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[jalview.git] / src / jalview / io / AnnotationFile.java

2015-08-10	Jim Procter	Merge branch 'release/2_9_documentation' into develop	blob \| commitdiff
2015-07-23	Jim Procter	JAL-1819 commented out debugging message to stderr bug/JAL-1819_isNaN	blob \| commitdiff \| diff to current
2015-07-23	Jim Procter	JAL-1819 use Float.isNaN() to check for NaNs!	blob \| commitdiff \| diff to current
2015-06-30	Jim Procter	JAL-1682 JAL-1645 remove references to 2.8.3	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	JAL-1683 replace year/version strings with tokens in...	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	reassign features already created/documented for 2...	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...	blob \| commitdiff \| diff to current
2015-01-23	Jim Procter	JAL-1628 tweak signature of core annotation printer...	blob \| commitdiff \| diff to current
2015-01-23	Jim Procter	JAL-1628 drop getShowAnnotation accessor in favour...	blob \| commitdiff \| diff to current
2015-01-18	Jim Procter	JAL-1628 new entry point for reading annotation files...	blob \| commitdiff \| diff to current
2015-01-18	Jim Procter	JAL-1628 formatting and javadoc	blob \| commitdiff \| diff to current
2014-12-15	Jim Procter	JAL-1620 version bump and release notes	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 source formatting	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 fix copyright for 2.8.2	blob \| commitdiff \| diff to current
2014-06-05	Jim Procter	JAL-1517 update copyright to version 2.8.2	blob \| commitdiff \| diff to current
2014-05-22	Jim Procter	JAL-1503 update version in GPL header	blob \| commitdiff \| diff to current
2014-04-21	Jim Procter	fix for JAL-1478	blob \| commitdiff \| diff to current
2014-01-29	Jim Procter	JAL-1432 updated copyright notices	blob \| commitdiff \| diff to current
2013-06-21	Jim Procter	JAL-1325 JAL-1294 resolve SEQUENCE_REF and GROUP_REF...	blob \| commitdiff \| diff to current
2013-06-21	Jim Procter	JAL-1294 JAL-1325 store graphline for individual annota...	blob \| commitdiff \| diff to current
2013-05-24	Jim Procter	patch for JAL-1300 fixes JAL-1294: read and write COMBI...	blob \| commitdiff \| diff to current
2013-05-24	Jim Procter	JAL-1299 fix: ensure a new graphGroup is created if...	blob \| commitdiff \| diff to current
2013-05-24	Jim Procter	fix for JAL-1297: COMBINE output now follows specificat...	blob \| commitdiff \| diff to current
2013-05-24	Jim Procter	JAL-1070 - [ not a real patch ] - include offending...	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
2012-05-30	jprocter	JAL-1114 - refactor methods handling Vectors and Hashta...	blob \| commitdiff \| diff to current
2011-10-21	jprocter	todo	blob \| commitdiff \| diff to current
2011-10-10	jprocter	update author list in license for (JAL-826)	blob \| commitdiff \| diff to current
2011-10-04	jprocter	Merge remote-tracking branch 'remotes/origin/2_5_1_rna_...	blob \| commitdiff \| diff to current
2011-09-27	jprocter	apply version 2.7 copyright	blob \| commitdiff \| diff to current
2011-07-25	janengelhardt	JAL-841; Structure trigger token in jalview.io.Alignmen...	blob \| commitdiff \| diff to current
2011-01-05	jprocter	JAL-727	blob \| commitdiff \| diff to current
2010-12-15	jprocter	more accurate determination of annotation modification	blob \| commitdiff \| diff to current
2010-12-15	jprocter	refactored key calc for hash to separate function	blob \| commitdiff \| diff to current
2010-11-14	jprocter	import annotation file from datasource	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
2010-06-06	jprocter	patch for JAL-542	blob \| commitdiff \| diff to current
2010-06-03	jprocter	patch and error reports re JAL-554	blob \| commitdiff \| diff to current
2010-04-30	jprocter	jalview 2.5 release banner	blob \| commitdiff \| diff to current
2010-04-28	jprocter	group/annotation association	blob \| commitdiff \| diff to current
2010-04-23	jprocter	skips any annotation that appears to be identical to...	blob \| commitdiff \| diff to current
2010-04-23	jprocter	next attempt for Bug #36198 - appears to work reproducibly	blob \| commitdiff \| diff to current
2010-04-16	jprocter	patch for bug #36198 - more to follow on Monday.	blob \| commitdiff \| diff to current
