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

2005-12-07	jprocter	Submissions for secondary structure prediction are... vamsasDemo	blob \| commitdiff
2005-12-06	amwaterhouse	Clear highlighted residues	blob \| commitdiff \| diff to current
2005-12-06	amwaterhouse	Paste this makes new sequence	blob \| commitdiff \| diff to current
2005-12-05	amwaterhouse	Save Feature Rendering	blob \| commitdiff \| diff to current
2005-12-02	amwaterhouse	Remove comments	blob \| commitdiff \| diff to current
2005-11-29	amwaterhouse	Features added removed from alignment	blob \| commitdiff \| diff to current
2005-11-24	amwaterhouse	Don't parse input id, leave it as it is	blob \| commitdiff \| diff to current
2005-11-17	amwaterhouse	Hidden tabs and vamsas refs for beta release	blob \| commitdiff \| diff to current
2005-11-17	amwaterhouse	Hide Tab settings for build	blob \| commitdiff \| diff to current
2005-11-11	amwaterhouse	SequenceFetcher new class	blob \| commitdiff \| diff to current
2005-11-10	amwaterhouse	AlignSeq takes printstream as arg	blob \| commitdiff \| diff to current
2005-11-08	amwaterhouse	getVersion added for Castor mapping	blob \| commitdiff \| diff to current
2005-11-04	amwaterhouse	Use visible id for sorting	blob \| commitdiff \| diff to current
2005-11-01	jprocter	dataset reference propagated to new MsaWS alignment.	blob \| commitdiff \| diff to current
2005-11-01	amwaterhouse	Adjust seq limits for visual and dataset sequences	blob \| commitdiff \| diff to current
2005-10-31	amwaterhouse	dbPrefix and jvsuffix added	blob \| commitdiff \| diff to current
2005-10-27	amwaterhouse	Allow old style groups file	blob \| commitdiff \| diff to current
2005-10-26	amwaterhouse	Groups file is now feature file	blob \| commitdiff \| diff to current
2005-10-26	amwaterhouse	vamsasDemo new branch	blob \| commitdiff \| diff to current
2005-10-03	amwaterhouse	Remove development code	blob \| commitdiff \| diff to current
2005-09-30	amwaterhouse	Remove redundancy in Eclipse	blob \| commitdiff \| diff to current
2005-09-22	amwaterhouse	Create instance of FormatAdapter	blob \| commitdiff \| diff to current
2005-09-22	amwaterhouse	If Mac user hasnt selected file format, give warning	blob \| commitdiff \| diff to current
2005-09-21	amwaterhouse	Sequences must be aligned before PCA	blob \| commitdiff \| diff to current
2005-09-20	amwaterhouse	PCAPanel just requires viewport	blob \| commitdiff \| diff to current
2005-09-19	amwaterhouse	Dont add ServiceListeners if desktop is null	blob \| commitdiff \| diff to current
2005-09-15	amwaterhouse	remove system.out	blob \| commitdiff \| diff to current
2005-09-14	amwaterhouse	Copy and paste uses FASTA format	blob \| commitdiff \| diff to current
2005-09-14	amwaterhouse	PCA is in outofmemory try-catch	blob \| commitdiff \| diff to current
2005-09-12	amwaterhouse	Remove gaps in regions, not char by char	blob \| commitdiff \| diff to current
2005-09-12	amwaterhouse	Update overview in alignmentChanged	blob \| commitdiff \| diff to current
2005-09-08	amwaterhouse	Move tree property change to treePanel	blob \| commitdiff \| diff to current
2005-09-08	amwaterhouse	If no consensus, disable certain colour options	blob \| commitdiff \| diff to current
2005-09-01	amwaterhouse	firePropertyChange if sequences deleted	blob \| commitdiff \| diff to current
2005-09-01	amwaterhouse	Use propertyListener for alignment edits	blob \| commitdiff \| diff to current
2005-08-30	amwaterhouse	Update colours after remove left, cut, paste	blob \| commitdiff \| diff to current
2005-08-29	amwaterhouse	Reset all colour schemes after gaps removed	blob \| commitdiff \| diff to current
2005-08-29	amwaterhouse	Keep startRes the same after removing columns	blob \| commitdiff \| diff to current
2005-08-29	amwaterhouse	Reset ClustalX after removing gaps	blob \| commitdiff \| diff to current
2005-08-26	amwaterhouse	When saving, use print instead of println	blob \| commitdiff \| diff to current
2005-08-23	amwaterhouse	Dont make new frame reference in Buildwebservicemenu	blob \| commitdiff \| diff to current
2005-08-23	amwaterhouse	Set size and location of frame before visible	blob \| commitdiff \| diff to current
2005-08-22	amwaterhouse	Check for null colour	blob \| commitdiff \| diff to current
2005-08-22	amwaterhouse	Conservation colour scheme is no more	blob \| commitdiff \| diff to current
2005-08-18	amwaterhouse	Add name and mouse listener to new user colour menuitems	blob \| commitdiff \| diff to current
2005-08-18	amwaterhouse	Blosum62 PID and conservation bug fixed	blob \| commitdiff \| diff to current
2005-08-18	jprocter	GUI typo	blob \| commitdiff \| diff to current
2005-08-17	jprocter	Gui Modifications for Service Discovery.	blob \| commitdiff \| diff to current
2005-08-17	amwaterhouse	updateUserColourMenu	blob \| commitdiff \| diff to current
2005-08-15	amwaterhouse	IgnoreGapsConsensus	blob \| commitdiff \| diff to current
