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[jalview.git] / src / jalview / io /
2007-09-29 jprocteralways update PDBEntry list if DBRefEntries might have... tree | commitdiff
2007-09-28 jprocterbetter support for TreeNode binding tree | commitdiff
2007-09-27 jproctermodifiable lock check tree | commitdiff
2007-09-25 jprocterascii file tree | commitdiff
2007-09-25 jprocterbeginning of vamsas/local object synchronization patter... tree | commitdiff
2007-09-25 jprocteradded store of undo/redo hash for each alignment so... tree | commitdiff
2007-09-18 jprocterfix class-cast exception and added beginnings of DBRef... tree | commitdiff
2007-09-14 jprocterbetter reproduction of compact newick files (removal... tree | commitdiff
2007-09-07 jprocterMaps are usually added to DbRefs which are added to... tree | commitdiff
2007-09-06 jprocterbootstrap regex 'fixed' and ugly hack to try and get... tree | commitdiff
2007-09-04 jprocterbasic fix for pfelkers problem with ':' in the last... tree | commitdiff
2007-09-04 jproctergff parsing when no start or end position is defined. tree | commitdiff
2007-08-31 jprocteradded CSV export of annotation rows to application. tree | commitdiff
2007-08-30 jproctersequenceMappings go on boh datasets involved in a mappi... tree | commitdiff
2007-08-30 jprocterimproved vamsas treenode node binding support tree | commitdiff
2007-08-23 jprocterproper vamsas style binding of alignment sequence objec... tree | commitdiff
2007-08-22 jprocterintroduce beginning of bug fix for parsing atv style... tree | commitdiff
2007-08-22 jprocteradded facility for sending non-fatal warnings back... tree | commitdiff
2007-08-06 jproctercomment concerning null exceptions generated when annot... tree | commitdiff
2007-08-01 jprocterjavadoc tree | commitdiff
2007-07-25 jproctertodo comment tree | commitdiff
2007-07-25 jprocterbetter vamsas tree io (for when there are no nodemappings) tree | commitdiff
2007-07-25 jprocterbugfix for vamsas demo tree | commitdiff
2007-07-25 jprocterIO rearrangement for AMSAFile output tree | commitdiff
2007-07-13 jprocterpreliminary IO classes - read javadoc for purpose tree | commitdiff
2007-07-13 jprocternew DBRef management and generalised source and entry... tree | commitdiff
2007-07-13 jprocterupdated to iscb demo vamsas-client version tree | commitdiff
2007-07-13 jprocterrefactored form of vamsas document interaction code tree | commitdiff
2007-06-18 jprocter1.1 methods tree | commitdiff
2007-06-17 jproctervamsas-client-1.2 schema (mappings and Treenodes) and... tree | commitdiff
2007-06-17 jprocterJnetFIle is a readable format tree | commitdiff
2007-06-17 jprocterscore only annotation IO tree | commitdiff
2007-06-04 jprocterfix for 'RF' annotation tags and ensured parser is... tree | commitdiff
2007-05-22 jprocterrefactored document objects and bugfix on jvdataset... tree | commitdiff
2007-05-18 jprocterfixed getObject(VorbaId) lookup in vamsas-client tree | commitdiff
2007-05-18 jprocterupdate to and from document (and remove deprecated... tree | commitdiff
2007-05-17 jprocteruse of proper vamsas client API by Jalview tree | commitdiff
2007-05-17 jproctermodified castor-1.1 library and refactored uk.ac.vamsas tree | commitdiff
2007-05-10 jprocterapparent bug in JpredFile parser where annotation was... tree | commitdiff
2007-05-09 jproctermain method for running from command line and better... tree | commitdiff
2007-05-08 amwaterhouseaddElement tree | commitdiff
2007-05-02 jprocterpublic debug report log message to gather any cases... tree | commitdiff
2007-05-02 amwaterhouseAMSA input set padgaps true tree | commitdiff
2007-05-01 amwaterhouseMake sure annots are alignment width tree | commitdiff
2007-04-30 jprocter'no sources selected' calls method on feature settings... tree | commitdiff
2007-04-30 jprocterparse alignment properties and add annotation rows... tree | commitdiff
2007-04-30 jprocteralignment properties and embedded newick strings can... tree | commitdiff
2007-04-27 jprocterblc header lines inserted as 'comment' alignment property tree | commitdiff
