javadoc
281 lines of code changed in:
rejiggered loadDataFile and parseFeatureFile so JNet annotation parsing is attempted before feature file parsing (avoids additional exception reports on stderr)
34 lines of code changed in:
added bugfix todo
1209 lines of code changed in:
concise files can now be read as a normal alignment, and will be displayed with annotation. See javadoc for usage notes.
23 lines of code changed in:
added a quieter bailout for cases when the featuresFile is really not going to manage to parse the file - consider revoking this in the future if it hinders debugging of features file input to jalview
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factored out reference to parent alignFrame (so all views can be closed whilst a job is in progress)
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beginnings of view definition capability for annotations file
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javadoc
1 lines of code changed in:
error message associated with an alignment file loading failure is passed back to user (finally!)
263 lines of code changed in:
introduce new type to pass around featureRendererSettings
39 lines of code changed in:
nullpointer bug fix on consensus thread
2 lines of code changed in:
javadoc on webservice discovery method
6 lines of code changed in:
fix parsing of embl entries like S75919 which have feature properties with no values
11 lines of code changed in:
bugfix for alignments without aligned codon frames
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begin process of allowing for column selection in wrapped mode.
12 lines of code changed in:
fix display of hidden sequence markers in applet
384 lines of code changed in:
must do any modification to menus before they are embedded onto a panel.
1 lines of code changed in:
new option on annotation export dialog box
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enabled platform dependent embedding of menuBar with EmbmenuFrame
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windowclose handler now calls EmbmenuFrame garbage collector.
5 lines of code changed in:
fixed bootstrap value rendering to occur only when non-negative bootstrap is attached to node.
16 lines of code changed in:
refactored embedded menu machinery
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enabled platform dependent embedding of menuBar with EmbmenuFrame
654 lines of code changed in:
refactored embedded menu machinery
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add mac dependent use of embedded menu bar rather than AWT toolbar for the non-embedded applet alignframe windows
42 lines of code changed in:
use new utility class for platform info
940 lines of code changed in:
new applet and application utility class for platform information
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fixed applet API calls so they operate on the embedded applet instance if no other views have input focus.
62 lines of code changed in:
updated client which allows XML validation flags to be controlled (to ensure that application only writes a valid document back to the session)
26 lines of code changed in:
thread for product retrieval
57 lines of code changed in:
ensure PDB ids are updated on the dataset sequence
9 lines of code changed in:
individual query error/exception report and bugfix
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add parsed PDB reference to sequences
48 lines of code changed in:
null pointer exception and warning for update of tree
6 lines of code changed in:
javadoc
9 lines of code changed in:
test autobuild of release
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contains java properties read by ant build automation
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file containing the cvs tag for the latest release
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new features or newly shown group features are placed at top of feature stack
10 lines of code changed in:
added separator parameter with default of '|' to control the list separator to use, and better debug output.
71 lines of code changed in:
remove conflict on javascript api
39 lines of code changed in:
javac.debug passed through to applet build to preserve line numbers when obfuscation is not performed.
1 lines of code changed in:
static debug flag controlling output of excessive info. showfeaturegroups and hidefeaturegroups parameters.
55 lines of code changed in:
pass up the errormessage in the exception when a datasource is not readable.
10 lines of code changed in:
jnlp amsa extension and donotobfuscate property conditional for jalviewLite build
20 lines of code changed in:
featureGroup show/hide and newView methods for applet's javascript API
1727 lines of code changed in:
selected region output also supports generation of annotations
39 lines of code changed in:
refactored list of file extensions and file format descriptions
45 lines of code changed in:
edit label/displayChar contains existing character(s) of sites to be edited
47 lines of code changed in:
refactored invertColumnSelection as an object method
4 lines of code changed in:
added colSel as a parameter formatAdaptor print function to allow editing of annotation embedded in output.
13 lines of code changed in:
convenience constructor for duplicating an annotation and editing it for hidden columns
16 lines of code changed in:
javadoc and operator for editing AlignmentAnnotation to remove hidden columns
0 lines of code changed in:
javadoc
8 lines of code changed in: