Examples with PropertyConfig edu.ucsf.rbvi.clusterMaker2.internal.treeview.PropertyConfig used on opensource projects

Example 1 with PropertyConfig

use of edu.ucsf.rbvi.clusterMaker2.internal.treeview.PropertyConfig in project clusterMaker2 by RBVI.

the class HeatMapView method startup.

protected void startup() {
    CyProperty cyProperty = manager.getService(CyProperty.class, "(cyPropertyName=cytoscape3.props)");
    List<String> nodeAttributeList = context.attributeList.getNodeAttributeList();
    String edgeAttribute = context.attributeList.getEdgeAttribute();
    if (nodeAttributeList == null && edgeAttribute == null) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Must select either one edge column or two or more node columns");
        return;
    }
    if (nodeAttributeList != null && nodeAttributeList.size() > 0 && edgeAttribute != null) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Can't have both node and edge columns selected");
        return;
    }
    if (nodeAttributeList != null && nodeAttributeList.size() < 2) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Must have at least two node columns for cluster weighting");
        return;
    }
    String[] nodeArray;
    // Handle selected only
    if (!context.selectedOnly) {
        nodeArray = new String[myNetwork.getNodeCount()];
        int index = 0;
        for (CyNode node : myNetwork.getNodeList()) {
            nodeArray[index++] = ModelUtils.getName(myNetwork, node);
        }
    } else {
        if (edgeAttribute != null && edgeAttribute.length() > 0) {
            List<CyEdge> selectedEdges = CyTableUtil.getEdgesInState(myNetwork, CyNetwork.SELECTED, true);
            Set<CyNode> nodesSeen = new HashSet<CyNode>();
            for (CyEdge edge : selectedEdges) {
                nodesSeen.add(edge.getSource());
                nodesSeen.add(edge.getTarget());
            }
            int index = 0;
            nodeArray = new String[nodesSeen.size()];
            for (CyNode node : nodesSeen) nodeArray[index++] = ModelUtils.getName(myNetwork, node);
        } else {
            List<CyNode> selectedNodes = CyTableUtil.getNodesInState(myNetwork, CyNetwork.SELECTED, true);
            nodeArray = new String[selectedNodes.size()];
            int index = 0;
            for (CyNode node : selectedNodes) {
                nodeArray[index++] = ModelUtils.getName(myNetwork, node);
            }
        }
    }
    Arrays.sort(nodeArray);
    ModelUtils.createAndSetLocal(myNetwork, myNetwork, ClusterManager.NODE_ORDER_ATTRIBUTE, Arrays.asList(nodeArray), List.class, String.class);
    // Edge attribute?
    if (edgeAttribute != null && edgeAttribute.length() > 0) {
        ModelUtils.createAndSetLocal(myNetwork, myNetwork, ClusterManager.ARRAY_ORDER_ATTRIBUTE, Arrays.asList(nodeArray), List.class, String.class);
        ModelUtils.createAndSetLocal(myNetwork, myNetwork, ClusterManager.CLUSTER_EDGE_ATTRIBUTE, "edge." + edgeAttribute, String.class, null);
    } else {
        int index = 0;
        Collections.sort(nodeAttributeList);
        ModelUtils.createAndSetLocal(myNetwork, myNetwork, ClusterManager.ARRAY_ORDER_ATTRIBUTE, nodeAttributeList, List.class, String.class);
    }
    // Get our data model
    dataModel = new TreeViewModel(monitor, myNetwork, myView, manager);
    // Set up the global config
    setConfigDefaults(new PropertyConfig(cyProperty, globalConfigName(), "ProgramConfig"));
    // Set up our configuration
    PropertyConfig documentConfig = new PropertyConfig(cyProperty, getShortName(), "DocumentConfig");
    dataModel.setDocumentConfig(documentConfig);
    // Create our view frame
    TreeViewFrame frame = new TreeViewFrame(this, appName);
    // Set the data model
    frame.setDataModel(dataModel);
    frame.setLoaded(true);
    frame.addWindowListener(this);
    frame.setVisible(true);
    geneSelection = frame.getGeneSelection();
    geneSelection.addObserver(this);
    arraySelection = frame.getArraySelection();
    arraySelection.addObserver(this);
    manager.registerService(this, RowsSetListener.class, new Properties());
}

Example 2 with PropertyConfig

use of edu.ucsf.rbvi.clusterMaker2.internal.treeview.PropertyConfig in project clusterMaker2 by RBVI.

the class KnnView method startup.

