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2006-10-24	jprocter	fixes bug reported by Christopher Tan (help@jalview...	commit \| commitdiff \| tree
2006-10-15	jprocter	fixed array out of bounds exception in copy constructor	commit \| commitdiff \| tree
2006-10-11	jprocter	fixes exception (array index out of bounds - due to...	commit \| commitdiff \| tree
2006-10-10	jprocter	refined id matching to pick the closest match (by length...	commit \| commitdiff \| tree
2006-10-10	jprocter	debug message bugfix on duplicate tree leaf names.	commit \| commitdiff \| tree
2006-10-10	jprocter	bugfix for dodgy trees which contain the same leafname...	commit \| commitdiff \| tree
2006-10-09	jprocter	fixed log4j complaints for vamsas logging (again)	commit \| commitdiff \| tree
2006-10-09	jprocter	fixed log4j complaints for vamsas logging.	commit \| commitdiff \| tree
2006-10-09	jprocter	excluded log4j properties.	commit \| commitdiff \| tree
2006-10-09	jprocter	java 1.4 compliant classes.	commit \| commitdiff \| tree
2006-10-09	jprocter	imported Vamsas bindings and alpha vamsas client code...	commit \| commitdiff \| tree
2006-10-09	jprocter	set firstColumn property for an alignmentView object.	commit \| commitdiff \| tree
2006-10-09	jprocter	fixed getCompactAlignment method to return proper cigarArray...	commit \| commitdiff \| tree
2006-10-06	jprocter	Added filter so that input to a JPred job is *solely...	commit \| commitdiff \| tree
2006-10-06	jprocter	javadoc	commit \| commitdiff \| tree
2006-10-06	jprocter	new getVisibleContigs method mirrors the getVisibleContigs...	commit \| commitdiff \| tree
2006-09-27	jprocter	fixed tree building exception when one residue or a...	commit \| commitdiff \| tree
2006-09-07	jprocter	added copy consensus sequence to consensus annotation...	commit \| commitdiff \| tree
2006-09-05	jprocter	getVisibleContigs() returns start and end positions...	commit \| commitdiff \| tree
2006-09-05	jprocter	javadoc on contigs	commit \| commitdiff \| tree
2006-08-22	jprocter	documentation - adding new Input data menu entries.	commit \| commitdiff \| tree
2006-08-22	jprocter	added note on column-separability	commit \| commitdiff \| tree
2006-08-22	jprocter	documentation	commit \| commitdiff \| tree
2006-08-22	jprocter	getSequenceStrings() bug fixed.	commit \| commitdiff \| tree
2006-08-22	jprocter	hidden region recovery in JPred and new hidden region...	commit \| commitdiff \| tree
2006-08-22	jprocter	off by one bug in hiden column unmarshalling	commit \| commitdiff \| tree
2006-08-21	jprocter	Refactored Jnet and added hidden columns support.	commit \| commitdiff \| tree
2006-08-21	jprocter	fixed undo-redo bug, hidden columns are moved with...	commit \| commitdiff \| tree
2006-08-21	jprocter	removeGaps method can record changes in alignment columns...	commit \| commitdiff \| tree
2006-08-21	jprocter	fix for truncation of sequence associated annotation...	commit \| commitdiff \| tree
2006-08-21	jprocter	added shiftList to record changes in alignment column...	commit \| commitdiff \| tree
2006-08-21	jprocter	remove gaps method from AlignFrame.remove_gaps_actionPerformed	commit \| commitdiff \| tree
2006-08-21	jprocter	inverse ShiftList and SequenceI.gapMap->ShiftList methods.	commit \| commitdiff \| tree
2006-08-21	jprocter	avoid null pointer exceptions	commit \| commitdiff \| tree
2006-08-20	jprocter	javadoc	commit \| commitdiff \| tree
2006-08-17	jprocter	moved visible sub-alignment extraction and update from...	commit \| commitdiff \| tree
2006-08-17	jprocter	javadoc	commit \| commitdiff \| tree
2006-08-15	jprocter	make annotation label font size follow alignment font...	commit \| commitdiff \| tree
2006-08-15	jprocter	first stage of adapting JNet client to hidden regions...	commit \| commitdiff \| tree
2006-08-15	jprocter	fixed alignment ordering name.	commit \| commitdiff \| tree
2006-08-15	jprocter	ensure that close widget is available for jobs that...	commit \| commitdiff \| tree
2006-08-14	jprocter	refactored to create generic polling thread and subjobs	commit \| commitdiff \| tree
2006-08-14	jprocter	function to indicate job has finished but no results...	commit \| commitdiff \| tree
2006-08-14	jprocter	multiple subjobs can be cancelled and gui only allows...	commit \| commitdiff \| tree
2006-08-14	jprocter	fixed off by one bug in end sequence from getSubSequence...	commit \| commitdiff \| tree
2006-08-14	jprocter	end<start for empty sequences in Sequence[] from SeqCigar[]	commit \| commitdiff \| tree
2006-08-14	jprocter	fixing residue clip bug in MsaWSThread and adding minimum...	commit \| commitdiff \| tree
2006-08-13	jprocter	fixed end-residue bug and subjob panel names bug	commit \| commitdiff \| tree
