Cytoscape WikiIn Cytoscape 2.2, there is currently no support for bundling the properties files vizmap.props and cytoscape.props into web start bundles. We're looking into that. In the meantime, this page describes what behavior you can expect with Cytoscape, web start, and properties files.
For web start users
1. If the web start user does not have a local cytoscape configuration directory (~/.cytoscape on Unix systems), or if the directory does not vizmap.props and/or cytoscape.props, they will be created and filled with default values.
2. If the web start user has cytoscape.props and/or vizmap.props files in the cytoscape configuration directory, they will be used.
3. If the visual styles and/or the global properties are changed while the user is running Cytoscape via web start, and if Cytoscape exits normally (i.e. through Exit), then the user's local properties files will be modified.
For plugin developers
If you have a plugin designed for use with web start, but require specific global properties and/or visual styles, you will need to define them programatically within your plugin. See the archives of the cytoscape-discuss mailing list for more information on this. Be aware that if the user exits Cytoscape normally, these changes will be saved in the user's configuration files unless you clean them up on exit.