blob | commitdiff | diff to current
2016-07-04 gmungocJAL-2110 use shared dataset when copying alignment... blob | commitdiff | diff to current
2016-07-04 gmungocRevert "JAL-2110 use shared alignment dataset when... blob | commitdiff | diff to current
2016-07-04 gmungocJAL-2110 use shared alignment dataset when copying... blob | commitdiff | diff to current
2016-07-01 gmungocJAL-2110 bug fixing and tidying for get cross-refs blob | commitdiff | diff to current
2016-07-01 gmungocJAL-2110 add 'products' parameter to filter results... blob | commitdiff | diff to current
2016-06-23 Jim ProcterMerge branch 'develop' into merge_JAL-2110 blob | commitdiff | diff to current
2016-06-22 gmungocJAL-1982 defensive checks for null annotations array blob | commitdiff | diff to current
2016-06-16 Jim ProcterJAL-2110 throw implementation error if not given a... blob | commitdiff | diff to current
2016-06-14 gmungocJAL-2110 fixes to dbref resolution and mappings, use... blob | commitdiff | diff to current
2016-06-09 gmungocJAL-2110 work in progress blob | commitdiff | diff to current
2016-05-31 gmungocJAL-2023 adjustments to mappings added for split frame... blob | commitdiff | diff to current
2016-05-18 gmungocJAL-2049 set sequence feature group to "Jalview" for... blob | commitdiff | diff to current
2016-05-18 gmungocJAL-2049 use HGVS notation for variant on protein residue blob | commitdiff | diff to current
2016-04-14 gmungocJAL-2041 add ID,clinical_significance to feature attrib... blob | commitdiff | diff to current
2016-04-14 gmungocJAL-2049 revised computePeptideVariants to transfer... blob | commitdiff | diff to current
2016-04-12 gmungocJAL-2049 separate protein variant per dna variant ... blob | commitdiff | diff to current
2016-04-01 gmungocJAL-1705 ensure the right mapping is used to align... blob | commitdiff | diff to current
2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and... blob | commitdiff | diff to current
2016-03-11 gmungocJAL-1705 refactoring etc for fetching Ensembl --> Uniprot blob | commitdiff | diff to current
2016-03-07 gmungocJAL-2023 CDS sequences added to / share alignment dataset blob | commitdiff | diff to current
2016-03-03 gmungocJAL-1705 include stop codons in derived CDS; support... blob | commitdiff | diff to current
2016-03-02 gmungocJAL-1705 include any unmapped protein start 'X' when... blob | commitdiff | diff to current
2016-03-01 gmungocJAL-1705 align CDS to transcripts blob | commitdiff | diff to current
2016-02-01 gmungocJAL-1705 JAL-1191 SequenceOntologyLite added as hard... blob | commitdiff | diff to current
2016-01-28 gmungocJAL-1705 refine feature copying to including 5' and... blob | commitdiff | diff to current
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge blob | commitdiff | diff to current
2016-01-23 gmungocJAL-1705 compute peptide variants from dna; add "conseq... blob | commitdiff | diff to current
2016-01-21 gmungocJAL-1705 transfer features to the dataset sequence... blob | commitdiff | diff to current
2016-01-21 gmungocJAL-1705 features transferred to CDS sequence; makeExon... blob | commitdiff | diff to current
2015-12-22 gmungocJAL-653 AlignedCodonFrame collections changed from... blob | commitdiff | diff to current
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