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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
2006-04-09	jprocter	doco writing.	commit \| commitdiff \| tree
2006-04-07	jprocter	added full keyset for cursorMode	commit \| commitdiff \| tree
2006-04-06	jprocter	added cursorMode feature page and rearranged keystrokes...	commit \| commitdiff \| tree
2006-04-06	jprocter	removed dross, added a safety check to buildextclients...	commit \| commitdiff \| tree
2006-03-20	jprocter	added example jnlp to memory settings help	commit \| commitdiff \| tree
2006-03-20	jprocter	added link to example jnlp file	commit \| commitdiff \| tree
2006-03-20	jprocter	example jnlp file for users to edit and save locally	commit \| commitdiff \| tree
2006-03-17	jprocter	jnet method description correction.	commit \| commitdiff \| tree
2006-03-16	jprocter	added description of alignment quality scores and separated	commit \| commitdiff \| tree
2006-03-14	jprocter	methods for searching DBRef lists	commit \| commitdiff \| tree
2006-03-13	jprocter	fixes bug 0013013 but reveals lack of a 'features retrieved...	commit \| commitdiff \| tree
2006-03-13	jprocter	bug fix for 0013013	commit \| commitdiff \| tree
2006-03-01	jprocter	fixed after refactoring of SequenceFeature[] seq.getSequence...	commit \| commitdiff \| tree
2006-03-01	jprocter	propagate SearchResult object use to MCView's highlighted...	commit \| commitdiff \| tree
2006-01-12	jprocter	PIR file IO now preserves and parses Modeller style...	commit \| commitdiff \| tree
2006-01-12	jprocter	DBRefEntry made for sequences retrieved from the PDB	commit \| commitdiff \| tree
2006-01-12	jprocter	<No Comment Entered>	commit \| commitdiff \| tree
2006-01-12	jprocter	ensured properties are loaded before loggers are initialised.	commit \| commitdiff \| tree
2006-01-11	jprocter	refactored Alignframe padGaps code to Alignment and...	commit \| commitdiff \| tree
2005-12-16	jprocter	Todo notes for feature issue: 0011711	commit \| commitdiff \| tree
2005-12-09	jprocter	added description of how PDB structures can be associated...	commit \| commitdiff \| tree
2005-12-09	jprocter	Rearranged 'What's new' and debugged/verified the sequence...	commit \| commitdiff \| tree
2005-12-09	jprocter	fixed pdbentry creation and multiple uniprot or pdb...	commit \| commitdiff \| tree
2005-12-08	jprocter	context dependent title for when called from desktop...	commit \| commitdiff \| tree
2005-12-08	jprocter	changed WhatsNew to a folder and modified preferences...	commit \| commitdiff \| tree
2005-12-08	jprocter	added some error checking and instruction dialogs	commit \| commitdiff \| tree
2005-12-08	jprocter	modified jnet parsing exception report string.	commit \| commitdiff \| tree
2005-12-08	jprocter	exception checks for (de)uniquify	commit \| commitdiff \| tree
2005-11-18	jprocter	Fixed bug http://dragonfly.compbio.dundee.ac.uk/mantis...	commit \| commitdiff \| tree
2005-11-18	jprocter	added 3 letter IUB codes for ambiguous residues/bases	commit \| commitdiff \| tree
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