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Discussion Title : Cytoscape 3.0 Model

About this document

This document should serve to begin the discussion about the Cytoscape 3.0 model. At the 2007 Retreat, it was agreed that we would investigate a new class model for Cytoscape objects to replace the current, complicated combination of cytoscape, giny, ding, and fing models that currently provide the API for Cytoscape. Our goal at this point should be to design a model that provides a clean interface to cytoscape objects and provides the cleanest interface we can imagine for plugin writers.

General Notes

References

I have included a [attachment:Cytoscape3.cys Cytoscape session file] that demonstrates the class hierarchy. The session includes a custom Link Out URL that will pull up the JavaDoc file for that interface. I have currently written proposed interfaces for CyNetwork, CyNode, CyEdge, CyModeObject, CyGroup, CyProject, and CyModelObject. Here is an image from the session: attachment:Cytoscape3ClassHierarchy.png

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