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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / analysis / AlignmentUtils.java
2016-06-23 Jim ProcterMerge branch 'develop' into merge_JAL-2110 commit | commitdiff
2016-06-22 gmungocJAL-1982 defensive checks for null annotations array commit | commitdiff
2016-06-16 Jim ProcterJAL-2110 throw implementation error if not given a... commit | commitdiff
2016-06-14 gmungocJAL-2110 fixes to dbref resolution and mappings, use... commit | commitdiff
2016-06-09 gmungocJAL-2110 work in progress commit | commitdiff
2016-05-31 gmungocJAL-2023 adjustments to mappings added for split frame... commit | commitdiff
2016-05-18 gmungocJAL-2049 set sequence feature group to "Jalview" for... commit | commitdiff
2016-05-18 gmungocJAL-2049 use HGVS notation for variant on protein residue commit | commitdiff
2016-04-14 gmungocJAL-2041 add ID,clinical_significance to feature attrib... commit | commitdiff
2016-04-14 gmungocJAL-2049 revised computePeptideVariants to transfer... commit | commitdiff
2016-04-12 gmungocJAL-2049 separate protein variant per dna variant ... commit | commitdiff
2016-04-01 gmungocJAL-1705 ensure the right mapping is used to align... commit | commitdiff
2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and... commit | commitdiff
2016-03-11 gmungocJAL-1705 refactoring etc for fetching Ensembl --> Uniprot commit | commitdiff
2016-03-07 gmungocJAL-2023 CDS sequences added to / share alignment dataset commit | commitdiff
2016-03-03 gmungocJAL-1705 include stop codons in derived CDS; support... commit | commitdiff
2016-03-02 gmungocJAL-1705 include any unmapped protein start 'X' when... commit | commitdiff
2016-03-01 gmungocJAL-1705 align CDS to transcripts commit | commitdiff
2016-02-01 gmungocJAL-1705 JAL-1191 SequenceOntologyLite added as hard... commit | commitdiff
2016-01-28 gmungocJAL-1705 refine feature copying to including 5' and... commit | commitdiff
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge commit | commitdiff
2016-01-23 gmungocJAL-1705 compute peptide variants from dna; add "conseq... commit | commitdiff
2016-01-21 gmungocJAL-1705 transfer features to the dataset sequence... commit | commitdiff
2016-01-21 gmungocJAL-1705 features transferred to CDS sequence; makeExon... commit | commitdiff
2015-12-22 gmungocJAL-653 AlignedCodonFrame collections changed from... commit | commitdiff
2015-11-30 gmungocJAL-653 small comment change only commit | commitdiff
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2 commit | commitdiff
2015-10-15 tcofoegbuJAL-1479 refactored SequenceI interface - changed getDB... commit | commitdiff
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright commit | commitdiff
2015-10-08 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch commit | commitdiff
2015-10-07 Jim ProcterJAL-1894 source formatting commit | commitdiff
2015-09-22 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch commit | commitdiff
2015-09-14 gmungocJAL-1880 handle sequence offsets properly when mapping... commit | commitdiff
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin... commit | commitdiff
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports commit | commitdiff
2015-09-09 gmungocJAL-1619 'align protein as cDNA' now leaves unmapped... commit | commitdiff
2015-09-07 gmungocJAL-1636 translate stop codon as '*', mouseover * as... commit | commitdiff
2015-08-17 gmungocJAL-1800 separated SearchResults.getCharacters() from... commit | commitdiff
2015-06-04 gmungocJAL-1544 spelling in javadoc only commit | commitdiff
2015-05-12 gmungocJAL-1712 fixes/tests for Castor binding and 'show flank... commit | commitdiff
2015-04-21 gmungocJAL-1693 mappings added back to the original alignment commit | commitdiff
2015-04-14 gmungocJAL-1693 generate multiple exon sequences for 1-many... commit | commitdiff
2015-04-13 gmungocJAL-1693 make exon alignment for get-xref splitframe... commit | commitdiff
2015-03-30 gmungocJAL-1264 remove broken applet build dependencies commit | commitdiff
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch commit | commitdiff
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in... commit | commitdiff
2014-12-22 Jim ProcterMerge: 497958b 68dcaa7 commit | commitdiff
2014-12-15 Jim ProcterJAL-1620 version bump and release notes commit | commitdiff
2014-11-27 Jim ProcterJAL-674 add sequence associated annotation rows to... commit | commitdiff
2014-10-30 gmungocJAL-1152 prototype of new Annotations menu with sort... commit | commitdiff
2014-06-06 Jim ProcterJAL-1517 source formatting commit | commitdiff
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2 commit | commitdiff
2014-04-21 Jim ProcterJAL-1466 don't include empty columns if no upstream... commit | commitdiff
2014-04-21 Jim ProcterJAL-1466 improved test and patched off by one that... commit | commitdiff
2014-04-21 Jim ProcterJAL-1466 new calculation menu option to recover the... commit | commitdiff