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2007-10-31	jprocter	added bugfix todo	commit \| commitdiff \| tree
2007-10-31	jprocter	concise files can now be read as a normal alignment...	commit \| commitdiff \| tree
2007-10-31	jprocter	added a quieter bailout for cases when the featuresFile...	commit \| commitdiff \| tree
2007-10-31	jprocter	factored out reference to parent alignFrame (so all...	commit \| commitdiff \| tree
2007-10-31	jprocter	beginnings of view definition capability for annotations...	commit \| commitdiff \| tree
2007-10-31	jprocter	javadoc	commit \| commitdiff \| tree
2007-10-31	jprocter	error message associated with an alignment file loading...	commit \| commitdiff \| tree
2007-10-31	jprocter	introduce new type to pass around featureRendererSettings	commit \| commitdiff \| tree
2007-10-31	jprocter	nullpointer bug fix on consensus thread	commit \| commitdiff \| tree
2007-10-31	jprocter	javadoc on webservice discovery method	commit \| commitdiff \| tree
2007-10-31	jprocter	fix parsing of embl entries like S75919 which have...	commit \| commitdiff \| tree
2007-10-29	jprocter	bugfix for alignments without aligned codon frames	commit \| commitdiff \| tree
2007-10-28	jprocter	begin process of allowing for column selection in wrapped...	commit \| commitdiff \| tree
2007-10-28	jprocter	fix display of hidden sequence markers in applet	commit \| commitdiff \| tree
2007-10-27	jprocter	must do any modification to menus before they are embedded...	commit \| commitdiff \| tree
2007-10-27	jprocter	new option on annotation export dialog box	commit \| commitdiff \| tree
2007-10-27	jprocter	enabled platform dependent embedding of menuBar with...	commit \| commitdiff \| tree
2007-10-27	jprocter	windowclose handler now calls EmbmenuFrame garbage...	commit \| commitdiff \| tree
2007-10-27	jprocter	fixed bootstrap value rendering to occur only when...	commit \| commitdiff \| tree
2007-10-27	jprocter	refactored embedded menu machinery	commit \| commitdiff \| tree
2007-10-26	jprocter	add mac dependent use of embedded menu bar rather than...	commit \| commitdiff \| tree
2007-10-26	jprocter	use new utility class for platform info	commit \| commitdiff \| tree
2007-10-26	jprocter	new applet and application utility class for platform...	commit \| commitdiff \| tree
2007-10-26	jprocter	fixed applet API calls so they operate on the embedded...	commit \| commitdiff \| tree
2007-10-26	jprocter	updated client which allows XML validation flags to...	commit \| commitdiff \| tree
2007-10-24	jprocter	thread for product retrieval	commit \| commitdiff \| tree
2007-10-24	jprocter	ensure PDB ids are updated on the dataset sequence	commit \| commitdiff \| tree
2007-10-24	jprocter	individual query error/exception report and bugfix	commit \| commitdiff \| tree
2007-10-24	jprocter	add parsed PDB reference to sequences	commit \| commitdiff \| tree
2007-10-24	jprocter	null pointer exception and warning for update of tree	commit \| commitdiff \| tree
2007-10-24	jprocter	javadoc	commit \| commitdiff \| tree
2007-10-19	jprocter	test autobuild of release	commit \| commitdiff \| tree
2007-10-19	jprocter	contains java properties read by ant build automation	commit \| commitdiff \| tree
2007-10-19	jprocter	file containing the cvs tag for the latest release	commit \| commitdiff \| tree
2007-10-15	jprocter	new features or newly shown group features are placed...	commit \| commitdiff \| tree
2007-10-12	jprocter	added separator parameter with default of '\|' to control...	commit \| commitdiff \| tree
2007-10-11	jprocter	remove conflict on javascript api	commit \| commitdiff \| tree
2007-10-11	jprocter	javac.debug passed through to applet build to preserve...	commit \| commitdiff \| tree
2007-10-11	jprocter	static debug flag controlling output of excessive info...	commit \| commitdiff \| tree
2007-10-11	jprocter	pass up the errormessage in the exception when a datasource...	commit \| commitdiff \| tree
2007-10-10	jprocter	jnlp amsa extension and donotobfuscate property conditional...	commit \| commitdiff \| tree
2007-10-10	jprocter	featureGroup show/hide and newView methods for applet...	commit \| commitdiff \| tree
2007-10-04	jprocter	selected region output also supports generation of...	commit \| commitdiff \| tree
2007-10-04	jprocter	refactored list of file extensions and file format...	commit \| commitdiff \| tree
2007-10-04	jprocter	edit label/displayChar contains existing character...	commit \| commitdiff \| tree
2007-10-04	jprocter	refactored invertColumnSelection as an object method	commit \| commitdiff \| tree
2007-10-02	jprocter	added colSel as a parameter formatAdaptor print function...	commit \| commitdiff \| tree
2007-10-02	jprocter	convenience constructor for duplicating an annotation...	commit \| commitdiff \| tree
2007-10-02	jprocter	javadoc and operator for editing AlignmentAnnotation...	commit \| commitdiff \| tree
