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