Cytoscape Wiki
About this document
This is an official Request for Comment (RFC) for a Cytoscape Quick Find Feature.
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
Open for public comment.
How to Comment
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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
This RFC proposes a new Cytoscape Quick Find feature. The goal of the feature is to enable Cytoscape users to quickly find nodes, and select them in the network view.
The feature will be based loosely on [http://www.google.com/webhp?complete=1&hl=en Google Suggest]. In Google Suggest, a user types a few characters, and Google automatically provides matching search terms which begin with these characters. Along the same lines, a Cytoscape users will type a few characters into a text box, and Cytoscape will automatically provide matching nodes which begin with these characters. The user can then select one of these matching terms, and the nodes will be automatically selected in the network view.
Here is a screenshot of my current prototype in action:
attachment:quick_find.png
Features
By default, Quick Find will automatically index nodes based on Semantics.CANONICAL_NAME, and matching nodes will automatically be selected in the network view.
For more advanced users, the Quick Find feature will also support the following:
- Users will be able to index nodes based on any attribute. Only those attributes on type: String or Simple List of Strings will be available for indexing.
- Users will be able to select from the following set of "actions":
- Select Matching Nodes.
- Select Node Neighborhood (and keep all other nodes visible).
- Select Node Neighborhood (and hide all other nodes).
For the last two action options, the user will also be able to select a radius size for the neighborhood.
Quick Find will work with all Cytoscape plugins, so long as those plugins use CyAttributes to store attribute values.
Biological Questions / Use Cases
Quick Find addresses numerous use cases.
Deferred Items
None defined yet.
Open Issues
None defined yet.
Backward Compatibility
As this is a new feature, there are no backward compatibility issues.
References
Implementation Plan
Comments
Please add your comments below.