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Managing Properties
Important! If you have used previous versions of Cytoscape, you will notice that handling of properties has changed. The most important change is that properties are no longer saved by default to the current directory or to your home .cytoscape directory. Properties are stored by default in Cytoscape session files (.cys extension). The cytoscape.props file still exists in the .cytoscape directory but is only written to when the user explicitly requests that the current settings be made the defaults for all future sessions of Cytoscape. Unless you have something important in your .cytoscape/cytoscape.props file, your best bet will be to delete the file and use the defaults. |
The Cytoscape Properties editor, accessed via Edit → Preferences → Properties…, is used to specify general and default properties. Properties are now stored in Cytoscape session files, so changes to general properties will be saved as part of the current session, but will only carry over to subsequent sessions if they are set as defaults or exported using the File → Export function.
Cytoscape properties are configurable via Add, Modify and Delete operations.
- attachment:prefs_editor.png
Some common properties are described below.
Property name |
Default value |
Valid values |
defaultSpeciesName |
PleaseSpecify |
Species name. This value must match the name in the first line of the file specified in the bioDataServer’s manifest for synonyms, e.g., specify Saccharomyces cerevisiae for yeast synonyms |
bioDataServer |
PleaseSpecify |
annotation/manifest, and other manifest file locations |
viewThreshold |
10000 |
integer > 0 |
secondaryViewThreshold |
30000 |
integer > 0 |
viewType |
tabbed |
tabbed |
plugins |
|
comma-separated list of jar files containing plugins, or URLs to jar files containing plugins (e.g., http://server/my-plugin.jar) |
defaultWebBrowser |
|
A path to the web browser on your system. This only needs to be specified if Cytoscape can’t find the web browser on your system. |
The specification of plugins to be loaded into Cytoscape at startup time is also supported in cytoscape.props and accessible under the plugins section. In this special case, the plugins property specifies a comma-separated list of jar files or URLs to jar files containing plugins. This property is parsed and presented and managed in the plugins table.
Setting Default Properties
It is possible to alter the default properties for Cytoscape.
Edit the properties via Edit → Preferences → Properties... and check the Make Current Cytoscape Properties Default checkbox. This will save the current properties to the .cytoscape directory, where they will then be applied to all of your Cytoscape sessions from that point on. Otherwise, Cytoscape will automatically save the properties used in a particular session inside its .cys session file, while the default properties will be applied at the beginning of subsequent sessions.
Managing Bookmarks
Cytoscape contains a pre-defined list of bookmarks, which point to sample network files located on the Cytoscape web server. Users may add, modify, and delete bookmarks through the Bookmark manager, accessed by going to Edit → Preferences → Bookmarks… .
attachment:BookmarkManager.PNG
There are currently two types of bookmarks: network and annotation. Network bookmarks are URLs pointing to network files available on the Internet. These are nomal networks that can be loaded into Cytoscape. The annotation bookmarks are URLs pointing to ontology annotation files. The annotation bookmarks are only used when importing an ontology.
Managing Proxy Servers
You can define and configure a proxy server for Cytoscape by going to Edit → Preferences → Proxies… .
attachment:ProxyServerSetting.PNG
After the proxy server is set, all network traffic related to loading a network from URL will pass through the proxy server. Other plugins use this capability as well.