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| === About this Document === | === About this Document: === |
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10/4/2005, Version 0.2 of the proposal is below. This represents a beta version of the API, with input from: Nerius, Iliana, Rowan, Gary and Ethan. '''This API is officially open for public comment until __Thursday, October 13, 2005__. After that time, we will take into account all comments, generate a revised API, and the Cytostaff group will vote to accept/reject {{{CyAttributes}}} into the core.''' |
'''On 10/13/2005, the Cytoscape Developers group unanimously voted to accept {{{CyAttributes}}} into the Cytoscape core. Work on implementation has begun, and the RFC is now officially __closed to public comment__. You can still add comments, but we can't guarantee that those comments will be accepted into the API until our next Cytoscape release.''' |
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=== Proposed API: === * Version 0.2 of {{{CyAttributes}}} is now checked in CVS at: src/cytoscape/data/ * [http://cbio.mskcc.org/~cerami/cyto/docs/cytoscape/data/CyAttributes.html View Proposed JavaDocs] |
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* '''Open Item:''' support for Labels (Rowan has this feature in the current implementation of {{{CytoscapeData}}}) ["/RFC1 Comment Labels"] * '''Open Item:''' recommended attribute names ["/RFC1 Comment Attribute Names"] |
* Misc items that didn't fit in any existing category: ["/RFC1 Comment API"] |
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| * Misc items that didn't fit in any existing category: ["/RFC1 Comment API"] | === Deferred Items: === |
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| References: |
* Recommended attribute names. ["/RFC1 Comment Attribute Names"] * Support for attribute labels or categories. ["/RFC1 Comment Labels"] === References: === |
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| === Proposed API: Version 0.1 === | === Implementation Plan: === |
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* Version 0.2 of {{{CyAttributes}}} is now checked in CVS at: src/cytoscape/data/ * [http://cbio.mskcc.org/~cerami/cyto/docs/cytoscape/data/CyAttributes.html View Proposed JavaDocs] |
* ["/RFC1 Implementation Plan"] |
About this Document:
This is an official Request for Comment (RFC) for replacing GraphObjAttributes. RFCs represent one possible mechanism for soliciting feedback for core features / refactoring. 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:
On 10/13/2005, the Cytoscape Developers group unanimously voted to accept CyAttributes into the Cytoscape core. Work on implementation has begun, and the RFC is now officially closed to public comment. You can still add comments, but we can't guarantee that those comments will be accepted into the API until our next Cytoscape release.
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.
Proposed API:
Version 0.2 of CyAttributes is now checked in CVS at: src/cytoscape/data/
[http://cbio.mskcc.org/~cerami/cyto/docs/cytoscape/data/CyAttributes.html View Proposed JavaDocs]
General Notes:
The following represents Version 0.2 notes, as agreed by Nerius, Iliana and Ethan:
The new interface is now called CyAttributes. ["/RFC1 Comment Name"]
CyData is now called MultiHashMap. We wanted to give it a name that reflected its role as a core data structure. ["/RFC1 Comment CyData Name"]
CyAttributes uses a MultiHashMap as a back-end data store, but does not extend MultiHashMap. ["/RFC1 Comment Complex Data Structures"]
CyAttributes provides several overloaded versions of setAttribute, one for each basic data type, e.g. setAttribute(String id, String attributeName, Double value). It also provides several varients of getAttribute, e.g. Double getDoubleAttribute(String id, String attributeName). ["/RFC1 Comment Getters Setters"]
CyAttributes provides support for 'simple' lists. A 'simple' list is defined as follows:
- All items within the list are of the same type, and are chosen from one of the following: Boolean, Integer, Double or String. ["/RFC1 Comment Lists"]
CyAttributes provides support for 'simple' maps. A 'simple' map is defined as follows:
- All keys within the map are of type: String.
- All values within the map are of the same type, and are chosen from one of the following: Boolean, Integer, Double or String. ["/RFC1 Comment Maps"]
To do complicated things, such as create arbitarily complex data structures, you can obtain the MultiHashMap and MultiHashMapDataDefinition from CyAttributes. ["/RFC1 Comment Complex Data Structures"]
Event / Listener Framework: Coders who wish to register for attribute events can use the existing listener API provided by MultiHashMap. ["/RFC1 Comment Event Framework"]
- Misc items that didn't fit in any existing category: ["/RFC1 Comment API"]
Open Item: how to access global node / edge attributes ["/RFC1 Comment Global Attribute Access"]
Deferred Items:
- Recommended attribute names. ["/RFC1 Comment Attribute Names"]
- Support for attribute labels or categories. ["/RFC1 Comment Labels"]
References:
[http://java.sun.com/j2se/1.5.0/docs/guide/javadoc/deprecation/deprecation.html How and When To Deprecate APIs] (Java Sun Site).
Implementation Plan:
- ["/RFC1 Implementation Plan"]