Iliana: Here is my opinion on each of the proposed data structures:

*GaryBader - if we don't use the GINY implementation, then what will happen to all of the child and parent methods in GINY? Should they disappear? If so, the CyNetwork definition changes (becomes much simpler), since it would no longer support a compound graph structure.

* IlianaAvila - The question is, should GINY be a simple graph (nodes, edges, and nothing else) and additional complexity added on a different layer, or, should GINY be a complex graph (with support for nested graphs). I don't think there is a right/wrong answer. Many factors need to be considered, like, API cleanliness, code performance, etc. Maybe Nerius could tell us about this, since he seems to be rewriting our graph API.

API/CommentDataStructure (last edited 2009-02-12 01:03:38 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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