2010-03-22	jprocter	See note in Mantis bug #55537 : inconsistency between...	blob \| commitdiff \| diff to current
2010-03-12	jprocter	1.1 compatibility	blob \| commitdiff \| diff to current
2010-03-11	jprocter	new ROWPROPERTIES statement for setting an individual...	blob \| commitdiff \| diff to current
2010-01-28	jprocter	quick fix for very broken checkin - see Mantis bug...	blob \| commitdiff \| diff to current
2010-01-28	jprocter	more rigorous annotation row content check to limit...	blob \| commitdiff \| diff to current
2009-09-22	jprocter	allow the display character below a graph to be explici...	blob \| commitdiff \| diff to current
2009-07-24	jprocter	todo	blob \| commitdiff \| diff to current
2009-06-08	jprocter	apply gpl development license	blob \| commitdiff \| diff to current
2009-02-06	jprocter	showUnconserved IO	blob \| commitdiff \| diff to current
2008-11-04	jprocter	beginning of implementation of new properties for hide...	blob \| commitdiff \| diff to current
2008-09-24	jprocter	fixed sequence associated annotation reading bug where...	blob \| commitdiff \| diff to current
2008-09-04	jprocter	merge from 2_4_Release branch	blob \| commitdiff \| diff to current
2008-08-20	jprocter	Use 0f rather than NaN to specify non-valued annotation...	blob \| commitdiff \| diff to current
2008-07-18	jprocter	resolve 1:many mappings for sequence associated annotat...	blob \| commitdiff \| diff to current
2008-07-18	jprocter	comment	blob \| commitdiff \| diff to current
2008-07-18	jprocter	annotation file format updated to take idColour and...	blob \| commitdiff \| diff to current
2007-10-31	jprocter	beginnings of view definition capability for annotation...	blob \| commitdiff \| diff to current
2007-08-31	jprocter	added CSV export of annotation rows to application.	blob \| commitdiff \| diff to current
2007-08-06	jprocter	comment concerning null exceptions generated when annot...	blob \| commitdiff \| diff to current
2007-06-17	jprocter	score only annotation IO	blob \| commitdiff \| diff to current
2007-04-27	amwaterhouse	one colour flag in annotation export	blob \| commitdiff \| diff to current
2007-04-26	jprocter	use hasScore method to test presence of score in annota...	blob \| commitdiff \| diff to current
2007-04-25	amwaterhouse	properties + colours	blob \| commitdiff \| diff to current
2007-04-25	jprocter	AlignmentAnnotation: added annotation score attribute...	blob \| commitdiff \| diff to current
2007-04-23	amwaterhouse	Check displayChar is not null	blob \| commitdiff \| diff to current
2007-04-18	amwaterhouse	dont set seqref null if index incorrect	blob \| commitdiff \| diff to current
2007-04-18	amwaterhouse	adjustForAlignment on new seq ref	blob \| commitdiff \| diff to current
2007-02-07	amwaterhouse	Formatting	blob \| commitdiff \| diff to current
2007-02-05	amwaterhouse	applet can define groups as parameters	blob \| commitdiff \| diff to current
2007-02-02	amwaterhouse	Dont add group if seqs not found	blob \| commitdiff \| diff to current
2007-01-30	amwaterhouse	Output groups in annotation file	blob \| commitdiff \| diff to current
2007-01-29	amwaterhouse	SequenceGroup parsing added to annotation file	blob \| commitdiff \| diff to current
2007-01-19	amwaterhouse	Need to know protocol to load anntotations	blob \| commitdiff \| diff to current
2007-01-18	amwaterhouse	Descriptions can be added to annotations	blob \| commitdiff \| diff to current
2006-12-14	amwaterhouse	set sequence_ref alignment	blob \| commitdiff \| diff to current
2006-12-14	amwaterhouse	Are the labels all secondary Strutures? are the display...	blob \| commitdiff \| diff to current
2006-12-11	jprocter	fixed introduced bug (doh)	blob \| commitdiff \| diff to current
2006-12-11	jprocter	clarified help documentation for annotation file format...	blob \| commitdiff \| diff to current
2006-12-05	amwaterhouse	Sequence is char []	blob \| commitdiff \| diff to current
2006-08-29	amwaterhouse	createMapping alreadyMapped	blob \| commitdiff \| diff to current
2006-07-07	amwaterhouse	Dont discard label if different to H or E	blob \| commitdiff \| diff to current
2006-07-07	amwaterhouse	Dont write graph type twice	blob \| commitdiff \| diff to current
2006-06-09	amwaterhouse	Annotation/feature exporter	blob \| commitdiff \| diff to current

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