2007-10-02	jprocter	javadoc	commit \| commitdiff \| tree
2007-09-29	jprocter	always update PDBEntry list if DBRefEntries might have...	commit \| commitdiff \| tree
2007-09-29	jprocter	updatePDBEntry method to add any PDBEntry from the...	commit \| commitdiff \| tree
2007-09-29	jprocter	use pdb refsource string	commit \| commitdiff \| tree
2007-09-29	jprocter	javadoc	commit \| commitdiff \| tree
2007-09-29	jprocter	friendlier sequence names for protein products	commit \| commitdiff \| tree
2007-09-28	jprocter	better support for TreeNode binding	commit \| commitdiff \| tree
2007-09-28	jprocter	javadoc for jalview_properties tags	commit \| commitdiff \| tree
2007-09-27	jprocter	switched to apache zip tool for doc IO	commit \| commitdiff \| tree
2007-09-27	jprocter	modifiable lock check	commit \| commitdiff \| tree
2007-09-25	jprocter	ascii file	commit \| commitdiff \| tree
2007-09-25	jprocter	beginning of vamsas/local object synchronization pattern...	commit \| commitdiff \| tree
2007-09-25	jprocter	added store of undo/redo hash for each alignment so...	commit \| commitdiff \| tree
2007-09-25	jprocter	primitive methods for getting current undo/redo state...	commit \| commitdiff \| tree
2007-09-18	jprocter	fix class-cast exception and added beginnings of DBRef...	commit \| commitdiff \| tree
2007-09-18	jprocter	pathological vamsas archive update fix ?	commit \| commitdiff \| tree
2007-09-14	jprocter	ascii file	commit \| commitdiff \| tree
2007-09-14	jprocter	added support for loading a vamsas document into a...	commit \| commitdiff \| tree
2007-09-14	jprocter	better reproduction of compact newick files (removal...	commit \| commitdiff \| tree
2007-09-10	jprocter	choose a particular vamsas session, load, or create...	commit \| commitdiff \| tree
2007-09-10	jprocter	ensure dbrefs are added to dataset sequence.	commit \| commitdiff \| tree
2007-09-07	jprocter	client update to fix appData read triggering document...	commit \| commitdiff \| tree
2007-09-07	jprocter	formatting and ensure that dataset is actually searched...	commit \| commitdiff \| tree
2007-09-07	jprocter	added action for saving the current session as a vamsas...	commit \| commitdiff \| tree
2007-09-07	jprocter	Maps are usually added to DbRefs which are added to...	commit \| commitdiff \| tree
2007-09-07	jprocter	added a more general DBRef search interface	commit \| commitdiff \| tree
2007-09-06	jprocter	bootstrap regex 'fixed' and ugly hack to try and get...	commit \| commitdiff \| tree
2007-09-06	jprocter	args for emblfile parser main method	commit \| commitdiff \| tree
2007-09-06	jprocter	fixes bootstrap bug noted by Chunlong Chen in email...	commit \| commitdiff \| tree
2007-09-04	jprocter	removed href in the jnlp generation	commit \| commitdiff \| tree
2007-09-04	jprocter	basic fix for pfelkers problem with ':' in the last...	commit \| commitdiff \| tree
2007-09-04	jprocter	gff parsing when no start or end position is defined.	commit \| commitdiff \| tree
2007-08-31	jprocter	added CSV export of annotation rows to application.	commit \| commitdiff \| tree
2007-08-31	jprocter	appdata bugfix in vamsas client library	commit \| commitdiff \| tree
2007-08-30	jprocter	really make sure database references are stored and...	commit \| commitdiff \| tree
2007-08-30	jprocter	ensure codon mappings and database references are merged...	commit \| commitdiff \| tree
2007-08-30	jprocter	sequenceMappings go on boh datasets involved in a mapping...	commit \| commitdiff \| tree
2007-08-30	jprocter	refactored and ensured alCodonMappings are propagated...	commit \| commitdiff \| tree
2007-08-30	jprocter	store dataset references, sequence dataset ids, and...	commit \| commitdiff \| tree
2007-08-30	jprocter	improved vamsas treenode node binding support	commit \| commitdiff \| tree
2007-08-30	jprocter	moved dataset sequence creation onto sequence method	commit \| commitdiff \| tree
2007-08-30	jprocter	create dataset sequence method	commit \| commitdiff \| tree
2007-08-30	jprocter	removed autogenerated todo	commit \| commitdiff \| tree
2007-08-30	jprocter	updated source generation for castor-1.1-cycle patched	commit \| commitdiff \| tree
2007-08-30	jprocter	added aligned codon frames, and dataset reference ids...	commit \| commitdiff \| tree
2007-08-29	jprocter	applet and application menu entry differences and consensus...	commit \| commitdiff \| tree
2007-08-24	jprocter	dataset alignments have a reference count which must...	commit \| commitdiff \| tree
2007-08-24	jprocter	remove null pointer exception when embl file is not...	commit \| commitdiff \| tree
2007-08-24	jprocter	todo comments	commit \| commitdiff \| tree
2007-08-23	jprocter	proper vamsas style binding of alignment sequence objects...	commit \| commitdiff \| tree
2007-08-23	jprocter	slightly faster validation patch (logging message concatenat...	commit \| commitdiff \| tree
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