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2007-02-09	jprocter	running jalview from the command line.	commit \| commitdiff \| tree
2007-02-09	jprocter	added command line help documentation and preferences...	commit \| commitdiff \| tree
2007-02-09	jprocter	added 'show overview' preference.	commit \| commitdiff \| tree
2007-02-08	jprocter	fix on newquestionaire notification bug (again)	commit \| commitdiff \| tree
2007-02-06	jprocter	hardwired default user questionnaire url and by default...	commit \| commitdiff \| tree
2007-02-06	jprocter	more bugfixes.	commit \| commitdiff \| tree
2007-02-06	jprocter	debug log message	commit \| commitdiff \| tree
2007-02-05	jprocter	simplified and refactored along with cgi-script.	commit \| commitdiff \| tree
2007-02-05	jprocter	command line hook for questionnaire url argument.	commit \| commitdiff \| tree
2007-02-05	jprocter	kkv change	commit \| commitdiff \| tree
2007-02-05	jprocter	client side machinery for user questionnaire responses	commit \| commitdiff \| tree
2007-01-26	jprocter	preliminary documentation for DNA->protein codon features...	commit \| commitdiff \| tree
2007-01-26	jprocter	added doc for PDBResNum features	commit \| commitdiff \| tree
2007-01-25	jprocter	reinstating class implementation.	commit \| commitdiff \| tree
2007-01-25	jprocter	checks for irreflexive mapping in main tester	commit \| commitdiff \| tree
2007-01-24	jprocter	refactored to use jalview.analysis.Finder for searching...	commit \| commitdiff \| tree
2007-01-24	jprocter	kkv change	commit \| commitdiff \| tree
2007-01-24	jprocter	Map arbitrary series of non-overlapping integer intervals...	commit \| commitdiff \| tree
2007-01-23	jprocter	refactoring (added seqIndex/resIndex state for incremental...	commit \| commitdiff \| tree
2007-01-23	jprocter	refactored search algorithm from gui classes	commit \| commitdiff \| tree
2007-01-23	jprocter	transfer resnum features now returns features (could...	commit \| commitdiff \| tree
2007-01-19	jprocter	reoganization of PDB sequence fetching for sequence...	commit \| commitdiff \| tree
2007-01-19	jprocter	PDBChain maintains reference to dataset of sequences...	commit \| commitdiff \| tree
2007-01-19	jprocter	datasetSequence derive method and some checks	commit \| commitdiff \| tree
2007-01-19	jprocter	javadoc	commit \| commitdiff \| tree
2007-01-19	jprocter	added sequence feature copy constructor.	commit \| commitdiff \| tree
2007-01-18	jprocter	transfer and update of sequenceFeatures for associated...	commit \| commitdiff \| tree
2007-01-18	jprocter	random ';'	commit \| commitdiff \| tree
2007-01-18	jprocter	transfer and update of sequenceFeatures for associated...	commit \| commitdiff \| tree
2007-01-18	jprocter	fixed last-residue bug and added sequence feature creation...	commit \| commitdiff \| tree
2007-01-18	jprocter	added resNum+insCode string field for truly unambiguous...	commit \| commitdiff \| tree
2007-01-17	jprocter	made atom attributes public (rather than put in get...	commit \| commitdiff \| tree
2006-12-21	jprocter	type change	commit \| commitdiff \| tree
2006-12-21	jprocter	description from vamsas sequence and file type change	commit \| commitdiff \| tree
2006-12-21	jprocter	type change	commit \| commitdiff \| tree
2006-12-11	jprocter	fixed introduced bug (doh)	commit \| commitdiff \| tree
2006-12-11	jprocter	clarified help documentation for annotation file format...	commit \| commitdiff \| tree
2006-12-06	jprocter	type change	commit \| commitdiff \| tree
2006-12-06	jprocter	typo fix.	commit \| commitdiff \| tree
2006-12-06	jprocter	general pairwise substitution score models for pairwise...	commit \| commitdiff \| tree
2006-12-04	jprocter	random notes on putting a Groovy interpreter into Jalview.	commit \| commitdiff \| tree
2006-11-30	jprocter	fix bad grammar in new alignment title	commit \| commitdiff \| tree
2006-11-28	jprocter	EBI web service interface update (and SequenceFetcher...	commit \| commitdiff \| tree
