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

2017-08-28	kiramt	Merge remote-tracking branch 'origin/develop' into...	blob \| commitdiff
2017-08-28	kiramt	Merge remote-tracking branch 'origin/releases/Release_2...	blob \| commitdiff
2017-08-28	kiramt	JAL-2665 Changes for review comments; printing with... bug/JAL-2665	blob \| commitdiff \| diff to current
2017-08-16	Jim Procter	JAL-2418 source formatting	blob \| commitdiff \| diff to current
2017-08-16	kiramt	JAL-2665 Added hidden columns group selection - almost...	blob \| commitdiff \| diff to current
2017-08-16	kiramt	JAL-2665 Added sequence group update event.	blob \| commitdiff \| diff to current
2017-06-08	gmungoc	JAL-2386 JAL-2570 use ResidueShader copy constructor... bug/JAL-2386groupConservationColouring	blob \| commitdiff \| diff to current
2017-06-07	gmungoc	JAL-2386 ensure group conservation shading is applied...	blob \| commitdiff \| diff to current
2017-05-30	gmungoc	JAL-2570 don't zap group colour scheme when mapping...	blob \| commitdiff \| diff to current
2017-05-24	kiramt	JAL-2034 Added isDefined flag to SequenceGroup	blob \| commitdiff \| diff to current
2017-04-27	Jim Procter	JAL-2494 fix: updated behaviour for SequenceGroup.findA...	blob \| commitdiff \| diff to current
2017-03-31	gmungoc	JAL-2405 additional checks for circular reference in...	blob \| commitdiff \| diff to current
2017-02-15	Jim Procter	JAL-2374 new contains methods for seq and seq,apos	blob \| commitdiff \| diff to current
2017-02-09	gmungoc	JAL-2405 check for circular reference in SequenceGroup...	blob \| commitdiff \| diff to current
2017-01-27	gmungoc	JAL-2371 CollectionColourScheme renamed ResidueShader...	blob \| commitdiff \| diff to current
2017-01-27	gmungoc	JAL-2360 JAL-2371 updates from review CR-JAL-1	blob \| commitdiff \| diff to current
2017-01-09	gmungoc	JAL-2371 pull up isNucleotide to SequenceCollectionI	blob \| commitdiff \| diff to current
2017-01-05	gmungoc	JAL-2371 tests added	blob \| commitdiff \| diff to current
2017-01-04	gmungoc	JAL-2371 CollectionColourScheme wraps ColourSchemeI	blob \| commitdiff \| diff to current
2016-12-21	gmungoc	JAL-2360 Javadoc and test cases for findAnnotation	blob \| commitdiff \| diff to current
2016-11-17	gmungoc	JAL-98 ProfilesI container for profiles for columns	blob \| commitdiff \| diff to current
2016-11-02	gmungoc	JAL-98 JAL-1854 encapsulate 'magic number' threshold...	blob \| commitdiff \| diff to current
2016-11-02	gmungoc	JAL-98 ProfileI interface for Profile	blob \| commitdiff \| diff to current
2016-11-02	gmungoc	JAL-98 Profile and ResidueCount moved from analysis...	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
2016-10-03	gmungoc	JAL-98 use Profile to store consensus, ResidueCount...	blob \| commitdiff \| diff to current
2016-09-22	gmungoc	JAL-1421 typed ResidueProperties.propHash; JAL-2176...	blob \| commitdiff \| diff to current
2016-08-31	Jim Procter	JAL-2034 fix logic so recalcConservation(true) returns...	blob \| commitdiff \| diff to current
2016-07-19	Jim Procter	Merge branch 'develop' into efficiency/JAL-2034_JAL...	blob \| commitdiff \| diff to current
2016-06-20	Jim Procter	JAL-1551 tidy	blob \| commitdiff \| diff to current
2016-06-20	Jim Procter	JAL-2068 avoid ArrayIndexOutOfBounds when consensus...	blob \| commitdiff \| diff to current
2016-03-25	Jim Procter	JAL-2034 make colour scheme update optional when group...	blob \| commitdiff \| diff to current
2016-03-25	Jim Procter	JAL-1551	blob \| commitdiff \| diff to current
2015-11-05	tcofoegbu	JAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc...	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
2015-10-08	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
2015-04-01	gmungoc	JAL-845 fixed start/end range of a mapped SequenceGroup	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
2015-02-12	Jim Procter	JAL-1115 List rather than vector for sequence groups...	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
