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2007-05-07	amwaterhouse	Use id hash to add pdb mappings back to alignment	commit \| commitdiff \| tree
2007-05-07	amwaterhouse	tIndex prevented deletion of last annotation	commit \| commitdiff \| tree
2007-05-07	amwaterhouse	Dont use gold colouring for highlight	commit \| commitdiff \| tree
2007-05-07	amwaterhouse	Use PDB id for grouping mappings	commit \| commitdiff \| tree
2007-05-07	amwaterhouse	PDBViewer available if necessary	commit \| commitdiff \| tree
2007-05-04	amwaterhouse	Check bounds of loaded comp	commit \| commitdiff \| tree
2007-05-04	amwaterhouse	remove system.out	commit \| commitdiff \| tree
2007-05-04	amwaterhouse	added	commit \| commitdiff \| tree
2007-05-04	amwaterhouse	Add dbrefs before zero length features	commit \| commitdiff \| tree
2007-05-04	amwaterhouse	lastCommand check	commit \| commitdiff \| tree
2007-05-04	amwaterhouse	Rename AppJMol to AppJmol - also AppJmol works with...	commit \| commitdiff \| tree
2007-05-04	amwaterhouse	Renamed to AppJmol	commit \| commitdiff \| tree
2007-05-04	amwaterhouse	New example file for version 2.3	commit \| commitdiff \| tree
2007-05-04	amwaterhouse	New example file for version 2.3	commit \| commitdiff \| tree
2007-05-04	amwaterhouse	Splash screen is not added using normal method, prevents...	commit \| commitdiff \| tree
2007-05-04	amwaterhouse	Annotations do not extend when full alignment is adjusted	commit \| commitdiff \| tree
2007-05-03	amwaterhouse	pdb id toUpperCase	commit \| commitdiff \| tree
2007-05-03	amwaterhouse	optimize repaints	commit \| commitdiff \| tree
2007-05-03	amwaterhouse	remove system.out	commit \| commitdiff \| tree
2007-05-02	amwaterhouse	Allow expansion of textarea for many sequence input	commit \| commitdiff \| tree
2007-05-02	amwaterhouse	AMSA input set padgaps true	commit \| commitdiff \| tree
2007-05-02	amwaterhouse	convert space to gapchar	commit \| commitdiff \| tree
2007-05-02	amwaterhouse	Padgaps is false by default	commit \| commitdiff \| tree
2007-05-01	amwaterhouse	setVisible flag sent to EditNameDialog	commit \| commitdiff \| tree
2007-05-01	amwaterhouse	Pad gaps method	commit \| commitdiff \| tree
2007-05-01	amwaterhouse	Make sure annots are alignment width	commit \| commitdiff \| tree
2007-05-01	amwaterhouse	use jalviewLite to addFrame	commit \| commitdiff \| tree
2007-05-01	amwaterhouse	remove system.out	commit \| commitdiff \| tree
2007-05-01	amwaterhouse	set chains available	commit \| commitdiff \| tree
2007-05-01	amwaterhouse	Multiple views/hidden region/undo out of index bug	commit \| commitdiff \| tree
2007-05-01	amwaterhouse	Can specify PDB chain to map sequence to - only used...	commit \| commitdiff \| tree
2007-05-01	amwaterhouse	Save seqset properties	commit \| commitdiff \| tree
2007-05-01	amwaterhouse	Seqset properties saved	commit \| commitdiff \| tree
2007-04-30	amwaterhouse	setVisible replaces show	commit \| commitdiff \| tree
2007-04-30	amwaterhouse	Version 11.0.2	commit \| commitdiff \| tree
2007-04-30	amwaterhouse	REmoved	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	remove excessive painting	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	REmove excessive painting	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	Repaint after feature added	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	Prevent err when editing and overview drawing	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	FeatureRenderer mixups fixed	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	Remove system.out AppletPDBViewer.java	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	Check pdbid size >0	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	Trouble with featureRenderers fixed	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	Move repaint in thread	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	Put alignmentProperties in scrollpane	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	Check feature group is visible for mouse over features	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	remove System.out	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	Add param to Jmol path	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	padGaps moved	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	Make sure mainContainer and owner are not null	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	Must check that featureGroup is visible for mouse over...	