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[jalview.git] / src / jalview / analysis / AlignmentUtils.java

2018-03-07	Jim Procter	Merge branch 'releases/Release_2_10_4_Branch' into...	blob \| commitdiff
2018-02-09	gmungoc	JAL-2789 avoid using transcript (with no UTR) as CDS... bug/JAL-2666	blob \| commitdiff \| diff to current
2018-02-09	gmungoc	JAL-2789 code format changes only (before functional...	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
2018-01-30	gmungoc	JAL-2897 formatting change only prior to functional...	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
2017-10-04	gmungoc	JAL-2738 match consequence "Allele" to VCF allele;...	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
2017-09-25	gmungoc	JAL-2738 one constant in codebase for "alleles" attribu...	blob \| commitdiff \| diff to current
2017-09-21	gmungoc	JAL-2738 compute VCF on peptide, extract AF (allele...	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
2017-09-01	gmungoc	JAL-2617 omit stop codon from synthesized CDS sequence	blob \| commitdiff \| diff to current
2017-08-21	gmungoc	Merge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList	blob \| commitdiff \| diff to current
2017-08-16	Jim Procter	JAL-2418 source formatting	blob \| commitdiff \| diff to current
2017-06-14	gmungoc	JAL-2598 Sequence.getSequence return a copy of the...	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-2050 make SequenceFeature.score final, adjust const...	blob \| commitdiff \| diff to current
2017-05-15	gmungoc	JAL-2480 redundant code removed	blob \| commitdiff \| diff to current
2017-05-12	gmungoc	JAL-2525 get sequence features for Ontology term(s...	blob \| commitdiff \| diff to current
2017-05-09	gmungoc	JAL-2505 use constructors to set (what will be) final...	blob \| commitdiff \| diff to current
2017-03-01	gmungoc	Merge branch 'features/JAL-2295setChimeraAttributes...	blob \| commitdiff \| diff to current
2016-12-16	gmungoc	JAL-1705 JAL-98 use SortedMap as more accurate type...	blob \| commitdiff \| diff to current
2016-11-08	gmungoc	JAL-2295 make RangeComparator a top level class for...	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 source formatting	blob \| commitdiff \| diff to current
2016-09-27	gmungoc	JAL-2230 use correct mapping to transfer features 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
2016-08-29	Jim Procter	JAL-2154 don’t synthesise multiple CDS\|<Acc> sequences...	blob \| commitdiff \| diff to current
2016-08-26	Jim Procter	JAL-2154 don’t add any remaining xrefed sequences of...	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-2154 JAL-2106 transfer primary refs to CDS for...	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 removed setSourceDBRef, refactor getSourceDBRe...	blob \| commitdiff \| diff to current
2016-08-23	Jim Procter	JAL-2154 propagate from contig to CDS after constructin...	blob \| commitdiff \| diff to current
2016-08-23	Jim Procter	JAL-2154 should only add mappings between dataset sequences	blob \| commitdiff \| diff to current
2016-08-23	Jim Procter	JAL-2154 - only copy DBRef from contig to new CDS seque...	blob \| commitdiff \| diff to current
2016-08-22	gmungoc	JAL-2011 adjust method to fix failing unit test	blob \| commitdiff \| diff to current
2016-07-14	Jim Procter	JAL-2110 JAL-2147 JAL-2145 - pad CDS alignment reconstr...	blob \| commitdiff \| diff to current
2016-07-12	Jim Procter	JAL-2110 test demonstrating limitation of current imple...	blob \| commitdiff \| diff to current
2016-07-12	Jim Procter	JAL-2110 javadoc	blob \| commitdiff \| diff to current
2016-07-12	Jim Procter	JAL-2110 scalability todo	blob \| commitdiff \| diff to current
2016-07-12	Jim Procter	JAL-1381 JAL-2110 efficiency TODO	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 AlignmentUtils.alignCdsAsProtein implemented	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	JAL-2110 use shared dataset when copying alignment...	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 bug fixing and tidying for get cross-refs	blob \| commitdiff \| diff to current
2016-07-01	gmungoc	JAL-2110 add 'products' parameter to filter results...	blob \| commitdiff \| diff to current
2016-06-23	Jim Procter	Merge branch 'develop' into merge_JAL-2110	blob \| commitdiff \| diff to current
2016-06-22	gmungoc	JAL-1982 defensive checks for null annotations array	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
2016-06-09	gmungoc	JAL-2110 work in progress	blob \| commitdiff \| diff to current
2016-05-31	gmungoc	JAL-2023 adjustments to mappings added for split frame...	blob \| commitdiff \| diff to current
2016-05-18	gmungoc	JAL-2049 set sequence feature group to "Jalview" for...	blob \| commitdiff \| diff to current
2016-05-18	gmungoc	JAL-2049 use HGVS notation for variant on protein residue	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 include stop codons in derived CDS; support...	blob \| commitdiff \| diff to current
2016-03-02	gmungoc	JAL-1705 include any unmapped protein start 'X' when...	blob \| commitdiff \| diff to current
2016-03-01	gmungoc	JAL-1705 align CDS to transcripts	blob \| commitdiff \| diff to current
2016-02-01	gmungoc	JAL-1705 JAL-1191 SequenceOntologyLite added as hard...	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
2016-01-23	gmungoc	JAL-1705 compute peptide variants from dna; add "conseq...	blob \| commitdiff \| diff to current
2016-01-21	gmungoc	JAL-1705 transfer features to the dataset sequence...	blob \| commitdiff \| diff to current
2016-01-21	gmungoc	JAL-1705 features transferred to CDS sequence; makeExon...	blob \| commitdiff \| diff to current
2015-12-22	gmungoc	JAL-653 AlignedCodonFrame collections changed from...	blob \| commitdiff \| diff to current
2015-11-30	gmungoc	JAL-653 small comment change only	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
2015-10-08	Jim Procter	Merge branch 'develop' into Release_2_9_0b1_Branch	blob \| commitdiff \| diff to current
2015-10-07	Jim Procter	JAL-1894 source formatting	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-1800 separated SearchResults.getCharacters() from...	blob \| commitdiff \| diff to current
2015-06-04	gmungoc	JAL-1544 spelling in javadoc only	blob \| commitdiff \| diff to current
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