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JAL-1551 formatting

[jalview.git] / src / jalview / analysis /
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
2015-05-29 Jim ProcterJAL-1755 fix for NPE when setting up temporary variables tree | commitdiff
2015-05-15 gmungocJAL-1737 ignore non-positional annotations for display tree | commitdiff
2015-05-15 gmungocJAL-1270 added test for regex actually used; include... tree | commitdiff
2015-05-15 gmungocJAL-1270 main methods converted to JUnit tree | commitdiff
2015-05-12 gmungocJAL-1712 fixes/tests for Castor binding and 'show flank... tree | commitdiff
2015-04-21 gmungocJAL-1693 mappings added back to the original alignment tree | commitdiff
2015-04-14 gmungocJAL-1693 generate multiple exon sequences for 1-many... tree | commitdiff
2015-04-13 gmungocJAL-1693 make exon alignment for get-xref splitframe... tree | commitdiff
2015-03-30 gmungocJAL-1264 remove broken applet build dependencies tree | commitdiff
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch tree | commitdiff
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in... tree | commitdiff
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e... tree | commitdiff
2015-02-19 gmungocJAL-1665 refactored Sequence.getSequenceFeatures features/sequenceFeatureRefactor tree | commitdiff
2015-02-12 Jim ProcterJAL-1350 cloned method and tested equivalence for using... tree | commitdiff
2015-02-12 Jim ProcterJAL-1115 switch to lists in SequenceGroup tree | commitdiff
2015-02-02 Charles OfoegbuMerge branch 'bug/JAL-1644_Finder-logic-improvement... tree | commitdiff
2015-02-02 Charles OfoegbuJAL-1644 added null check for sequence description... tree | commitdiff
2015-02-02 Charles OfoegbuMerge commit tree | commitdiff
2015-02-02 Charles OfoegbuJAL-1644 revised Finder's implementation to use a flag... tree | commitdiff
2015-02-02 Charles OfoegbuMerge branch 'bug/JAL-1644_Finder-logic-improvement... tree | commitdiff
2015-02-02 Charles OfoegbuJAL-1644 improvment of finder logic to include the... tree | commitdiff
2015-01-28 Jim Procter JAL-674 patch to make Mapping.compareTransferredToR... tree | commitdiff
2015-01-07 Jim ProcterJAL-1483 patches to make test case pass: hamming distan... tree | commitdiff
2015-01-07 Jim ProcterJAL-1483 source formatting tree | commitdiff
2015-01-07 Jim ProcterJAL-1483 refactor NJTree constructor to allow preconfig... tree | commitdiff
2015-01-07 Jim ProcterJAL-1483 organise imports tree | commitdiff
2014-12-22 Jim ProcterMerge: 497958b 68dcaa7 tree | commitdiff
2014-12-15 Jim ProcterJAL-1620 version bump and release notes tree | commitdiff
2014-11-27 Jim ProcterJAL-674 add sequence associated annotation rows to... tree | commitdiff
2014-11-23 Jim ProcterMerge branch 'JAL-1569_wuss_vienna_broke' into develop tree | commitdiff
2014-11-23 Jim ProcterMerge branch 'JAL-1569_wuss_vienna_broke' into Release_... tree | commitdiff
2014-11-23 Jim ProcterJAL-1152 avoid NPE on null alignment annotation vector tree | commitdiff
2014-11-20 Jim ProcterJAL-1569 remove log output during RNA secondary structu... tree | commitdiff
2014-11-18 Jim ProcterJAL-674 make temperature factor, local secondary struct... tree | commitdiff
2014-11-14 Jim ProcterMerge branch 'develop' into JAL-1483_featureBasedTreeCalc tree | commitdiff
2014-11-12 Jim ProcterJAL-674 patch broken getMapping function tree | commitdiff
2014-11-04 gmungocJAL-1152 annotation sort algorithm optimisation tree | commitdiff
2014-11-03 gmungocMerge branch 'features/JAL-1152annotationSorting' of... tree | commitdiff
2014-11-03 gmungocJAL-1152 annotation sorting preferences and help docume... tree | commitdiff
2014-11-03 Jim ProcterMerge branch 'develop' into features/JAL-1152annotation... tree | commitdiff
2014-10-31 gmungocJAL-1152 bug fix for 'no sort' case + tests for autocal... tree | commitdiff
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