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2008-08-06	jprocter	extra checks for datasetsequence for when getDbRefs...	commit \| commitdiff \| tree
2008-08-06	jprocter	getDBRefs now always returns DBRefArray if it exists...	commit \| commitdiff \| tree
2008-08-05	jprocter	vamsas documentation	commit \| commitdiff \| tree
2008-08-05	jprocter	new vamsas session does not open a dialog box	commit \| commitdiff \| tree
2008-08-05	jprocter	web services and sequence fetcher added to contents	commit \| commitdiff \| tree
2008-08-05	jprocter	added sequence fetcher and sequence features retrieval...	commit \| commitdiff \| tree
2008-08-05	jprocter	updated statement of limitations for interactive annotation...	commit \| commitdiff \| tree
2008-08-05	jprocter	new sequence fetcher documentation	commit \| commitdiff \| tree
2008-08-05	jprocter	ensure das sequence sources are refreshed when das...	commit \| commitdiff \| tree
2008-08-05	jprocter	showbutton default is true	commit \| commitdiff \| tree
2008-08-04	jprocter	stackoverflow fix	commit \| commitdiff \| tree
2008-08-04	jprocter	PFAM retrieval and new applet parameter	commit \| commitdiff \| tree
2008-08-04	jprocter	pfam seed and full alignment retrieval and nicer ordering...	commit \| commitdiff \| tree
2008-08-04	jprocter	added 'showbutton' applet parameter	commit \| commitdiff \| tree
2008-08-01	jprocter	update to feature list (more to come here for 2.4 release)	commit \| commitdiff \| tree
2008-08-01	jprocter	new SequenceFetcher gui and visual delay indication...	commit \| commitdiff \| tree
2008-08-01	jprocter	updated jalview version of dasobert 1.53e client and...	commit \| commitdiff \| tree
2008-08-01	jprocter	todo	commit \| commitdiff \| tree
2008-08-01	jprocter	interface for windows that display progress bars	commit \| commitdiff \| tree
2008-07-31	jprocter	use canonical DbSource name in GUI box, and ensure...	commit \| commitdiff \| tree
2008-07-31	jprocter	refactored method for registering instance of a dbSource...	commit \| commitdiff \| tree
2008-07-31	jprocter	quick fix for the new uniprot name schema - description...	commit \| commitdiff \| tree
2008-07-31	jprocter	added specific retrieval arguments to SequneceFetcher...	commit \| commitdiff \| tree
2008-07-18	jprocter	resolve 1:many mappings for sequence associated annotation...	commit \| commitdiff \| tree
2008-07-18	jprocter	resolve 1:many mappings from feature sequence ID to...	commit \| commitdiff \| tree
2008-07-18	jprocter	allow findSeq to begin after a given sequence in...	commit \| commitdiff \| tree
2008-07-18	jprocter	Sequence label colour stored for each sequence group	commit \| commitdiff \| tree
2008-07-18	jprocter	comment	commit \| commitdiff \| tree
2008-07-18	jprocter	annotation file format updated to take idColour and...	commit \| commitdiff \| tree
2008-07-18	jprocter	Sequence label colour stored for each sequence group	commit \| commitdiff \| tree
2008-07-18	jprocter	User defined colourschemes are automatically generated...	commit \| commitdiff \| tree
2008-07-18	jprocter	prevent exception when no default timeout is specified	commit \| commitdiff \| tree
2008-07-11	jprocter	ensure annotationElements in non-graphical annotation...	commit \| commitdiff \| tree
2008-06-30	jprocter	javadoc and constraint to ensure annotation labels...	commit \| commitdiff \| tree
2008-06-30	jprocter	java 1.1 compatibility	commit \| commitdiff \| tree
2008-06-30	jprocter	timing of 'on load' output before any gui thread operations	commit \| commitdiff \| tree
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
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