Cytoscape WikiRFC Name : ... |
Editor(s): ... |
About this document
This is an official Request for Comment (RFC) for Fixing the loading and saving of the vizmap.props file
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
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: ["/Comment"].
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.
Introduction
The vizmap.props file is currently loaded from at least 2 different default locations. One is the cytoscape installation directory and the other is the users .cytoscape directory in their home directory. Figuring out these locations, learning when files get saved to certain locations, and when files get loaded from certain locations is difficult for users.
This document is an attempt to develop a new scheme for loading and saving vizmap.props files.
Biological Questions / Use Cases
- Users want to save a set of visual properties they have spent many hours developing.
- Users want to load the visual properties they spent yesterday creating.
- Users want the same visual properties to be applied to the same network.
Proposal
- Have a default vizmap.props file that is included in and loaded from cytoscape.jar.
- Save all changes to vizmap.props in the project (.cys) file.
- Have the ability to import/export vizmap.props through menu items, command line options, etc. for the rare instances that saving the properties in the .cys file isn't sufficient ( e.g. when you want to share a set of visual properties you came up with).
Do away with all of the existing default handling and placement of vizmap.props files. This means no saving in $HOME, no saving in the cytoscape install directory, and no loading from places that a user doesn't explicitly request.
- Generalize the loading of vizmap.props to loading parameters and preferences. See ["generic preferences system"] for details.
Requirements
- Support loading of vizmap.props from webstart bundles.
Backward Compatibility
In the proposal above, backwards compatibility is achieved by the user importing his or her favorite vizmap.props file.
Implementation Plan
- ["/Implementation Plan"]