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Contents

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Swing Application
Model
View Model
VizMapper
I/O
1. How to build a network reader to support my own format?
Work
1. How to use the Cytoscape task monitor to show the progress of my job?
2. How to issue non-blocking, informational messages to users?
Session
1. How to save/restore app states?
2. How to add CyProperty to save values across sessions?
Events
1. How to handle events from a network
Equations
1. How to add new attribute functions via a Cytoscape App?
Web Services
1. How to use a web service client?
2. How to write a web service client?
Help
1. How to add plug-in specific help to the Cytoscape main help system?
OSGi
1. An easier way to construct service properties
2. Including packages accessed via reflection (e.g. JDBC, SAX parsers, XML utilities)

Swing Application

How to add a tabbed Panel to Control panel?

In Cytoscape desktop, there are three CytoPanels, Control panel, data panel and result panel, located at West, south and east, respectively. New tabbed panel can be easily added to the CytoPanel. All the app developer should do is (1) defines a JPanel, which implements the CytoPanelComponnet; (2) register the new panel as OSGi service. The internal CytoPanel manager will automatically pick up the newly registered service identified as CytoPanelComponent and adds the new panel to the specified target CytoPanel.

Step 1

// Define a CytoPanel class
public class MyCytoPanel extends JPanel implements CytoPanelComponent {

    ...
    @Override
    public CytoPanelName getCytoPanelName() {
        return CytoPanelName.WEST;
    }
     ...
}

Step 2

// In the start method of your CyActivator class:
//   Create an instance:
MyCytoPanel myPanel = new MyPanel();
//   Register it as a service:
registerService(bc,myCytoPanel,CytoPanelComponent.class, new Properties());

Look at a sample App, Here.

How to add an image icon (menu item) to the toolbar?

Sometimes, an app needs to add an menu item to the cytoscape menu or add an image icon on the Cytoscape toolbar. In such case, app developer needs to (1) define a class, which implements CyAction or extends AbstractCyAction; (2) and register the class as an OSGi service. The internal CyAction manger of Cytoscape will pick up the registered service and create the menu item as defined. Note the methods isInToolbar() and isInMenu(), its return value true or false will determine if menu item or image icon will be created or not.

Step 1

// Define a CyAction class
public class AddImageIconAction extends AbstractCyAction {
        
    public AddImageIconAction(CySwingApplication desktopApp){
        ...
        ImageIcon icon = new ImageIcon(getClass().getResource("/images/tiger.jpg"));

        putValue(LARGE_ICON_KEY, icon);
       ...
    }

    public boolean isInToolBar() {
        return true;
    }
    ...
}

Step 2

// In the start method of your CyActivator class:
//   Create an instance:
AddImageIconAction addImageIconAction = new AddImageIconAction(cytoscapeDesktopService);
//   Register it as a service:
registerService(bc,addImageIconAction,CyAction.class, new Properties());

Look at a sample App, Here.

How to create a submenu?

The way to define a submenu item is similar to define a menu item. Besides the definition of menu item itself, it is also necessary to define its parent menu item, see below.

Step 1

// Define a CyAction class
public class MySubMenuItemAction extends AbstractCyAction {
    ...
    public MySubMenuItemAction(CySwingApplication desktopApp){
                super("My Sub MenuItem...");
                setPreferredMenu("Apps.My MenuItem");
                //setMenuGravity(2.0f);
        ...
    }

Step 2

                // In the start method of your CyActivator class:
                //   Create an instance:
                MySubMenuItemAction action = new MySubMenuItemAction(cytoscapeDesktopService);

                //   Register it as a service:
                registerService(bc,action,CyAction.class, new Properties());

Look at a sample App, here.

Model

How to create, modify, and destroy a network, nodes, and edges?

To create a network, get a reference to the CyNetworkFactory service, and tell it to create a network. With the new network, nodes and edges can be created through the CyNetwork interface.

  // To get a reference of CyNetworkFactory at CyActivator class of the App
  CyNetworkFactory networkFactory = getService(bc, CyNetworkFactory.class);
...

  // Create a new network
  CyNetwork myNet = networkFactory.createNetwork();
  
  // Set name for network
  myNet.getRow(net).set(CyNetwork.NAME, "My network");
...

  // Add two nodes to the network
  CyNode node1 = myNet.addNode();
  CyNode node2 = myNet.addNode();
                
  // Set name for new nodes
  myNet.getRow(node1).set(CyNetwork.NAME, "Node1");
  myNet.getRow(node2).set(CyNetwork.NAME, "Node2");
                
  // Add an edge
  myNet.addEdge(node1, node2, true);

  // Add the network to Cytoscape
  CyNetworkManager networkManager = getService(bc, CyNetworkManager.class);
  networkManager.addNetwork(myNet);

Destroying networks is done through the CyNetworkManager service.

