FileParse object can be re-used to read different files concatenated together
[jalview.git] / src / jalview /
2007-10-02 jprocterconvenience constructor for duplicating an annotation...
2007-10-02 jprocterjavadoc and operator for editing AlignmentAnnotation...
2007-10-02 jprocterjavadoc
2007-09-29 jprocteralways update PDBEntry list if DBRefEntries might have...
2007-09-29 jprocterupdatePDBEntry method to add any PDBEntry from the...
2007-09-29 jprocteruse pdb refsource string
2007-09-29 jprocterjavadoc
2007-09-29 jprocterfriendlier sequence names for protein products
2007-09-28 jprocterbetter support for TreeNode binding
2007-09-28 jprocterjavadoc for jalview_properties tags
2007-09-27 jproctermodifiable lock check
2007-09-25 jprocterascii file
2007-09-25 jprocterbeginning of vamsas/local object synchronization patter...
2007-09-25 jprocteradded store of undo/redo hash for each alignment so...
2007-09-25 jprocterprimitive methods for getting current undo/redo state...
2007-09-18 jprocterfix class-cast exception and added beginnings of DBRef...
2007-09-14 jprocteradded support for loading a vamsas document into a...
2007-09-14 jprocterbetter reproduction of compact newick files (removal...
2007-09-10 jprocterchoose a particular vamsas session, load, or create...
2007-09-10 jprocterensure dbrefs are added to dataset sequence.
2007-09-07 jprocterformatting and ensure that dataset is actually searched...
2007-09-07 jprocteradded action for saving the current session as a vamsas...
2007-09-07 jprocterMaps are usually added to DbRefs which are added to...
2007-09-07 jprocteradded a more general DBRef search interface
2007-09-06 jprocterbootstrap regex 'fixed' and ugly hack to try and get...
2007-09-06 jprocterargs for emblfile parser main method
2007-09-06 jprocterfixes bootstrap bug noted by Chunlong Chen in email...
2007-09-04 jprocterbasic fix for pfelkers problem with ':' in the last...
2007-09-04 jproctergff parsing when no start or end position is defined.
2007-08-31 jprocteradded CSV export of annotation rows to application.
2007-08-30 jprocter*really* make sure database references are stored and...
2007-08-30 jprocterensure codon mappings and database references are merge...
2007-08-30 jproctersequenceMappings go on boh datasets involved in a mappi...
2007-08-30 jprocterrefactored and ensured alCodonMappings are propagated...
2007-08-30 jprocterstore dataset references, sequence dataset ids, and...
2007-08-30 jprocterimproved vamsas treenode node binding support
2007-08-30 jproctermoved dataset sequence creation onto sequence method
2007-08-30 jproctercreate dataset sequence method
2007-08-30 jprocterremoved autogenerated todo
2007-08-30 jprocteradded aligned codon frames, and dataset reference ids...
2007-08-24 jprocterdataset alignments have a reference count which must...
2007-08-24 jprocterremove null pointer exception when embl file is not...
2007-08-24 jproctertodo comments
2007-08-23 jprocterproper vamsas style binding of alignment sequence objec...
2007-08-22 jprocterpopup for non-fatal tree parsing error
2007-08-22 jprocterquick fix for exceptions due to invalid embl refs
2007-08-22 jprocterfix serious repetitive exceptions if user closes colour...
2007-08-22 jproctercatch occasional -ve imgWidth exception
2007-08-22 jprocteradded failsafe fix for cases where null sequence names...
2007-08-22 jprocterintroduce beginning of bug fix for parsing atv style...
2007-08-22 jprocteradded facility for sending non-fatal warnings back...
2007-08-13 jprocterfixed typo in new 2_3 startup file default value
2007-08-08 jproctergeneralise name of prediction method
2007-08-08 jprocterhistidine should be midblue (noticed by Peter Knight...
2007-08-06 jproctercomment concerning null exceptions generated when annot...
2007-08-06 jprocternull pointer exception blocked redraw of annotation...
2007-08-02 jprocterjavadoc and bugfix for 'save' when jalview is default...
2007-08-01 jprocteradded the '-tree' parameter to open a tree from the...
2007-08-01 jprocterjavadoc
2007-08-01 jprocterensure current dataset reference is passed to the cross...
2007-08-01 jprocteradded tree as an applet to application servlet parameter
2007-08-01 jprocternull pointer exception bug fix
2007-07-31 jprocterdebugging cross references and duplicate sequence db...
2007-07-30 jproctertest cc change revoked.
2007-07-30 jproctertest cc
2007-07-30 jprocterjavadoc
2007-07-25 jproctertodo comment
2007-07-25 jprocterfix crossRef retrieval so either protein OR nucleotide
2007-07-25 jprocteruniprot synonym
2007-07-25 jprocterbetter vamsas tree io (for when there are no nodemappings)
2007-07-25 jprocterbugfix for vamsas demo
2007-07-25 jprocterIO rearrangement for AMSAFile output
2007-07-25 jprocterbugfix for vamsas demo and IO rearrangement for AMSAFil...
2007-07-13 jprocterpreliminary IO classes - read javadoc for purpose
2007-07-13 jprocterpickmanager on sequence and alignment position, vamsas...
2007-07-13 jprocternew DBRef management and generalised source and entry...
2007-07-13 jproctermore semantic groupings of dbs
2007-07-13 jprocterdebugged mappings and translated sequence recovery
2007-07-13 jprocterpreliminary states for pca distribution io
2007-07-13 jprocterpreliminary methods for detecting internal sequence...
2007-07-13 jprocterbugfix
2007-07-13 jproctermapping bug fixes
2007-07-13 jprocterbasic idea for recognising that a feature is a coding...
2007-07-13 jprocterbugfixes, partially working code for translation using...
2007-07-13 jproctercomments for future viz/detection of internal sequence...
2007-07-13 jprocterupdated to iscb demo vamsas-client version
2007-07-13 jprocterrefactored form of vamsas document interaction code
2007-07-13 jproctermethods for traversing database reference space
2007-07-13 jprocternew search method for finding references like other...
2007-07-13 jprocterbugfix and comments
2007-07-13 jproctermoved to castor-1.1-cycle - a specially patched version...
2007-06-18 jprocterensure lines are drawn from first alignment column.
2007-06-18 jprocter1.1 methods
2007-06-17 jproctervamsas-client-1.2 schema (mappings and Treenodes) and...
2007-06-17 jproctervamsas mouseOvers
2007-06-17 jprocterenable mouseover between DNA coding regions and transla...
2007-06-17 jprocterenable mouseover between DNA coding regions and transla...
2007-06-17 jprocterfix aligned DNA codon translation bug(s) and generate...
2007-06-17 jprocterrecovery of identical dataset sequence object on undo...
2007-06-17 jprocterAlignedCodonFrame holds mapping information between...
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