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das source browser uses local source method from jalview.bin.Cache and methods refact...
[jalview.git]
/
src
/
jalview
/
2007-11-12
jprocter
publicly accessible flag to indicate if a registry...
tree
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commitdiff
2007-11-12
jprocter
bugfix for occasional race condition causing exception...
tree
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commitdiff
2007-11-12
jprocter
comments
tree
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commitdiff
2007-11-12
jprocter
begun adding string constants for source properties
tree
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commitdiff
2007-11-12
jprocter
javadoc
tree
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commitdiff
2007-11-08
jprocter
end must be greater than blockstart
tree
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commitdiff
2007-11-08
jprocter
initialise treeCanvas before starting loading thread
tree
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commitdiff
2007-11-07
jprocter
fix accidental breakage of annotation panel redraw...
tree
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commitdiff
2007-11-07
jprocter
attempt to make fastPaint method thread safe
tree
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commitdiff
2007-11-05
jprocter
refactored syncing of alignment sequences - still buggy
tree
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commitdiff
2007-11-05
jprocter
vamsas connects and updates are threaded with a progres...
tree
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commitdiff
2007-10-31
jprocter
javadoc
tree
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commitdiff
2007-10-31
jprocter
rejiggered loadDataFile and parseFeatureFile so JNet...
tree
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commitdiff
2007-10-31
jprocter
added bugfix todo
tree
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commitdiff
2007-10-31
jprocter
concise files can now be read as a normal alignment...
tree
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commitdiff
2007-10-31
jprocter
added a quieter bailout for cases when the featuresFile...
tree
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commitdiff
2007-10-31
jprocter
factored out reference to parent alignFrame (so all...
tree
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commitdiff
2007-10-31
jprocter
beginnings of view definition capability for annotation...
tree
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commitdiff
2007-10-31
jprocter
javadoc
tree
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commitdiff
2007-10-31
jprocter
error message associated with an alignment file loading...
tree
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commitdiff
2007-10-31
jprocter
introduce new type to pass around featureRendererSettings
tree
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commitdiff
2007-10-31
jprocter
nullpointer bug fix on consensus thread
tree
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commitdiff
2007-10-31
jprocter
javadoc on webservice discovery method
tree
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commitdiff
2007-10-31
jprocter
fix parsing of embl entries like S75919 which have...
tree
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commitdiff
2007-10-29
jprocter
bugfix for alignments without aligned codon frames
tree
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commitdiff
2007-10-28
jprocter
begin process of allowing for column selection in wrapp...
tree
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commitdiff
2007-10-28
jprocter
fix display of hidden sequence markers in applet
tree
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commitdiff
2007-10-27
jprocter
must do any modification to menus before they are embed...
tree
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commitdiff
2007-10-27
jprocter
enabled platform dependent embedding of menuBar with...
tree
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commitdiff
2007-10-27
jprocter
windowclose handler now calls EmbmenuFrame garbage...
tree
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commitdiff
2007-10-27
jprocter
fixed bootstrap value rendering to occur only when...
tree
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commitdiff
2007-10-27
jprocter
refactored embedded menu machinery
tree
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commitdiff
2007-10-26
jprocter
add mac dependent use of embedded menu bar rather than...
tree
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commitdiff
2007-10-26
jprocter
use new utility class for platform info
tree
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commitdiff
2007-10-26
jprocter
new applet and application utility class for platform...
tree
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commitdiff
2007-10-26
jprocter
fixed applet API calls so they operate on the embedded...
tree
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commitdiff
2007-10-26
jprocter
updated client which allows XML validation flags to...
tree
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commitdiff
2007-10-24
jprocter
thread for product retrieval
tree
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commitdiff
2007-10-24
jprocter
ensure PDB ids are updated on the dataset sequence
tree
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commitdiff
2007-10-24
jprocter
individual query error/exception report and bugfix
tree
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commitdiff
2007-10-24
jprocter
add parsed PDB reference to sequences
tree
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commitdiff
2007-10-24
jprocter
null pointer exception and warning for update of tree
tree
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commitdiff
2007-10-24
jprocter
javadoc
tree
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commitdiff
2007-10-15
jprocter
new features or newly shown group features are placed...
tree
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commitdiff
2007-10-12
jprocter
added separator parameter with default of '|' to contro...
tree
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commitdiff
2007-10-11
jprocter
remove conflict on javascript api
tree
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commitdiff
2007-10-11
jprocter
static debug flag controlling output of excessive info...
tree
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commitdiff
2007-10-11
jprocter
pass up the errormessage in the exception when a dataso...
tree
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commitdiff
2007-10-10
jprocter
featureGroup show/hide and newView methods for applet...
tree
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commitdiff
2007-10-04
jprocter
selected region output also supports generation of...