First, in the start method of your CyActivator class:

  // Get a CyNetworkManager
  CyNetworkManager netMgr = getService(bc,CyNetworkManager.class);

Now you can use CyNetworkManager in your code:

  // Destroy a network with NetworkManager
  netMgr.destroyNetwork(myNet); 

Look at a sample App, here.

How to determine which nodes are currently selected on a network?

The selection state of a node or edge is saved in the table associated with the network. Its attribute or column name is “selected”. Therefore, to determine the selection state of a node, we need to get the CyRow of the node and check the value of column “selected”.

There is a util class CyTableUtil. We can use this class to get the list of selected nodes in a network

//Get the selected nodes
  List<CyNode> nodes = CyTableUtil.getNodesInState(myNetwork,"selected",true);

Look at a sample App, Here.

How to set the name of a network?

The network name is kept in the table associated with the network, and its column name is “name”. To set the network name, first we need to get the CyRow of the network object, then set the “name” attribute of this row.

  CyNetwork net = ...;
  String name = ...;
  net.getRow(net).set(CyNetwork.NAME, name);

Look at a sample App, here.

How to get the name of a network?

The network title is kept in the table associated with the network, and its column name is “name”. To set the network name/title, first we need to get the CyRow of the network object, then get the “name” attribute of this row.

  CyNetwork net = ...;
  String name = net.getRow(net).get(CyNetwork.NAME, String.class);

How to set the name of a node?

The name of a node is kept in the CyRow of the table associated with the network, and its column name is “name”. To set the node name, first we need to get the CyRow of the node object, then set the “name” attribute of this row.

  CyNode node = ...;
  String myNodeName = ...;
  net.getRow(node).set(CyNetwork.NAME, myNodeName);

Look at a sample App, here.

How to get the name of a node?

The name of a node is kept in the CyRow of the table associated with the network, and its column name is “name”. To get the node name, first we need to get the CyRow of the node object, then get the “name” attribute of this row.

  CyNode node = ...;
  String myNodeName = net.getRow(node).get(CyNetwork.NAME, String.class);

How to load attribute data?

// Define a task
public class CreateTableTask extends AbstractTask {
    ....
    @Override
    public void run(TaskMonitor tm) throws IOException {
        // Step 1: create a new table
        CyTable table = tableFactory.createTable("MyAttrTable " + Integer.toString(numImports++), 
                                   "name", String.class, true, true);

        // create a column for the table
        String attributeName = "MyAttributeName"; 
        table.createColumn(attributeName, Integer.class, false);
                
        // Step 2: populate the table with some data
        String[] keys = {"YLL021W","YBR170C","YLR249W"}; //map to the the "name" column
        CyRow row = table.getRow(keys[0]);
        row.set(attributeName, new Integer(2));

        row = table.getRow(keys[1]);
        row.set(attributeName, new Integer(3));

        row = table.getRow(keys[2]);
        row.set(attributeName, new Integer(4));

        // We are loading node attribute
        Class<? extends CyTableEntry> type = CyNode.class;

        // Step 3: pass the new table to MapNetworkAttrTask
        super.insertTasksAfterCurrentTask( new MapNetworkAttrTask(type,table,netMgr,appMgr,rootNetworkManager) );
    }
    ....
}

Look at a sample App, Look at a sample App, here.

How to remove attributes?

Step 1: get the CyTable through the network

    // case for Node table
    CyTable nodeTable = network.getDefaultNodeTable();

Step 2: Find the column and delete it

    if(nodeTable.getColumn(columnName)!= null){
        nodeTable.deleteColumn(columnName);
    }   

Look at a sample App, here.

How to get all the nodes with a specific attribute value?

Copy this method in your code:

    /**
     * Get all the nodes with a given attribute value.
     *
     * This method is effectively a wrapper around {@link CyTable#getMatchingRows}.
     * It converts the table's primary keys (assuming they are node SUIDs) back to
     * nodes in the network.
     *
     * Here is an example of using this method to find all nodes with a given name:
     *
     * {@code
     *   CyNetwork net = ...;
     *   String nodeNameToSearchFor = ...;
     *   Set<CyNode> nodes = getNodesWithValue(net, net.getDefaultNodeTable(), "name", nodeNameToSearchFor);
     *   // nodes now contains all CyNodes with the name specified by nodeNameToSearchFor
     * }
     * @param net The network that contains the nodes you are looking for.
     * @param table The node table that has the attribute value you are looking for;
     * the primary keys of this table <i>must</i> be SUIDs of nodes in {@code net}.
     * @param colname The name of the column with the attribute value
     * @param value The attribute value
     * @return A set of {@code CyNode}s with a matching value, or an empty set if no nodes match.
     */
    private static Set<CyNode> getNodesWithValue(
            final CyNetwork net, final CyTable table,
            final String colname, final Object value)
    {
        final Collection<CyRow> matchingRows = table.getMatchingRows(colname, value);
        final Set<CyNode> nodes = new HashSet<CyNode>();
        final String primaryKeyColname = table.getPrimaryKey().getName();
        for (final CyRow row : matchingRows)
        {
            final Long nodeId = row.get(primaryKeyColname, Long.class);
            if (nodeId == null)
                continue;
            final CyNode node = net.getNode(nodeId);
            if (node == null)
                continue;
            nodes.add(node);
        }
        return nodes;
    }

How to use model objects (CyNetwork, CyNode, etc.) when writing tests?

