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JAL-2422 save/restore ChimeraX session
[jalview.git] / src / jalview / datamodel / Sequence.java
2016-04-05 Jim ProcterJAL-2046 add/delete SequenceFeature operate on dataset... blob | commitdiff | diff to current
2016-04-05 Jim ProcterJAL-2046 setSequenceFeature contract implementation... blob | commitdiff | diff to current
2016-04-05 Jim ProcterJAL-2046 remove javadoc blob | commitdiff | diff to current
2016-04-05 Jim ProcterJAL-2046 simpler deriveSequence - promote to dataset... blob | commitdiff | diff to current
2016-04-05 Jim ProcterJAL-2046 clarify contract for copy constructor and... blob | commitdiff | diff to current
2016-04-05 Jim ProcterJAL-2046 explicitly copy char[] when cloning sequence... blob | commitdiff | diff to current
2016-04-05 Jim ProcterJAL-2046 safer createDatasetSequence manipulates privat... blob | commitdiff | diff to current
2016-03-21 tcofoegbudevelop merge blob | commitdiff | diff to current
2016-03-03 tcofoegbuJAL-1919 fixed bug causing PDBfile test failure blob | commitdiff | diff to current
2016-03-03 tcofoegbuJAL-1919 PDBfile and JmolParser refactor blob | commitdiff | diff to current
2016-03-01 gmungocJAL-1705 align CDS and peptide products to transcripts blob | commitdiff | diff to current
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge blob | commitdiff | diff to current
2016-01-23 gmungocJAL-1705 todo comment re writing DBRefEntry/SequenceFea... blob | commitdiff | diff to current
2015-11-30 gmungocJAL-1421 use generics JAL-1551 @Override annotations... blob | commitdiff | diff to current
2015-11-05 tcofoegbuJAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc... blob | commitdiff | diff to current
2015-10-29 tcofoegbuJAL-1926 JAL-1479 updated PDBfile fetcher to add source... blob | commitdiff | diff to current
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2 blob | commitdiff | diff to current
2015-10-15 tcofoegbuJAL-1479 refactored SequenceI interface - changed getDB... blob | commitdiff | diff to current
2015-10-14 tcofoegbuJAL-1926 added supporting model changes to enable savin... blob | commitdiff | diff to current
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright blob | commitdiff | diff to current
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin... blob | commitdiff | diff to current
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports blob | commitdiff | diff to current
2015-08-07 tcofoegbuJAL-1824 updated caching procedure for pdb entries... blob | commitdiff | diff to current
2015-08-04 tcofoegbuJAL-1821 updated the reference sequence column of struc... blob | commitdiff | diff to current
2015-07-08 gmungocJAL-1759 merge from develop blob | commitdiff | diff to current
2015-07-01 gmungocJAL-1802 handle slide sequences edits in split frame... blob | commitdiff | diff to current
2015-06-17 Jim ProcterMerge branch 'develop' into features/JAL-653_gffalignments features/JAL-653_gffalignments blob | commitdiff | diff to current
2015-06-12 tcofoegbuJAL-1641 refactor blob | commitdiff | diff to current
2015-06-06 Jim ProcterJAL-653 allow a dummy sequence to take on attributes... blob | commitdiff | diff to current
2015-06-05 tcofoegbuJAL-1760 JAL-1641 Serialisation of Hidden Seqs and... blob | commitdiff | diff to current
2015-06-05 Jim ProcterJAL-653 refactor sequence interface to separate concret... blob | commitdiff | diff to current
2015-05-12 gmungocJAL-1712 fixes/tests for Castor binding and 'show flank... blob | commitdiff | diff to current
2015-04-30 tcofoegbuJAL-1717 updated the PDBEntry model and updated the... blob | commitdiff | diff to current
2015-04-13 gmungocJAL-1693 make exon alignment for get-xref splitframe... blob | commitdiff | diff to current
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch blob | commitdiff | diff to current
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in... blob | commitdiff | diff to current
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e... blob | commitdiff | diff to current
2015-02-19 gmungocJAL-1665 refactored Sequence.getSequenceFeatures features/sequenceFeatureRefactor blob | commitdiff | diff to current
2015-01-18 Jim ProcterJAL-1628 new method to get a list of insertions in... blob | commitdiff | diff to current
2015-01-18 Jim ProcterJAL-1372 JAL-1114 JAL-1628 tidy sequenceI/sequence blob | commitdiff | diff to current
2014-12-22 Jim ProcterMerge: 497958b 68dcaa7 blob | commitdiff | diff to current
2014-12-15 Jim ProcterJAL-1620 version bump and release notes blob | commitdiff | diff to current
2014-11-28 gmungocJAL-1610 check reference annotations against alignment... blob | commitdiff | diff to current
2014-11-12 Jim Procterjavadoc blob | commitdiff | diff to current
2014-10-23 gmungocJAL-1264 further refactoring and tests blob | commitdiff | diff to current
2014-10-10 gmungocJAL-1264 added getAlignmentAnnotations(calcId, label) blob | commitdiff | diff to current
2014-10-06 Jim ProcterJAL-654 JAL-1264 sequence associated annotation is... blob | commitdiff | diff to current
