Cytoscape Wiki
Cytoscape RFC #1: Replacing Graph Obj Attributes
This is an official Request for Comment (RFC) for replacing GraphObjAttributes.
Status
9/30/2005, Version 0.1 of the proposal is below. This represents Ethan's first stab at creating a new API.
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: ["/RFC1 Comment Name"].
Try to keep your comments as concrete and constructive as possible. For example, if you find a part of the API makes no sense, please say so, but don't stop there. Take the extra step and propose alternatives.
General Notes:
I propose that the interface be called AttributeData, rather than CytoscapeData. I think this is more descriptive, and besides, not all our classes have to have the word Cytoscape in it. ["/RFC1 Comment Name"]
We provide several overloaded version of setAttribute, one for each basic data type, e.g. setAttribute(String id, String attributeName, double value). We also provide several varients of getAttribute, e.g. Double getDoubleAttribute(String id, String attributeName). ["/RFC1 Comment Getters Setters"]
AttributeData provides support for 'simple' lists. By simple, I mean that each list can only contain Objects of type: Boolean, Integer, Double and String, and each item must be of the same data type. AttributeData enforces this requirement explicitly. See proposed API below. ["/RFC1 Comment Lists"]
AttributeData provides support for 'simple' maps. By simple, I mean that all keys in the map must be of type String, and all values must be of the same type, and must be one of: Boolean, Integer, Double, and String. AttributeData enforces these requirement explicitly. See proposed API below. ["/RFC1 Comment Maps"]
To do complicated things, such as create arbitarily complex data structures, you can obtain a copy of CyData and CyDataDefinition from AttributeData. Advanced users who need this functionality can read through the CyData and CyDataDefinition Javadocs. ["/RFC1 Comment Complex Data Structures"]
- Item not yet covered: Event / Listener Framework ["/RFC1 Comment Event Framework"]
Item not yet covered: support for Labels (Rowan has this feature in the current implementation of CytoscapeData) ["/RFC1 Comment Labels"]
- Item not yet covered: recommended attribute names ["/RFC1 Comment Attribute Names"]
- ["/RFC1 Comment API"]