Step 1. Include the JUnit framework as a dependency in your pom.xml:

<dependency>
    <groupId>junit</groupId>
    <artifactId>junit</artifactId>
    <scope>test</scope>
</dependency>

Step 2. Include the model-impl package as a dependency in your pom.xml:

<dependency>
    <groupId>org.cytoscape</groupId>
    <artifactId>model-impl</artifactId>
    <version>${cytoscape.api.version}</version>
    <scope>test</scope>
</dependency>

Step 3. In your testing code, use NetworkTestSupport to get a CyNetwork instance:

import org.cytoscape.model.NetworkTestSupport;

...

final NetworkTestSupport nts = new NetworkTestSupport();
final CyNetwork network = nts.getNetwork();

// Now you have a CyNetwork!

View Model

Getting node views for newly created nodes?

After creating a node and edge, this is how to get its view:

  CyNetworkView networkView = ...;
  CyNetwork network = networkView.getModel();
  CyEventHelper eventHelper = ...;
  CyNode newNode = network.addNode();
  network.getRow(newNode).set(CyNetwork.NAME, "New Node");
  eventHelper.flushPayloadEvents();
  View<CyNode> newNodeView = networkView.getNodeView(newNode);

After creating the node in CyNetwork, you have to call CyEventHelper's flushPayloadEvents so that the new node gets a node view. If flushPayloadEvents is not called, getNodeView may return null.

If you are creating a bunch of nodes at once, call flushPayloadEvents after you have finished creating all the nodes, not after each node is created. Example:

  CyNetworkView networkView = ...;
  CyNetwork network = networkView.getModel();
  CyEventHelper eventHelper = ...;
  
  for (int i = 1; i <= 100; i++) {
    CyNode node = network.addNode();
    network.getRow(newNode).set(CyNetwork.NAME, "Node " + i);
  }
  eventHelper.flushPayloadEvents();

How to create, modify, and destroy a network view?

To create a network, get a reference to the CyNetworkViewFactory service, and tell it to create a network view.

First, in the start method of your CyActivator class:

  // Get a CyNetworkViewFactory
  CyNetworkViewFactory networkViewFactory = getService(bc, CyNetworkViewFactory.class);

Now you can use CyNetworkViewFactory in your code:

  // Create a new network view
  CyNetworkView myView = networkViewFactory.createNetworkView(myNet);

  // Add view to Cytoscape
  CyNetworkViewManager networkViewManager = getService(bc, CyNetworkViewManager.class);
  networkViewManager.addNetworkView(myView);

Destroying network views is done through the CyNetworkViewManager service.

First, in the start method of your CyActivator class:

  // get a CyNetworkViewManager
  CyNetworkViewManager networkViewManager = getService(bc, CyNetworkViewManager.class);

Now you can use CyNetworkViewManager in your code:

  // destroy a network view through NetworkViewManager
  networkViewManager.destroyNetworkView(myView);

Look at a sample App, here.

How to change the background color of a view?

Network background color is changed as a _visual property_.

  // Set the background of current view to RED  
  view.setVisualProperty(BasicVisualLexicon.NETWORK_BACKGROUND_PAINT, Color.red);
  view.updateView(); 

Look at a sample App, here.

How to zoom a network view?

// Get the scale and adjust
double newScale = view.getVisualProperty(NETWORK_SCALE_FACTOR).doubleValue() * scale;
view.setVisualProperty(NETWORK_SCALE_FACTOR, newScale);
...     
view.updateView();

Look at a sample App, here.

How to get and set node coordinate positions?

Given a View<CyNode>, here's how to get its x and y coordinate positions:

View<CyNode> nodeView = ...;
Double x = nodeView.getVisualProperty(BasicVisualLexicon.NODE_X_LOCATION);
Double y = nodeView.getVisualProperty(BasicVisualLexicon.NODE_Y_LOCATION);

Here's how to set the x and y coordinate positions:

View<CyNode> nodeView = ...;
double x = ...;
double y = ...;
nodeView.setVisualProperty(BasicVisualLexicon.NODE_X_LOCATION, x);
nodeView.setVisualProperty(BasicVisualLexicon.NODE_Y_LOCATION, y);

Look at a sample App, here.

How to write a layout algorithm?

First define a layout class, which implements CyLayoutAlgorithm interface or extends AbstractLayoutAlgorithm class. Then register the layout class as a service.

  // Define a layout class
  public class MyLayout extends AbstractLayoutAlgorithm {
    ...
  }


  // Define a layout task class
  public class MyLayoutTask extends AbstractLayoutTask {
    ...

