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

2015-07-30	tcofoegbu	JAL-1443 modified exception notifications	blob \| commitdiff
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
2007-04-25	amwaterhouse	alignmentProperties added	blob \| commitdiff \| diff to current
2007-04-23	amwaterhouse	remove seqref annotations	blob \| commitdiff \| diff to current
2007-04-17	jprocter	copy constructors and AlignmentAnnotation sequenceRef...	blob \| commitdiff \| diff to current
2007-04-02	amwaterhouse	Destroy alignment moved to finalize	blob \| commitdiff \| diff to current
2007-04-02	amwaterhouse	Destroy aligment method added	blob \| commitdiff \| diff to current
2007-02-07	amwaterhouse	Formatting	blob \| commitdiff \| diff to current
2007-01-26	amwaterhouse	Only set the sequence oncecvs diff datamodel/Alignment...	blob \| commitdiff \| diff to current
2007-01-25	amwaterhouse	Annotation adjustment moved to EditCommand	blob \| commitdiff \| diff to current
2007-01-24	amwaterhouse	AdjustAnnotations needs position, number and insert	blob \| commitdiff \| diff to current
2007-01-23	amwaterhouse	Hidden representatives moved from sequence to viewport	blob \| commitdiff \| diff to current
2006-12-21	amwaterhouse	remove unnecessary import	blob \| commitdiff \| diff to current
2006-12-05	amwaterhouse	Sequence is char []	blob \| commitdiff \| diff to current
2006-11-23	amwaterhouse	Dont make groups of hidden sequences	blob \| commitdiff \| diff to current
2006-11-13	amwaterhouse	Sequence colour moved to viewport	blob \| commitdiff \| diff to current
2006-11-08	amwaterhouse	currentSeq and set description in dataset	blob \| commitdiff \| diff to current
2006-11-03	amwaterhouse	Consensus may already have been removed	blob \| commitdiff \| diff to current
2006-10-27	amwaterhouse	New padgaps works out number of gaps to insert, delete	blob \| commitdiff \| diff to current
2006-10-25	amwaterhouse	We can delete sequence 0	blob \| commitdiff \| diff to current
2006-10-24	amwaterhouse	maxIdLength redundant, deleteCols, trimLeft, removeGaps...	blob \| commitdiff \| diff to current
2006-10-12	amwaterhouse	HiddenSequences now array, not hashtable	blob \| commitdiff \| diff to current
2006-10-09	jprocter	fixed getCompactAlignment method to return proper cigar...	blob \| commitdiff \| diff to current
2006-10-06	amwaterhouse	AAFrequency optimized	blob \| commitdiff \| diff to current
2006-08-21	amwaterhouse	header updated	blob \| commitdiff \| diff to current
2006-08-21	jprocter	removeGaps method can record changes in alignment colum...	blob \| commitdiff \| diff to current
2006-08-18	amwaterhouse	dont remove all representative seqs on delete groups	blob \| commitdiff \| diff to current
2006-08-18	amwaterhouse	remove all representative seqs on delete groups	blob \| commitdiff \| diff to current
2006-08-15	amwaterhouse	Move features to dataset	blob \| commitdiff \| diff to current
2006-08-14	amwaterhouse	findSequenceMatch returns multiple sequences	blob \| commitdiff \| diff to current
2006-08-09	jprocter	alignment from seqCigars will correctly mark deleted...	blob \| commitdiff \| diff to current
2006-08-04	jprocter	recover original data for tree and pca as alignment...	blob \| commitdiff \| diff to current
2006-07-28	amwaterhouse	1.1 compatible	blob \| commitdiff \| diff to current
2006-07-26	jprocter	Implemented CIGAR representation of an Alignment view...	blob \| commitdiff \| diff to current
2006-07-26	amwaterhouse	seqs[j] replaces current	blob \| commitdiff \| diff to current
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