Cytoscape Wiki|
Size: 524
Comment:
|
Size: 2711
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| This is an official Request for Comment (RFC) for the new Cytoscape Data API. |
## page was renamed from RFC1 HOME ## page was renamed from CytoscapeData RFC [[TableOfContents([2])]] |
| Line 3: | Line 5: |
| '''Status:''' Version 0.1 of the proposal is below. This represents Ethan's first stab at creating a new API. | === About this Document === |
| Line 5: | Line 7: |
| '''How to Comment:''' To view/add comments, click on any of the links below, and add your comments directly to the Wiki. | This is an official Request for Comment (RFC) for replacing {{{GraphObjAttributes}}}. |
| Line 7: | Line 9: |
| '''General Notes:''' | === Status === |
| Line 9: | Line 11: |
| * The interface is now 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. |
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 new interface is now called {{{CyAttributes}}}. ["/RFC1 Comment Name"] * The API provides several overloaded version 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 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"] === Proposed API: Version 0.1 === |
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 new interface is now called CyAttributes. ["/RFC1 Comment Name"]
The API provides several overloaded version 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 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"]