    //Perform actual layout task
    final protected void doLayout(final TaskMonitor taskMonitor) {
      ...   
    }
    ...
  }


  // Register the layout class as a service in CyActivator class
  Properties myLayoutProps = new Properties();
  myLayoutProps.setProperty("preferredMenu","My Layouts");
  registerService(bc,myLayout,CyLayoutAlgorithm.class, myLayoutProps);

Look at a sample App, here.

How to add components to the node view, edge view, and attribute browser context menus?

To add a context menu to a NodeView, define a class, which extends AbstractNodeViewTaskFactory, and register the NodeViewTaskFactory as service. We can add the title of menu item by setting the service property when we register the nodeViewTaskFactory.

To add context menu to the table browser, define a class, which extends AbstractTableCellTaskFactory. Create an instance and register it as service (Note register as TableCellTaskFactory).

  // Define a class MyNodeViewTaskFactory 
  public class MyNodeViewTaskFactory extends AbstractNodeViewTaskFactory {
    ...
  }


  // Register myNodeViewTaskFactory as a service in CyActivator
  Properties myNodeViewTaskFactoryProps = new Properties();
  myNodeViewTaskFactoryProps.setProperty("title","My context menu title");
  registerService(bc,myNodeViewTaskFactory,NodeViewTaskFactory.class, myNodeViewTaskFactoryProps);

Look at a sample App, AddNodeViewContextMenuItem.

Look at a sample App, CreateNetworkViewContextMenu.

VizMapper

How to use the VizMapper programmatically?

Cytosape provides services for using visual mapping programming. There services are VisualMappingManager, VisualStyleFactory and VisualMappingFunctionFactory. App should get references to these services in CyActivator class, the entry point of the app. We can create new visualStyle with VisualStyleFactory and create mapping function with VisualMappingFunctionFactory very easily. After a new visual style is created, it should register with the VisualMappingManger, in this way the new visual style will be available throughout Cytoscape.

  // To get references to services in CyActivator class
  VisualMappingManager vmmServiceRef = getService(bc,VisualMappingManager.class);
                
  VisualStyleFactory visualStyleFactoryServiceRef = getService(bc,VisualStyleFactory.class);
                
  VisualMappingFunctionFactory vmfFactoryC = getService(bc,VisualMappingFunctionFactory.class, "(mapping.type=continuous)");
  VisualMappingFunctionFactory vmfFactoryD = getService(bc,VisualMappingFunctionFactory.class, "(mapping.type=discrete)");
  VisualMappingFunctionFactory vmfFactoryP = getService(bc,VisualMappingFunctionFactory.class, "(mapping.type=passthrough)");


  // To create a new VisualStyle object and set the mapping function
  VisualStyle vs= this.visualStyleFactoryServiceRef.createVisualStyle("My visual style");


  //Use pass-through mapping
  String ctrAttrName1 = "SUID";
  PassthroughMapping pMapping = (PassthroughMapping) vmfFactoryP.createVisualMappingFunction(ctrAttrName1, String.class, attrForTest, BasicVisualLexicon.NODE_LABEL);

  vs.addVisualMappingFunction(pMapping);                        


  // Add the new style to the VisualMappingManager
  vmmServiceRef.addVisualStyle(vs);


  // Apply the visual style to a NetwokView
  vs.apply(myNetworkView);
  myNetworkView.updateView();

Look at a sample App, here.

How to apply a continuous color gradient to nodes according to their degree?

  
  // Set node color map to attribute "Degree"
  ContinuousMapping mapping = (ContinuousMapping)
                this.continuousMappingFactoryServiceRef.createVisualMappingFunction("Degree", Integer.class, BasicVisualLexicon.NODE_FILL_COLOR);

  // Define the points
  Double val1 = 2d;
  BoundaryRangeValues<Paint> brv1 = new BoundaryRangeValues<Paint>(Color.RED, Color.GREEN, Color.PINK);

  Double val2 = 12d;
  BoundaryRangeValues<Paint> brv2 = new BoundaryRangeValues<Paint>(Color.WHITE, Color.YELLOW, Color.BLACK);
                
  // Set the points
  mapping.addPoint(val1, brv1);
  mapping.addPoint(val2, brv2);

  // add the mapping to visual style            
  vs.addVisualMappingFunction(mapping); 

Look at a sample App, here.

How to load a visual properties file?

Cytoscape provide a service 'LoadVizmapFileTaskFactory' for loading visual styles definded in a property file.

  // get a reference to Cytoscape service -- LoadVizmapFileTaskFactory 
  LoadVizmapFileTaskFactory loadVizmapFileTaskFactory =  getService(bc,LoadVizmapFileTaskFactory.class);

  // Use the service to load visual style, 'f' is the File object to hold the visual properties 
  Set<VisualStyle> vsSet = loadVizmapFileTaskFactory.loadStyles(f);

Look at a sample App, here.

