Examples with LayoutNode org.cytoscape.view.layout.LayoutNode used on opensource projects

Example 11 with LayoutNode

use of org.cytoscape.view.layout.LayoutNode in project cytoscape-impl by cytoscape.

the class BioLayoutFRAlgorithmTask method doOneIteration.

/**
 * This executes a single iteration of the FR algorithm.
 *
 * @param iteration The current interation.
 * @param temp The current temperature factor.
 * @return an updated temperature factor.
 */
public double doOneIteration(int iteration, double temp) {
    double xAverage = 0;
    double yAverage = 0;
    double zAverage = 0;
    // Calculate repulsive forces
    for (LayoutNode v : partition.getNodeList()) {
        if (!v.isLocked()) {
            xAverage += v.getX() / partition.nodeCount();
            yAverage += v.getY() / partition.nodeCount();
            zAverage += v.getZ() / partition.nodeCount();
        }
    }
    for (LayoutNode v : partition.getNodeList()) {
        if (!v.isLocked()) {
            calculateRepulsion(v);
            if (gravity_constant != 0)
                calculateGravity(v, xAverage, yAverage, zAverage);
        }
    }
    // / for e in E do begin
    for (LayoutEdge e : partition.getEdgeList()) {
        calculateAttraction(e);
    }
    // / end
    // attractProfile.checkpoint();
    // Dump the current displacements
    // print_disp();
    // Dampen & update
    double xDispTotal = 0;
    double yDispTotal = 0;
    // / for v in V do begin
    for (LayoutNode v : partition.getNodeList()) {
        if (v.isLocked())
            continue;
        calculatePosition(v, temp);
        xDispTotal += Math.abs(v.getXDisp());
        yDispTotal += Math.abs(v.getYDisp());
    }
    // hit our completion criteria
    if (complete(xDispTotal, yDispTotal))
        return 0;
    // t := cool(t)
    return cool(temp, iteration);
}

Example 12 with LayoutNode

use of org.cytoscape.view.layout.LayoutNode in project cytoscape-impl by cytoscape.

the class BioLayoutKKAlgorithmTask method simpleMoveNode.

private void simpleMoveNode(PartialDerivatives partials) {
    LayoutNode node = partials.node;
    if (node.isLocked()) {
        return;
    }
    double denominator = ((partials.xx * partials.yy) - (partials.xy * partials.xy));
    if (((float) denominator) == 0.0) {
        return;
    // throw new RuntimeException("denominator too close to 0 for node "+node);
    }
    // System.out.println(partials.printPartial());
    double deltaX = (((-partials.x * partials.yy) - (-partials.y * partials.xy)) / denominator);
    double deltaY = (((-partials.y * partials.xx) - (-partials.x * partials.xy)) / denominator);
    /* System.out.println("Moving node "+node.getIdentifier()+" from "+node.getX()+", "+node.getY()+
		                    " to "+(node.getX()+deltaX)+", "+(node.getY()+deltaY)); */
    node.setLocation(node.getX() + deltaX, node.getY() + deltaY);
}

Example 13 with LayoutNode

use of org.cytoscape.view.layout.LayoutNode in project cytoscape-impl by cytoscape.

the class BioLayoutKKAlgorithmTask method calculateNodeDistances.

private int[][] calculateNodeDistances() {
    int[][] distances = new int[m_nodeCount][];
    LinkedList<Integer> queue = new LinkedList<Integer>();
    boolean[] completedNodes = new boolean[m_nodeCount];
    int toNode;
    int fromNode;
    int neighbor;
    int toNodeDistance;
    int neighborDistance;
    for (LayoutNode v : partition.getNodeList()) {
        fromNode = v.getIndex();
        if (distances[fromNode] == null)
            distances[fromNode] = new int[m_nodeCount];
        Arrays.fill(distances[fromNode], Integer.MAX_VALUE);
        distances[fromNode][fromNode] = 0;
        Arrays.fill(completedNodes, false);
        queue.add(Integer.valueOf(fromNode));
        while (!(queue.isEmpty())) {
            int index = ((Integer) queue.removeFirst()).intValue();
            if (completedNodes[index])
                continue;
            completedNodes[index] = true;
            toNode = index;
            toNodeDistance = distances[fromNode][index];
            if (index < fromNode) {
                // Oh boy.  We've already got every distance from/to this node.
                int distanceThroughToNode;
                for (int i = 0; i < m_nodeCount; i++) {
                    if (distances[index][i] == Integer.MAX_VALUE)
                        continue;
                    distanceThroughToNode = toNodeDistance + distances[index][i];
                    if (distanceThroughToNode <= distances[fromNode][i]) {
                        // calculated from fromNode never will, and is thus complete.
                        if (distances[index][i] == 1)
                            completedNodes[i] = true;
                        distances[fromNode][i] = distanceThroughToNode;
                    }
                }
                // the previous calculation.
                continue;
            }
            // End if toNode has already had all of its distances calculated.
            List<LayoutNode> neighborList = v.getNeighbors();
            for (LayoutNode neighbor_v : neighborList) {
                neighbor = neighbor_v.getIndex();
                // We've already done everything we can here.
                if (completedNodes[neighbor])
                    continue;
                neighborDistance = distances[fromNode][neighbor];
                if ((toNodeDistance != Integer.MAX_VALUE) && (neighborDistance > (toNodeDistance + 1))) {
                    distances[fromNode][neighbor] = toNodeDistance + 1;
                    queue.addLast(Integer.valueOf(neighbor));
                }
            }
        }
    }
    return distances;
}

