File: TODO

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mauve-aligner 2.4.0+4736-1
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DON'T USE THIS!!!!!  I'm only keeping this for updating changes or whatever.

CLOSED ISSUES
(DEFECT) Can't scroll at max zoom
	Resolution: added some code in SeqPanel.zoomAndMove for when move is less than 1 symbol.
(DEFECT) Printout of "doubleclick.net" when a double-click is detected.
	Resolution: Got rid of junk double-click handling code in RRSequencePanel	
(DEFECT) Errors printed when click to left or right of genome
	Resolution: Added exception-handling code to RearrangementPanel.alignView()
(FEATURE) file checks (missing, unreadable, wrong format) for loading genbank files
	Resolution: Added checks to FeaturePanel
(DEFECT) FeaturePanel displays at wrong zoom initially, then resizes.
	Resolution: Added hack to FeaturePanel.setBounds()	
(FEATURE) Validate length of Genbank sequence for target.
	Resolution: Added check at file-loading time.
(DEFECT) Reasonably fast-moving mouse causes clicks to be lost.
	Resolution: Greatly improved mouseover performance, by eliminating unnecessary repainting and using threading.
(USABILITY) How about a scrollbar instead of left-right arrows?
	Resolution: Not done, because it will take too many resources.	
(USABILITY) Extremely slow and memory-hungry when showing features at low magnification
	Resolution: Currently okay again, with changes to mouse-handling.
(DESIGN) Some panels might be getting unnecessarily repainted.
	Resolution: Reviewed calls to repaintSeqPanels(), a very expensive call, eliminated one.
(FEATURE) Show feature details for CDS, rRNA, tRNA and misc_RNA in popup window.
	Resolution: Added QualifierPanel
(DEFECT) Off by one in alignment file writing
	Resolution: fixed by Aaron.		
(DEFECT) FeaturePanel currently assumes genbank file will be one larger than sequence (interim fix for alignment file off by one problem).
	Resolution: fixed by Paul, after above fix.	
(DEFECT) NullPointerExceptions when dealing with .mauve and .mums files.
	Resolution: revised highlighting routine	
(DEFECT) No product qualifier for a feature causes java.util.NoSuchElementException for mouseovers.
	Resolution: Qualifier is checked for, and only location of feature shown if not present.
(FEATURE) Show feature symbols on single line.
	Resolution: Using biojava features to render on one line.	
(FEATURE) If RRSequencePanel double-clicked, do something like move the annotation browser window onto this section of sequence.
	Resolution: Apparently, this describes the feature popup.
(DEFECT) Rearrangement of .mums sequences fails
	Resolution: Pushed down fix for reordering / LCB problem.		
(USABILITY) Maybe restore variable-sized label for sequence
	Resolution: Eh, why bother?
(FEATURE) Update licensing to GPL.
	Replaced COPYING with the GPL text
(DEFECT) Text information in bottom toolbar doesn't go away when file is closed
	Added a clear() method to LCBStatusBar, call it when final RearrangementPanel is being closed
(DEFECT) ArrayIndexOutOfBounds exceptions when clicking on .mauve sequences after adjusting LCB weight
	References to LCBs weren't being properly updated in filterLCBs; now they are.
(DEFECT) When too many sequences need to fit in window need to be displayed, display punks out.
	Taken care of by adding scrolling.		
(USABILITY) Allow use of scrollbar for set of sequence panels.
	Added a scrollPane to mauveFrame.
(DEFECT) Moving LCB slider after rearranging sequences makes everything go to hell.
	Added call to updateLCBweight() after rearrangement, in LcbViewerModel.
(DEFECT) Selecting "LCB" color option when viewing MUMS format breaks display.
	Initialization of color_selector is now later, when model is known, and LCB is omitted.
(DEFECT) Slider use also breaks color picker when viewing .mauve files.
	Added reapplication of color scheme after updating LCB weight.
(DEFECT) Ruler shows the same number twice for different ticks at high magnification.
	Replaced home-grown ruler panel with Ruler from biojava.
(DEFECT) Printing output is very small.
	Replaced some printing code, added an x-scaling.
(USABILITY) Multi-threading viewer panels for usability during alignment
	Silly idea, ignored.	
(USABILITY) Ruler units float around too much, even take fractional values at high magnification
	Taken care of by replacement
(DEFECT) Output file name text (in AlignFrame.java) doesn't scroll right with long file names
	Changed TextArea (?) to TextField; this was probably just a typo.