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2007-07-25	jprocter	bugfix for vamsas demo and IO rearrangement for AMSAFile...	commit \| commitdiff \| tree
2007-07-13	jprocter	ignore random stuff to do with eclipse	commit \| commitdiff \| tree
2007-07-13	jprocter	preliminary IO classes - read javadoc for purpose	commit \| commitdiff \| tree
2007-07-13	jprocter	pickmanager on sequence and alignment position, vamsas...	commit \| commitdiff \| tree
2007-07-13	jprocter	refactor	commit \| commitdiff \| tree
2007-07-13	jprocter	new DBRef management and generalised source and entry...	commit \| commitdiff \| tree
2007-07-13	jprocter	more semantic groupings of dbs	commit \| commitdiff \| tree
2007-07-13	jprocter	debugged mappings and translated sequence recovery	commit \| commitdiff \| tree
2007-07-13	jprocter	preliminary states for pca distribution io	commit \| commitdiff \| tree
2007-07-13	jprocter	preliminary methods for detecting internal sequence...	commit \| commitdiff \| tree
2007-07-13	jprocter	bugfix	commit \| commitdiff \| tree
2007-07-13	jprocter	mapping bug fixes	commit \| commitdiff \| tree
2007-07-13	jprocter	basic idea for recognising that a feature is a coding...	commit \| commitdiff \| tree
2007-07-13	jprocter	bugfixes, partially working code for translation using...	commit \| commitdiff \| tree
2007-07-13	jprocter	comments for future viz/detection of internal sequence...	commit \| commitdiff \| tree
2007-07-13	jprocter	updated to iscb demo vamsas-client version	commit \| commitdiff \| tree
2007-07-13	jprocter	refactored form of vamsas document interaction code	commit \| commitdiff \| tree
2007-07-13	jprocter	methods for traversing database reference space	commit \| commitdiff \| tree
2007-07-13	jprocter	new search method for finding references like other...	commit \| commitdiff \| tree
2007-07-13	jprocter	bugfix and comments	commit \| commitdiff \| tree
2007-07-13	jprocter	moved to castor-1.1-cycle - a specially patched version...	commit \| commitdiff \| tree
2007-06-18	jprocter	ensure lines are drawn from first alignment column.	commit \| commitdiff \| tree
2007-06-18	jprocter	1.1 methods	commit \| commitdiff \| tree
2007-06-17	jprocter	vamsas-client-1.2 schema (mappings and Treenodes) and...	commit \| commitdiff \| tree
2007-06-17	jprocter	vamsas mouseOvers	commit \| commitdiff \| tree
2007-06-17	jprocter	enable mouseover between DNA coding regions and translated...	commit \| commitdiff \| tree
2007-06-17	jprocter	enable mouseover between DNA coding regions and translated...	commit \| commitdiff \| tree
2007-06-17	jprocter	fix aligned DNA codon translation bug(s) and generate...	commit \| commitdiff \| tree
2007-06-17	jprocter	recovery of identical dataset sequence object on undo...	commit \| commitdiff \| tree
2007-06-17	jprocter	AlignedCodonFrame holds mapping information between...	commit \| commitdiff \| tree
2007-06-17	jprocter	fix modeller generated PDB file reading bug (missing...	commit \| commitdiff \| tree
2007-06-17	jprocter	JnetFIle is a readable format	commit \| commitdiff \| tree
2007-06-17	jprocter	score only annotation IO	commit \| commitdiff \| tree
2007-06-17	jprocter	mouseOver highlighting and broadcasting efficiency	commit \| commitdiff \| tree
2007-06-17	jprocter	thread safety during repaint	commit \| commitdiff \| tree
2007-06-17	jprocter	null pointer exception fix	commit \| commitdiff \| tree
2007-06-17	jprocter	searchresult highlighting on common dataset or specific...	commit \| commitdiff \| tree
2007-06-17	jprocter	correct construction of new dataset sequence when residues...	commit \| commitdiff \| tree
2007-06-17	jprocter	javadoc	commit \| commitdiff \| tree
2007-06-04	jprocter	fix for 'RF' annotation tags and ensured parser is...	commit \| commitdiff \| tree
2007-05-28	jprocter	prototype DBRef and Feature Type semantics (for annotating...	commit \| commitdiff \| tree
2007-05-28	jprocter	moved castor-mapping.xsd to schemas	commit \| commitdiff \| tree
2007-05-28	jprocter	jalview source development documentation	commit \| commitdiff \| tree
2007-05-28	jprocter	fix compact annotation array routine	commit \| commitdiff \| tree
2007-05-28	jprocter	castor mapping file schema (for mappings in resources...	commit \| commitdiff \| tree
2007-05-28	jprocter	mapping file change for castor-1.1 upgrade	commit \| commitdiff \| tree
2007-05-28	jprocter	castor mapping unmarshalling logging	commit \| commitdiff \| tree
2007-05-28	jprocter	loglevel property constants and castor validation logger...	commit \| commitdiff \| tree
2007-05-24	jprocter	castor-1.1 classes (descriptors moved to subpackage)	commit \| commitdiff \| tree