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	amendFeatures	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	paintAlignment(true)	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	Place new feature on top of existing features	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	Make sure sequence is in mouse over alignment	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	Amend Features	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	ColourByStructure not ready yet	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	aligned boxes	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	ThresholdIsMin available in applet	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	Set black if colour null	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	Alignment properties available	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	hide the initial window after selection made	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	one colour flag in annotation export	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	Annotation gradient will use direct colours if no graph...	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	Allow threshold to be min/max	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	hide annotation colouring options	commit \| commitdiff \| tree
2007-04-27	amwaterhouse	Dont colour labels	commit \| commitdiff \| tree
2007-04-26	amwaterhouse	check for null ss character	commit \| commitdiff \| tree
2007-04-26	amwaterhouse	colourText = false	commit \| commitdiff \| tree
2007-04-26	amwaterhouse	Edit seqs	commit \| commitdiff \| tree
2007-04-26	amwaterhouse	remove should be removeElement	commit \| commitdiff \| tree
2007-04-26	amwaterhouse	Alignment Properties required for annotation file	commit \| commitdiff \| tree
2007-04-25	amwaterhouse	properties + colours	commit \| commitdiff \| tree
2007-04-25	amwaterhouse	Show scores	commit \| commitdiff \| tree
2007-04-25	amwaterhouse	Export annotations with properties	commit \| commitdiff \| tree
2007-04-25	amwaterhouse	View Properties	commit \| commitdiff \| tree
2007-04-25	amwaterhouse	fix recent file type bug	commit \| commitdiff \| tree
2007-04-25	amwaterhouse	alignmentProperties added	commit \| commitdiff \| tree
2007-04-23	amwaterhouse	getColour method added	commit \| commitdiff \| tree
2007-04-23	amwaterhouse	Check for null displayCharacters	commit \| commitdiff \| tree
2007-04-23	amwaterhouse	Dbref fetcher takes sequences, not alignment	commit \| commitdiff \| tree
2007-04-23	amwaterhouse	getColour added to structures	commit \| commitdiff \| tree
2007-04-23	amwaterhouse	Test out new arrangement	commit \| commitdiff \| tree
2007-04-23	amwaterhouse	Get colour from structure added	commit \| commitdiff \| tree
2007-04-23	amwaterhouse	check dispalyChar is not null	commit \| commitdiff \| tree
2007-04-23	amwaterhouse	Check displayChar is not null	commit \| commitdiff \| tree
2007-04-23	amwaterhouse	Colour is null	commit \| commitdiff \| tree
2007-04-23	amwaterhouse	remove seqref annotations	commit \| commitdiff \| tree
2007-04-23	amwaterhouse	remove alignmentAnnotation added	commit \| commitdiff \| tree
2007-04-23	amwaterhouse	Only fetch refs for seelcted sequences	commit \| commitdiff \| tree
2007-04-19	amwaterhouse	REPLACE added to edit command	commit \| commitdiff \| tree
2007-04-19	amwaterhouse	Only setDropTarget if Desktop is not null	commit \| commitdiff \| tree
2007-04-18	amwaterhouse	Validate range for all annotations	commit \| commitdiff \| tree
2007-04-18	amwaterhouse	Redundant code commented out	commit \| commitdiff \| tree
2007-04-18	amwaterhouse	hastext = false	commit \| commitdiff \| tree
2007-04-18	amwaterhouse	dont set seqref null if index incorrect	commit \| commitdiff \| tree
2007-04-18	amwaterhouse	featureGroups not null	commit \| commitdiff \| tree
2007-04-18	amwaterhouse	Pad gaps when annotation editing	commit \| commitdiff \| tree
2007-04-18	amwaterhouse	quality has text false	commit \| commitdiff \| tree
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