source.jalview.org Git - jalview.git/history

git://source.jalview.org / jalview.git / history

2007-06-04	jprocter	fix for 'RF' annotation tags and ensured parser is...	tree \| commitdiff
2007-05-22	jprocter	refactored document objects and bugfix on jvdataset...	tree \| commitdiff
2007-05-18	jprocter	fixed getObject(VorbaId) lookup in vamsas-client	tree \| commitdiff
2007-05-18	jprocter	update to and from document (and remove deprecated...	tree \| commitdiff
2007-05-17	jprocter	use of proper vamsas client API by Jalview	tree \| commitdiff
2007-05-17	jprocter	modified castor-1.1 library and refactored uk.ac.vamsas	tree \| commitdiff
2007-05-10	jprocter	apparent bug in JpredFile parser where annotation was...	tree \| commitdiff
2007-05-09	jprocter	main method for running from command line and better...	tree \| commitdiff
2007-05-08	amwaterhouse	addElement	tree \| commitdiff
2007-05-02	jprocter	public debug report log message to gather any cases...	tree \| commitdiff
2007-05-02	amwaterhouse	AMSA input set padgaps true	tree \| commitdiff
2007-05-01	amwaterhouse	Make sure annots are alignment width	tree \| commitdiff
2007-04-30	jprocter	'no sources selected' calls method on feature settings...	tree \| commitdiff
2007-04-30	jprocter	parse alignment properties and add annotation rows...	tree \| commitdiff
2007-04-30	jprocter	alignment properties and embedded newick strings can...	tree \| commitdiff
2007-04-27	jprocter	blc header lines inserted as 'comment' alignment property	tree \| commitdiff
2007-04-27	jprocter	parsers can generate alignment properties	tree \| commitdiff
2007-04-27	amwaterhouse	one colour flag in annotation export	tree \| commitdiff
2007-04-26	jprocter	use hasScore method to test presence of score in annota...	tree \| commitdiff
2007-04-26	jprocter	quick fix for verbose fortranesque comments in preamble...	tree \| commitdiff
2007-04-26	jprocter	fixed bug in prefix extraction for application	tree \| commitdiff
2007-04-25	amwaterhouse	properties + colours	tree \| commitdiff
2007-04-25	amwaterhouse	fix recent file type bug	tree \| commitdiff
2007-04-25	jprocter	AlignmentAnnotation: added annotation score attribute...	tree \| commitdiff
2007-04-23	amwaterhouse	Check displayChar is not null	tree \| commitdiff
2007-04-23	amwaterhouse	Only fetch refs for seelcted sequences	tree \| commitdiff
2007-04-20	jprocter	annotation and seqs vectors are protected members for...	tree \| commitdiff
2007-04-18	amwaterhouse	dont set seqref null if index incorrect	tree \| commitdiff
2007-04-18	amwaterhouse	adjustForAlignment on new seq ref	tree \| commitdiff
2007-04-18	jprocter	java 1.1 compliance	tree \| commitdiff
2007-04-17	jprocter	bugfix.	tree \| commitdiff
2007-04-17	jprocter	use of suffix string (filename.blc#suffixstring) to...	tree \| commitdiff
2007-04-17	jprocter	refactored to allow seeks on a FileParse datasource...	tree \| commitdiff
2007-04-17	jprocter	javadoc	tree \| commitdiff
2007-04-13	amwaterhouse	FeatureRenderer takes alignmentPanel	tree \| commitdiff
2007-04-05	amwaterhouse	Pasted file doesnt have title and not reloadable	tree \| commitdiff
2007-04-05	amwaterhouse	call getAllframes on desktop instance	tree \| commitdiff
2007-04-04	amwaterhouse	flag for dasCoordSysFound added	tree \| commitdiff
2007-03-19	jprocter	DAS features mapped to local reference frame	tree \| commitdiff
2007-03-19	jprocter	disambiguate jalview.datamodel.Mapping from castor...	tree \| commitdiff
2007-02-27	amwaterhouse	Use paintAlignment	tree \| commitdiff
2007-02-27	amwaterhouse	remove p+3 < query.length	tree \| commitdiff
2007-02-07	amwaterhouse	Formatting	tree \| commitdiff
2007-02-05	amwaterhouse	applet can define groups as parameters	tree \| commitdiff
2007-02-02	amwaterhouse	Dont add group if seqs not found	tree \| commitdiff
2007-01-30	amwaterhouse	Any character non aa or nucleotide is a space	tree \| commitdiff
2007-01-30	amwaterhouse	Use util toHexString	tree \| commitdiff
2007-01-30	amwaterhouse	Output groups in annotation file	tree \| commitdiff
