Cytoscape APIs

Cytoscape Provided Services

Plugin Implemented Services

The APIs for these services are defined as interfaces in Cytoscape. The interfaces are as follows:

UI Services

Interactive - provide an option to bring up before or after action has run Action to create panel Action to be triggered by the panel 

// the service interface
interface UIPanel {
  JPanel getJPanel();
}

// in the plugin
// meta data defining where/how to use the panel
Hashtable dict = new HashTable();
dict.put("panel.location","control");
dict.put("panel.name","hello world");
dict.put("service.pid","myuipanel.persistent.id");

bundleContext.registerService(UIPanel.class.getName(), new MyUIPanel(), dict);

Single Action 

// The factory is the service.  The factory will return individual action objects
// that can store internal state.  If we didn't have a factory, then the individual
// actions wouldn't be able to store their state because they'd persist as services.
interface CytoscapeActionFactory {
  CytoscapeAction createAction(context of some sort);
  List<Tunable> createParameters(possibly some context);
 boolean isEnabled(context of some sort);
}

interface CytoscapeAction {
   void run();
}

// meta data defining where/how to use the action
Hashtable dict = new HashTable();
dict.put("preferred.menu","whereever/submenu");
dict.put("action.panel","myuipanel.persistent.id"); // so that it can get the exact panel
dict.put("menu.label","asdfasdf");
dict.put("icon", new Icon("my.png"));

bundleContext.registerService(CytoscapeActionFactory.class.getName(), new MyCyActionFactory(), dict);

Menu Action flow of events

  1. MenuItem is created.

  2. Click on a menu

  3. The menuSelected() method checks the CytoscapeActionFactory metadata to see if the menu item should be enabled/disabled. The Action could just declare what attributes need to exist in the world in the metadata of the CytoscapeActionFactory. For example, you could define metadata like requiresNetwork, requiresNetworkView, requiresNodeSelection, requiresEdgeSelection, etc.. There could also a overriding metadatum called isEnabled that could be forced to be true if necessary.

  4. The menu would be displayed if the action is enabled.

  5. The menu looks for a registered service for CytoscapeActionFactory. The individual factory returned is determined based on a parameter to the MenuItem. This happens dynamically based on how the CytoscapeActionFactories are defined.

  6. First call createParameters() that creates some sort of UI (e.g. a GUI that allows input values or a command line that reads a config file or queries a database or reads a command line, etc.). This data is specified by the user and is then passed into the action that is created next.
  7. The factory.createAction() method is called with all of the appropriate params (e.g. currentNetwork, currentNetworkView, etc.).

  8. The CytoscapeAction object can now be run at your leisure.

CytoscapeAction can implement additional interfaces, e.g. ProgressTrackable, which would mean a progress monitor could be added.

A CytoscapeAction needs it's basic inputs (current network, current view, or possibly a DataManager), but it also may need separate parameters. These should be defined as some sort of Tunable or List<Tunable> or a JPanel that returns some sort of configuration object, e.g. a Dictionary of key -> value pairs.

The action context could be a DataManager interface that provides methods like getCurrentNetwork, getCurrentNetworkView, etc.. Alternatively, you could provide an Context object (e.g. CIShellContext) which could provide access to all Cytoscape services. This isn't an osgi context that worries about bundles, but is an application specific context that provides services appropriate for how the application is currently being run.

Scripting

This Action model needs to be separated from the GUI so that it can be used in a scripting context (i.e headless mode) as well.

MetaData could also be used to specify where the Action can be used. For example you could set a requiresGUI (or even requiresSwing) element that would disable the action if the current running context doesn't support a GUI.

the Solution

[http://cishell.org CIShell] does all of this now.

Action Services

General Bundle Organization

Breakdown of Cytoscape Services

Currently supported by Cytoscape.java.

NOT Currently provided by Cytoscape.java

"Services" currently existing elsewhere that would be transformed into OSGi services.

Visual Styles

A VisualStyle consists of a NodeAppearanceCalculator, EdgeAppearanceCalculator, and GlobalAppearanceCalculator.

NodeAppearanceCalculators and EdgeAppearanceCalculators consist of lists of Calculator objects. Each calculator has a specific VisualPropertyType. Only one Calculator of a given VisualPropertyType is allowed in either NodeAppearanceCalculators or EdgeAppearanceCalculators.

Possible Improvements for VisualStyles

Current Cytoscape Actions

Algorithm Workflow

  1. Click Top-level menu
  2. Check algorithm meta data to see if menu item should be enabled.
  3. Click menu item.

  4. MenuManager checks Algorithm meta data to UI service id.

  5. MenuManager associates a GUI instance with an Algorithm through Algorithm meta data.

  6. MenuManager creates a GUIController object that knows about the Algorithm and the GUI.

  7. MenuManager creates GUI based on the UI service id. MenuManager creates the GUI with a GUIController object.

  8. GUI intializes itself from UI.getFallBackInterface().
  9. User does stuff to the GUI setting the various Tunables.
  10. User clicks submit().

  11. GUI calls GUIController.execute(List<Tunables>).

  12. GUIController.close() gets called some point to close the GUI.

  13. GUIController gets all associated algorithms with GUI and calls AlgorithmFactory.createAlgorithm(List<Tunable>).execute().

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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