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[jalview.git] / src / jalview / gui / Jalview2XML.java

2014-04-25	Jim Procter	JAL-1177 patches to loader to cope with dataset only...	blob \| commitdiff
2014-04-25	Jim Procter	JAL-1177 new flag to write a dataset only jalview XML...	blob \| commitdiff \| diff to current
2014-04-21	Jim Procter	patch v2 for JAL-1474 add the newly recovered dataset...	blob \| commitdiff \| diff to current
2014-04-21	Jim Procter	patch v1 for JAL-1474 - make sure we actually set the...	blob \| commitdiff \| diff to current
2014-04-21	Jim Procter	JAL-1474 note about buggy 'merge sequence' operation...	blob \| commitdiff \| diff to current
2014-02-03	Jim Procter	Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge	blob \| commitdiff \| diff to current
2014-01-29	Jim Procter	JAL-1432 updated copyright notices	blob \| commitdiff \| diff to current
2013-10-17	Jim Procter	JAL-1397 make sure annotation colourscheme is up to...	blob \| commitdiff \| diff to current
2013-10-17	Jim Procter	JAL-1397 store colour by sequence and originalColour...	blob \| commitdiff \| diff to current
2013-09-25	Jim Procter	JAL-1270 nominal jalview version string for projects...	blob \| commitdiff \| diff to current
2012-11-08	jprocter	JAL-1193 ensure the 'loadedComplete' method gets called...	blob \| commitdiff \| diff to current
2012-11-08	jprocter	tidy imports	blob \| commitdiff \| diff to current
2012-10-24	jprocter	JAL-1193 call setLoadingFromArchiveFinished(true) for...	blob \| commitdiff \| diff to current
2012-10-22	jprocter	Jalview 2.8 Source Header	blob \| commitdiff \| diff to current
2012-10-03	jprocter	formatting	blob \| commitdiff \| diff to current
2012-09-06	jprocter	JAL-958 flag indicating if visualization settings for...	blob \| commitdiff \| diff to current
2012-09-06	jprocter	JAL-958 store/recover normalised flag	blob \| commitdiff \| diff to current
2012-09-05	jprocter	JAL-976 fix AACon name typo in source and GUI	blob \| commitdiff \| diff to current
2012-08-29	jprocter	JAL-1153 new runtime property set to first non-null...	blob \| commitdiff \| diff to current
2012-08-28	jprocter	formatting	blob \| commitdiff \| diff to current
2012-08-28	jprocter	JAL-1136 sometimes there are no parameters associated...	blob \| commitdiff \| diff to current
2012-08-28	jprocter	JAL-1148 reinstate sequence references for annotation...	blob \| commitdiff \| diff to current
2012-08-03	jprocter	JAL-1136 Ensure asynchronously calculated autoannotatio...	blob \| commitdiff \| diff to current
2012-08-03	jprocter	JAL-1136 JAL-811 JAL-812 store/recover autocalc alignme...	blob \| commitdiff \| diff to current
2012-08-03	jprocter	JAL-1136 fix logic for recovering AACons params	blob \| commitdiff \| diff to current
2012-08-03	jprocter	JAL-1136 store ws-parameter list as XML element content...	blob \| commitdiff \| diff to current
2012-07-08	jprocter	a209409239 (JAL-976 - add support for storing service...	blob \| commitdiff \| diff to current
2012-07-01	jprocter	JAL-1117 alleviate lock starvation	blob \| commitdiff \| diff to current
2012-06-13	jprocter	JAL-1115 refactor base collection for Alignment from...	blob \| commitdiff \| diff to current
2012-06-13	jprocter	javatidy	blob \| commitdiff \| diff to current
2012-05-30	jprocter	updated schema to store and recover belowAlignment...	blob \| commitdiff \| diff to current
2012-05-30	jprocter	JAL-1114 - refactor methods handling Vectors and Hashta...	blob \| commitdiff \| diff to current
2012-03-01	jprocter	Merge branch 'Release_2_7_Branch' into develop	blob \| commitdiff \| diff to current
2012-02-12	Jim Procter	(JAL-1022) reverted to original strategy of escaping...	blob \| commitdiff \| diff to current
2012-02-12	Jim Procter	(JAL-1050) ensure all filenames passed in to the load...	blob \| commitdiff \| diff to current
2012-02-12	Jim Procter	(JAL-1025 JAL-1022) File based equivalence used to...	blob \| commitdiff \| diff to current
2012-02-12	Jim Procter	(JAL-1049) only store state reference for sequence...	blob \| commitdiff \| diff to current
2011-10-27	jprocter	(JAL-969) refactored alignmentViewport base class to...	blob \| commitdiff \| diff to current
2011-10-10	jprocter	update author list in license for (JAL-826)	blob \| commitdiff \| diff to current
2011-09-27	jprocter	apply version 2.7 copyright	blob \| commitdiff \| diff to current
2011-09-16	jprocter	JAL-747 - made warning message friendlier and more...	blob \| commitdiff \| diff to current
2011-09-14	jprocter	patch for NPE (not clear if NPE is evidence of deeper...	blob \| commitdiff \| diff to current
2011-08-15	jprocter	JAL-747 - warning dialog if Jalview can't resolve filen...	blob \| commitdiff \| diff to current
2011-05-17	jprocter	refactor to allow distinct StructureSelectionManager...	blob \| commitdiff \| diff to current
2011-04-25	jprocter	JAL-824 - patch to schema to allow jmol colouring state...	blob \| commitdiff \| diff to current
2011-04-22	jprocter	comments re JAL-823 legacy issue	blob \| commitdiff \| diff to current
2011-04-21	jprocter	save and recover graph height, visibility and row posit...	blob \| commitdiff \| diff to current
2011-02-18	jprocter	bugfixing for JAL-778	blob \| commitdiff \| diff to current
2010-09-23	jprocter	apply jalview code style	blob \| commitdiff \| diff to current
2010-09-23	jprocter	Jalview 2.6 source licence	blob \| commitdiff \| diff to current
2010-09-22	jprocter	trap out of memory errors specifically associated with...	blob \| commitdiff \| diff to current
2010-09-08	jprocter	JAL-634	blob \| commitdiff \| diff to current
2010-08-27	jprocter	revised sequence/structure binding so one structure...	blob \| commitdiff \| diff to current
2010-08-20	jprocter	avoid race condition by setting sequence logo flag...	blob \| commitdiff \| diff to current
2010-08-18	jprocter	thread safe construction of Jmol instance and hack...	blob \| commitdiff \| diff to current
2010-06-29	jprocter	jmol 12 patch - ensure we replace the correct filename...	blob \| commitdiff \| diff to current
2010-06-11	jprocter	patched for JAL-531 - only display full symbol distribu...	blob \| commitdiff \| diff to current
2010-06-06	jprocter	patch for JAL-542	blob \| commitdiff \| diff to current
2010-06-03	jprocter	patch re JAL-554	blob \| commitdiff \| diff to current
2010-06-01	jprocter	patches for # JAL-254 and JAL-548	blob \| commitdiff \| diff to current
2010-04-30	jprocter	jalview 2.5 release banner	blob \| commitdiff \| diff to current
2010-04-14	jprocter	profile visualizations are now logos	blob \| commitdiff \| diff to current
2010-04-05	jprocter	Extend XML model for graduated feature colours, group...	blob \| commitdiff \| diff to current
2009-10-14	jprocter	quick fix for nullpointer in column selection when...	blob \| commitdiff \| diff to current
2009-10-13	jprocter	safer OOM handling when importing from XML	blob \| commitdiff \| diff to current
2009-06-12	jprocter	recover pdb from jalview-xml in vamsas doc	blob \| commitdiff \| diff to current
2009-06-08	jprocter	debug messages and graceful recovery when structure...	blob \| commitdiff \| diff to current
2009-03-31	jprocter	prototype for store/restore of feature colour gradient...	blob \| commitdiff \| diff to current
2009-02-06	jprocter	showUnconserved view and group setting	blob \| commitdiff \| diff to current
2008-12-15	jprocter	warning for failed parsing of newick strings	blob \| commitdiff \| diff to current
2008-11-12	jprocter	selection sending and receiving, autoscrolling to highl...	blob \| commitdiff \| diff to current
2008-09-04	jprocter	merge from 2_4_Release branch	blob \| commitdiff \| diff to current
2008-08-19	jprocter	beginning of fix for embl/cds/highlighting IO in https...	blob \| commitdiff \| diff to current
2008-05-12	jprocter	fixed Jalview project archive bug where alignment view...	blob \| commitdiff \| diff to current
2008-02-22	jprocter	sequenceId is a string, not an integer - allows generat...	blob \| commitdiff \| diff to current
2008-01-29	jprocter	flag to indicate if errors are raised as warning dialog...	blob \| commitdiff \| diff to current
2007-11-28	jprocter	bugfix	blob \| commitdiff \| diff to current
2007-11-12	jprocter	bugfix for occasional race condition causing exception...	blob \| commitdiff \| diff to current
2007-08-30	jprocter	really make sure database references are stored and...	blob \| commitdiff \| diff to current
2007-08-30	jprocter	ensure codon mappings and database references are merge...	blob \| commitdiff \| diff to current
2007-08-30	jprocter	store dataset references, sequence dataset ids, and...	blob \| commitdiff \| diff to current
2007-05-10	amwaterhouse	visibility setting	blob \| commitdiff \| diff to current
2007-05-10	amwaterhouse	Visible state of annotation	blob \| commitdiff \| diff to current
2007-05-07	amwaterhouse	Use id hash to add pdb mappings back to alignment	blob \| commitdiff \| diff to current
2007-05-04	amwaterhouse	Check bounds of loaded comp	blob \| commitdiff \| diff to current
2007-05-04	amwaterhouse	Rename AppJMol to AppJmol - also AppJmol works with...	blob \| commitdiff \| diff to current
2007-05-01	amwaterhouse	Can specify PDB chain to map sequence to - only used...	blob \| commitdiff \| diff to current
2007-05-01	amwaterhouse	Save seqset properties	blob \| commitdiff \| diff to current
2007-04-26	jprocter	use hasScore method to test presence of score in annota...	blob \| commitdiff \| diff to current
2007-04-26	amwaterhouse	check for null ss character	blob \| commitdiff \| diff to current
2007-04-25	jprocter	AlignmentAnnotation: added annotation score attribute...	blob \| commitdiff \| diff to current
2007-04-17	jprocter	pdb files are global to all alignments with new mapping...	blob \| commitdiff \| diff to current
2007-04-02	jprocter	feature group state and type order preference storage...	blob \| commitdiff \| diff to current
2007-03-26	amwaterhouse	Add seq mapping for multiple seq 2 pdbs	blob \| commitdiff \| diff to current
2007-03-22	amwaterhouse	Saves structures	blob \| commitdiff \| diff to current
2007-02-12	amwaterhouse	Hashtable for previously loaded pdb files	blob \| commitdiff \| diff to current
2007-02-07	amwaterhouse	Formatting	blob \| commitdiff \| diff to current
2007-01-31	amwaterhouse	Consensus, conservation, quality labels may have changed	blob \| commitdiff \| diff to current
2007-01-30	amwaterhouse	Check seqs in group exist in this alignment	blob \| commitdiff \| diff to current
2007-01-25	amwaterhouse	Annotations move when full alignment edited	blob \| commitdiff \| diff to current
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