2007-05-24	jprocter	castor-1.1 compatible classes from ant task	commit \| commitdiff \| tree
2007-05-24	jprocter	jalview 2.0 XML schema versions for backwards compatibility...	commit \| commitdiff \| tree
2007-05-24	jprocter	New file for /homes/www-jalview	commit \| commitdiff \| tree
2007-05-22	jprocter	fixed jalview 2.3 bug where gapped aligned codons were...	commit \| commitdiff \| tree
2007-05-22	jprocter	1.4 version of vamsas-client	commit \| commitdiff \| tree
2007-05-22	jprocter	refactored document objects and bugfix on jvdataset...	commit \| commitdiff \| tree
2007-05-21	jprocter	vamsas svn 14.55 May 21	commit \| commitdiff \| tree
2007-05-18	jprocter	fixed getObject(VorbaId) lookup in vamsas-client	commit \| commitdiff \| tree
2007-05-18	jprocter	update to and from document (and remove deprecated...	commit \| commitdiff \| tree
2007-05-18	jprocter	removed uneccessary vamsasLoad commented out.	commit \| commitdiff \| tree
2007-05-17	jprocter	refining - still debugging.	commit \| commitdiff \| tree
2007-05-17	jprocter	updated source generator properties for castor-1.1	commit \| commitdiff \| tree
2007-05-17	jprocter	use of proper vamsas client API by Jalview	commit \| commitdiff \| tree
2007-05-17	jprocter	modified castor-1.1 library and refactored uk.ac.vamsas	commit \| commitdiff \| tree
2007-05-10	jprocter	apparent bug in JpredFile parser where annotation was...	commit \| commitdiff \| tree
2007-05-10	jprocter	ensure that only annotation referenced in given alignment...	commit \| commitdiff \| tree
2007-05-10	jprocter	documentation	commit \| commitdiff \| tree
2007-05-10	jprocter	bugfix on copy only referenced annotation in copy constructor	commit \| commitdiff \| tree
2007-05-10	jprocter	fixed array index out of bounds when not removing alignment...	commit \| commitdiff \| tree
2007-05-09	jprocter	main method for running from command line and better...	commit \| commitdiff \| tree
2007-05-09	jprocter	reword jmol state storage	commit \| commitdiff \| tree
2007-05-09	jprocter	image size	commit \| commitdiff \| tree
2007-05-09	jprocter	new binary image	commit \| commitdiff \| tree
2007-05-08	jprocter	removed cdna coding region 'new feature'	commit \| commitdiff \| tree
2007-05-08	jprocter	embl mapping and das feature retrieval	commit \| commitdiff \| tree
2007-05-08	jprocter	optimise order	commit \| commitdiff \| tree
2007-05-08	jprocter	multiple view pdb view association	commit \| commitdiff \| tree
2007-05-08	jprocter	formatting and wording	commit \| commitdiff \| tree
2007-05-08	jprocter	grammar, clarity and typos	commit \| commitdiff \| tree
2007-05-08	jprocter	typo	commit \| commitdiff \| tree
2007-05-08	jprocter	formatting	commit \| commitdiff \| tree
2007-05-08	jprocter	page setup entry	commit \| commitdiff \| tree
2007-05-08	jprocter	dialog box menu item naming	commit \| commitdiff \| tree
2007-05-08	jprocter	correct menu entry names and typos	commit \| commitdiff \| tree
2007-05-08	jprocter	PID distance measure and finishing sentence.	commit \| commitdiff \| tree
2007-05-08	jprocter	sort by score	commit \| commitdiff \| tree
2007-05-08	jprocter	rightalign and italic ids docs	commit \| commitdiff \| tree
2007-05-08	jprocter	added jmol documentation	commit \| commitdiff \| tree
2007-05-02	jprocter	feature locations are retrieved by associated accession...	commit \| commitdiff \| tree
2007-05-02	jprocter	feature locations are retrieved by associated accession...	commit \| commitdiff \| tree
2007-05-02	jprocter	public debug report log message to gather any cases...	commit \| commitdiff \| tree
2007-05-02	jprocter	fixed getIntervals bug to ensure it returns range from...	commit \| commitdiff \| tree
2007-05-02	jprocter	documentation and proxy call to util.MapList.getToWord...	commit \| commitdiff \| tree
2007-05-02	jprocter	extractScores menu item disabled for release	commit \| commitdiff \| tree
2007-05-02	jprocter	only return non-empty subsequences when getting selection...	commit \| commitdiff \| tree
2007-05-02	jprocter	undo stackempty error fix, refactored do and undo(...	commit \| commitdiff \| tree
2007-05-02	jprocter	refactored do and undo() method to take array of alignments...	commit \| commitdiff \| tree
2007-05-02	jprocter	copy only the sequence associated alignment annotation...	commit \| commitdiff \| tree
2007-05-02	jprocter	subsequence bound checks and constructor for selectively...	commit \| commitdiff \| tree
2007-05-02	jprocter	return flag indicating if annotations were actually...	commit \| commitdiff \| tree
2007-05-02	jprocter	checks for negative start column in restrict	commit \| commitdiff \| tree
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