Release of new versions of group plugins: GroupTool, NamesSelection, and MetaNodePlugin2

[Scooter Morris]

The RBVI at UCSF is pleased to release new versions of the Cytoscape group plugins.  These new versions all support the new network-specific groups that were part of Cytoscape 2.8.  In addition to network specific groups, major changes include:

• the addition of CyCommands for NamedSelection and MetaNodePlugin;
• significant reworking of the internals of the MetaNodePlugin for robustness and correctness.  MetaNodes now behave much better, in general;
• support for NodeCharts in the MetaNodePlugin to provide a visual representation of the attributes of child nodes;
• UI improvements in the MetaNodePlugin settings dialog;
• corrections and improvements to the way settings are handled by the MetaNodePlugin.

All three plugins may be found under the "Other" section of the Plugin Manager.  Detailed documentation is available at http://www.cgl.ucsf.edu/cytoscape/groups/, and the source is available at http://chianti.ucsd.edu/svn/csplugins/trunk/ucsf/scooter/

We would like to specifically thank Alex Pico of the Gladstone Institutes for his contributions and Jon Kornhauser of Cell Signaling Technology for being a patient (and persistent) tester of the many iterations of the MetaNodePlugin.

-- scooter

Detailed changes:

groupTool:

•  Additions for 2.8 network-specific groups

namedSelectionPlugin:

• Additions for 2.8 network-specific groups
• Updates to make panel look more like other CytoPanel west panels.
• Fix-ups to support metanodes better
• Added extra layer to support multiple viewers.  Also added commands to simplify interaction with other viewers.

metaNodePlugin2:

•  Updated to reflect changes in how metanode-specific settings are handled.
•  Change option order to improve usability
•  Changed so that individual metanodes remember whether they are aggregating or not.
•  Rework settings dialog significantly to separate setting defaults from setting values for a particular context.
•  Fixed opacity settings. works with nested networks too!
•  Fixed impl of expandAll/collapseAll per network view. This is critical for distinguishing operations on nested network views of metanodes. Addresses NPE at MetaNode.expand.
•  "apply to selected" now applies to metanodes whose children are selected. This allows settings to be applied to metanodes in expanded states, e.g., going from expanded to nested.
•  Added comment where opacity trail is lost for nested metanodes. Couldn't figure out how to set opacity on GroupNode.
•  Added cycommands for 'Apply to All' and 'Apply to Selected'. Without these you can not actually apply the default appearance settings.
•  Make AttributeManager an instance class so we can independently control attributes aggregation for each meta node
•  Add create command and clean up list tunables a little.
•  Fix deep nesting of metanodes
•  Consistent case on tunable "metanodeOpacity". Resolves RuntimeException: can't find tunable for metaNodeOpacity
•  appearance commands should use CHARTATTR, not ATTRIBUTE, for nodechart
•  impl expandAll and collapseAll per network (other than current) and corresponding CyCommands
•   added tunable setting and result message for SETDEFAULTAGG when enabled=true
•  Add any new edges as OuterEdges so that they get saved
•  Make sure to remember edges that user's add between metanodes and other nodes.
•  Added basic commands, but it pointed out that I need to enhance the attribute aggregation stuff to allow for metanode-specific overrides!
•  If we're calling recollapse, we need to force collapsed = true
•  Node chart and collapse/expand fixes
•  Added NodeChart functionality
•  Clean-up in conjunction with new CyGroup cleanup.
•  Fixes for opacity and attribute aggregation