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[jalview.git] / src / jalview / datamodel / Sequence.java

2016-11-14	gmungoc	JAL-2296 report whether SequenceFeature actually added...	blob \| commitdiff
2016-10-25	Jim Procter	JAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch	blob \| commitdiff \| diff to current
2016-10-06	Jim Procter	JAL-2089 Merge branch releases/Release_2_10_Branch...	blob \| commitdiff \| diff to current
2016-10-05	Jim Procter	JAL-2189 source formatting	blob \| commitdiff \| diff to current
2016-10-03	gmungoc	JAL-2110 additional tests for setDatasetSequence, javad...	blob \| commitdiff \| diff to current
2016-09-28	Jim Procter	JAL-2235 raise exceptions if self reference or referenc...	blob \| commitdiff \| diff to current
2016-09-28	Jim Procter	JAL-2210 instrument setDBRefs to call ensurePrimaries	blob \| commitdiff \| diff to current
2016-09-27	Jim Procter	JAL-2210 promote direct dbrefs from verified sources...	blob \| commitdiff \| diff to current
2016-09-27	Jim Procter	JAL-2210 resolve todo - addDBRef adds to dataset sequen...	blob \| commitdiff \| diff to current
2016-09-16	gmungoc	JAL-2157 JAL-1803 refactored Sequence.updatePDBIds...	blob \| commitdiff \| diff to current
2016-09-07	Jim Procter	JAL-1803 first pass at updatePDBEntry	blob \| commitdiff \| diff to current
2016-09-06	gmungoc	JAL-2106 DBRefEntry.isPrimary() renamed isPrimaryCandid...	blob \| commitdiff \| diff to current
2016-09-05	gmungoc	JAL-2106 increased coverage for testGetPrimaryDbRefs	blob \| commitdiff \| diff to current
2016-08-31	Jim Procter	JAL-1926 JAL-2106 fix PDB primary DBRef semantics:...	blob \| commitdiff \| diff to current
2016-08-26	Jim Procter	JAL-2106 fix (last one!) remove the Sequence.sourceDBRe... bug/JAL-2154projectMappings	blob \| commitdiff \| diff to current
2016-08-25	Jim Procter	JAL-2106 tighten DBRefEntry primary seq test for PDB	blob \| commitdiff \| diff to current
2016-08-25	Jim Procter	Merge branch 'refactor/JAL-2106_sourceDbRef_revision...	blob \| commitdiff \| diff to current
2016-08-24	Jim Procter	JAL-2106 removed setSourceDBRef, refactor getSourceDBRe...	blob \| commitdiff \| diff to current
2016-08-24	Jim Procter	JAL-2106 rejig test to minimally verify patch that...	blob \| commitdiff \| diff to current
2016-08-04	Jim Procter	JAL-2046 stack trace for implementation warning	blob \| commitdiff \| diff to current
2016-08-02	Jim Procter	JAL-2046 additional logic to suppress spurious implemen...	blob \| commitdiff \| diff to current
2016-06-23	Jim Procter	JAL-2110 SequenceI.isProtein method	blob \| commitdiff \| diff to current
2016-05-31	gmungoc	JAL-2110 refactor + tests to allow a dbref version...	blob \| commitdiff \| diff to current
2016-04-05	Jim Procter	JAL-2046 add/delete SequenceFeature operate on dataset...	blob \| commitdiff \| diff to current
2016-04-05	Jim Procter	JAL-2046 setSequenceFeature contract implementation...	blob \| commitdiff \| diff to current
2016-04-05	Jim Procter	JAL-2046 remove javadoc	blob \| commitdiff \| diff to current
2016-04-05	Jim Procter	JAL-2046 simpler deriveSequence - promote to dataset...	blob \| commitdiff \| diff to current
2016-04-05	Jim Procter	JAL-2046 clarify contract for copy constructor and...	blob \| commitdiff \| diff to current
2016-04-05	Jim Procter	JAL-2046 explicitly copy char[] when cloning sequence...	blob \| commitdiff \| diff to current
2016-04-05	Jim Procter	JAL-2046 safer createDatasetSequence manipulates privat...	blob \| commitdiff \| diff to current
2016-03-21	tcofoegbu	develop merge	blob \| commitdiff \| diff to current
