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| 9/30/2005, Version 0.1 of the proposal is below. This represents Ethan's first stab at creating a new API. | 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. |
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| * 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"] | The following represents Version 0.2 notes, as agreed by Nerius, Iliana and Ethan: |
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| * 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"] |
* 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"] |
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| * {{{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"] | * {{{CyAttributes}}} uses a {{{MultiHashMap}}} as a back-end data store, but does not extend {{{MultiHashMap}}}. ["/RFC1 Comment Complex Data Structures"] |
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| * {{{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"] | * {{{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"] |
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| * 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"] |
* {{{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"] |
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| * Item not yet covered: Event / Listener Framework ["/RFC1 Comment Event Framework"] |
* {{{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"] |
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| ["/RFC1 Comment API"] | * Misc items that didn't fit in any existing category: ["/RFC1 Comment API"] |
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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] |
About this Document
This is an official Request for Comment (RFC) for replacing GraphObjAttributes.
Status
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.
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:
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"]
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"]
- Misc items that didn't fit in any existing category: ["/RFC1 Comment API"]
Proposed API: Version 0.1
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]