We count the number of open GUIs because we may want to terminate the currently running JVM if this drops to zero. (Or otherwise warn if we do so to update gMCP or ...)
Added two R CMD check notes.
Code for the R/gMCP bundle.
Updated ToDo.
Fixed: NumberFormatException during editing component graph weights are caught.
Added reference to Bonferroni to "No information about correlation".
Always initialize new nodes for entangled graphs with the correct number of weights.
Substitute epsilon edges for entangled graphs.
RUnit tests for entangled graphs.
Corrected upscale parameter.
Load matrix from main GUI if it is specified there.
WIP: For now load and save config file in user home directory.
Now also the first graph of an entangled graph can be removed. (Easier than I thought to implement.)
Fixed highlighting for different layers of entangled graphs and changed linewidth of highlighted edges to 3 (from 5).
Clean up and better description of extended RUnit tests.
Some work on annotations. All objects are of class Annotation. They can be saved as JSON strings and created from those. (Therefore there is a new java library javax.json-api-1.0.jar for all older systems.)
New annotation `Legend`. Not sure whether and how this will be constucted by using the base classes.
Requiring CommonJavaJars 1.0.5 and loading json jar.
Replaced API with Runtime in CommonJavaJars.
First progress on reading and writing annotations to JSON.