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JAL-2154 test for CDS->protein map
[jalview.git] / src / jalview / analysis /
2016-07-20 gmungocJAL-2023 JAL-1681 fixed bug in computing '+' for co... tree | commitdiff
2016-07-19 gmungocJAL-391 corrected handling of gapped sequences tree | commitdiff
2016-07-18 Jim ProcterJAL-2145 improvement: ensure conservation calculation... tree | commitdiff
2016-07-14 Jim ProcterJAL-2110 JAL-2147 JAL-2145 - pad CDS alignment reconstr... tree | commitdiff
2016-07-12 Jim ProcterJAL-2110 test demonstrating limitation of current imple... tree | commitdiff
2016-07-12 Jim ProcterJAL-2110 javadoc tree | commitdiff
2016-07-12 Jim ProcterJAL-2110 scalability todo tree | commitdiff
2016-07-12 Jim ProcterJAL-1381 JAL-2110 efficiency TODO tree | commitdiff
2016-07-07 gmungocJAL-2110 added alignAsSameSequences to handle 'direct... tree | commitdiff
2016-07-07 gmungocJAL-2110 field 'cf' moved to stack tree | commitdiff
2016-07-06 gmungocJAL-2110 AlignmentUtils.alignCdsAsProtein implemented tree | commitdiff
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds tree | commitdiff
2016-07-04 gmungocJAL-2110 use shared dataset when copying alignment... tree | commitdiff
2016-07-04 gmungocRevert "JAL-2110 use shared alignment dataset when... tree | commitdiff
2016-07-04 gmungocJAL-2110 use shared alignment dataset when copying... tree | commitdiff
2016-07-04 gmungocJAL-2110 bug fix / test for searchDataset mappings... tree | commitdiff
2016-07-01 gmungocJAL-2110 bug fixing and tidying for get cross-refs tree | commitdiff
2016-07-01 gmungocJAL-2110 add 'products' parameter to filter results... tree | commitdiff
2016-06-23 Jim ProcterMerge branch 'develop' into merge_JAL-2110 tree | commitdiff
2016-06-23 Jim ProcterJAL-2110 make indirect xref searches work by not filter... tree | commitdiff
2016-06-23 Jim ProcterJAL-2110 warning message when routine finds non-ds... tree | commitdiff
2016-06-23 Jim ProcterJAL-2110 clarify javadoc tree | commitdiff
2016-06-23 Jim ProcterJAL-2110 refactor to split SequenceFetcher from x-ref... tree | commitdiff
2016-06-23 Jim ProcterJAL-2110 use SequenceI.isProtein() tree | commitdiff
2016-06-22 gmungocJAL-1982 defensive checks for null annotations array tree | commitdiff
2016-06-22 Jim ProcterJAL-2110 remove hardwired detection of search context... tree | commitdiff
2016-06-19 Jim ProcterJAL-2110 JAL-2131 JAL-1765 remove reference to jalview... tree | commitdiff
2016-06-16 Jim ProcterJAL-2110 throw implementation error if not given a... tree | commitdiff
2016-06-14 gmungocJAL-2110 fixes to dbref resolution and mappings, use... tree | commitdiff
2016-06-09 gmungocJAL-2110 work in progress tree | commitdiff
2016-06-03 gmungocJAL-2110 random stuff tree | commitdiff
2016-06-02 gmungocMerge branch 'develop' into features/JAL-2110_makeSense... tree | commitdiff
2016-06-01 Jim ProcterJAL-2038 ensure bare Strings are lowercased before... tree | commitdiff
2016-05-31 gmungocJAL-2023 adjustments to mappings added for split frame... tree | commitdiff
2016-05-30 tcofoegbuJAL-2038 fix to enable case-insensitive file name ... tree | commitdiff
2016-05-26 gmungocJAL-1797 non-case-sensitive counting of residues /... tree | commitdiff
2016-05-25 gmungocJAL-2110 wip CrossRefs rewrite of CrossRef tree | commitdiff
2016-05-20 gmungocJAL-2110 unit tests for and minor refactoring of CrossRef tree | commitdiff
2016-05-18 gmungocJAL-2049 set sequence feature group to "Jalview" for... tree | commitdiff
2016-05-18 gmungocJAL-2049 use HGVS notation for variant on protein residue tree | commitdiff
2016-04-29 gmungocJAL-2051 better checking of retrieved / duplicated... tree | commitdiff
2016-04-23 Jim ProcterJAL-2075 fix: use AlignmentView.getVisibleContigs and... tree | commitdiff
2016-04-14 gmungocJAL-2041 add ID,clinical_significance to feature attrib... tree | commitdiff
2016-04-14 gmungocJAL-2049 revised computePeptideVariants to transfer... tree | commitdiff
2016-04-13 Jim ProcterJAL-2046 fix: patched SeqsetUtils so sequence features... tree | commitdiff
2016-04-12 gmungocJAL-2049 separate protein variant per dna variant ... tree | commitdiff
2016-04-01 gmungocJAL-1705 ensure the right mapping is used to align... tree | commitdiff
2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and... tree | commitdiff
2016-03-21 gmungocJAL-2029 further fixes to get correct xrefs and xrefs... tree | commitdiff
2016-03-21 gmungocJAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings tree | commitdiff
