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

2017-01-06	gmungoc	Merge branch 'develop' into features/JAL-2360colourSche...	blob \| commitdiff
2017-01-05	gmungoc	JAL-2374 fix popup out by one and multiple groups bugs	blob \| commitdiff \| diff to current
2016-12-14	gmungoc	JAL-2360 added check for null annotations array	blob \| commitdiff \| diff to current
2016-12-12	gmungoc	JAL-2360 simplify nucleotide flag, remove setter	blob \| commitdiff \| diff to current
2016-11-25	gmungoc	Merge branch 'develop' into trialMerge	blob \| commitdiff \| diff to current
2016-10-28	Jim Procter	JAL-966 JAL-1738 JAL-345 interfaces for SearchResults...	blob \| commitdiff \| diff to current
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
2016-10-04	gmungoc	JAL-2232 JAL-2154 update dbrefs to newly created datase...	blob \| commitdiff \| diff to current
2016-09-22	gmungoc	JAL-2216 finalize() refactored so not called programmat...	blob \| commitdiff \| diff to current
2016-08-30	gmungoc	Merge branch 'develop' into features/filetypeEnum	blob \| commitdiff \| diff to current
2016-08-22	Jim Procter	JAL-2154 always check dataset sequence for sequence...	blob \| commitdiff \| diff to current
2016-08-19	Jim Procter	JAL-2154 refactor setSequenceAt to replaceSequenceAt...	blob \| commitdiff \| diff to current
2016-08-07	Jim Procter	JAL-2154 add in missing class for createDatasetAlignmen...	blob \| commitdiff \| diff to current
2016-08-04	Jim Procter	JAL-2154 make sure all sequences referenced via DBRefEn...	blob \| commitdiff \| diff to current
2016-07-18	Jim Procter	JAL-2121 cleanup TODO	blob \| commitdiff \| diff to current
2016-07-14	Jim Procter	JAL-1115 change implementation to avoid possibility...	blob \| commitdiff \| diff to current
2016-07-14	Jim Procter	JAL-1270 test coverage TODO Alignment.append(AlignmentI)	blob \| commitdiff \| diff to current
2016-07-12	Jim Procter	JAL-2110 javadoc and TODO re shortcomings of implementation	blob \| commitdiff \| diff to current
2016-07-06	gmungoc	JAL-2110 ensuring mapped dbrefs between protein and cds	blob \| commitdiff \| diff to current
2016-07-04	gmungoc	JAL-2110 unused method removed	blob \| commitdiff \| diff to current
2016-06-20	Jim Procter	JAL-2110 copy alcodonframes only if copy constructor...	blob \| commitdiff \| diff to current
2016-06-19	Jim Procter	JAL-2110 JAL-2131 JAL-1765 remove reference to jalview...	blob \| commitdiff \| diff to current
2016-06-16	Jim Procter	JAL-2110 todo - select mappings involving sequences...	blob \| commitdiff \| diff to current
2016-05-31	gmungoc	JAL-2023 adjustments to mappings added for split frame...	blob \| commitdiff \| diff to current
2016-04-11	tcofoegbu	JAL-2054 Renamed getStartEnd in AlignFrame to getVisibl...	blob \| commitdiff \| diff to current
2016-04-01	gmungoc	JAL-1705 reworked AlignmentUtils.makeCdsAlignment and...	blob \| commitdiff \| diff to current
2015-12-22	gmungoc	JAL-653 realise virtual mappings and align when adding...	blob \| commitdiff \| diff to current
2015-12-03	gmungoc	JAL-653 mappings always reside on the dataset alignment...	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
2015-10-08	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
2015-07-30	tcofoegbu	JAL-1443 modified exception notifications	blob \| commitdiff \| diff to current
2015-07-21	tcofoegbu	JAL-1443 bugfix to prevent loading of unidentifiable...	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
2015-01-09	Jim Procter	Merge branch 'JAL-1372_referenceseq' into feature_29...	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
2014-11-17	Jim Procter	formatting	blob \| commitdiff \| diff to current
2014-11-17	Jim Procter	JAL-1587 JAL-407 instrument setDataset to add dataset...	blob \| commitdiff \| diff to current
2014-10-10	gmungoc	JAL-1264 reverted (removed added method)	blob \| commitdiff \| diff to current
2014-10-08	gmungoc	Merge branch 'Release_2_8_2_Branch' into	blob \| commitdiff \| diff to current
2014-10-07	gmungoc	JAL-1264 wip	blob \| commitdiff \| diff to current
2014-09-27	darolmar	JAL-1355	blob \| commitdiff \| diff to current
2014-09-23	darolmar	JAL-1355	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
2014-05-22	Jim Procter	JAL-1503 update version in GPL header	blob \| commitdiff \| diff to current