tree
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commitdiff
2007-10-04
jprocter
refactored list of file extensions and file format...
tree
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commitdiff
2007-10-04
jprocter
edit label/displayChar contains existing character...
tree
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commitdiff
2007-10-04
jprocter
refactored invertColumnSelection as an object method
tree
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commitdiff
2007-10-02
jprocter
added colSel as a parameter formatAdaptor print functio...
tree
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commitdiff
2007-10-02
jprocter
convenience constructor for duplicating an annotation...
tree
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commitdiff
2007-10-02
jprocter
javadoc and operator for editing AlignmentAnnotation...
tree
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commitdiff
2007-10-02
jprocter
javadoc
tree
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commitdiff
2007-09-29
jprocter
always update PDBEntry list if DBRefEntries might have...
tree
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commitdiff
2007-09-29
jprocter
updatePDBEntry method to add any PDBEntry from the...
tree
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commitdiff
2007-09-29
jprocter
use pdb refsource string
tree
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commitdiff
2007-09-29
jprocter
javadoc
tree
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commitdiff
2007-09-29
jprocter
friendlier sequence names for protein products
tree
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commitdiff
2007-09-28
jprocter
better support for TreeNode binding
tree
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commitdiff
2007-09-28
jprocter
javadoc for jalview_properties tags
tree
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commitdiff
2007-09-27
jprocter
modifiable lock check
tree
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commitdiff
2007-09-25
jprocter
ascii file
tree
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commitdiff
2007-09-25
jprocter
beginning of vamsas/local object synchronization patter...
tree
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commitdiff
2007-09-25
jprocter
added store of undo/redo hash for each alignment so...
tree
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commitdiff
2007-09-25
jprocter
primitive methods for getting current undo/redo state...
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commitdiff
2007-09-18
jprocter
fix class-cast exception and added beginnings of DBRef...
tree
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commitdiff
2007-09-14
jprocter
added support for loading a vamsas document into a...
tree
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commitdiff
2007-09-14
jprocter
better reproduction of compact newick files (removal...
tree
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commitdiff
2007-09-10
jprocter
choose a particular vamsas session, load, or create...
tree
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commitdiff
2007-09-10
jprocter
ensure dbrefs are added to dataset sequence.
tree
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commitdiff
2007-09-07
jprocter
formatting and ensure that dataset is actually searched...
tree
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commitdiff
2007-09-07
jprocter
added action for saving the current session as a vamsas...
tree
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commitdiff
2007-09-07
jprocter
Maps are usually added to DbRefs which are added to...
tree
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commitdiff
2007-09-07
jprocter
added a more general DBRef search interface
tree
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commitdiff
2007-09-06
jprocter
bootstrap regex 'fixed' and ugly hack to try and get...
tree
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commitdiff
2007-09-06
jprocter
args for emblfile parser main method
tree
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commitdiff
2007-09-06
jprocter
fixes bootstrap bug noted by Chunlong Chen in email...
tree
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commitdiff
2007-09-04
jprocter
basic fix for pfelkers problem with ':' in the last...
tree
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commitdiff
2007-09-04
jprocter
gff parsing when no start or end position is defined.
tree
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commitdiff
2007-08-31
jprocter
added CSV export of annotation rows to application.
tree
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commitdiff
2007-08-30
jprocter
*really* make sure database references are stored and...
tree
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commitdiff
2007-08-30
jprocter
ensure codon mappings and database references are merge...
tree
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commitdiff
2007-08-30
jprocter
sequenceMappings go on boh datasets involved in a mappi...
tree
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commitdiff
2007-08-30
jprocter
refactored and ensured alCodonMappings are propagated...
tree
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commitdiff
2007-08-30
jprocter
store dataset references, sequence dataset ids, and...
tree
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commitdiff
2007-08-30
jprocter
improved vamsas treenode node binding support
tree
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commitdiff
2007-08-30
jprocter
moved dataset sequence creation onto sequence method
tree
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commitdiff
2007-08-30
jprocter
create dataset sequence method
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commitdiff
2007-08-30
jprocter
removed autogenerated todo
tree
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commitdiff
2007-08-30
jprocter
added aligned codon frames, and dataset reference ids...
tree
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commitdiff
2007-08-24
jprocter
dataset alignments have a reference count which must...
tree
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commitdiff
2007-08-24
jprocter
remove null pointer exception when embl file is not...
tree
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commitdiff
2007-08-24
jprocter
todo comments
tree
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commitdiff
2007-08-23
jprocter
proper vamsas style binding of alignment sequence objec...
tree
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commitdiff
2007-08-22
jprocter
popup for non-fatal tree parsing error
tree
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commitdiff
2007-08-22
jprocter
quick fix for exceptions due to invalid embl refs
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commitdiff
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