Example 14 with LayoutNode

use of org.cytoscape.view.layout.LayoutNode in project cytoscape-impl by cytoscape.

the class CoSELayoutAlgorithmTask method layoutPartition.

@Override
public void layoutPartition(final LayoutPartition partition) {
    if (cancelled)
        return;
    final CyGroupManager groupManager = serviceRegistrar.getService(CyGroupManager.class);
    final CyNetwork network = networkView.getModel();
    // Create the CoSE model
    // (see http://www.cs.bilkent.edu.tr/~ivis/chilay/ChiLay-2.0-PG.pdf)
    cose = new CoSELayout();
    cose.addProgressListener(new ProgressListener() {

        @Override
        public void update(double value) {
            taskMonitor.setProgress(value);
        }
    });
    final LGraphManager gm = cose.getGraphManager();
    final LGraph root = gm.addRoot();
    // Index all LayoutNodes by CyNode for future reference
    final Map<CyNode, LayoutNode> layoutNodeMap = new HashMap<>();
    for (LayoutNode n : partition.getNodeList()) layoutNodeMap.put(n.getNode(), n);
    // Create all CoSE nodes
    final Map<CyNode, LNode> lNodeMap = new HashMap<>();
    for (LayoutNode n : partition.getNodeList()) {
        // If this node does not belong to a CyGroup, let's traverse its potential compound node tree.
        if (groupManager.getGroupsForNode(n.getNode(), network).isEmpty())
            traverseLNodeTree(n, root, cose, lNodeMap, layoutNodeMap, groupManager);
    }
    if (cancelled)
        return;
    // Create all CoSE edges
    final Map<CyEdge, LEdge> lEdgeMap = new HashMap<>();
    final Iterator<LayoutEdge> edgeIter = partition.edgeIterator();
    while (edgeIter.hasNext() && !cancelled) {
        final LayoutEdge e = edgeIter.next();
        createLEdge(e, cose, lNodeMap, lEdgeMap);
    }
    if (cancelled)
        return;
    // Run the layout
    try {
        cose.runLayout();
    } catch (Exception e) {
        logger.error("Error running CoSE Layout", e);
        return;
    }
    if (cancelled)
        return;
    // Move all Node Views to the new positions
    for (LayoutNode n : partition.getNodeList()) partition.moveNodeToLocation(n);
}

Example 15 with LayoutNode

use of org.cytoscape.view.layout.LayoutNode in project cytoscape-impl by cytoscape.

the class CoSELayoutAlgorithmTask method traverseLNodeTree.

private void traverseLNodeTree(final LayoutNode layoutNode, final LGraph graph, final CoSELayout cose, final Map<CyNode, LNode> lNodeMap, final Map<CyNode, LayoutNode> layoutNodeMap, final CyGroupManager groupManager) {
    if (lNodeMap.containsKey(layoutNode.getNode()))
        // This node has already been visited!
        return;
    final LNode ln = createLNode(layoutNode, graph, cose, lNodeMap);
    if (groupManager.isGroup(layoutNode.getNode(), networkView.getModel())) {
        final CyGroup group = groupManager.getGroup(layoutNode.getNode(), networkView.getModel());
        if (group != null) {
            final LGraphManager gm = cose.getGraphManager();
            final LGraph subGraph = gm.add(cose.newGraph("G" + group.getGroupNetwork().getSUID()), ln);
            for (CyNode childNode : group.getNodeList()) {
                final LayoutNode childLayoutNode = layoutNodeMap.get(childNode);
                if (childLayoutNode != null)
                    traverseLNodeTree(childLayoutNode, subGraph, cose, lNodeMap, layoutNodeMap, groupManager);
            }
        }
    }
}