I/O

How to build a network reader to support my own format?

First, we should define the format of my network file and its file extension. Let's say, each line in our network file has two columns, tab-delimited. And we define file extension '.tc', stands for 'two columns'.

  //1. define a file filter (BasicCyFileFilter), to support the reader to read the file with extension '.tc'
  HashSet<String> extensions = new HashSet<String>();
  extensions.add("tc");
  HashSet<String> contentTypes = new HashSet<String>();
  contentTypes.add("txt");
  String description = "My test filter";
  DataCategory category = DataCategory.NETWORK;
  BasicCyFileFilter filter = new BasicCyFileFilter(extensions,contentTypes, description, category, swingAdapter.getStreamUtil());


  //2. Create an instance of the ReaderFactory
  // Note that extends TCReaderFactory  must implement the interface InputStreamTaskFactory or extends the class  AbstractInputStreamTaskFactory.
  // And the defined task must implement CyNetworkReader
  TCReaderFactory factory = new TCReaderFactory(filter, swingAdapter.getCyNetworkFactory(), swingAdapter.getCyNetworkViewFactory());

  

  //3. register the ReaderFactory as an InputStreamTaskFactory.
  Properties props = new Properties();
  props.setProperty("readerDescription","TC file reader");
  props.setProperty("readerId","tcNetworkReader");
  swingAdapter.getCyServiceRegistrar().registerService(factory, InputStreamTaskFactory.class, props);

Compile the following sample App, and install the app in Cytoscape. When we try to import a network from a file (File-->Import-->Network-->File..), we will find file type '.tc' is listed as one of the file types supported by Cytoscape.

Look at a sample App, here.

Work

How to use the Cytoscape task monitor to show the progress of my job?

Get a Cytoscape service DialogTaskManager and execute the task through the taskManager.

  // Get a Cytoscape service 'DialogTaskManager' in CyActivator class
  DialogTaskManager dialogTaskManager = getService(bc, DialogTaskManager.class);


  // Define a task and set the progress in the run() method
  public class MyTask extends AbstractTask {
    ...
    public void run(final TaskMonitor taskMonitor) {
        // Give the task a title.
        taskMonitor.setTitle("My task");
        ...
        taskMonitor.setProgress(0.1);

        // do something here

        ...
        taskMonitor.setProgress(1.0);
  }


  // Execute the task through the TaskManager
  DialogTaskManager.execute(myTaskFactory);

Look at a sample App, here.

How to issue non-blocking, informational messages to users?

Cytoscape 3.0 has a status bar at the bottom of the Cytoscape desktop window. Tasks can put messages into the status bar. These messages wouldn't require immediate user attention but are informational. Debug messages useful for developers do not belong in the status bar.

To issue user messages to the status bar:

Step 1. Include the SLF4J library as a dependency in your pom.xml file.

<dependency>
  <groupId>org.slf4j</groupId>
  <artifactId>slf4j-api</artifactId>
  <version>1.6.6</version>
</dependency>
<dependency>
  <groupId>org.slf4j</groupId>
  <artifactId>slf4j-simple</artifactId>
</dependency>

Step 2. Obtain an instance of the CyUserMessages log.

import org.slf4j.LoggerFactory;
import org.slf4j.Logger;
...
Logger userMessagesLogger = LoggerFactory.getLogger("CyUserMessages");

Step 3. Issue log messages to the CyUserMessages log.

int lineError = 12;
userMessagesLogger.warn("Parse error on line {}", lineError);

The message will appear in the status bar.

Session

How to save/restore app states?

There are two events, which are important for saving/restoring App state. The two evetns are SessionAboutToBeSavedEvent and SessionLoadedEvent. App should implement the two listeners and register them.

  // Implements the session event listeners
  public class MyClass implements SessionAboutToBeSavedListener, SessionLoadedListener {

      // Save app state in a file
      public void handleEvent(SessionAboutToBeSavedEvent e){
          // save app state file "myAppStateFile"
          ...
      }

      // restore app state from a file
      public void handleEvent(SessionLoadedEvent e){

        if (e.getLoadedSession().getAppFileListMap() == null || e.getLoadedSession().getAppFileListMap().size() ==0){
            return;
        }       
        List<File> files = e.getLoadedSession().getAppFileListMap().get("myAppStateFile");
        ...
       }
  }
 

  // Register the two listeners in the CyActivator class
  registerService(bc,myClass,SessionAboutToBeSavedListener.class, new Properties());
  registerService(bc,myClass,SessionLoadedListener.class, new Properties());

Look at a sample App, here.

How to add CyProperty to save values across sessions?

CyProperty acts as a container to save properties of the type (key, value) across sessions. They are available for the user to manually change in the preference menu option.

        //1. Adding a property which saves the node border width selected by the user.
        public static String NodeBorderWidthInPaths = "NODE_BORDER_WIDTH_IN_PATHS";
        public static Double NodeBorderWidthInPathsValue = 20.0;
        public static Properties nodeBorderWidthProps = new Properties();

        //2. Find if the CyProperty already exists, if not create one with default value.
        CyProperty<Properties> nodeBorderWidthProperty = null;
        CySessionManager mySessionManager;
        mySessionManager = adapter.getCySessionManager();
        CySession session;
        session = mySessionManager.getCurrentSession();
        if(session.equals(null))
                System.out.println("session null");
                
        //3. Get all properties and loop through to find your own.
        Set<CyProperty<?>> props = new HashSet<CyProperty<?>>();
        props = session.getProperties();
        if(props.equals(null))
                System.out.println("props null");
        boolean flag = false;
        
        for (CyProperty<?> prop : props) {
            if (prop.getName() != null){
                if (prop.getName().equals(NodeBorderWidthInPaths)) {
                nodeBorderWidthProperty = (CyProperty<Properties>) prop;
                flag = true;
                break;
                }
            }
        }
        
        //4. If the property does not exists, create nodeBorderWidthProperty
        if (!flag)
        {
                nodeBorderWidthProps.setProperty(NodeBorderWidthInPaths, NodeBorderWidthInPathsValue.toString());
                nodeBorderWidthProperty = new 
                                SimpleCyProperty(NodeBorderWidthInPaths, 
                                                nodeBorderWidthProps, Float.TYPE, CyProperty.SavePolicy.SESSION_FILE_AND_CONFIG_DIR );
        }
        //5. If not null, property exists, get value from it and set NodeBorderWidthInPathsValue
        else
        {
                nodeBorderWidthProps = nodeBorderWidthProperty.getProperties();
                NodeBorderWidthInPathsValue = Double.valueOf((String)nodeBorderWidthProps.get(NodeBorderWidthInPaths));
        }

        //6. Register the CyProperty nodeBorderWidthProperty as OSGi service
        registerService(bc,nodeBorderWidthProperty,CyProperty.class, new Properties());

Events

How to handle events from a network

Step 1

  // Define a class, which implements a listener interface
  public class MyListenerClass implements NetworkAddedListener {
    ....
    public void handleEvent(NetworkAddedEvent e){
        // do something here
    }
  }

Step 2

  // In the `start` method of your `CyActivator` class,
  // register the listener in the CyActivator class
  registerService(bc,myListenerClass, NetworkAddedListener.class, new Properties());

Look at a sample App, here.

Equations

How to add new attribute functions via a Cytoscape App?

Here we will go through all the steps necessary to create a new built-in function IXOR(). The complete example code and can be downloaded from here. The easiest part is writing the actual plug-in class, which look similar to this:

  import org.cytoscape.equations.EquationCompiler;
  import org.cytoscape.equations.Interpreter;
  import org.cytoscape.equations.EquationParser;

  public class Sample23 {

        public Sample23(EquationCompiler eqCompilerRef, Interpreter interpreterRef){
                final EquationParser theParser = eqCompilerRef.getParser();
                theParser.registerFunction(new IXor());
        }
  }

Here we register a new built-in function called IXor. You can also register multiple built-in functions if you prefer.

The next part is creating one class each for every new built-in. Each such class has to implement the org.cytoscape.equations.Function interface usually via org.cytoscape.equations.AbstractFunction. The easiest way to get started is to peruse the existing built-ins in equations Cytoscape core library and look for a function with a similar or identical argument list. If you can't find one it may still be instructive to read through the implementation of a couple of existing functions.

First you have to create the constructor where you describe the arguments that your function will take:

public IXor() {
        super(new ArgDescriptor[] {
                        new ArgDescriptor(ArgType.INT, "arg1", "A quantity that can be converted to an integer."),
                        new ArgDescriptor(ArgType.INT, "arg2", "A quantity that can be converted to an integer."),
                });

The most trivial to implement methods are getName(), and getFunctionSummary().

/**                                                                                                                                                                                                                                                  
 *  Used to parse the function string.  This name is treated in a case-insensitive manner!                                                                                                                                                           
 *  @return the name by which you must call the function when used in an attribute equation.                                                                                                                                                        
 */
public String getName() { return "IXOR"; }

/**                                                                                                                                                                                                                                                  
  *  Used to provide help for users.                                                                                                                                                                                                                  
  *  @return a description of what this function does                                                                                                                                                                                                
  */
public String getFunctionSummary() { return "Returns an integer value that is the exclusive-or of 2 other integer values."; }

The next method is still simple but already touches on the one area that is somewhat complicated in attribute functions: data types and data type conversions!

public Class getReturnType() { return Long.class; }

Our example function is supposed to return an integer value. Integers in equation functions are represented as instances of class java.lang.Long. Therefore it is imperative not to return Integer.class! The user of the function can be blissfully unaware of this distinction. Just remember to always substitute Long for Integer and you should be fine.

The next method evaluateFunction() is the one that gets called when an expression is being evaluated. No argument type-checking is needed here because the compiler already took care of that for us. But, we need to handle all possible valid argument types and counts. (N.B., functions may be overloaded and/or variadic.) In this example the arguments can be any combination of Long and Double.

public Object evaluateFunction(final Object[] args) {
        long arg1;
        try {
                arg1 = FunctionUtil.getArgAsLong(args[0]);
        } catch (final Exception e) {
                throw new IllegalArgumentException("IXOR: can't convert the 1st argument to an integer!");
        }

        long arg2;
        try {
                arg2 = FunctionUtil.getArgAsLong(args[0]);
        } catch (final Exception e) {
                throw new IllegalArgumentException("IXOR: can't convert the 2nd argument to an integer!");
        }

        final long result = arg1 ^ arg2;
        return (Long)result;
}

This tutorial on how to write attribute functions may also be helpful.

Look at a sample App, here.

Web Services

How to use a web service client?

First define a listener of web service client and register it as service -- WebServiceHelper. This class will keep tracker of web service clients available using a Map.

  public class WebServiceHelper {
  ...
        public void addWebServiceClient(final WebServiceClient newFactory,
                        final Map properties)
        {
                webserviceMap.put(newFactory, properties);
        }

        public void removeWebServiceClient(final WebServiceClient factory,
                        final Map properties)
        {
                webserviceMap.remove(factory);
        }
  ...
  }  

At running time, check if the needed service is available by looking at the map.

  Iterator<WebServiceClient> it = webserviceMap.keySet().iterator();
                
  while (it.hasNext()){
    WebServiceClient client = it.next();
    // Based on the serviceLocation, we can find if the client we are looking for is available
    System.out.println("WebService CLient client: DisplayName() is "+client.getDisplayName());
    System.out.println("WebService CLient client: ServiceLocation() is "+client.getServiceLocation());
    ....  
  }

If the needed client is found, then we can construct the query and execute the query through the API of the client.

Look at a sample App, here.

How to write a web service client?

Step 1: Define a UI class for the setting of the client. This UI may listen to Cytoscape events

  public class MyWebserviceClientPanel extends JPanel implements ColumnCreatedListener, ColumnDeletedListener,
    SetCurrentNetworkListener {
  ...
}

Step 2: Define a client class, which must implement WebServiceClient and pass the UI class defined at previous step to the client. If UI is not defined, the default UI will be used.

  public class MyWebserviceClient extends AbstractWebServiceGUIClient implements TableImportWebServiceClient {
  ...
  }

Step 3: After the client is registered as service, the client can be find under File-->Import->Table-->Public databases...

Look at a sample App, here.

Help

How to add plug-in specific help to the Cytoscape main help system?

If you download CreateHelp and instal and copy the jar to the deploy directory fo your running Cytoscape, you will see topic Sample 24 help is added to your help panel (Help --> Contents...). In order to make it simpler, you can download the help directory and copy this folder to your project's resources folder. Next you need to get the CyHelpBroker service in your CyActivator class. The code in CreateHelp:

import java.util.Properties;

import org.cytoscape.application.swing.CyHelpBroker;
import org.cytoscape.service.util.AbstractCyActivator;
import org.osgi.framework.BundleContext;

public class CyActivator extends AbstractCyActivator {

        @Override
        public void start(BundleContext context) throws Exception {
                
                CyHelpBroker cyHelpBroker = getService(context, CyHelpBroker.class);

                AppHelp action = new AppHelp(cyHelpBroker);
                registerAllServices(context, action, new Properties());
        }

}

In the main entry point of your plug-in, add the following function:

...
import java.net.URL;
import org.cytoscape.application.swing.CyHelpBroker;
import javax.help.HelpSet;
...
        /**
         *  Hook plugin help into the Cytoscape main help system:
         */
        private void addHelp() {
                final String HELP_SET_NAME = "/help/jhelpset";
                final ClassLoader classLoader = AppHelp.class.getClassLoader();
                URL helpSetURL;
                try {
                        helpSetURL = HelpSet.findHelpSet(classLoader, HELP_SET_NAME);
                        final HelpSet newHelpSet = new HelpSet(classLoader, helpSetURL);
                        cyHelpBroker.getHelpSet().add(newHelpSet);
                } catch (final Exception e) {
                        System.err.println("Sample24: Could not find help set: \"" + HELP_SET_NAME + "!");
                }
        }

Invoke this function somewhere in the constructor for the class. Finally, edit the files in the help directory. Most likely you would want to edit the files named jhelpmap.jhm and Topic.html. You may consider removing both, SubTopic.html and the reference to it in jhelpmap.jhm. You can also add additional topics, if you want. The effect this will have is to add a new topic at the very bottom of the Cytoscape help index. You may have a help button in your plug-in, in which case you would probably want to add code similar to the following:

       ...
import cytoscape.view.CyHelpBroker;
       ...
       CyHelpBroker.getHelpBroker().enableHelpOnButton(helpButton, "Topic", null);
       ...

