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[jalview.git] / src / jalview / gui / AlignViewport.java

2014-10-31	gmungoc	JAL-1152 menu tweaks plus new option to put Autocalc...	blob \| commitdiff \| diff to current
2014-10-30	gmungoc	JAL-1152 with sticky annotation sort order that updates...	blob \| commitdiff \| diff to current
2014-08-08	j.procter@dundee...	JAL-1483 move show sequence feature and sequence featur...	blob \| commitdiff \| diff to current
2014-08-08	j.procter@dundee...	JAL-1483 model and api for feature display list on...	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
2014-02-03	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
2013-10-07	Jim Procter	JAL-1385 JAL-535 refactor sequence colour settings...	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
2012-09-24	jprocter	formatting	blob \| commitdiff \| diff to current
2012-09-05	jprocter	JAL-976 fix AACon name typo in source and GUI	blob \| commitdiff \| diff to current
2012-08-07	jprocter	Debug message associated with TODO for JAL-1136 - re...	blob \| commitdiff \| diff to current
2012-07-08	jprocter	JAL-976 - storing service parameters on the view model	blob \| commitdiff \| diff to current
2012-06-19	jprocter	JAL-975 - bespoke AACons settings object to save curren...	blob \| commitdiff \| diff to current
2012-05-30	jprocter	JAL-969 - refactor colourscheme machinery from GUI...	blob \| commitdiff \| diff to current
2012-05-30	jprocter	JAL-1114 - refactor methods handling Vectors and Hashta...	blob \| commitdiff \| diff to current
2011-10-28	jprocter	JAL-969 - refactor initialisation of automatic annotati...	blob \| commitdiff \| diff to current
2011-10-27	jprocter	(JAL-969) refactored alignmentViewport base class to...	blob \| commitdiff \| diff to current
2011-10-21	jprocter	Refactored alignment viewport to use common base, exten...	blob \| commitdiff \| diff to current
2011-10-14	jprocter	(JAL-958) - normalised sequence logo for applet	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
2011-10-04	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
2011-08-10	janengelhardt	JAL-885; Structure conservation row is just added if...	blob \| commitdiff \| diff to current
2011-08-08	janengelhardt	JAL-891; structure logo is adapted to two char's; Missi...	blob \| commitdiff \| diff to current
2011-08-08	janengelhardt	JAL-891; sequence logos are available on structure...	blob \| commitdiff \| diff to current
2011-07-31	janengelhardt	JAL-885; StructureConservation row is displayed at...	blob \| commitdiff \| diff to current
2011-07-29	janengelhardt	JAL-885; Implementation of StructureFrequency.java...	blob \| commitdiff \| diff to current
2011-07-09	jprocter	refactored from PopupMenu (for JAL-860)	blob \| commitdiff \| diff to current
2011-05-17	jprocter	refactor to allow distinct StructureSelectionManager...	blob \| commitdiff \| diff to current
2011-02-18	jprocter	JAL-574	blob \| commitdiff \| diff to current
2011-02-04	jprocter	javadoc	blob \| commitdiff \| diff to current
2011-01-18	jprocter	refactored VamsasListener to allow the source of the...	blob \| commitdiff \| diff to current
2010-12-09	jprocter	refactored and added methods for getting richer Alignme...	blob \| commitdiff \| diff to current
2010-11-12	jprocter	patch for JAL-699 so conservation/consensus threads...	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
2010-08-20	jprocter	avoid race condition by setting sequence logo flag...	blob \| commitdiff \| diff to current
2010-06-11	jprocter	patched for JAL-531 - only display full symbol distribu...	blob \| commitdiff \| diff to current
2010-06-08	jprocter	followSelections flag now set via user preferences...	blob \| commitdiff \| diff to current
2010-04-30	jprocter	jalview 2.5 release banner	blob \| commitdiff \| diff to current
2010-04-29	jprocter	new selection manipulation method	blob \| commitdiff \| diff to current
2010-04-14	jprocter	profile visualizations are now logos	blob \| commitdiff \| diff to current
2010-04-05	jprocter	javadoc	blob \| commitdiff \| diff to current
2010-03-30	jprocter	group autoannotation and consensus display settings	blob \| commitdiff \| diff to current
2009-10-14	jprocter	quick fix for nullpointer in column selection when...	blob \| commitdiff \| diff to current
2009-08-21	jprocter	viewport setting for displaying sequence logos	blob \| commitdiff \| diff to current
2009-07-24	jprocter	refactored conservation thread, added showgroupannotati...	blob \| commitdiff \| diff to current