2014-05-02	Jim Procter	Merge branch 'Release_2_8_1_Branch' into JAL-1372_refer...	blob \| commitdiff \| diff to current
2014-05-01	Jim Procter	JAL-1492 JAL-1397 make AnnotatedCollectionI context...	blob \| commitdiff \| diff to current
2014-01-29	Jim Procter	JAL-1432 updated copyright notices	blob \| commitdiff \| diff to current
2013-10-11	Jim Procter	JAL-1114 promote start/end attributes to gettable field...	blob \| commitdiff \| diff to current
2013-08-30	Jim Procter	JAL-1367 promote the existing representative sequence...	blob \| commitdiff \| diff to current
2013-06-23	Jim Procter	JAL-1230 proxy method for synchronising internal Alignm...	blob \| commitdiff \| diff to current
2013-05-31	Jim Procter	JAL-1259 patch to avoid NPE	blob \| commitdiff \| diff to current
2013-05-31	Jim Procter	JAL-1259 patch to avoid NPE	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
2012-07-03	jprocter	JAL-961 allow calcId to be specified independently...	blob \| commitdiff \| diff to current
2012-06-13	jprocter	javatidy	blob \| commitdiff \| diff to current
2012-06-12	jprocter	JAL-1115 refactor reordering code operating directly...	blob \| commitdiff \| diff to current
2012-06-12	jprocter	JAL-1115 refactor base collection for Alignment from...	blob \| commitdiff \| diff to current
2012-05-30	jprocter	JAL-1114 - refactor methods handling Vectors and Hashta...	blob \| commitdiff \| diff to current
2012-05-23	jprocter	JAL-961 - annotatable datamodel objects can be queried...	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
2011-10-04	jprocter	Merge remote-tracking branch 'remotes/origin/2_5_1_rna_...	blob \| commitdiff \| diff to current
2011-09-27	jprocter	apply version 2.7 copyright	blob \| commitdiff \| diff to current
2011-08-15	janengelhardt	JAL-891; Sorting of Structure logo implemented; bug...	blob \| commitdiff \| diff to current
2011-08-11	janengelhardt	JAL-885; hasRNAStructure method was introduced to Align...	blob \| commitdiff \| diff to current
2011-04-21	jprocter	allow an alignment annotation row to be removed and...	blob \| commitdiff \| diff to current
2010-11-12	jprocter	patch for JAL-700	blob \| commitdiff \| diff to current
2010-09-23	jprocter	apply jalview code style	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
2010-04-29	jprocter	isAligned assertion (bug 0008144)	blob \| commitdiff \| diff to current
2010-04-28	jprocter	group/annotation association housekeeping	blob \| commitdiff \| diff to current
2009-07-24	jprocter	implement new insert annotation row method and ensure...	blob \| commitdiff \| diff to current
2009-06-08	jprocter	apply gpl development license	blob \| commitdiff \| diff to current
2008-12-19	jprocter	left and right justify method	blob \| commitdiff \| diff to current
2008-12-05	jprocter	support for multiple accession retrieval from a databas...	blob \| commitdiff \| diff to current
2008-11-12	jprocter	javadoc and new method to get alignment sequence index...	blob \| commitdiff \| diff to current
2008-09-04	jprocter	merge from 2_4_Release branch	blob \| commitdiff \| diff to current
2008-07-18	jprocter	allow findSeq to begin after a given sequence in...	blob \| commitdiff \| diff to current
2007-11-30	jprocter	case invariant matching of seqeunce feature to sequence...	blob \| commitdiff \| diff to current
2007-08-30	jprocter	moved dataset sequence creation onto sequence method	blob \| commitdiff \| diff to current
2007-08-24	jprocter	dataset alignments have a reference count which must...	blob \| commitdiff \| diff to current
2007-07-13	jprocter	mapping bug fixes	blob \| commitdiff \| diff to current
2007-06-17	jprocter	AlignedCodonFrame holds mapping information between...	blob \| commitdiff \| diff to current
2007-05-10	jprocter	fixed array index out of bounds when not removing align...	blob \| commitdiff \| diff to current
2007-05-07	amwaterhouse	tIndex prevented deletion of last annotation	blob \| commitdiff \| diff to current
2007-05-02	jprocter	return flag indicating if annotations were actually...	blob \| commitdiff \| diff to current
2007-05-01	jprocter	removeAlignmentAnnotation only removes annotation objec...	blob \| commitdiff \| diff to current
2007-04-27	jprocter	documentation and getProperties method	blob \| commitdiff \| diff to current
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