2007-04-27 jprocterparsers can generate alignment properties tree | commitdiff
2007-04-27 amwaterhouseone colour flag in annotation export tree | commitdiff
2007-04-26 jprocteruse hasScore method to test presence of score in annota... tree | commitdiff
2007-04-26 jprocterquick fix for verbose fortranesque comments in preamble... tree | commitdiff
2007-04-26 jprocterfixed bug in prefix extraction for application tree | commitdiff
2007-04-25 amwaterhouseproperties + colours tree | commitdiff
2007-04-25 amwaterhousefix recent file type bug tree | commitdiff
2007-04-25 jprocterAlignmentAnnotation: added annotation score attribute... tree | commitdiff
2007-04-23 amwaterhouseCheck displayChar is not null tree | commitdiff
2007-04-23 amwaterhouseOnly fetch refs for seelcted sequences tree | commitdiff
2007-04-20 jprocterannotation and seqs vectors are protected members for... tree | commitdiff
2007-04-18 amwaterhousedont set seqref null if index incorrect tree | commitdiff
2007-04-18 amwaterhouseadjustForAlignment on new seq ref tree | commitdiff
2007-04-18 jprocterjava 1.1 compliance tree | commitdiff
2007-04-17 jprocterbugfix. tree | commitdiff
2007-04-17 jprocteruse of suffix string (filename.blc#suffixstring) to... tree | commitdiff
2007-04-17 jprocterrefactored to allow seeks on a FileParse datasource... tree | commitdiff
2007-04-17 jprocterjavadoc tree | commitdiff
2007-04-13 amwaterhouseFeatureRenderer takes alignmentPanel tree | commitdiff
2007-04-05 amwaterhousePasted file doesnt have title and not reloadable tree | commitdiff
2007-04-05 amwaterhousecall getAllframes on desktop instance tree | commitdiff
2007-04-04 amwaterhouseflag for dasCoordSysFound added tree | commitdiff
2007-03-19 jprocterDAS features mapped to local reference frame tree | commitdiff
2007-03-19 jprocterdisambiguate jalview.datamodel.Mapping from castor... tree | commitdiff
2007-02-27 amwaterhouseUse paintAlignment tree | commitdiff
2007-02-27 amwaterhouseremove p+3 < query.length tree | commitdiff
2007-02-07 amwaterhouseFormatting tree | commitdiff
2007-02-05 amwaterhouseapplet can define groups as parameters tree | commitdiff
2007-02-02 amwaterhouseDont add group if seqs not found tree | commitdiff
2007-01-30 amwaterhouseAny character non aa or nucleotide is a space tree | commitdiff
2007-01-30 amwaterhouseUse util toHexString tree | commitdiff
2007-01-30 amwaterhouseOutput groups in annotation file tree | commitdiff
2007-01-29 amwaterhouseSequenceGroup parsing added to annotation file tree | commitdiff
2007-01-25 amwaterhouseRemove unneccessary lines tree | commitdiff
2007-01-25 amwaterhouseOnly output visible annotations tree | commitdiff
2007-01-25 jprocterreinstating class implementation. tree | commitdiff
2007-01-24 amwaterhouseoutput now takes alignment, not just sequences tree | commitdiff
2007-01-24 amwaterhouseExtension to fastaFile for myhits tree | commitdiff
2007-01-19 amwaterhouseNeed to know protocol to load anntotations tree | commitdiff
2007-01-18 amwaterhouseAdd the last sequence before annotations tree | commitdiff
2007-01-18 amwaterhouse1.1 enabled tree | commitdiff
2007-01-18 amwaterhouseFile Parsing returns Alignments, not Sequence[] tree | commitdiff
2007-01-18 amwaterhouseDescriptions can be added to annotations tree | commitdiff
2007-01-04 amwaterhouseReads in anything following seq id as a description tree | commitdiff
2007-01-04 amwaterhouseHEADER and ATOM must be position 0 tree | commitdiff
2006-12-21 jprocterdescription from vamsas sequence and file type change tree | commitdiff
2006-12-21 amwaterhouseremove unnecessary import tree | commitdiff
2006-12-19 amwaterhousedescription may be null tree | commitdiff
2006-12-14 amwaterhouseset sequence_ref alignment tree | commitdiff
2006-12-14 amwaterhouseAre the labels all secondary Strutures? are the display... tree | commitdiff
2006-12-11 jprocterfixed introduced bug (doh) tree | commitdiff
2006-12-11 jprocterclarified help documentation for annotation file format... tree | commitdiff
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