JAL-3454 tidy comments
[jalview.git] / src / jalview / analysis / AlignmentUtils.java
2019-01-29 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into trialMerge
2019-01-26 hansonrJalview.isJS() --> Platform.isJS(), DBRefEntry[] -...
2019-01-25 hansonrJSON refactoring
2019-01-18 gmungocJAL-3143 'id' not 'ID' attribute drives generation...
2018-06-20 hansonrJAL-3032 for (var var
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2018-02-09 gmungocJAL-2789 avoid using transcript (with no UTR) as CDS... bug/JAL-2666
2018-02-09 gmungocJAL-2789 code format changes only (before functional...
2018-02-05 gmungocJAL-2897 more informative description on synonymous...
2018-02-05 gmungocMerge branch 'spikes/mungo' into trialMerge
2018-02-05 gmungocJAL-2897 more informative description on synonymous...
2018-01-30 gmungocJAL-1793 update spike build to latest incl stop and...
2018-01-30 gmungocJAL-2898 show 'stop_gained' variants on peptide sequences
2018-01-30 gmungocJAL-2897 generate peptide variants for synonymous codon...
2018-01-30 gmungocJAL-2897 formatting change only prior to functional...
2017-10-27 gmungocJAL-1793 spike branch updated to latest
2017-10-26 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-10-05 gmungocJAL-2738 update spikes/mungo
2017-10-05 gmungocJAL-2755 transfer chromosomal reference from transcript...
2017-10-04 gmungocJAL-2738 match consequence "Allele" to VCF allele;...
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-09-26 gmungocJAL-2738 JAL-2154 add DBRef from transcript to synthesi...
2017-09-25 gmungocJAL-2738 one constant in codebase for "alleles" attribu...
2017-09-21 gmungocJAL-2738 compute VCF on peptide, extract AF (allele...
2017-09-04 gmungocJAL-2617 unit tests for CDS + stop codon, CDS with... bug/JAL-2617mappedStopCodon
2017-09-01 gmungocJAL-2617 omit stop codon from synthesized CDS sequence
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList
2017-08-16 Jim ProcterJAL-2418 source formatting
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the...
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-05-25 gmungocJAL-2050 make SequenceFeature.score final, adjust const...
2017-05-15 gmungocJAL-2480 redundant code removed
2017-05-12 gmungocJAL-2525 get sequence features for Ontology term(s...
2017-05-09 gmungocJAL-2505 use constructors to set (what will be) final...
2017-03-01 gmungocMerge branch 'features/JAL-2295setChimeraAttributes...
2016-12-16 gmungocJAL-1705 JAL-98 use SortedMap as more accurate type...
2016-11-08 gmungocJAL-2295 make RangeComparator a top level class for...
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch...
2016-10-05 Jim ProcterJAL-2189 source formatting
2016-09-27 gmungocJAL-2230 use correct mapping to transfer features to...
2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p...
2016-08-29 Jim ProcterJAL-2154 don’t synthesise multiple CDS|<Acc> sequences...
2016-08-26 Jim ProcterJAL-2154 don’t add any remaining xrefed sequences of...
2016-08-26 gmungocJAL-2049 set Ensembl variant source to ENSEMBL if ...
2016-08-25 Jim ProcterJAL-2154 JAL-2106 transfer primary refs to CDS for...
2016-08-25 Jim ProcterMerge branch 'trailm' into trial_fixMakeCDSDBRefPropagation
2016-08-25 Jim ProcterMerge branch 'develop' into refactor/JAL-2106_sourceDbR...
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
2016-08-23 Jim ProcterJAL-2154 propagate from contig to CDS after constructin...
2016-08-23 Jim ProcterJAL-2154 should only add mappings between dataset sequences
2016-08-23 Jim ProcterJAL-2154 - only copy DBRef from contig to new CDS seque...
2016-08-22 gmungocJAL-2011 adjust method to fix failing unit test
2016-07-14 Jim ProcterJAL-2110 JAL-2147 JAL-2145 - pad CDS alignment reconstr...
2016-07-12 Jim ProcterJAL-2110 test demonstrating limitation of current imple...
2016-07-12 Jim ProcterJAL-2110 javadoc
2016-07-12 Jim ProcterJAL-2110 scalability todo
2016-07-12 Jim ProcterJAL-1381 JAL-2110 efficiency TODO
2016-07-07 gmungocJAL-2110 added alignAsSameSequences to handle 'direct...
2016-07-06 gmungocJAL-2110 AlignmentUtils.alignCdsAsProtein implemented
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds
2016-07-04 gmungocJAL-2110 use shared dataset when copying alignment...
2016-07-04 gmungocRevert "JAL-2110 use shared alignment dataset when...
2016-07-04 gmungocJAL-2110 use shared alignment dataset when copying...
2016-07-01 gmungocJAL-2110 bug fixing and tidying for get cross-refs
2016-07-01 gmungocJAL-2110 add 'products' parameter to filter results...
2016-06-23 Jim ProcterMerge branch 'develop' into merge_JAL-2110
2016-06-22 gmungocJAL-1982 defensive checks for null annotations array
2016-06-16 Jim ProcterJAL-2110 throw implementation error if not given a...
2016-06-14 gmungocJAL-2110 fixes to dbref resolution and mappings, use...
2016-06-09 gmungocJAL-2110 work in progress
2016-05-31 gmungocJAL-2023 adjustments to mappings added for split frame...
2016-05-18 gmungocJAL-2049 set sequence feature group to "Jalview" for...
2016-05-18 gmungocJAL-2049 use HGVS notation for variant on protein residue
2016-04-14 gmungocJAL-2041 add ID,clinical_significance to feature attrib...
2016-04-14 gmungocJAL-2049 revised computePeptideVariants to transfer...
2016-04-12 gmungocJAL-2049 separate protein variant per dna variant ...
2016-04-01 gmungocJAL-1705 ensure the right mapping is used to align...
2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and...
2016-03-11 gmungocJAL-1705 refactoring etc for fetching Ensembl --> Uniprot
2016-03-07 gmungocJAL-2023 CDS sequences added to / share alignment dataset
2016-03-03 gmungocJAL-1705 include stop codons in derived CDS; support...
2016-03-02 gmungocJAL-1705 include any unmapped protein start 'X' when...
2016-03-01 gmungocJAL-1705 align CDS to transcripts
2016-02-01 gmungocJAL-1705 JAL-1191 SequenceOntologyLite added as hard...
2016-01-28 gmungocJAL-1705 refine feature copying to including 5' and...
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge
2016-01-23 gmungocJAL-1705 compute peptide variants from dna; add "conseq...
2016-01-21 gmungocJAL-1705 transfer features to the dataset sequence...
2016-01-21 gmungocJAL-1705 features transferred to CDS sequence; makeExon...
2015-12-22 gmungocJAL-653 AlignedCodonFrame collections changed from...
2015-11-30 gmungocJAL-653 small comment change only
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2
2015-10-15 tcofoegbuJAL-1479 refactored SequenceI interface - changed getDB...
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright
2015-10-08 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch
2015-10-07 Jim ProcterJAL-1894 source formatting
2015-09-22 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch
2015-09-14 gmungocJAL-1880 handle sequence offsets properly when mapping...
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
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