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

2019-03-04	gmungoc	Merge branch 'bug/JAL-3099alignmentVisibleWidth' into...	blob \| commitdiff
2018-11-28	gmungoc	JAL-3164 redraw complement overview on hide columns bug/JAL-3164complementOverview	blob \| commitdiff \| diff to current
2018-09-10	gmungoc	JAL-3099 new method AlignmentI.getVisibleWidth()	blob \| commitdiff \| diff to current
2018-02-21	kiramt	JAL-2778 Revert back to old synchronisation	blob \| commitdiff \| diff to current
2018-01-26	kiramt	JAL-2778 try another way to draw sequences with reduced...	blob \| commitdiff \| diff to current
2018-01-19	kiramt	JAL-2759 Moved propagateInsertions out of HiddenColumns	blob \| commitdiff \| diff to current
2018-01-15	kiramt	JAL-2759 Refactor of hideInsertionsFor after review	blob \| commitdiff \| diff to current
2017-10-03	gmungoc	JAL-2738 copy to spikes/mungo	blob \| commitdiff \| diff to current
2017-09-04	Jim Procter	JAL-2675 source license	blob \| commitdiff \| diff to current
2017-07-24	gmungoc	spike branch updated from latest features/JAL-2446	blob \| commitdiff \| diff to current
2017-06-09	gmungoc	JAL-2446 merged to spike branch	blob \| commitdiff \| diff to current
2017-06-07	kiramt	JAL-2591 More refactoring (incomplete)	blob \| commitdiff \| diff to current
2017-04-24	kiramt	JAL-2388 Hidden cols separated from column selection...	blob \| commitdiff \| diff to current
2017-03-10	kiramt	JAL-2437 Fixed reordering of sequences when hiding...	blob \| commitdiff \| diff to current
2017-03-03	kiramt	JAL-2388 Initial removal of hidden cols/seqs out of...	blob \| commitdiff \| diff to current
2017-02-15	Jim Procter	JAL-2374 javadoc - qualify that sequence argument to...	blob \| commitdiff \| diff to current
2017-01-09	gmungoc	JAL-2371 pull up isNucleotide to SequenceCollectionI	blob \| commitdiff \| diff to current
2017-01-06	gmungoc	Merge branch 'develop' into features/JAL-2360colourSche...	blob \| commitdiff \| diff to current
2017-01-05	gmungoc	JAL-2374 fix popup out by one and multiple groups bugs	blob \| commitdiff \| diff to current
2016-12-12	gmungoc	JAL-2360 simplify nucleotide flag, remove setter	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
2016-08-19	Jim Procter	JAL-2154 refactor setSequenceAt to replaceSequenceAt...	blob \| commitdiff \| diff to current
2016-07-18	Jim Procter	JAL-2145 documentation of getWidth()	blob \| commitdiff \| diff to current
2016-07-04	gmungoc	JAL-2110 unused method removed	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
2016-05-31	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
2015-12-22	gmungoc	JAL-653 realise virtual mappings and align when adding...	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
2015-07-21	tcofoegbu	JAL-1443 bugfix to prevent loading of unidentifiable...	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
2014-12-15	Jim Procter	JAL-1620 version bump and release notes	blob \| commitdiff \| diff to current
2014-10-07	gmungoc	JAL-1264 wip	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
2014-01-29	Jim Procter	JAL-1432 updated copyright notices	blob \| commitdiff \| diff to current
2013-06-23	Jim Procter	JAL-1230 proxy method for synchronising internal Alignm...	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
2011-08-11	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
2010-09-23	jprocter	apply jalview code style	blob \| commitdiff \| diff to current
2010-09-23	jprocter	Jalview 2.6 source licence	blob \| commitdiff \| diff to current
2010-06-03	jprocter	javadoc re JAL-554	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
2009-07-24	jprocter	insert annotation at specific position	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
2007-06-17	jprocter	AlignedCodonFrame holds mapping information between...	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	javadoc	blob \| commitdiff \| diff to current
2007-05-01	jprocter	removeAlignmentAnnotation only removes annotation objec...	blob \| commitdiff \| diff to current
2007-04-27	jprocter	getProperties returns nullk for no properties	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
2007-04-19	jprocter	javadoc note on padding AlignmentAnnotation to alignmen...	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
2007-01-25	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
2006-12-21	amwaterhouse	remove unnecessary import	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
2006-10-06	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
2006-08-14	amwaterhouse	findSequenceMatch returns multiple sequences	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	Remove left, right, empty cols work on hidden reps	blob \| commitdiff \| diff to current
2006-07-12	amwaterhouse	sequences are private in SequenceGroup	blob \| commitdiff \| diff to current
2006-07-07	amwaterhouse	Redundant Remove Redundancy Removed	blob \| commitdiff \| diff to current
2006-06-09	amwaterhouse	getSequencesArray	blob \| commitdiff \| diff to current
2006-05-10	amwaterhouse	addAnnotation with seqRef	blob \| commitdiff \| diff to current
2006-03-16	amwaterhouse	getHiddenSequences	blob \| commitdiff \| diff to current
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