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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
2007-04-19	jprocter	copying sequenceMapping, restrict(alstart/end) and...	commit \| commitdiff \| tree
2007-04-18	jprocter	made compileApplet and obfuscate depend on the presence...	commit \| commitdiff \| tree
2007-04-18	jprocter	java 1.1 compliance	commit \| commitdiff \| tree
2007-04-17	jprocter	bugfix for jalviewApplet run from command line.	commit \| commitdiff \| tree
2007-04-17	jprocter	bugfix.	commit \| commitdiff \| tree
2007-04-17	jprocter	jmol lib dependency for proguard and castorbinding...	commit \| commitdiff \| tree
2007-04-17	jprocter	use of suffix string (filename.blc#suffixstring) to...	commit \| commitdiff \| tree
2007-04-17	jprocter	refactored to allow seeks on a FileParse datasource...	commit \| commitdiff \| tree
2007-04-17	jprocter	javadoc	commit \| commitdiff \| tree
2007-04-17	jprocter	ascii type	commit \| commitdiff \| tree
2007-04-17	jprocter	paste adds or creates full copies of objects in clipboard...	commit \| commitdiff \| tree
2007-04-17	jprocter	pdb files are global to all alignments with new mapping...	commit \| commitdiff \| tree
2007-04-17	jprocter	paste/cut now adds or removes associated AlignmentAnnotation.	commit \| commitdiff \| tree
2007-04-17	jprocter	copy constructors and AlignmentAnnotation sequenceRef...	commit \| commitdiff \| tree
2007-04-17	jprocter	copy constructor and ascii type change.	commit \| commitdiff \| tree
2007-04-17	jprocter	proper copy constructor (not clone)	commit \| commitdiff \| tree
2007-04-12	jprocter	basic support for multi-exon CDS features	commit \| commitdiff \| tree
2007-04-11	jprocter	fixed for display of 'null' group features	commit \| commitdiff \| tree
2007-04-11	jprocter	fixed base lookup bug in dna pairwise alignment and...	commit \| commitdiff \| tree
2007-04-02	jprocter	doco change.	commit \| commitdiff \| tree
2007-04-02	jprocter	update settings for new groups (always displayed) and...	commit \| commitdiff \| tree
2007-04-02	jprocter	bugfix + create/amend whilst feature panel open (still...	commit \| commitdiff \| tree
2007-04-02	jprocter	typo fix.	commit \| commitdiff \| tree
2007-04-02	jprocter	featuresAdded method introduced for consistency with...	commit \| commitdiff \| tree
2007-04-02	jprocter	fr==null check.	commit \| commitdiff \| tree
2007-04-02	jprocter	feature group state and type order preference storage...	commit \| commitdiff \| tree
2007-04-02	jprocter	featuresAdded call for transferred PDB features	commit \| commitdiff \| tree
2007-04-02	jprocter	featuresAdded() method, state change support between...	commit \| commitdiff \| tree
2007-04-02	jprocter	added feature type order preference attribute and visible...	commit \| commitdiff \| tree
2007-03-26	jprocter	fix single sequence features added rendering bug.	commit \| commitdiff \| tree
2007-03-26	jprocter	PDB residue numberings transfered and alignment view...	commit \| commitdiff \| tree
2007-03-26	jprocter	grammar.	commit \| commitdiff \| tree
2007-03-23	jprocter	generalised feature attribute parsing slightly (no...	commit \| commitdiff \| tree
2007-03-23	jprocter	bugfix for 1.1 conversion.	commit \| commitdiff \| tree
2007-03-23	jprocter	reenable canceldas after a cancel and subsequence fetch	commit \| commitdiff \| tree
2007-03-23	jprocter	lastSeq==null to force refresh of sequencefeature array...	commit \| commitdiff \| tree
2007-03-23	jprocter	removed Iterator usage.	commit \| commitdiff \| tree
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