IlianaAvila 3-29-06. I have put some more thought on this whole grouping/metanode problem, and I have a new approach for 2.3. Please read my /NewApiApproachForMetaNodes. Thanks.

The following content was created before 3-29-06:

Please review the Java-Docs at http://db.systemsbiology.net/cytoscape/grouping/gdoc/ and comment.

To give you a better idea of how the interfaces work together, here is an example:

{{{
// Example 1. Algorithm calculated groups:

CyNetwork [] groups = someAlgorithm.calculateGroups(someArgs);
groupManager.addGroupsToNetwork(myNetwork);
GroupingStrategy collapsingStrategy = 
     GroupingStrategyFactory.createGroupingStrategy(GroupingStrategyFactory.COLLAPSING_STRATEGY);
GroupingStrategy stackingStrategy =
     GroupingStrategyFactory.createGroupingStrategy(GroupingStrategyFactory.STACKING_STRATEGY);
for(int i = 0; i < groups.length; i++){

   // Layout the nodes in a column
   stackingStrategy.group(myNetwork,groups[i]);

   if(groups[i].nodeCount() > SOME_LIMIT)
        // collapse groups that are too large
        collapsingStrategy.group(myNetwork,groups[i]); 
}
}}}

/CommentInterfaces

Notes:

 1. I decided to name the interfaces in this API using the {{{group}}} word instead of the {{{MetaNode}}} word. A {{{MetaNode}}} is a way of grouping nodes/edges in a graph. The more general concept is grouping.

/CommentSemantics (is {{{Group}}} a good word to use? what other wording would you suggest?)

 1. The {{{GroupingManager}}} is an interface to the data structure that stores groups for Cytoscape networks. We have not decided what data structure will do this. Alternatives that have been mentioned in the past are:
  * {{{CyAttributes}}}
  * {{{CyNodes}}} (as it is done currently)
  * A new data structure

/CommentDataStructure