protected void startup() {
    CyProperty cyProperty = manager.getService(CyProperty.class, "(cyPropertyName=cytoscape3.props)");
    // Get our data model
    dataModel = new KnnViewModel(monitor, myNetwork, myView, manager);
    // Set up the global config
    setConfigDefaults(new PropertyConfig(cyProperty, globalConfigName(), "ProgramConfig"));
    // Set up our configuration
    PropertyConfig documentConfig = new PropertyConfig(cyProperty, getShortName(), "DocumentConfig");
    dataModel.setDocumentConfig(documentConfig);
    // Create our view frame
    KnnViewFrame frame = new KnnViewFrame(this, appName);
    // Set the data model
    frame.setDataModel(dataModel);
    frame.setLoaded(true);
    frame.addWindowListener(this);
    frame.setVisible(true);
    geneSelection = frame.getGeneSelection();
    geneSelection.addObserver(this);
    arraySelection = frame.getArraySelection();
    arraySelection.addObserver(this);
    manager.registerService(this, RowsSetListener.class, new Properties());
}

Example 3 with PropertyConfig

use of edu.ucsf.rbvi.clusterMaker2.internal.treeview.PropertyConfig in project clusterMaker2 by RBVI.

the class BiclusterView method startup.

protected void startup() {
    CyProperty cyProperty = manager.getService(CyProperty.class, "(cyPropertyName=cytoscape3.props)");
    /*
		Map<Integer, List<String>> clusterNodes = getBiclusterNodes();
		Map<Integer, List<String>> clusterAttrs = getBiclusterAttributes();
		
		
		ArrayList<String> nodeArrayL = new ArrayList<String>();
		for(Integer key:clusterNodes.keySet()){
			List<String> bicluster =  clusterNodes.get(key);
			for(String node:bicluster){
				nodeArrayL.add(node);
			}			
		}
		
		// ModelUtils.createAndSetLocal(myNetwork, myNetwork, ClusterManager.NODE_ORDER_ATTRIBUTE, 
    //             nodeArrayL, List.class, String.class);
		
		ArrayList<String> attrArrayL = new ArrayList<String>();
		for(Integer key:clusterAttrs.keySet()){
			List<String> bicluster =  clusterAttrs.get(key);
			for(String attr:bicluster){
				attrArrayL.add(attr);
			}			
		}
		// ModelUtils.createAndSetLocal(myNetwork, myNetwork, ClusterManager.ARRAY_ORDER_ATTRIBUTE, 
		// 		attrArrayL, List.class, String.class);
		*/
    /*
		//Using the overlapping and reordering for node and array order attributes
		mergeBiclusters(clusterNodes,clusterAttrs);
		ModelUtils.createAndSetLocal(myNetwork, myNetwork, ClusterManager.NODE_ORDER_ATTRIBUTE, 
                rowList, List.class, String.class);
		ModelUtils.createAndSetLocal(myNetwork, myNetwork, ClusterManager.ARRAY_ORDER_ATTRIBUTE, 
				colList, List.class, String.class);
		*/
    // Get our data model
    // FIXME: Can't use the KnnViewModel because it's going to
    // fill in all of the data for each cell and we only want to
    // fill in the data for the cells within the bicluster
    dataModel = new KnnViewModel(monitor, myNetwork, myView, manager);
    // Set up the global config
    setConfigDefaults(new PropertyConfig(cyProperty, globalConfigName(), "ProgramConfig"));
    // Set up our configuration
    PropertyConfig documentConfig = new PropertyConfig(cyProperty, getShortName(), "DocumentConfig");
    dataModel.setDocumentConfig(documentConfig);
    // Create our view frame
    KnnViewFrame frame = new KnnViewFrame(this, appName);
    // Set the data model
    frame.setDataModel(dataModel);
    frame.setLoaded(true);
    frame.addWindowListener(this);
    frame.setVisible(true);
    geneSelection = frame.getGeneSelection();
    geneSelection.addObserver(this);
    arraySelection = frame.getArraySelection();
    arraySelection.addObserver(this);
    manager.registerService(this, RowsSetListener.class, new Properties());
}

Example 4 with PropertyConfig

use of edu.ucsf.rbvi.clusterMaker2.internal.treeview.PropertyConfig in project clusterMaker2 by RBVI.

the class TreeView method startup.

protected void startup() {
    CyProperty cyProperty = manager.getService(CyProperty.class, "(cyPropertyName=cytoscape3.props)");
    // Get our data model
    dataModel = new TreeViewModel(monitor, myNetwork, myView, manager);
    // Set up the global config
    setConfigDefaults(new PropertyConfig(cyProperty, globalConfigName(), "ProgramConfig"));
    // Set up our configuration
    PropertyConfig documentConfig = new PropertyConfig(cyProperty, getShortName(), "DocumentConfig");
    dataModel.setDocumentConfig(documentConfig);
    // Create our view frame
    TreeViewFrame frame = new TreeViewFrame(this, appName);
    // Set the data model
    frame.setDataModel(dataModel);
    frame.setLoaded(true);
    frame.addWindowListener(this);
    frame.setVisible(true);
    geneSelection = frame.getGeneSelection();
    geneSelection.addObserver(this);
    arraySelection = frame.getArraySelection();
    arraySelection.addObserver(this);
    manager.registerService(this, RowsSetListener.class, new Properties());
}