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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
2007-08-23	jprocter	bugfixed and removed some inefficiencies in marshalling	commit \| commitdiff \| tree
2007-08-22	jprocter	popup for non-fatal tree parsing error	commit \| commitdiff \| tree
2007-08-22	jprocter	quick fix for exceptions due to invalid embl refs	commit \| commitdiff \| tree
2007-08-22	jprocter	fix serious repetitive exceptions if user closes colour...	commit \| commitdiff \| tree
2007-08-22	jprocter	catch occasional -ve imgWidth exception	commit \| commitdiff \| tree
2007-08-22	jprocter	added failsafe fix for cases where null sequence names...	commit \| commitdiff \| tree
2007-08-22	jprocter	introduce beginning of bug fix for parsing atv style...	commit \| commitdiff \| tree
2007-08-22	jprocter	added facility for sending non-fatal warnings back...	commit \| commitdiff \| tree
2007-08-13	jprocter	fixed typo in new 2_3 startup file default value	commit \| commitdiff \| tree
2007-08-08	jprocter	give treeviewer description its own contents entry...	commit \| commitdiff \| tree
2007-08-08	jprocter	generalise name of prediction method	commit \| commitdiff \| tree
2007-08-08	jprocter	ensure default source dist is relative to basedir of...	commit \| commitdiff \| tree
2007-08-08	jprocter	allow source dist archive to be an absolute filename	commit \| commitdiff \| tree
2007-08-08	jprocter	added source-dist task	commit \| commitdiff \| tree
2007-08-08	jprocter	histidine should be midblue (noticed by Peter Knight...	commit \| commitdiff \| tree
2007-08-06	jprocter	comment concerning null exceptions generated when annotation...	commit \| commitdiff \| tree
2007-08-06	jprocter	null pointer exception blocked redraw of annotation...	commit \| commitdiff \| tree
2007-08-02	jprocter	javadoc and bugfix for 'save' when jalview is default...	commit \| commitdiff \| tree
2007-08-02	jprocter	updated vamsas library (version for iscb demo)	commit \| commitdiff \| tree
2007-08-01	jprocter	ignore contents of this directory	commit \| commitdiff \| tree
2007-08-01	jprocter	added the '-tree' parameter to open a tree from the...	commit \| commitdiff \| tree
2007-08-01	jprocter	javadoc	commit \| commitdiff \| tree
2007-08-01	jprocter	ensure current dataset reference is passed to the crossRefer...	commit \| commitdiff \| tree
2007-08-01	jprocter	added tree as an applet to application servlet parameter	commit \| commitdiff \| tree
2007-08-01	jprocter	null pointer exception bug fix	commit \| commitdiff \| tree
2007-07-31	jprocter	debugging cross references and duplicate sequence db...	commit \| commitdiff \| tree
2007-07-30	jprocter	test cc change revoked.	commit \| commitdiff \| tree
2007-07-30	jprocter	test cc	commit \| commitdiff \| tree
2007-07-30	jprocter	javadoc	commit \| commitdiff \| tree
2007-07-30	jprocter	property for including debug info in classes	commit \| commitdiff \| tree
2007-07-25	jprocter	todo comment	commit \| commitdiff \| tree
2007-07-25	jprocter	fix crossRef retrieval so either protein OR nucleotide	commit \| commitdiff \| tree
2007-07-25	jprocter	uniprot synonym	commit \| commitdiff \| tree
2007-07-25	jprocter	better vamsas tree io (for when there are no nodemappings)	commit \| commitdiff \| tree
2007-07-25	jprocter	bugfix for vamsas demo	commit \| commitdiff \| tree
2007-07-25	jprocter	IO rearrangement for AMSAFile output	commit \| commitdiff \| tree
2007-07-25	jprocter	bugfix for vamsas demo and IO rearrangement for AMSAFile...	commit \| commitdiff \| tree
2007-07-13	jprocter	ignore random stuff to do with eclipse	commit \| commitdiff \| tree
2007-07-13	jprocter	preliminary IO classes - read javadoc for purpose	commit \| commitdiff \| tree
2007-07-13	jprocter	pickmanager on sequence and alignment position, vamsas...	commit \| commitdiff \| tree
2007-07-13	jprocter	refactor	commit \| commitdiff \| tree
2007-07-13	jprocter	new DBRef management and generalised source and entry...	commit \| commitdiff \| tree
2007-07-13	jprocter	more semantic groupings of dbs	commit \| commitdiff \| tree
2007-07-13	jprocter	debugged mappings and translated sequence recovery	commit \| commitdiff \| tree
2007-07-13	jprocter	preliminary states for pca distribution io	commit \| commitdiff \| tree
2007-07-13	jprocter	preliminary methods for detecting internal sequence...	commit \| commitdiff \| tree
2007-07-13	jprocter	bugfix	commit \| commitdiff \| tree
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