2006-11-28	jprocter	2.2 documentation	commit \| commitdiff \| tree
2006-11-28	jprocter	2.2 documentation	commit \| commitdiff \| tree
2006-11-28	jprocter	2.2 documentation	commit \| commitdiff \| tree
2006-11-28	jprocter	2.2 documentation	commit \| commitdiff \| tree
2006-11-27	jprocter	2.2 documentation	commit \| commitdiff \| tree
2006-11-27	jprocter	2.2 documentation	commit \| commitdiff \| tree
2006-11-27	jprocter	2.2 documentation	commit \| commitdiff \| tree
2006-11-27	jprocter	* keyword substitution change *	commit \| commitdiff \| tree
2006-11-27	jprocter	2.2 documentation	commit \| commitdiff \| tree
2006-11-27	jprocter	2.2 documentation	commit \| commitdiff \| tree
2006-11-26	jprocter	2.2 documentation	commit \| commitdiff \| tree
2006-11-24	jprocter	new and corrected docs for 2.2 release	commit \| commitdiff \| tree
2006-11-21	jprocter	corrected subtree colour dialogbox title	commit \| commitdiff \| tree
2006-11-21	jprocter	fix unselectable tree leaf nodes when node mapping...	commit \| commitdiff \| tree
2006-10-24	jprocter	fixes bug reported by Christopher Tan (help@jalview...	commit \| commitdiff \| tree
2006-10-15	jprocter	fixed array out of bounds exception in copy constructor	commit \| commitdiff \| tree
2006-10-11	jprocter	fixes exception (array index out of bounds - due to...	commit \| commitdiff \| tree
2006-10-10	jprocter	refined id matching to pick the closest match (by length...	commit \| commitdiff \| tree
2006-10-10	jprocter	debug message bugfix on duplicate tree leaf names.	commit \| commitdiff \| tree
2006-10-10	jprocter	bugfix for dodgy trees which contain the same leafname...	commit \| commitdiff \| tree
2006-10-09	jprocter	fixed log4j complaints for vamsas logging (again)	commit \| commitdiff \| tree
2006-10-09	jprocter	fixed log4j complaints for vamsas logging.	commit \| commitdiff \| tree
2006-10-09	jprocter	excluded log4j properties.	commit \| commitdiff \| tree
2006-10-09	jprocter	java 1.4 compliant classes.	commit \| commitdiff \| tree
2006-10-09	jprocter	imported Vamsas bindings and alpha vamsas client code...	commit \| commitdiff \| tree
2006-10-09	jprocter	set firstColumn property for an alignmentView object.	commit \| commitdiff \| tree
2006-10-09	jprocter	fixed getCompactAlignment method to return proper cigarArray...	commit \| commitdiff \| tree
2006-10-06	jprocter	Added filter so that input to a JPred job is *solely...	commit \| commitdiff \| tree
2006-10-06	jprocter	javadoc	commit \| commitdiff \| tree
2006-10-06	jprocter	new getVisibleContigs method mirrors the getVisibleContigs...	commit \| commitdiff \| tree
2006-09-27	jprocter	fixed tree building exception when one residue or a...	commit \| commitdiff \| tree
2006-09-07	jprocter	added copy consensus sequence to consensus annotation...	commit \| commitdiff \| tree
2006-09-05	jprocter	getVisibleContigs() returns start and end positions...	commit \| commitdiff \| tree
2006-09-05	jprocter	javadoc on contigs	commit \| commitdiff \| tree
2006-08-22	jprocter	documentation - adding new Input data menu entries.	commit \| commitdiff \| tree
2006-08-22	jprocter	added note on column-separability	commit \| commitdiff \| tree
2006-08-22	jprocter	documentation	commit \| commitdiff \| tree
2006-08-22	jprocter	getSequenceStrings() bug fixed.	commit \| commitdiff \| tree
2006-08-22	jprocter	hidden region recovery in JPred and new hidden region...	commit \| commitdiff \| tree
2006-08-22	jprocter	off by one bug in hiden column unmarshalling	commit \| commitdiff \| tree
2006-08-21	jprocter	Refactored Jnet and added hidden columns support.	commit \| commitdiff \| tree
2006-08-21	jprocter	fixed undo-redo bug, hidden columns are moved with...	commit \| commitdiff \| tree
2006-08-21	jprocter	removeGaps method can record changes in alignment columns...	commit \| commitdiff \| tree
2006-08-21	jprocter	fix for truncation of sequence associated annotation...	commit \| commitdiff \| tree
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
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