2016-03-11 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... tree | commitdiff
2016-03-11 gmungocJAL-1270 unit test for SequenceIdMatcher.SeqIdName tree | commitdiff
2016-03-11 gmungocJAL-1705 refactoring etc for fetching Ensembl --> Uniprot tree | commitdiff
2016-03-07 gmungocJAL-2023 CDS sequences added to / share alignment dataset tree | commitdiff
2016-03-03 gmungocJAL-1705 include stop codons in derived CDS; support... tree | commitdiff
2016-03-02 gmungocJAL-1705 include any unmapped protein start 'X' when... tree | commitdiff
2016-03-01 gmungocJAL-1705 align CDS to transcripts tree | commitdiff
2016-02-19 gmungocJAL-1705 refactor show products, set initial split... tree | commitdiff
2016-02-12 gmungocJAL-1705 various refactoring towards Uniprot-to-Ensembl... tree | commitdiff
2016-02-12 gmungocJAL-2008 updates for String[] to List<String> change tree | commitdiff
2016-02-12 gmungocJAL-2008 avoid unnecessary repaints; signatures changed... tree | commitdiff
2016-02-04 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... tree | commitdiff
2016-02-04 gmungocJAL-2005 added (stable) sort methods parameterised by tree | commitdiff
2016-02-01 gmungocJAL-1705 JAL-1191 SequenceOntologyLite added as hard... tree | commitdiff
2016-01-28 gmungocJAL-1705 refine feature copying to including 5' and... tree | commitdiff
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge tree | commitdiff
2016-01-27 gmungocJAL-1705 add exon name to features and render on peptid... tree | commitdiff
2016-01-23 gmungocJAL-1705 compute peptide variants from dna; add "conseq... tree | commitdiff
2016-01-21 gmungocJAL-1705 transfer features to the dataset sequence... tree | commitdiff
2016-01-21 gmungocJAL-1705 features transferred to CDS sequence; makeExon... tree | commitdiff
2016-01-21 gmungocJAL-1705 get xrefs only for dna/peptide; code tidy tree | commitdiff
2015-12-22 gmungocJAL-391 new Calculate options to Reverse, Reverse Compl... tree | commitdiff
2015-12-22 gmungocJAL-653 AlignedCodonFrame collections changed from... tree | commitdiff
2015-12-22 gmungocJAL-653 AlignedCodonFrame internal refactor, merge... tree | commitdiff
2015-11-30 gmungocJAL-1421 generics loop syntax; 'bug?' comment added tree | commitdiff
2015-11-30 gmungocJAL-653 small comment change only tree | commitdiff
2015-11-30 gmungocJAL-652 refactored to remove one method tree | commitdiff
2015-10-28 tcofoegbuJAL-1952 bugfix tree | commitdiff
2015-10-22 tcofoegbuJAL-1479 added basic support for SIFTs mapping - more... tree | commitdiff
2015-10-15 tcofoegbuJAL-1479 refactored SequenceI interface - changed getDB... tree | commitdiff
2015-10-14 tcofoegbuJAL-1926 added supporting model changes to enable savin... tree | commitdiff
2015-10-07 Jim ProcterJAL-1894 source formatting tree | commitdiff
2015-09-14 gmungocJAL-1880 handle sequence offsets properly when mapping... tree | commitdiff
2015-09-10 Jim ProcterJAL-1645 licencing for new files in src tree | commitdiff
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports tree | commitdiff
2015-09-09 gmungocJAL-1619 'align protein as cDNA' now leaves unmapped... tree | commitdiff
2015-09-07 gmungocJAL-1636 translate stop codon as '*', mouseover * as... tree | commitdiff
2015-09-07 gmungocJAL-1152 check 'autocalculated' not 'null sequenceRef... tree | commitdiff
2015-08-17 gmungocJAL-1800 separated SearchResults.getCharacters() from... tree | commitdiff
2015-08-10 Jim ProcterJAL-736 relocate group associated conservation symbols... tree | commitdiff
2015-08-10 Jim ProcterJAL-736 source formatting tree | commitdiff
2015-08-07 tcofoegbuJAL-1824 updated caching procedure for pdb entries... tree | commitdiff
2015-07-23 Jim ProcterJAL-1819 use Float.isNaN() to check for NaNs! tree | commitdiff
2015-07-08 gmungocJAL-1759 merge from develop tree | commitdiff
2015-07-01 gmungocJAL-1681 more condensed tooltip where codons share... tree | commitdiff
2015-06-05 Jim ProcterMerge branch 'develop' into features/JAL-653_gffalignments tree | commitdiff
2015-06-05 Jim ProcterJAL-1115 JAL-653 partial introduction of List interface... tree | commitdiff
2015-06-04 gmungocJAL-1750 small tidy of AlignSeq.printMapping (+Junit) tree | commitdiff
2015-06-04 gmungocJAL-1544 spelling in javadoc only tree | commitdiff
2015-05-29 Jim ProcterMerge branch 'JAL-1755_npe_groupconsensus' into develop tree | commitdiff
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