2007-01-29	amwaterhouse	SequenceGroup parsing added to annotation file	tree \| commitdiff
2007-01-25	amwaterhouse	Remove unneccessary lines	tree \| commitdiff
2007-01-25	amwaterhouse	Only output visible annotations	tree \| commitdiff
2007-01-25	jprocter	reinstating class implementation.	tree \| commitdiff
2007-01-24	amwaterhouse	output now takes alignment, not just sequences	tree \| commitdiff
2007-01-24	amwaterhouse	Extension to fastaFile for myhits	tree \| commitdiff
2007-01-19	amwaterhouse	Need to know protocol to load anntotations	tree \| commitdiff
2007-01-18	amwaterhouse	Add the last sequence before annotations	tree \| commitdiff
2007-01-18	amwaterhouse	1.1 enabled	tree \| commitdiff
2007-01-18	amwaterhouse	File Parsing returns Alignments, not Sequence[]	tree \| commitdiff
2007-01-18	amwaterhouse	Descriptions can be added to annotations	tree \| commitdiff
2007-01-04	amwaterhouse	Reads in anything following seq id as a description	tree \| commitdiff
2007-01-04	amwaterhouse	HEADER and ATOM must be position 0	tree \| commitdiff
2006-12-21	jprocter	description from vamsas sequence and file type change	tree \| commitdiff
2006-12-21	amwaterhouse	remove unnecessary import	tree \| commitdiff
2006-12-19	amwaterhouse	description may be null	tree \| commitdiff
2006-12-14	amwaterhouse	set sequence_ref alignment	tree \| commitdiff
2006-12-14	amwaterhouse	Are the labels all secondary Strutures? are the display...	tree \| commitdiff
2006-12-11	jprocter	fixed introduced bug (doh)	tree \| commitdiff
2006-12-11	jprocter	clarified help documentation for annotation file format...	tree \| commitdiff
2006-12-05	amwaterhouse	Sequence is char []	tree \| commitdiff
2006-11-30	amwaterhouse	DasRegistry moved again	tree \| commitdiff
2006-11-28	jprocter	EBI web service interface update (and SequenceFetcher...	tree \| commitdiff
2006-11-21	amwaterhouse	Memory check on loading file	tree \| commitdiff
2006-11-21	amwaterhouse	Set fsettings in constuctor	tree \| commitdiff
2006-11-20	amwaterhouse	Cancel added	tree \| commitdiff
2006-11-14	amwaterhouse	Single seq Blc file detection	tree \| commitdiff
2006-11-13	amwaterhouse	Use j not i	tree \| commitdiff
2006-11-13	amwaterhouse	Fasta files with * read not identified as BLC	tree \| commitdiff
2006-11-13	amwaterhouse	Querystring made from line tokenized seq name, seq...	tree \| commitdiff
2006-11-09	amwaterhouse	alignFrame.setFileName	tree \| commitdiff
2006-11-06	amwaterhouse	Remember fileName in alignFrame	tree \| commitdiff
2006-11-02	amwaterhouse	dasregistry is now dasregistry.org	tree \| commitdiff
2006-10-30	amwaterhouse	Append html	tree \| commitdiff
2006-10-24	amwaterhouse	Only send one call per sequence at the moment	tree \| commitdiff
2006-10-18	amwaterhouse	Wait for response from server before next sequence	tree \| commitdiff
2006-10-18	amwaterhouse	parseDescriptionHTML	tree \| commitdiff
2006-10-10	amwaterhouse	aaIndex replaces aaHash	tree \| commitdiff
2006-10-09	jprocter	imported Vamsas bindings and alpha vamsas client code...	tree \| commitdiff
2006-10-06	jprocter	Added filter so that input to a JPred job is *solely...	tree \| commitdiff
2006-10-05	amwaterhouse	BatchSize now 10	tree \| commitdiff
2006-10-05	amwaterhouse	OutOfMemoryError test	tree \| commitdiff
2006-10-03	amwaterhouse	Send DAS requests in batches of 20	tree \| commitdiff
2006-10-03	amwaterhouse	DB seqs may be lower or upper case	tree \| commitdiff
2006-08-30	amwaterhouse	jnet file is 1 to 1 mapping	tree \| commitdiff
2006-08-29	amwaterhouse	No stacktrace	tree \| commitdiff
2006-08-29	amwaterhouse	createMapping alreadyMapped	tree \| commitdiff
2006-08-21	amwaterhouse	header updated	tree \| commitdiff
2006-08-21	amwaterhouse	Remove system.out	tree \| commitdiff
2006-08-18	amwaterhouse	Jalview features format adds links as hrefs	tree \| commitdiff
2006-08-17	amwaterhouse	OptionPane invokeLater	tree \| commitdiff
2006-08-15	amwaterhouse	Acknowledgement	tree \| commitdiff
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