2005-07-29	amwaterhouse	Correct label for end res in copy	blob \| commitdiff \| diff to current
2005-07-18	amwaterhouse	Copy seq ordering bug fixed	blob \| commitdiff \| diff to current
2005-07-11	amwaterhouse	Must check if group.sequences are null in remove gaps	blob \| commitdiff \| diff to current
2005-07-11	amwaterhouse	check groupsize is non zero	blob \| commitdiff \| diff to current
2005-07-07	amwaterhouse	Remove all gaps must check jSize	blob \| commitdiff \| diff to current
2005-06-30	amwaterhouse	Formatting changes	blob \| commitdiff \| diff to current
2005-06-16	amwaterhouse	Sort Groups modified	blob \| commitdiff \| diff to current
2005-06-16	amwaterhouse	remove gaps applies to selected area	blob \| commitdiff \| diff to current
2005-06-14	jprocter	pad-1 gaps fixed.	blob \| commitdiff \| diff to current
2005-06-14	amwaterhouse	Deselect sets annotationPanel activeres null	blob \| commitdiff \| diff to current
2005-06-14	amwaterhouse	PaintRefresher must be sent alignment	blob \| commitdiff \| diff to current
2005-06-14	amwaterhouse	Returns TreePanel when opening Newick	blob \| commitdiff \| diff to current
2005-06-08	amwaterhouse	Recalc accelerated	blob \| commitdiff \| diff to current
2005-06-08	amwaterhouse	Formatted source	blob \| commitdiff \| diff to current
2005-06-08	amwaterhouse	GPL license added	blob \| commitdiff \| diff to current
2005-06-03	jprocter	Reinstated 'create tree from selected region only'...	blob \| commitdiff \| diff to current
2005-06-02	amwaterhouse	Name of xml file changed	blob \| commitdiff \| diff to current
2005-05-30	jprocter	Added clustalW 'realignment' (primitive)	blob \| commitdiff \| diff to current
2005-05-30	jprocter	added default ClustalWS or MuscleWS to remove gaps.	blob \| commitdiff \| diff to current
2005-05-30	jprocter	fixed stacktrace potential for pairwise alignment action.	blob \| commitdiff \| diff to current
2005-05-27	jprocter	right ordering for RedundancyPanel constructor	blob \| commitdiff \| diff to current
2005-05-27	jprocter	recovered changes from v 1.84	blob \| commitdiff \| diff to current
2005-05-27	amwaterhouse	New cut and paste	blob \| commitdiff \| diff to current
2005-05-26	jprocter	fixed redundancy Undo and allowed it to work on UNALIGN...	blob \| commitdiff \| diff to current
2005-05-26	jprocter	bug fix in jpred client. TreeViewer display state and...	blob \| commitdiff \| diff to current
2005-05-25	amwaterhouse	usercolours changed	blob \| commitdiff \| diff to current
2005-05-25	jprocter	tidied up system.out messages and moved many to stderr.	blob \| commitdiff \| diff to current
2005-05-24	jprocter	Added more firePropertyChange calls - mainly for sequen...	blob \| commitdiff \| diff to current
2005-05-24	jprocter	added PropertyChangeListeners for alignviewport.alignme...	blob \| commitdiff \| diff to current
2005-05-24	amwaterhouse	setDefaultFileFormat	blob \| commitdiff \| diff to current
2005-05-23	jprocter	Added PadGaps and made treeSortMenu dynamic (it gets...	blob \| commitdiff \| diff to current
2005-05-23	amwaterhouse	new savestate method	blob \| commitdiff \| diff to current
2005-05-23	amwaterhouse	historyitem added	blob \| commitdiff \| diff to current
2005-05-22	jprocter	include MsaWS ordering but not perfect (undo destroys...	blob \| commitdiff \| diff to current
2005-05-22	jprocter	Added alignment ordering option to 'Sort by' and implem...	blob \| commitdiff \| diff to current
2005-05-20	amwaterhouse	copy order maintained	blob \| commitdiff \| diff to current
2005-05-20	amwaterhouse	Fasta FASTA	blob \| commitdiff \| diff to current
2005-05-19	amwaterhouse	loading/saving changes	blob \| commitdiff \| diff to current
2005-05-03	amwaterhouse	formatAdapter.formatSequences and maintain annotation...	blob \| commitdiff \| diff to current
2005-04-29	amwaterhouse	preferences moved to desktop	blob \| commitdiff \| diff to current
2005-04-28	amwaterhouse	Preferences panel added	blob \| commitdiff \| diff to current
2005-04-28	jprocter	added MuscleWS and did a bit more standardisation of...	blob \| commitdiff \| diff to current
2005-04-25	amwaterhouse	Overviewpanel allows for large alignments	blob \| commitdiff \| diff to current
2005-04-21	amwaterhouse	update conSlider when colour changes	blob \| commitdiff \| diff to current
2005-04-18	amwaterhouse	show sliders when first selecting conservation,PID	blob \| commitdiff \| diff to current
2005-04-16	amwaterhouse	check if colourscheme is null	blob \| commitdiff \| diff to current
2005-04-16	amwaterhouse	AlignPanel RefreshPanels put into paintComponent	blob \| commitdiff \| diff to current
2005-04-15	amwaterhouse	clustalx exception in colourchange	blob \| commitdiff \| diff to current
2005-04-15	amwaterhouse	PID and conservation colouring changes	blob \| commitdiff \| diff to current
2005-04-14	amwaterhouse	use webservice info to display web service state	blob \| commitdiff \| diff to current
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