Diff for "groupAPI"

TableOfContents([2])

About this document

This is an official Request for Comment (RFC) for supporting groups in Cytoscape. This RFC encompasses and leverages the MetaNodes RFC (RFC 8) and the SimplifiedMetaNodeDataStructureRFC (RFC 9) by extending the notion of a metanode, to a more general group concept.

For details on RFCs in general, check out the [http://www.answers.com/main/ntquery?method=4&dsid=2222&dekey=Request+for+Comments&gwp=8&curtab=2222_1&linktext=Request%20for%20Comments Wikipedia Entry: Request for Comments (RFCs)]

Status

Not yet completely written

How to Comment

To view/add comments, click on any of 'Comment' links below. By adding your ideas to the Wiki directly, we can more easily organize everyone's ideas, and keep clear records. Be sure to include today's date and your name for each comment. Here is an example to get things started: ["/Comment"].

Try to keep your comments as concrete and constructive as possible. For example, if you find a part of the RFC makes no sense, please say so, but don't stop there. Take the extra step and propose alternatives.

Proposal

The goal is to provide a new package, e.g. cytoscape.groups, that suplants all direct calls to the giny metanodes methods, and extends the concept of metanodes in a structured manner. Similar to the MetaNodes implementation, there is a [http://www.cgl.ucsf.edu/Research/cytoscape/groupAPI/doc/edu/ucsf/groups/GroupUtils.html GroupUtils] class that should be the main interface for most developer. There are also three interfaces to allow a group to have different abstraction models and different visual properties. The three interfaces are:

• [http://www.cgl.ucsf.edu/Research/cytoscape/groupAPI/doc/edu/ucsf/groups/model/GroupAbstractionModel.html GroupAbstractionModel] - provides an interface for classes that handle the model associated with presentation of grouped nodes,

• [http://www.cgl.ucsf.edu/Research/cytoscape/groupAPI/doc/edu/ucsf/groups/view/GroupAbstractionViewer.html GroupAbstractionViewer] - an interface for classes that handle the actual presentation of groups, and

• [http://www.cgl.ucsf.edu/Research/cytoscape/groupAPI/doc/edu/ucsf/groups/data/GroupAttributesHandler.html GroupAttributesHandler] - an interface for classes that handle the node and edge attributes of groups.

This package must be in the core to provide direct, consistent access to the grouping API for the XGMML reader/writer, the Cytoscape Editor, and the Metanode Plugin (which will still be provided as one interface to grouping). An [http://www.cgl.ucsf.edu/Research/cytoscape/groupAPI/doc Overview] of the proposed API is available for comment.

Biological Questions / Use Cases

See the MetaNodes RFC for a list of common use cases.

Implementation Plan

• ["/Implementation Plan"]

Comments

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