2014-10-06 Jim ProcterJAL-1115 TODO remove use of java.util.Vector blob | commitdiff | diff to current
2014-06-06 Jim ProcterJAL-1517 source formatting blob | commitdiff | diff to current
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2 blob | commitdiff | diff to current
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2 blob | commitdiff | diff to current
2014-06-05 Jim ProcterMerge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch blob | commitdiff | diff to current
2014-05-22 Jim ProcterJAL-1503 update version in GPL header blob | commitdiff | diff to current
2014-04-25 Jim ProcterMerge branch 'JAL-1177_prop_rnasecstr' into develop blob | commitdiff | diff to current
2014-04-25 Jim ProcterJAL-1177 propagate sequence associated annotation to... blob | commitdiff | diff to current
2014-02-18 Jim ProcterMerge branch 'JAL-1445' into develop blob | commitdiff | diff to current
2014-02-03 Jim ProcterMerge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge blob | commitdiff | diff to current
2014-01-29 Jim ProcterJAL-1432 updated copyright notices blob | commitdiff | diff to current
2013-10-14 Jim ProcterMerge branch 'develop' into dev_from_2_8_1 blob | commitdiff | diff to current
2013-10-04 Jim Procterfix for JAL-1380 and efficiency todo for JAL-1381 blob | commitdiff | diff to current
2012-11-15 jprocterMerge branch 'develop' into menard blob | commitdiff | diff to current
2012-10-22 jprocterJalview 2.8 Source Header blob | commitdiff | diff to current
2012-10-03 jprocterformatting blob | commitdiff | diff to current
2012-08-31 jprocterMerge branch 'develop' into menard blob | commitdiff | diff to current
2012-08-28 jprocterjavadoc and note about broken semantics for findIndex blob | commitdiff | diff to current
2012-07-10 Anne Menardv2 blob | commitdiff | diff to current
2012-07-05 Anne MenardAdd support RNAML format blob | commitdiff | diff to current
2012-05-24 jprocterensure annotation isn't added twice - note - this could... blob | commitdiff | diff to current
2012-05-22 jprocterMerge remote-tracking branch 'origin/Tcoffee_JAL-1065... blob | commitdiff | diff to current
2011-10-10 jprocterupdate author list in license for (JAL-826) blob | commitdiff | diff to current
2011-09-27 jprocterapply version 2.7 copyright blob | commitdiff | diff to current
2011-02-27 jprocterfirst patch for JAL-774 - ensure end is a valid bound... blob | commitdiff | diff to current
2010-09-23 jprocterJalview 2.6 source licence blob | commitdiff | diff to current
2010-04-30 jprocterjalview 2.5 release banner blob | commitdiff | diff to current
2009-06-08 jprocterapply gpl development license blob | commitdiff | diff to current
2008-09-04 jproctermerge from 2_4_Release branch blob | commitdiff | diff to current
2008-08-06 jproctergetDBRefs now always returns DBRefArray if it exists... blob | commitdiff | diff to current
2008-01-22 jprocternew method to get map of sequence positions correspondi... blob | commitdiff | diff to current
2007-11-30 jprocterjavadoc and transferAnnotation method blob | commitdiff | diff to current
2007-10-24 jprocterensure PDB ids are updated on the dataset sequence blob | commitdiff | diff to current
2007-10-02 jprocterjavadoc blob | commitdiff | diff to current
2007-09-29 jprocterupdatePDBEntry method to add any PDBEntry from the... blob | commitdiff | diff to current
2007-08-30 jproctercreate dataset sequence method blob | commitdiff | diff to current
2007-08-22 jprocteradded failsafe fix for cases where null sequence names... blob | commitdiff | diff to current
2007-07-31 jprocterdebugging cross references and duplicate sequence db... blob | commitdiff | diff to current
2007-07-30 jprocterjavadoc blob | commitdiff | diff to current
2007-06-17 jproctercorrect construction of new dataset sequence when resid... blob | commitdiff | diff to current
2007-05-10 jprocterbugfix on copy only referenced annotation in copy const... blob | commitdiff | diff to current
2007-05-02 jproctersubsequence bound checks and constructor for selectivel... blob | commitdiff | diff to current
2007-04-26 jprocterget annotation by label string blob | commitdiff | diff to current
2007-04-26 amwaterhouseremove should be removeElement blob | commitdiff | diff to current
2007-04-23 amwaterhouseremove alignmentAnnotation added blob | commitdiff | diff to current
2007-04-18 jprocterjava 1.1 compliance blob | commitdiff | diff to current
2007-04-17 jproctercopy constructors and AlignmentAnnotation sequenceRef... blob | commitdiff | diff to current
2007-03-19 jprocterequals operation used for canonicalisation of DBRefList... blob | commitdiff | diff to current
2007-02-07 amwaterhouseFormatting blob | commitdiff | diff to current
2007-01-31 amwaterhousemake new dataset seq if residues deleted blob | commitdiff | diff to current
2007-01-23 amwaterhouseHidden representatives moved from sequence to viewport blob | commitdiff | diff to current
2007-01-19 jprocterdatasetSequence derive method and some checks blob | commitdiff | diff to current
2007-01-18 amwaterhouseSet description on copy blob | commitdiff | diff to current
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