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

Example 16 with CyEdge

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

the class UnHideCommandTask method getResults.

public Object getResults(Class type) {
    List<CyIdentifiable> identifiables = new ArrayList<>();
    if (nodes != null)
        identifiables.addAll(nodes);
    if (edges != null)
        identifiables.addAll(edges);
    if (type.equals(List.class)) {
        return identifiables;
    } else if (type.equals(String.class)) {
        if (identifiables.size() == 0)
            return "<none>";
        String ret = "";
        if (nodes != null && nodes.size() > 0) {
            ret += "Nodes unhidden: \n";
            for (CyNode node : nodes) {
                ret += "   " + network.getRow(node).get(CyNetwork.NAME, String.class) + "\n";
            }
        }
        if (edges != null && edges.size() > 0) {
            ret += "Edges unhidden: \n";
            for (CyEdge edge : edges) {
                ret += "   " + network.getRow(edge).get(CyNetwork.NAME, String.class) + "\n";
            }
        }
        return ret;
    } else if (type.equals(JSONResult.class)) {
        JSONResult res = () -> {
            if (identifiables == null || identifiables.size() == 0)
                return "{}";
            else {
                CyJSONUtil cyJSONUtil = serviceRegistrar.getService(CyJSONUtil.class);
                String result = "{\"nodes\":";
                if (nodes == null || nodes.size() == 0)
                    result += "[]";
                else
                    result += cyJSONUtil.cyIdentifiablesToJson(nodes);
                result += ", \"edges\":";
                if (edges == null || edges.size() == 0)
                    result += "[]";
                else
                    result += cyJSONUtil.cyIdentifiablesToJson(edges);
                result += "}";
                return result;
            }
        };
        return res;
    }
    return identifiables;
}

Example 17 with CyEdge

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

the class PasteEdit method redo.

@Override
public void redo() {
    List<CyIdentifiable> pastedObjects = null;
    if (this.xformPt == null)
        pastedObjects = clipboard.paste(view, 0.0, 0.0);
    else
        pastedObjects = clipboard.paste(view, xformPt.getX(), xformPt.getY());
    // Apply visual style
    final VisualMappingManager vmMgr = serviceRegistrar.getService(VisualMappingManager.class);
    VisualStyle vs = vmMgr.getVisualStyle(view);
    for (CyIdentifiable element : pastedObjects) {
        View<? extends CyIdentifiable> elementView = null;
        if (element instanceof CyNode)
            elementView = view.getNodeView((CyNode) element);
        else if (element instanceof CyEdge)
            elementView = view.getEdgeView((CyEdge) element);
        else
            continue;
        vs.apply(view.getModel().getRow(element), elementView);
    }
    view.updateView();
}

Example 18 with CyEdge

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

the class SIFInterpreterTask method run.

@Override
public void run(TaskMonitor tm) {
    if (sifString == null)
        throw new NullPointerException("SIF input string is null");
    String[] terms = sifString.split("\\s");
    if (terms != null) {
        if (terms.length > 0) {
            String name1 = terms[0].trim();
            if (!name1.equals(null)) {
                CyNode node1 = findNode(terms[0]);
                if (node1 == null) {
                    node1 = network.addNode();
                    network.getRow(node1).set("name", terms[0]);
                // nv1 = view.getNodeView(node1);
                // double[] nextLocn = new double[2];
                // nextLocn[0] = p.getX();
                // nextLocn[1] = p.getY();
                // view.xformComponentToNodeCoords(nextLocn);
                // nv1.setOffset(nextLocn[0], nextLocn[1]);
                } else {
                // nv1 = view.getNodeView(node1);
                }
                if (terms.length == 3) {
                    // simple case of 'A interaction B'
                    CyNode node2 = findNode(terms[2]);
                    if (node2 == null) {
                        node2 = network.addNode();
                        network.getRow(node2).set("name", terms[2]);
                    // nv2 = view.getNodeView(node2);
                    // nv2.setOffset(nv1.getXPosition() + spacing, nv1.getYPosition());
                    }
                    CyEdge edge = network.addEdge(node1, node2, true);
                    network.getRow(edge).set("name", terms[1]);
                } else if (terms.length > 3) {
                    // process multiple targets and one source
                    List<View<CyNode>> nodeViews = new ArrayList<View<CyNode>>();
                    String interactionType = terms[1];
                    for (int i = 2; i < terms.length; i++) {
                        CyNode node2 = findNode(terms[i]);
                        if (node2 == null) {
                            node2 = network.addNode();
                            network.getRow(node2).set("name", terms[i]);
                        // nv2 = view.getNodeView(node2);
                        // nv2.setOffset(nv1.getXPosition() + spacing, nv1
                        // .getYPosition());
                        }
                        CyEdge edge = network.addEdge(node1, node2, true);
                        network.getRow(edge).set("name", terms[1]);
                    // doCircleLayout(nodeViews, nv1);
                    }
                }
            }
            // Apply visual style
            final CyEventHelper eventHelper = serviceRegistrar.getService(CyEventHelper.class);
            // To make sure the edge view is created before applying the style
            eventHelper.flushPayloadEvents();
            final VisualMappingManager vmMgr = serviceRegistrar.getService(VisualMappingManager.class);
            VisualStyle vs = vmMgr.getVisualStyle(view);
            vs.apply(view);
            view.updateView();
        }
    }
}

Example 19 with CyEdge

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

the class ClipboardImplTest method addEdge.

private CyEdge addEdge(CyNetwork net, CyNode n1, CyNode n2, String name) {
    CyEdge edge = net.addEdge(n1, n2, true);
    net.getRow(edge).set(CyNetwork.NAME, name);
    return edge;
}

Example 20 with CyEdge

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

the class ClipboardImplTest method testCopyNodes_SameRoot.

@Test
public void testCopyNodes_SameRoot() throws Exception {
    CyNetworkView targetView = createNetworkAndView(sourceView.getModel());
    Set<CyNode> nodes = new HashSet<>(Arrays.asList(new CyNode[] { n1, n3 }));
    Set<CyEdge> edges = Collections.emptySet();
    ClipboardImpl clipboard = new ClipboardImpl(sourceView, nodes, edges, false, lexicon, serviceRegistrar);
    clipboard.paste(targetView, 0, 0);
    assertEquals(2, targetView.getModel().getNodeCount());
    assertEquals(0, targetView.getModel().getEdgeCount());
    assertNotNull(getNodeByName(targetView.getModel(), "n1"));
    assertNotNull(getNodeByName(targetView.getModel(), "n3"));
}