always update PDBEntry list if DBRefEntries might have changed
1 lines of code changed in:
updatePDBEntry method to add any PDBEntry from the list of DBRefEntries
73 lines of code changed in:
use pdb refsource string
0 lines of code changed in:
javadoc
3 lines of code changed in:
friendlier sequence names for protein products
8 lines of code changed in:
better support for TreeNode binding
2 lines of code changed in:
javadoc for jalview_properties tags
62 lines of code changed in:
switched to apache zip tool for doc IO
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modifiable lock check
2 lines of code changed in:
ascii file
1364 lines of code changed in:
beginning of vamsas/local object synchronization pattern implementation.
85 lines of code changed in:
ascii file
234 lines of code changed in:
added store of undo/redo hash for each alignment so local state changes can be detected. Dataset and alignment sequences are now synchronised with document on updates and commits.
235 lines of code changed in:
primitive methods for getting current undo/redo state and comparing with another (to be used for indicating if an alignment is unsaved since last changed, or in the vamsas synchronization mechanism)
35 lines of code changed in:
fix class-cast exception and added beginnings of DBRef inference mechanism
85 lines of code changed in:
pathological vamsas archive update fix ?
0 lines of code changed in:
ascii file
0 lines of code changed in:
added support for loading a vamsas document into a new vamsas session.
216 lines of code changed in:
better reproduction of compact newick files (removal of unecessary spaces)
7 lines of code changed in:
choose a particular vamsas session, load, or create a new session and export the current session.
201 lines of code changed in:
ensure dbrefs are added to dataset sequence.
4 lines of code changed in:
client update to fix appData read triggering document modification bug.
0 lines of code changed in:
formatting and ensure that dataset is actually searched for sequences with dbrefs that correspond to a dbref crossreference sequence being retrieved (still outstanding bug for embl->proteinprod->emblcds retrieval
0 lines of code changed in:
added action for saving the current session as a vamsas archive.
50 lines of code changed in:
Maps are usually added to DbRefs which are added to dataset sequences.
1 lines of code changed in:
added a more general DBRef search interface
183 lines of code changed in:
bootstrap regex 'fixed' and ugly hack to try and get comment skip working correctly for chunglong chen .branch file (sent to help at jalview)
36 lines of code changed in:
args for emblfile parser main method
11 lines of code changed in:
fixes bootstrap bug noted by Chunlong Chen in email to jalview-help
669 lines of code changed in:
removed href in the jnlp generation
2 lines of code changed in:
basic fix for pfelkers problem with ':' in the last saved file history - outstanding todo to ensure that user is prompted to choose a better filename.
296 lines of code changed in:
gff parsing when no start or end position is defined.
0 lines of code changed in: