Cytoscape 2.x Plugins Release Note

Plugin Name: AgilentLiteratureSearch

Version: 2.70

Release Note:

This version includes the following changes:

1) Changed so users can immediately see and use ALS menu items without having to perform Plugins->AgilentLiteratureSearch when they have previously answered proxy and legal questions (see Mantis Bug 1946).

Changed ALS to completely build itself when ALS is loaded and to enable menus for use if legal and proxy issues are taken care of.

2) Changed ALS to be more flexible in the Semantics.INTERACTION attribute associated with edges it creates.

The Semantics.INTERACTION attribute associated with ALS created edges can now be controlled by placing a property in the cytoscape.props file. Specifically, adding the property "AgilentLiteratureSearch.EdgeTypeToGenerate", with a given value, will cause ALS to add a Semantics.INTERACTION attribute with the given value to all edges it generates. For example, adding:

AgilentLiteratureSearch.EdgeTypeToGenerate ppi

would cause all ALS generated edges to have a Semantics.INTERACTION property with value "ppi".


3) Fixed various bugs with inconsistencies with enabling and disabling of Evidence From Literature popup menu and toolbar menu.

The menu is now always present after ALS is loaded, but may be disabled, if user hasn't finished legal agreement. Popup menu & toolbar menu have consistent behavior and use the same code base.

4) Moved ALS code into subpackages.

Added impl, actions, and menus subpackages. Migrated code to appropriate packages.

5) Fixed bug where Proxy was not being used for all network references (see Mantis Bug 1956).

6) Various changes and fixes to Extend Network from Literature:

a) Changed extend network operation to generate all appropriate attributes like a regular search.
b) Changed feedback to include the number of nodes created.

7) Changed ALS to generate a List of String aliases versus a String of all aliases.

The 'ALS-Aliases' attribute is used to hold the List of String aliases. These aliases can be seen as tooltips by changing the Node Tooltip visual style attribute to be a PassThrough filter that uses the ALS-Aliases attribute. We no longer use the 'Aliases' attribute, which was a String of all the aliases, seperated by commas.

8) Various extend network and gather evidence code cleanup.

This includes migrating setting and getting of node attributes to use LSPUtils, replacing use of ExtendNetworkMenuItemMonitor and ExtendNetworkFeedbackListener to use reused ALSMenuItemMonitor and ALSFeedbackListener, and some misc cleanup and refactoring.