Examples with CyEdge org.cytoscape.model.CyEdge used on opensource projects

Example 41 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-impl by cytoscape.

the class SelectAdjacentEdgesTask method run.

@Override
public void run(final TaskMonitor tm) {
    tm.setTitle("Select Adjacent Edges");
    tm.setProgress(0.0);
    final Collection<CyNetworkView> views = networkViewManager.getNetworkViews(network);
    CyNetworkView view = null;
    if (views.size() != 0)
        view = views.iterator().next();
    undoSupport.postEdit(new SelectionEdit(eventHelper, "Select Adjacent Edges", network, view, SelectionEdit.SelectionFilter.EDGES_ONLY));
    tm.setStatusMessage("Selecting Edges...");
    tm.setProgress(0.2);
    final Set<CyEdge> edgeSet = new HashSet<>();
    // Get the list of selected nodes
    for (CyNode node : CyTableUtil.getNodesInState(network, CyNetwork.SELECTED, true)) {
        // Get the list of edges connected to this node
        edgeSet.addAll(network.getAdjacentEdgeList(node, CyEdge.Type.ANY));
    }
    tm.setProgress(0.3);
    selectUtils.setSelectedEdges(network, edgeSet, true);
    tm.setStatusMessage("Updating View...");
    tm.setProgress(0.9);
    updateView();
    tm.setProgress(1.0);
}

Example 42 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-impl by cytoscape.

the class HideFromSelectionTask method run.

@Override
public void run(final TaskMonitor tm) {
    tm.setProgress(0.0);
    final CyNetwork network = view.getModel();
    final List<CyIdentifiable> elements = new ArrayList<>();
    List<CyNode> nodes = null;
    List<CyEdge> edges = null;
    if (hideNodes) {
        nodes = CyTableUtil.getNodesInState(network, CyNetwork.SELECTED, selectionValue);
        elements.addAll(nodes);
    }
    tm.setProgress(0.1);
    if (hideEdges) {
        edges = CyTableUtil.getEdgesInState(network, CyNetwork.SELECTED, selectionValue);
        elements.addAll(edges);
    }
    final UndoSupport undoSupport = serviceRegistrar.getService(UndoSupport.class);
    final CyEventHelper eventHelper = serviceRegistrar.getService(CyEventHelper.class);
    final VisualMappingManager vmMgr = serviceRegistrar.getService(VisualMappingManager.class);
    undoSupport.postEdit(new HideEdit(description, view, elements, false, eventHelper, vmMgr));
    tm.setProgress(0.4);
    if (nodes != null)
        HideUtils.setVisibleNodes(nodes, false, view);
    tm.setProgress(0.6);
    if (edges != null)
        HideUtils.setVisibleEdges(edges, false, view);
    tm.setProgress(0.8);
    VisualStyle style = vmMgr.getVisualStyle(view);
    for (CyIdentifiable e : elements) {
        View<? extends CyIdentifiable> ev = null;
        if (e instanceof CyNode)
            ev = view.getNodeView((CyNode) e);
        else if (e instanceof CyEdge)
            ev = view.getEdgeView((CyEdge) e);
        if (ev != null)
            style.apply(network.getRow(e), ev);
    }
    view.updateView();
    tm.setProgress(1.0);
}

Example 43 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-impl by cytoscape.

the class RenameEdgeTask method run.

@Override
public void run(final TaskMonitor taskMonitor) {
    if (network == null) {
        taskMonitor.showMessage(TaskMonitor.Level.ERROR, "Network must be specified");
        return;
    }
    if (edge == null) {
        taskMonitor.showMessage(TaskMonitor.Level.ERROR, "Edge name or suid must be specified");
        return;
    }
    if (newName == null) {
        taskMonitor.showMessage(TaskMonitor.Level.ERROR, "New name must be specified");
        return;
    }
    CyEdge renamedEdge = getEdge(network, edge);
    network.getRow(renamedEdge).set(CyNetwork.NAME, newName);
    taskMonitor.showMessage(TaskMonitor.Level.INFO, "Edge " + renamedEdge + " renamed to " + newName);
}

Example 44 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-impl by cytoscape.

the class LayoutEdgeTest method testLayoutEdgeConstructor2.

@Test
public void testLayoutEdgeConstructor2() {
    CyNetworkFactory nFactory = support.getNetworkFactory();
    CyNetwork newNetwork = nFactory.createNetwork();
    CyNode s = newNetwork.addNode();
    CyNode t = newNetwork.addNode();
    CyEdge e = newNetwork.addEdge(s, t, true);
    final CyNetworkViewFactory viewFactory = support.getNetworkViewFactory();
    CyNetworkView newView = viewFactory.createNetworkView(newNetwork);
    final View<CyNode> sourceView = newView.getNodeView(s);
    final View<CyNode> targetView = newView.getNodeView(t);
    assertNotNull(sourceView);
    assertNotNull(targetView);
    CyRow sRow = newNetwork.getRow(s);
    CyRow tRow = newNetwork.getRow(t);
    final LayoutNode layoutNodeS = new LayoutNode(sourceView, 0, sRow);
    final LayoutNode layoutNodeT = new LayoutNode(targetView, 1, tRow);
    final LayoutEdge layoutEdge2 = new LayoutEdge(e, layoutNodeS, layoutNodeT, newNetwork.getRow(e));
    assertNotNull(layoutEdge2);
}

Example 45 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-impl by cytoscape.

the class NetworkLineParser method parseEntry.

public void parseEntry(final String[] parts) {
    final CyNode source = createNode(parts, mapping.getSourceIndex());
    final CyNode target = createNode(parts, mapping.getTargetIndex());
    final SourceColumnSemantic[] types = mapping.getTypes();
    final List<Integer> srcAttrIdxs = new ArrayList<>();
    final List<Integer> tgtAttrIdxs = new ArrayList<>();
    final List<Integer> edgeAttrIdxs = new ArrayList<>();
    for (int i = 0; i < types.length; i++) {
        if (types[i] == SourceColumnSemantic.SOURCE_ATTR)
            srcAttrIdxs.add(i);
        else if (types[i] == SourceColumnSemantic.TARGET_ATTR)
            tgtAttrIdxs.add(i);
        else if (types[i] == SourceColumnSemantic.EDGE_ATTR || types[i] == SourceColumnSemantic.ATTR)
            edgeAttrIdxs.add(i);
    }
    if (source != null)
        addAttributes(source, parts, srcAttrIdxs);
    if (target != null)
        addAttributes(target, parts, tgtAttrIdxs);
    // Single column nodes list.  Just add nodes.
    if (source == null || target == null)
        return;
    final String interaction;
    if ((mapping.getInteractionIndex() == -1) || (mapping.getInteractionIndex() > (parts.length - 1)) || (parts[mapping.getInteractionIndex()] == null)) {
        interaction = mapping.getDefaultInteraction();
    } else {
        interaction = parts[mapping.getInteractionIndex()];
    }
    final CyEdge edge = network.addEdge(source, target, true);
    network.getRow(edge).set(CyEdge.INTERACTION, interaction);
    String edgeName = network.getRow(source).get(CyNetwork.NAME, String.class) + " (" + interaction + ") " + network.getRow(target).get(CyNetwork.NAME, String.class);
    network.getRow(edge).set(CyNetwork.NAME, edgeName);
    edgeList.add(edge.getSUID());
    if (edge != null)
        addAttributes(edge, parts, edgeAttrIdxs);
}