2006-08-11	jprocter	multiple web service jobs from visible blocks of an...	commit \| commitdiff \| tree
2006-08-09	jprocter	new SequenceI method for making a sub sequence from...	commit \| commitdiff \| tree
2006-08-09	jprocter	alignment from seqCigars will correctly mark deleted...	commit \| commitdiff \| tree
2006-08-09	jprocter	refactored hidden regions methods and made an AlignmentView...	commit \| commitdiff \| tree
2006-08-09	jprocter	fixed multiple shifts bug.	commit \| commitdiff \| tree
2006-08-08	jprocter	removed extraneous classes.	commit \| commitdiff \| tree
2006-08-08	jprocter	locally modified biojava-dasobert package is now org...	commit \| commitdiff \| tree
2006-08-07	jprocter	added commented out seqStrings comment.	commit \| commitdiff \| tree
2006-08-04	jprocter	recover original data for tree and pca as alignment...	commit \| commitdiff \| tree
2006-07-26	jprocter	accidental commit of a build	commit \| commitdiff \| tree
2006-07-26	jprocter	Ignore list created	commit \| commitdiff \| tree
2006-07-26	jprocter	Cigars for representing alignment view as used for...	commit \| commitdiff \| tree
2006-07-26	jprocter	CigarBase class and derivatives.	commit \| commitdiff \| tree
2006-07-26	jprocter	Implemented CIGAR representation of an Alignment view...	commit \| commitdiff \| tree
2006-07-26	jprocter	Compact Idiosyncratic Gapped Alignment Representation...	commit \| commitdiff \| tree
2006-07-24	jprocter	partly finished pods.	commit \| commitdiff \| tree
2006-07-21	jprocter	Item added to ignoreList	commit \| commitdiff \| tree
2006-07-21	jprocter	Item added to ignoreList	commit \| commitdiff \| tree
2006-07-21	jprocter	Ignore list created	commit \| commitdiff \| tree
2006-07-20	jprocter	annotation label font size change in applet.	commit \| commitdiff \| tree
2006-07-18	jprocter	use of GapChars	commit \| commitdiff \| tree
2006-06-08	jprocter	Introduced DbRefEntry to DasSourceCoordinateSystem...	commit \| commitdiff \| tree
2006-06-08	jprocter	DBRefEntry.source enum type	commit \| commitdiff \| tree
2006-06-08	jprocter	bugfixed and podded.	commit \| commitdiff \| tree
2006-06-08	jprocter	simplest conversion of gff to jalview annotation format...	commit \| commitdiff \| tree
2006-06-07	jprocter	broken link typo. (SEVENtwentyfour alert)	commit \| commitdiff \| tree
2006-05-18	jprocter	added future method comment	commit \| commitdiff \| tree
2006-05-17	jprocter	added the jnetfile parameter to specify a JNet concise...	commit \| commitdiff \| tree
2006-05-17	jprocter	added unofficial support for concise output parsing...	commit \| commitdiff \| tree
2006-05-17	jprocter	refactored code for creating JNet annotations	commit \| commitdiff \| tree
2006-05-17	jprocter	Refactored code for creating annotation objects from...	commit \| commitdiff \| tree
2006-05-16	jprocter	added popup warning when proxy settings must be configured.	commit \| commitdiff \| tree
2006-05-12	jprocter	rearranged discoverer to dynamically update on demand	commit \| commitdiff \| tree
2006-04-10	jprocter	load features/annotations typo.	commit \| commitdiff \| tree
2006-04-10	jprocter	added note about cursor mode disabling the popup menu.	commit \| commitdiff \| tree
2006-04-10	jprocter	typo and explanation for ignore gaps in consensus	commit \| commitdiff \| tree
2006-04-10	jprocter	reworded pad gaps	commit \| commitdiff \| tree
2006-04-10	jprocter	reworded pad gaps.	commit \| commitdiff \| tree
2006-04-10	jprocter	put modellerpir in correct place!	commit \| commitdiff \| tree
2006-04-10	jprocter	updated menus and rearranged seqfeatures (again)	commit \| commitdiff \| tree
2006-04-10	jprocter	fix links to complex html (that don't display) by quoting...	commit \| commitdiff \| tree
2006-04-10	jprocter	moved Modeller/PIR description to its own home.	commit \| commitdiff \| tree
2006-04-10	jprocter	moved modellerpir to io	commit \| commitdiff \| tree
2006-04-10	jprocter	describing the Modeller/PIR output.	commit \| commitdiff \| tree
2006-04-10	jprocter	Fixed table border and updated restrictions	commit \| commitdiff \| tree
2006-04-10	jprocter	added bit about modeller/pir	commit \| commitdiff \| tree
2006-04-10	jprocter	added annotationColouring to whats new and updated...	commit \| commitdiff \| tree
2006-04-10	jprocter	extended preamble and added new heading for user defined...	commit \| commitdiff \| tree
2006-04-10	jprocter	doco	commit \| commitdiff \| tree
2006-04-10	jprocter	doco changes.	commit \| commitdiff \| tree
2006-04-10	jprocter	added 2.08 application version dialog box.	commit \| commitdiff \| tree
2006-04-10	jprocter	feature settings dialog box for jalview 2.08 application	commit \| commitdiff \| tree
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