2014-10-10	gmungoc	JAL-1264 reverted (removed added method)	blob \| commitdiff \| diff to current
2014-10-07	gmungoc	JAL-1264 wip	blob \| commitdiff \| diff to current
2014-09-23	gmungoc	JAL-1264 first cut of panel for annotation show/hide...	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
2014-05-01	Jim Procter	JAL-1492 formatting and squash NPEs	blob \| commitdiff \| diff to current
2014-05-01	Jim Procter	JAL-1492 JAL-1397 make AnnotatedCollectionI context...	blob \| commitdiff \| diff to current
2014-05-01	Jim Procter	JAL-1492 JAL-1397 JAL-643 JAL-969 pull up global and...	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
2013-10-11	Jim Procter	Merge branch 'JAL-1164_disorderforselection' into Relea...	blob \| commitdiff \| diff to current
2013-10-11	Jim Procter	JAL-1114 javadoc	blob \| commitdiff \| diff to current
2013-09-02	Jim Procter	JAL-1373 pass size of sequence set to consensus renderi...	blob \| commitdiff \| diff to current
2013-07-11	Jim Procter	JAL-1347 make it efficient to call getConsensus to...	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
2012-05-30	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
2011-10-11	jprocter	normalised logo rendering (JAL-958)	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
2011-08-17	jprocter	JAL-813 fix - check whether conservation is applied...	blob \| commitdiff \| diff to current
2011-04-21	jprocter	allow an existing alignment annotation row to be bound...	blob \| commitdiff \| diff to current
2010-12-17	jprocter	javadoc	blob \| commitdiff \| diff to current
2010-12-09	jprocter	javadoc and additional convenience method for JAL-716	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
2010-06-11	jprocter	patched for JAL-531 - only display full symbol distribu...	blob \| commitdiff \| diff to current
2010-06-06	jprocter	patch for JAL-542	blob \| commitdiff \| diff to current
2010-04-30	jprocter	jalview 2.5 release banner	blob \| commitdiff \| diff to current
2010-04-29	jprocter	make sure references are intact when group annotation...	blob \| commitdiff \| diff to current
2010-04-14	jprocter	profile visualizations are now logos	blob \| commitdiff \| diff to current
2010-03-30	jprocter	name update for group autoannotation and consensus...	blob \| commitdiff \| diff to current
2010-03-26	jprocter	comments	blob \| commitdiff \| diff to current
2009-08-21	jprocter	basic implementation of profile display and todos	blob \| commitdiff \| diff to current
2009-07-24	jprocter	sequence groups carry their own conservation and consen...	blob \| commitdiff \| diff to current
2009-06-19	jprocter	intersect did not intersect (used in selection listener)	blob \| commitdiff \| diff to current
2009-06-08	jprocter	apply gpl development license	blob \| commitdiff \| diff to current
2009-02-24	jprocter	bugfix for occasional nullpointer exceptions when selec...	blob \| commitdiff \| diff to current
2009-02-06	jprocter	showUnconserved group attribute	blob \| commitdiff \| diff to current
2008-12-19	jprocter	avoid null pointer exception when groupName is not set	blob \| commitdiff \| diff to current
2008-11-12	jprocter	jdk1.2 compatibility	blob \| commitdiff \| diff to current
2008-11-12	jprocter	new copy constructor and intersect method	blob \| commitdiff \| diff to current
2008-11-04	jprocter	beginning of implementation of new properties for hide...	blob \| commitdiff \| diff to current
2008-09-04	jprocter	merge from 2_4_Release branch	blob \| commitdiff \| diff to current
2008-07-18	jprocter	Sequence label colour stored for each sequence group	blob \| commitdiff \| diff to current
2008-02-22	jprocter	javadoc	blob \| commitdiff \| diff to current
2007-11-16	jprocter	javadoc	blob \| commitdiff \| diff to current
2007-05-10	jprocter	ensure that only annotation referenced in given alignme...	blob \| commitdiff \| diff to current
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