That should be all that is needed to dynamically add your own help topic(s)!

Look at a sample App, here.

OSGi

An easier way to construct service properties

Writing code to put in service properties requires a lot of boilerplate. Here's an example:

public void start(BundleContext bc) {
  Properties props = new Properties();
  props.put(TITLE, "My app");
  props.put(PREFERRED_MENU, "Apps");
  TaskFactory myTaskFactory = ...;
  registerService(bc, myTaskFactory, props);
}

To avoid having to construct a Properties object manually for each service, you can use the ezProps method:

private static Properties ezProps(String... vals) {
    final Properties props = new Properties();
    for (int i = 0; i < vals.length; i += 2)
       props.put(vals[i], vals[i + 1]);
    return props;
}

The example above can be reworked using ezProps:

public void start(BundleContext bc) {
  TaskFactory myTaskFactory = ...;
  registerService(bc, myTaskFactory, ezProps(
    TITLE, "My app",
    PREFERRED_MENU, "Apps"));
}

Including packages accessed via reflection (e.g. JDBC, SAX parsers, XML utilities)

Some packages are not included in your Import-Package header in your manifest file. The maven-bundle-plugin or bndtool would normally generate this information for you. However, since both tools compute that metadata based on direct references in the compiled class files, they cannot detect packages that are accessed via reflection (e.g. using Class.forName). The old Java service model (which is used by SAX parsers, XML utilities and JDBC drivers) uses this a lot. The preferred option for getting around this is to manually add the problematic packages to your Import-Package header. For example, for the jdbc driver package, modify the maven-bundle-plugin configuration as follows:

<!-- Generates the OSGi metadata based on the osgi.bnd file. -->
<plugin>
        <groupId>org.apache.felix</groupId>
        <artifactId>maven-bundle-plugin</artifactId>
        <version>2.3.7</version>
        <extensions>true</extensions>
        <configuration>
                <instructions>
                        <Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
                        <Bundle-Version>${project.version}</Bundle-Version>
                        <Export-Package>${bundle.namespace}</Export-Package>
                        <Private-Package>${bundle.namespace}.internal.*</Private-Package>
                        <Bundle-Activator>${bundle.namespace}.internal.CyActivator</Bundle-Activator>                                           
                        <Embed-Dependency>mysql-connector-java;inline=true</Embed-Dependency>
                        <Import-Package>com.mysql.jdbc;version:=5.1.25,*;resolution:=optional</Import-Package>
                </instructions>
        </configuration>
</plugin>

and add the dependency as usual

<dependency>
        <groupId>mysql</groupId>
        <artifactId>mysql-connector-java</artifactId>
        <version>5.1.25</version>
        <optional>true</optional>
</dependency>

Cytoscape_3/AppDeveloper/Cytoscape_3_App_Cookbook (last edited 2020-02-05 19:54:29 by KristinaHanspers)

-  ← Revision 108 as of 2013-06-05 09:41:58 →
  Size: 43963
  Editor: PietMolenaar
  Comment: Changed import package directive according to suggestions of Jason
+  ← Revision 109 as of 2013-06-06 23:07:43 →
  Size: 44124
  Editor: server2
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 835:
-}}}
+ //6. Register the CyProperty nodeBorderWidthProperty as OSGi service

 registerService(bc,nodeBorderWidthProperty,CyProperty.class, new Properties());



}}}

Diff for "Cytoscape_3/AppDeveloper/Cytoscape_3_App_Cookbook"

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Swing Application

How to add a tabbed Panel to Control panel?

How to add an image icon (menu item) to the toolbar?

How to create a submenu?

Model

How to create, modify, and destroy a network, nodes, and edges?

How to determine which nodes are currently selected on a network?

How to set the name of a network?

How to get the name of a network?

How to set the name of a node?

How to get the name of a node?

How to load attribute data?

How to remove attributes?

How to get all the nodes with a specific attribute value?

How to use model objects (CyNetwork, CyNode, etc.) when writing tests?

View Model

Getting node views for newly created nodes?

How to create, modify, and destroy a network view?

How to change the background color of a view?

How to zoom a network view?

How to get and set node coordinate positions?

How to write a layout algorithm?

How to add components to the node view, edge view, and attribute browser context menus?

VizMapper

How to use the VizMapper programmatically?

How to apply a continuous color gradient to nodes according to their degree?

How to load a visual properties file?

I/O

How to build a network reader to support my own format?

Work

How to use the Cytoscape task monitor to show the progress of my job?

How to issue non-blocking, informational messages to users?

Session

How to save/restore app states?

How to add CyProperty to save values across sessions?

Events

How to handle events from a network

Equations

How to add new attribute functions via a Cytoscape App?

Web Services

How to use a web service client?

How to write a web service client?

Help

How to add plug-in specific help to the Cytoscape main help system?

OSGi

An easier way to construct service properties

Including packages accessed via reflection (e.g. JDBC, SAX parsers, XML utilities)