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added showUnconserved property to group and view attributes
[jalview.git] / src / jalview / io /
2009-01-08 jprocterfix broken parsing of non-positional features in GFF... tree | commitdiff
2008-12-19 jprocteravoid null pointer exception when no features visible tree | commitdiff
2008-12-15 jprocteradded (and enabled) switch to store gff source string... tree | commitdiff
2008-11-12 jprocterrefactored to propery separate addToDocument,addFromDoc... tree | commitdiff
2008-11-12 jprocternew viewport IDs and jalview XML storage/sync in vamsas... tree | commitdiff
2008-11-12 jprocteradded todo regarding import of GFF2 key=value attributes tree | commitdiff
2008-11-04 jprocterbeginning of implementation of new properties for hide... tree | commitdiff
2008-11-04 jprocterapplication specific validIOformat method tree | commitdiff
2008-09-24 jprocterfixed sequence associated annotation reading bug where... tree | commitdiff
2008-09-16 jprocterjava 1.1 compatibility tree | commitdiff
2008-09-16 jprocterfix exception raised when JNet concise files with no... tree | commitdiff
2008-09-04 jproctermerge from 2_4_Release branch tree | commitdiff
2008-08-27 jprocterno newline after licence comment tree | commitdiff
2008-08-20 jprocterUse 0f rather than NaN to specify non-valued annotation... tree | commitdiff
2008-08-06 jprocterextra checks for datasetsequence for when getDbRefs... tree | commitdiff
2008-07-18 jprocterresolve 1:many mappings for sequence associated annotat... tree | commitdiff
2008-07-18 jprocterresolve 1:many mappings from feature sequence ID to... tree | commitdiff
2008-07-18 jproctercomment tree | commitdiff
2008-07-18 jprocterannotation file format updated to take idColour and... tree | commitdiff
2008-07-11 jprocterensure annotationElements in non-graphical annotation... tree | commitdiff
2008-06-30 jproctertiming of 'on load' output before any gui thread operations tree | commitdiff
2008-04-29 jproctertrial fix for parsing NHX style trees to extract the... tree | commitdiff
2008-04-21 jprocterdocumented and refactored to facilitate headless featur... tree | commitdiff
2008-04-10 jprocterbug fix for Features/Annotations file parameter parsing... tree | commitdiff
2008-02-22 jproctervalid format for writing test tree | commitdiff
2008-01-29 jprocterminor change to output of main method for testing file IO tree | commitdiff
2008-01-29 jproctermemory usage information and flag to indicate if warnin... tree | commitdiff
2008-01-29 jprocteradd methods to read from current position of existing... tree | commitdiff
2008-01-29 jprocterensure mark is set before identification is started. tree | commitdiff
2008-01-29 jprocterFileParse object can be re-used to read different files... tree | commitdiff
2008-01-22 jproctertimings and memory usage for reading in a file tree | commitdiff
2008-01-22 jproctermore efficient parsing of large files, do not create... tree | commitdiff
2008-01-21 jprocterfix regex for annotation subtype to use non-whitespace... tree | commitdiff
2008-01-21 jprocterjavadoc and main method for testing file input routines tree | commitdiff
2008-01-21 jprocterjavadoc tree | commitdiff
2007-12-21 jprocterbugfixes tree | commitdiff
2007-12-13 jprocterjava 1.1 compatibility (again) tree | commitdiff
2007-12-13 jprocterjava 1.1 compatibility (again) tree | commitdiff
2007-11-30 jproctercase invariant matching of seqeunce feature to sequence... tree | commitdiff
2007-11-05 jprocterrefactored syncing of alignment sequences - still buggy tree | commitdiff
2007-10-31 jprocterconcise files can now be read as a normal alignment... tree | commitdiff
2007-10-31 jprocteradded a quieter bailout for cases when the featuresFile... tree | commitdiff
2007-10-31 jprocterbeginnings of view definition capability for annotation... tree | commitdiff
2007-10-31 jprocterjavadoc tree | commitdiff
2007-10-31 jproctererror message associated with an alignment file loading... tree | commitdiff
2007-10-24 jprocteradd parsed PDB reference to sequences tree | commitdiff
2007-10-24 jprocternull pointer exception and warning for update of tree tree | commitdiff
2007-10-24 jprocterjavadoc tree | commitdiff
2007-10-11 jprocterpass up the errormessage in the exception when a dataso... tree | commitdiff
2007-10-04 jprocterselected region output also supports generation of... tree | commitdiff
2007-10-04 jprocterrefactored list of file extensions and file format... tree | commitdiff
2007-10-02 jprocteradded colSel as a parameter formatAdaptor print functio... tree | commitdiff
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
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