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

Example 71 with CyEdge

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

the class HideCommandTask 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 hidden: \n";
            for (CyNode node : nodes) {
                ret += "   " + network.getRow(node).get(CyNetwork.NAME, String.class) + "\n";
            }
        }
        if (edges != null && edges.size() > 0) {
            ret += "Edges hidden: \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 72 with CyEdge

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

the class HideUtils method setVisibleEdges.

static void setVisibleEdges(Collection<CyEdge> edges, boolean visible, CyNetworkView view) {
    for (CyEdge e : edges) {
        final View<CyEdge> ev = view.getEdgeView(e);
        if (visible)
            ev.clearValueLock(EDGE_VISIBLE);
        else {
            ev.setLockedValue(EDGE_VISIBLE, false);
            view.getModel().getRow(ev.getModel()).set(CyNetwork.SELECTED, false);
        }
    }
}

Example 73 with CyEdge

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

the class HideUtils method setVisibleNodes.

static void setVisibleNodes(Collection<CyNode> nodes, boolean visible, CyNetworkView view) {
    final CyNetwork net = view.getModel();
    for (CyNode n : nodes) {
        if (visible)
            view.getNodeView(n).clearValueLock(NODE_VISIBLE);
        else {
            view.getModel().getRow(n).set(CyNetwork.SELECTED, false);
            view.getNodeView(n).setLockedValue(NODE_VISIBLE, false);
        }
        for (CyNode n2 : net.getNeighborList(n, CyEdge.Type.ANY)) {
            for (CyEdge e : net.getConnectingEdgeList(n, n2, CyEdge.Type.ANY)) {
                final View<CyEdge> ev = view.getEdgeView(e);
                if (visible)
                    ev.clearValueLock(EDGE_VISIBLE);
                else {
                    view.getModel().getRow(ev.getModel()).set(CyNetwork.SELECTED, false);
                    ev.setLockedValue(EDGE_VISIBLE, false);
                }
            }
        }
    }
}

Example 74 with CyEdge

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

the class AdjacencyTransformer method apply.

@Override
public void apply(CyNetwork network, CyIdentifiable element, TransformerSink<CyIdentifiable> sink) {
    if (action == Action.ADD)
        sink.collect(element);
    if (element instanceof CyNode) {
        CyNode currentNode = (CyNode) element;
        Iterable<CyEdge> adjacentEdges = network.getAdjacentEdgeIterable(currentNode, edgesAre.type());
        Filter<CyNetwork, CyIdentifiable> memoizedFilter = super.getMemoizedFilter();
        for (CyEdge edge : adjacentEdges) {
            CyNode node = otherNode(currentNode, edge);
            boolean pass;
            if (filterTarget == What.NODES) {
                pass = memoizedFilter.accepts(network, node);
            } else if (filterTarget == What.EDGES) {
                pass = memoizedFilter.accepts(network, edge);
            } else {
                // filterTarget == What.NODES_AND_EDGES
                pass = memoizedFilter.accepts(network, node) && memoizedFilter.accepts(network, edge);
            }
            if (pass) {
                if (output == What.NODES || output == What.NODES_AND_EDGES) {
                    sink.collect(node);
                }
                if (output == What.EDGES || output == What.NODES_AND_EDGES) {
                    sink.collect(edge);
                }
            }
        }
    }
}

Example 75 with CyEdge

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

the class RangeSelectionListener method onUserSelection.

/**
 * Indicates that the user has selected a text item within the QuickFind
 * Search Box.
 *
 * @param network the current CyNetwork.
 * @param hit     hit value chosen by the user.
 */
public void onUserSelection(final CyNetwork network, Hit hit) {
    SelectUtil.unselectAllNodes(network);
    SelectUtil.unselectAllEdges(network);
    // Assemble Hit Objects
    final Object[] graphObjects = hit.getAssociatedObjects();
    final List list = new ArrayList();
    for (int i = 0; i < graphObjects.length; i++) {
        list.add(graphObjects[i]);
    }
    // Fit Selected Content
    SwingUtilities.invokeLater(new Runnable() {

        public void run() {
            final CyNetwork cyNetwork = applicationManager.getCurrentNetwork();
            CyNetworkView networkView = applicationManager.getCurrentNetworkView();
            GenericIndex index = quickFind.getIndex(cyNetwork);
            if (index.getIndexType() == QuickFind.INDEX_NODES) {
                SelectUtil.setSelectedNodeState(network, list, true);
                final CyNetworkView currentView = applicationManager.getCurrentNetworkView();
                if (currentView != null)
                    currentView.fitSelected();
            } else {
                SelectUtil.setSelectedEdgeState(network, list, true);
                List<CyNode> nodeList = new ArrayList<CyNode>();
                for (int i = 0; i < list.size(); i++) {
                    CyEdge edge = (CyEdge) list.get(i);
                    CyNode sourceNode = edge.getSource();
                    CyNode targetNode = edge.getTarget();
                    nodeList.add(sourceNode);
                    nodeList.add(targetNode);
                }
                SelectUtil.setSelectedNodeState(network, nodeList, true);
                networkView.fitSelected();
            }
            // so that node does not take up whole screen.
            if (graphObjects.length == 1) {
                if (graphObjects[0] instanceof CyNode) {
                    CyNode node = (CyNode) graphObjects[0];
                    // Obtain dimensions of current InnerCanvas
                    RenderingEngine<CyNetwork> engine = applicationManager.getCurrentRenderingEngine();
                    VisualLexicon lexicon = engine.getVisualLexicon();
                    Double networkWidth = VisualPropertyUtil.get(lexicon, networkView, "NETWORK_WIDTH", BasicVisualLexicon.NETWORK, Double.class);
                    Double networkHeight = VisualPropertyUtil.get(lexicon, networkView, "NETWORK_HEIGHT", BasicVisualLexicon.NETWORK, Double.class);
                    View<CyNode> nodeView = networkView.getNodeView(node);
                    Double nodeWidth = VisualPropertyUtil.get(lexicon, nodeView, "NODE_WIDTH", BasicVisualLexicon.NODE, Double.class);
                    Double nodeHeight = VisualPropertyUtil.get(lexicon, nodeView, "NODE_HEIGHT", BasicVisualLexicon.NODE, Double.class);
                    double width = nodeWidth * NODE_SIZE_MULTIPLER;
                    double height = nodeHeight * NODE_SIZE_MULTIPLER;
                    double scaleFactor = Math.min(networkWidth / width, (networkHeight / height));
                // TODO: How do we set the zoom in the new API?
                // networkView.setZoom(scaleFactor);
                }
            }
            networkView.updateView();
        }
    });
}