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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
2007-05-01	jprocter	javadoc	commit \| commitdiff \| tree
2007-05-01	jprocter	removeAlignmentAnnotation only removes annotation objects...	commit \| commitdiff \| tree
2007-05-01	jprocter	sort-by-score works of sequence-annotation, not alignment...	commit \| commitdiff \| tree
2007-05-01	jprocter	2.3 what's new	commit \| commitdiff \| tree
2007-05-01	jprocter	preliminary EMBL and mapping documentation	commit \| commitdiff \| tree
2007-04-30	jprocter	'no sources selected' calls method on feature settings...	commit \| commitdiff \| tree
2007-04-30	jprocter	fixed deadlock	commit \| commitdiff \| tree
2007-04-30	jprocter	rebuild sort by scores menu when new annotation is...	commit \| commitdiff \| tree
2007-04-30	jprocter	pad should leave null annotations array null	commit \| commitdiff \| tree
2007-04-30	jprocter	convenient creation of 'score only' annotation.	commit \| commitdiff \| tree
2007-04-30	jprocter	parse alignment properties and add annotation rows...	commit \| commitdiff \| tree
2007-04-30	jprocter	alignment properties and embedded newick strings can...	commit \| commitdiff \| tree
2007-04-30	jprocter	dssp 7-state to three state lookup	commit \| commitdiff \| tree
2007-04-30	jprocter	javadoc	commit \| commitdiff \| tree
2007-04-27	jprocter	newlines in alignment properties converted to <br>	commit \| commitdiff \| tree
2007-04-27	jprocter	blc header lines inserted as 'comment' alignment property	commit \| commitdiff \| tree
2007-04-27	jprocter	parsers can generate alignment properties	commit \| commitdiff \| tree
2007-04-27	jprocter	getProperties returns nullk for no properties	commit \| commitdiff \| tree
2007-04-27	jprocter	documentation and getProperties method	commit \| commitdiff \| tree
2007-04-27	jprocter	bugfix for deleted annotation undo	commit \| commitdiff \| tree
2007-04-26	jprocter	added/tested sort by scores menu and added basic extractScor...	commit \| commitdiff \| tree
2007-04-26	jprocter	use hasScore method to test presence of score in annotation.	commit \| commitdiff \| tree
2007-04-26	jprocter	added 'sort by sequence associated annotation score'	commit \| commitdiff \| tree
2007-04-26	jprocter	bug fixed basic score extraction by regex on description...	commit \| commitdiff \| tree
2007-04-26	jprocter	get annotation by label string	commit \| commitdiff \| tree
2007-04-26	jprocter	fix '\0' bug from score-only positional annotation	commit \| commitdiff \| tree
2007-04-26	jprocter	score is a double, fix bugs for score only annotation...	commit \| commitdiff \| tree
2007-04-26	jprocter	double sort functions	commit \| commitdiff \| tree
2007-04-26	jprocter	total annotation score is a double for maximum precision.	commit \| commitdiff \| tree
2007-04-26	jprocter	score and visible copy construction	commit \| commitdiff \| tree
2007-04-26	jprocter	quick fix for verbose fortranesque comments in preamble...	commit \| commitdiff \| tree
2007-04-26	jprocter	fixed bug in prefix extraction for application	commit \| commitdiff \| tree
2007-04-26	jprocter	basic methods for adding scores extracted from description	commit \| commitdiff \| tree
2007-04-26	jprocter	fix for null annotations	commit \| commitdiff \| tree
2007-04-26	jprocter	groovy support without compile-time dependency.	commit \| commitdiff \| tree
2007-04-25	jprocter	moving word methods to MapList and begin bug-fix for...	commit \| commitdiff \| tree
2007-04-25	jprocter	getContentPane().add alignmentProperties popup.	commit \| commitdiff \| tree
2007-04-25	jprocter	Functions for parsing free text properties on sequences...	commit \| commitdiff \| tree
2007-04-25	jprocter	transfer of residue numbering as alignment annotation	commit \| commitdiff \| tree
2007-04-25	jprocter	AlignmentAnnotation: added annotation score attribute...	commit \| commitdiff \| tree
2007-04-24	jprocter	bugfix for sequence features mapped to multiple contigs...	commit \| commitdiff \| tree
2007-04-24	jprocter	updated mapping for EMBL_Services_V1.1.xsd and tested...	commit \| commitdiff \| tree
2007-04-23	jprocter	functions that operate on references to sequences in...	commit \| commitdiff \| tree
2007-04-23	jprocter	distinct methods for getting references to selected...	commit \| commitdiff \| tree
2007-04-20	jprocter	fix null annotation values	commit \| commitdiff \| tree
2007-04-20	jprocter	global dbref fetch option in web services menu.	commit \| commitdiff \| tree
2007-04-20	jprocter	value only annotation	commit \| commitdiff \| tree
2007-04-20	jprocter	adds annotation for display (with flag to set alignmentAnnot...	commit \| commitdiff \| tree
2007-04-20	jprocter	annotation and seqs vectors are protected members for...	commit \| commitdiff \| tree
2007-04-19	jprocter	tfactor annotation description includes full sequenceID	commit \| commitdiff \| tree
2007-04-19	jprocter	tfactor and occupancy extracted from PDB file, and...	commit \| commitdiff \| tree
2007-04-19	jprocter	bugfix	commit \| commitdiff \| tree
2007-04-19	jprocter	fixed column selection cut/paste and self paste.	commit \| commitdiff \| tree
2007-04-19	jprocter	sequence associated alignment annotation copy for column...	commit \| commitdiff \| tree
2007-04-19	jprocter	ensure edit command gapChar is updated and used for...	commit \| commitdiff \| tree
2007-04-19	jprocter	padGaps flag in copy constructor	commit \| commitdiff \| tree
2007-04-19	jprocter	javadoc note on padding AlignmentAnnotation to alignment...	commit \| commitdiff \| tree
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