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2008-06-30	jprocter	safer retrieval of groovy scripts from URLs	commit \| commitdiff \| tree
2008-06-30	jprocter	included includeGaps flag in clustalW colour calculation...	commit \| commitdiff \| tree
2008-06-26	jprocter	added URLEncoder.encode to properly escape CGI encoded...	commit \| commitdiff \| tree
2008-06-23	jprocter	local sequence properties are preserved in SeqCigar...	commit \| commitdiff \| tree
2008-05-26	jprocter	Uniprot is not actually a multi-acc capable source...	commit \| commitdiff \| tree
2008-05-26	jprocter	bugfix so MULTI_ACC capable sources value property...	commit \| commitdiff \| tree
2008-05-26	jprocter	minor bugfix for case when PDB sequence strings are...	commit \| commitdiff \| tree
2008-05-12	jprocter	fixed Jalview project archive bug where alignment view...	commit \| commitdiff \| tree
2008-05-02	jprocter	bugfix to avoid null pointer exceptions being raised...	commit \| commitdiff \| tree
2008-05-01	jprocter	fix for unicode char labels causing arrayOutOfBoundsExceptio...	commit \| commitdiff \| tree
2008-04-29	jprocter	comments and version wget ping timeout fix for when...	commit \| commitdiff \| tree
2008-04-29	jprocter	added SeqSearch service interface. Documented and refactored...	commit \| commitdiff \| tree
2008-04-29	jprocter	trial fix for parsing NHX style trees to extract the...	commit \| commitdiff \| tree
2008-04-25	jprocter	potential fix for hang on opening of application window...	commit \| commitdiff \| tree
2008-04-22	jprocter	typo on Jalview help url	commit \| commitdiff \| tree
2008-04-21	jprocter	documented and refactored to facilitate headless feature...	commit \| commitdiff \| tree
2008-04-21	jprocter	added centre column labels menu entry to format menu	commit \| commitdiff \| tree
2008-04-21	jprocter	added centre annotation labels menu entry (and commented...	commit \| commitdiff \| tree
2008-04-21	jprocter	centrecolumnlabels format menu item and parameter added...	commit \| commitdiff \| tree
2008-04-21	jprocter	castor debug option cleared	commit \| commitdiff \| tree
2008-04-17	jprocter	bugfix for refactoring (webservice windows wouldn't...	commit \| commitdiff \| tree
2008-04-17	jprocter	javadoc and refactor of setWebService method to allow...	commit \| commitdiff \| tree
2008-04-17	jprocter	todo for refactoring webservice GUI creation mechanism	commit \| commitdiff \| tree
2008-04-17	jprocter	javadoc for webservice client tutorial	commit \| commitdiff \| tree
2008-04-17	jprocter	todos	commit \| commitdiff \| tree
2008-04-17	jprocter	javadoc and quiet flag	commit \| commitdiff \| tree
2008-04-11	jprocter	fix JPred thread so job aborts if submission fails.	commit \| commitdiff \| tree
2008-04-10	jprocter	quick fix for conservation calculation when residue...	commit \| commitdiff \| tree
2008-04-10	jprocter	bug fix for Features/Annotations file parameter parsing...	commit \| commitdiff \| tree
2008-03-08	jprocter	first hack to get true DNA and Sequence highlighting...	commit \| commitdiff \| tree
2008-03-08	jprocter	correction to Jnet service documentation	commit \| commitdiff \| tree
2008-02-24	jprocter	sequenceId is a string, not an integer - allows generation...	commit \| commitdiff \| tree
2008-02-24	jprocter	sequenceId is a string, not an integer - allows generation...	commit \| commitdiff \| tree
2008-02-22	jprocter	sequenceId is a string, not an integer - allows generation...	commit \| commitdiff \| tree
2008-02-22	jprocter	valid format for writing test	commit \| commitdiff \| tree
2008-02-22	jprocter	probably unnecessary optimisation (SequenceGroup.addSequence...	commit \| commitdiff \| tree
2008-02-22	jprocter	On 'save' menu entry check to see if fileformat is...	commit \| commitdiff \| tree
2008-02-22	jprocter	CDS segment index	commit \| commitdiff \| tree
2008-02-22	jprocter	possible fix for stockhom ss-annotation re-creation...	commit \| commitdiff \| tree
2008-02-22	jprocter	index number for contiguous part of mapped sequence...	commit \| commitdiff \| tree
2008-02-22	jprocter	javadoc	commit \| commitdiff \| tree
2008-02-22	jprocter	typo for AXISLOGLEVEL constant	commit \| commitdiff \| tree
2008-02-22	jprocter	explicit quote of chaincode in errror message	commit \| commitdiff \| tree
2008-01-29	jprocter	minor change to output of main method for testing file IO	commit \| commitdiff \| tree
2008-01-29	jprocter	groovy from stdin	commit \| commitdiff \| tree
2008-01-29	jprocter	memory usage information and flag to indicate if warning...	commit \| commitdiff \| tree
2008-01-29	jprocter	add methods to read from current position of existing...	commit \| commitdiff \| tree
2008-01-29	jprocter	ensure mark is set before identification is started.	commit \| commitdiff \| tree
