Differences between revisions 10 and 11

Hackathon discussion issues

GINY Refactoring

Edge IDs should be addressable, just like node IDs
We should ensure that all of Cytoscape currently assumes directed edges - how/when do we deal with undirected edges?
GINY metanode refactoring: remove meta methods - all functionality will be present in the metanode/group API. This will significantly simplify the GINY API and data structure allowing developers to be more confident that their algorithms will work on CyNetwork in general.
Refactor the GINY interface/inheritance architecture: e.g. should we encapsulate GINY in CyNetwork? See ["CyNode Identification"]
Clean up depracated methods
More Unit tests for giny to help us make these changes
Clean up Cytoscape class – duplicated methods in CyNetwork vs. Cytoscape class and the general bloat of the Cytoscape class.

What features should be in 3.0? There has been some brief discussion that the addition of metanode (group) and hyperedge concepts to the core (including some support for these in the UI) would qualify for 3.0 status.
How can plugins know which attributes are relevant to which network?
How should we deal with name clashes for cyattributes? Can we somehow detect name clashes and automate fixing these? Is this mainly a plugin issue?

-  ← Revision 10 as of 2006-08-31 17:08:37 →
  Size: 1405
  Editor: cosiapat1
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+  ← Revision 11 as of 2006-08-31 17:09:34 →
  Size: 1632
  Editor: GaryBader
  Comment:
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+ * How can plugins know which attributes are relevant to which network?

 * How should we deal with name clashes for cyattributes?  Can we somehow detect name clashes and automate fixing these?  Is this mainly a plugin issue?