2016-03-03	tcofoegbu	JAL-1919 fixed bug causing PDBfile test failure	blob \| commitdiff \| diff to current
2016-03-03	tcofoegbu	JAL-1919 PDBfile and JmolParser refactor	blob \| commitdiff \| diff to current
2016-03-01	gmungoc	JAL-1705 align CDS and peptide products to transcripts	blob \| commitdiff \| diff to current
2016-01-28	gmungoc	Merge branch 'develop' into JAL-1705_trialMerge	blob \| commitdiff \| diff to current
2016-01-23	gmungoc	JAL-1705 todo comment re writing DBRefEntry/SequenceFea...	blob \| commitdiff \| diff to current
2015-11-30	gmungoc	JAL-1421 use generics JAL-1551 @Override annotations...	blob \| commitdiff \| diff to current
2015-11-05	tcofoegbu	JAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc...	blob \| commitdiff \| diff to current
2015-10-29	tcofoegbu	JAL-1926 JAL-1479 updated PDBfile fetcher to add source...	blob \| commitdiff \| diff to current
2015-10-16	Jim Procter	JAL-1925 update source version in license Release_2_9_0b2	blob \| commitdiff \| diff to current
2015-10-15	tcofoegbu	JAL-1479 refactored SequenceI interface - changed getDB...	blob \| commitdiff \| diff to current
2015-10-14	tcofoegbu	JAL-1926 added supporting model changes to enable savin...	blob \| commitdiff \| diff to current
2015-10-08	Jim Procter	JAL-1894 update year/version in copyright	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 source formatting and organise imports	blob \| commitdiff \| diff to current
2015-08-07	tcofoegbu	JAL-1824 updated caching procedure for pdb entries...	blob \| commitdiff \| diff to current
2015-08-04	tcofoegbu	JAL-1821 updated the reference sequence column of struc...	blob \| commitdiff \| diff to current
2015-07-08	gmungoc	JAL-1759 merge from develop	blob \| commitdiff \| diff to current
2015-07-01	gmungoc	JAL-1802 handle slide sequences edits in split frame...	blob \| commitdiff \| diff to current
2015-06-17	Jim Procter	Merge branch 'develop' into features/JAL-653_gffalignments features/JAL-653_gffalignments	blob \| commitdiff \| diff to current
2015-06-12	tcofoegbu	JAL-1641 refactor	blob \| commitdiff \| diff to current
2015-06-06	Jim Procter	JAL-653 allow a dummy sequence to take on attributes...	blob \| commitdiff \| diff to current
2015-06-05	tcofoegbu	JAL-1760 JAL-1641 Serialisation of Hidden Seqs and...	blob \| commitdiff \| diff to current
2015-06-05	Jim Procter	JAL-653 refactor sequence interface to separate concret...	blob \| commitdiff \| diff to current
2015-05-12	gmungoc	JAL-1712 fixes/tests for Castor binding and 'show flank...	blob \| commitdiff \| diff to current
2015-04-30	tcofoegbu	JAL-1717 updated the PDBEntry model and updated the...	blob \| commitdiff \| diff to current
2015-04-13	gmungoc	JAL-1693 make exon alignment for get-xref splitframe...	blob \| commitdiff \| diff to current
2015-03-26	gmungoc	Merge develop to Release_2_8_3_Branch	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	JAL-1683 replace year/version strings with tokens in...	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...	blob \| commitdiff \| diff to current
2015-02-19	gmungoc	JAL-1665 refactored Sequence.getSequenceFeatures features/sequenceFeatureRefactor	blob \| commitdiff \| diff to current
2015-01-18	Jim Procter	JAL-1628 new method to get a list of insertions in...	blob \| commitdiff \| diff to current
2015-01-18	Jim Procter	JAL-1372 JAL-1114 JAL-1628 tidy sequenceI/sequence	blob \| commitdiff \| diff to current
2014-12-22	Jim Procter	Merge: 497958b 68dcaa7	blob \| commitdiff \| diff to current