2009-06-08	jprocter	apply gpl development license	blob \| commitdiff \| diff to current
2009-03-17	jprocter	sortbytree view setting and action added - setting...	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 view and group setting	blob \| commitdiff \| diff to current
2009-01-09	jprocter	hack to completely disable calculation of consensus...	blob \| commitdiff \| diff to current
2008-12-19	jprocter	new sort by length method, justify edit menu entries...	blob \| commitdiff \| diff to current
2008-11-12	jprocter	selection sending and receiving, autoscrolling to highl...	blob \| commitdiff \| diff to current
2008-09-08	jprocter	view settings in view submenu and user preferences...	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
2008-04-21	jprocter	added centre annotation labels menu entry (and commente...	blob \| commitdiff \| diff to current
2007-10-31	jprocter	nullpointer bug fix on consensus thread	blob \| commitdiff \| diff to current
2007-10-04	jprocter	refactored invertColumnSelection as an object method	blob \| commitdiff \| diff to current
2007-09-25	jprocter	primitive methods for getting current undo/redo state...	blob \| commitdiff \| diff to current
2007-06-17	jprocter	enable mouseover between DNA coding regions and transla...	blob \| commitdiff \| diff to current
2007-05-03	amwaterhouse	optimize repaints	blob \| commitdiff \| diff to current
2007-05-02	jprocter	copy only the sequence associated alignment annotation...	blob \| commitdiff \| diff to current
2007-04-23	jprocter	distinct methods for getting references to selected...	blob \| commitdiff \| diff to current
2007-04-18	amwaterhouse	hastext = false	blob \| commitdiff \| diff to current
2007-04-18	amwaterhouse	Quality does not have text	blob \| commitdiff \| diff to current
2007-03-19	jprocter	convenience method to get visible selected region.	blob \| commitdiff \| diff to current
2007-02-27	amwaterhouse	Use paintAlignment	blob \| commitdiff \| diff to current
2007-02-07	amwaterhouse	Formatting	blob \| commitdiff \| diff to current
2007-01-29	amwaterhouse	ID_ITALICS option in preferences	blob \| commitdiff \| diff to current
2007-01-24	amwaterhouse	Conservation etc have autoCalculated flag set true	blob \| commitdiff \| diff to current
2007-01-23	amwaterhouse	Hidden representatives moved from sequence to viewport	blob \| commitdiff \| diff to current
2006-12-05	amwaterhouse	Sequence is char []	blob \| commitdiff \| diff to current
2006-11-24	amwaterhouse	Invert col sel with hidden cols bug fixed	blob \| commitdiff \| diff to current
2006-11-21	amwaterhouse	RightAlign ids from prefs	blob \| commitdiff \| diff to current
2006-11-15	amwaterhouse	right align ids	blob \| commitdiff \| diff to current
2006-11-13	amwaterhouse	sequence colours and text colours added	blob \| commitdiff \| diff to current
2006-11-07	amwaterhouse	Tidy up group size after alignmentChanged	blob \| commitdiff \| diff to current
2006-11-02	amwaterhouse	History is per viewport	blob \| commitdiff \| diff to current
2006-10-30	amwaterhouse	conservation lock	blob \| commitdiff \| diff to current
2006-10-27	amwaterhouse	Remove consensus annotation if out of memory	blob \| commitdiff \| diff to current
2006-10-27	amwaterhouse	updatingConsensus, updatingConservation is static ...	blob \| commitdiff \| diff to current
2006-10-27	amwaterhouse	Reset colour schemes and alignmentChanged moved to...	blob \| commitdiff \| diff to current
2006-10-26	amwaterhouse	showConservation, quality, identity not used	blob \| commitdiff \| diff to current
2006-10-25	amwaterhouse	Return if negative width, ie alignment deleted	blob \| commitdiff \| diff to current
2006-10-18	amwaterhouse	set conserve and quality null if outofmemory	blob \| commitdiff \| diff to current
2006-10-12	amwaterhouse	showQuality may be updated during archive file load	blob \| commitdiff \| diff to current
2006-10-10	amwaterhouse	Calculate alWidth earlier	blob \| commitdiff \| diff to current
2006-10-10	amwaterhouse	Must repaint whole alignPanel	blob \| commitdiff \| diff to current
2006-10-10	amwaterhouse	Consensus and conservation updated in threads	blob \| commitdiff \| diff to current
2006-10-09	jprocter	set firstColumn property for an alignmentView object.	blob \| commitdiff \| diff to current
2006-10-06	amwaterhouse	AAFrequency optimized	blob \| commitdiff \| diff to current
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