2008-01-29	jprocter	FileParse object can be re-used to read different files...	commit \| commitdiff \| tree
2008-01-29	jprocter	flag to indicate if errors are raised as warning dialog...	commit \| commitdiff \| tree
2008-01-29	jprocter	explicitly allow access to showMemoryUsage flag in...	commit \| commitdiff \| tree
2008-01-29	jprocter	javadoc	commit \| commitdiff \| tree
2008-01-29	jprocter	groovy scripts can be read from stdin	commit \| commitdiff \| tree
2008-01-29	jprocter	reinstated proper case insensitive searching for both...	commit \| commitdiff \| tree
2008-01-22	jprocter	timings and memory usage for reading in a file	commit \| commitdiff \| tree
2008-01-22	jprocter	more efficient parsing of large files, do not create...	commit \| commitdiff \| tree
2008-01-22	jprocter	ensured that seqeunce feature shift takes into account...	commit \| commitdiff \| tree
2008-01-22	jprocter	new method to get map of sequence positions corresponding...	commit \| commitdiff \| tree
2008-01-21	jprocter	fix regex for annotation subtype to use non-whitespace...	commit \| commitdiff \| tree
2008-01-21	jprocter	javadoc and main method for testing file input routines	commit \| commitdiff \| tree
2008-01-21	jprocter	javadoc	commit \| commitdiff \| tree
2008-01-15	jprocter	draft of 2.4 features in feature list	commit \| commitdiff \| tree
2008-01-11	jprocter	added groovy documentation to contents	commit \| commitdiff \| tree
2008-01-11	jprocter	jalview memory monitor instructions added	commit \| commitdiff \| tree
2008-01-11	jprocter	desktop tools menu updated	commit \| commitdiff \| tree
2008-01-11	jprocter	groovy and das fetching stuff in command line argument...	commit \| commitdiff \| tree
2008-01-11	jprocter	documentation for groovy console and basic groovy...	commit \| commitdiff \| tree
2008-01-11	jprocter	added groovy argument for launching a groovy script...	commit \| commitdiff \| tree
2008-01-11	jprocter	memory monitor, garbage collection and changed menu...	commit \| commitdiff \| tree
2007-12-21	jprocter	uniprotxml format comment (ebi changed service parameter)	commit \| commitdiff \| tree
2007-12-21	jprocter	source directory tree documentation	commit \| commitdiff \| tree
2007-12-21	jprocter	automatic dbref fetching and sequence validation for...	commit \| commitdiff \| tree
2007-12-21	jprocter	further bugfix and annotation transfer for dna/protein...	commit \| commitdiff \| tree
2007-12-21	jprocter	javadoc and bugfix	commit \| commitdiff \| tree
2007-12-21	jprocter	sequence db fetcher and db reference validation/annotation...	commit \| commitdiff \| tree
2007-12-21	jprocter	sequence db fetcher metadata for multiple sequence...	commit \| commitdiff \| tree
2007-12-21	jprocter	temporary bugfix ?	commit \| commitdiff \| tree
2007-12-21	jprocter	bugfix	commit \| commitdiff \| tree
2007-12-21	jprocter	equivalence for transferring/updating references	commit \| commitdiff \| tree
2007-12-21	jprocter	bugfixes	commit \| commitdiff \| tree
2007-12-18	jprocter	incorrect colour-by-sequence when gaps are present...	commit \| commitdiff \| tree
2007-12-13	jprocter	java 1.1 compatibility (again)	commit \| commitdiff \| tree
2007-12-13	jprocter	java 1.1 compatibility (again)	commit \| commitdiff \| tree
2007-11-30	jprocter	null pointer bugfix	commit \| commitdiff \| tree
2007-11-30	jprocter	bugfixed MapList (must be propagated to vamsas version...	commit \| commitdiff \| tree
2007-11-30	jprocter	javadoc and transferAnnotation method	commit \| commitdiff \| tree
2007-11-30	jprocter	case insensitive matching of database ids	commit \| commitdiff \| tree
2007-11-30	jprocter	case invariant matching of seqeunce feature to sequence...	commit \| commitdiff \| tree
2007-11-28	jprocter	bugfix	commit \| commitdiff \| tree
2007-11-24	jprocter	only show bootstrap values if they are valid!	commit \| commitdiff \| tree
2007-11-16	jprocter	typo	commit \| commitdiff \| tree
2007-11-16	jprocter	javadoc	commit \| commitdiff \| tree
2007-11-16	jprocter	added generic method for adding new database proxies...	commit \| commitdiff \| tree
2007-11-16	jprocter	refactored ebi soap client and AbstractSequenceFetcher...	commit \| commitdiff \| tree
2007-11-16	jprocter	todo for sortbyPID operating on current selection rather...	commit \| commitdiff \| tree
2007-11-16	jprocter	javadoc	commit \| commitdiff \| tree
2007-11-16	jprocter	refactor abstract sequence fetching and DBSource machinery...	commit \| commitdiff \| tree
2007-11-12	jprocter	crossrefs have properly updated pdbId lists	commit \| commitdiff \| tree
2007-11-12	jprocter	javadoc and introduction of dasserver and fetchdas...	commit \| commitdiff \| tree
2007-11-12	jprocter	added mechanism to initiate DAS feature fetching programmati...	commit \| commitdiff \| tree
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