2014-12-15	Jim Procter	JAL-1620 version bump and release notes	blob \| commitdiff \| diff to current
2014-11-28	gmungoc	JAL-1610 check reference annotations against alignment...	blob \| commitdiff \| diff to current
2014-11-12	Jim Procter	javadoc	blob \| commitdiff \| diff to current
2014-10-23	gmungoc	JAL-1264 further refactoring and tests	blob \| commitdiff \| diff to current
2014-10-10	gmungoc	JAL-1264 added getAlignmentAnnotations(calcId, label)	blob \| commitdiff \| diff to current
2014-10-06	Jim Procter	JAL-654 JAL-1264 sequence associated annotation is...	blob \| commitdiff \| diff to current
2014-10-06	Jim Procter	JAL-1115 TODO remove use of java.util.Vector	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 source formatting	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 fix copyright for 2.8.2	blob \| commitdiff \| diff to current
2014-06-05	Jim Procter	JAL-1517 update copyright to version 2.8.2	blob \| commitdiff \| diff to current
2014-06-05	Jim Procter	Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch	blob \| commitdiff \| diff to current
2014-05-22	Jim Procter	JAL-1503 update version in GPL header	blob \| commitdiff \| diff to current
2014-04-25	Jim Procter	Merge branch 'JAL-1177_prop_rnasecstr' into develop	blob \| commitdiff \| diff to current
2014-04-25	Jim Procter	JAL-1177 propagate sequence associated annotation to...	blob \| commitdiff \| diff to current
2014-02-18	Jim Procter	Merge branch 'JAL-1445' into develop	blob \| commitdiff \| diff to current
2014-02-03	Jim Procter	Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge	blob \| commitdiff \| diff to current
2014-01-29	Jim Procter	JAL-1432 updated copyright notices	blob \| commitdiff \| diff to current
2013-10-14	Jim Procter	Merge branch 'develop' into dev_from_2_8_1	blob \| commitdiff \| diff to current
2013-10-04	Jim Procter	fix for JAL-1380 and efficiency todo for JAL-1381	blob \| commitdiff \| diff to current
2012-11-15	jprocter	Merge branch 'develop' into menard	blob \| commitdiff \| diff to current
2012-10-22	jprocter	Jalview 2.8 Source Header	blob \| commitdiff \| diff to current
2012-10-03	jprocter	formatting	blob \| commitdiff \| diff to current
2012-08-31	jprocter	Merge branch 'develop' into menard	blob \| commitdiff \| diff to current
2012-08-28	jprocter	javadoc and note about broken semantics for findIndex	blob \| commitdiff \| diff to current
2012-07-10	Anne Menard	v2	blob \| commitdiff \| diff to current
2012-07-05	Anne Menard	Add support RNAML format	blob \| commitdiff \| diff to current
2012-05-24	jprocter	ensure annotation isn't added twice - note - this could...	blob \| commitdiff \| diff to current
2012-05-22	jprocter	Merge remote-tracking branch 'origin/Tcoffee_JAL-1065...	blob \| commitdiff \| diff to current
2011-10-10	jprocter	update author list in license for (JAL-826)	blob \| commitdiff \| diff to current
2011-09-27	jprocter	apply version 2.7 copyright	blob \| commitdiff \| diff to current
2011-02-27	jprocter	first patch for JAL-774 - ensure end is a valid bound...	blob \| commitdiff \| diff to current
2010-09-23	jprocter	Jalview 2.6 source licence	blob \| commitdiff \| diff to current
2010-04-30	jprocter	jalview 2.5 release banner	blob \| commitdiff \| diff to current
2009-06-08	jprocter	apply gpl development license	blob \| commitdiff \| diff to current
2008-09-04	jprocter	merge from 2_4_Release branch	blob \| commitdiff \| diff to current
2008-08-06	jprocter	getDBRefs now always returns DBRefArray if it exists...	blob \| commitdiff \| diff to current
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