Examples with LNode org.ivis.layout.LNode used on opensource projects

Example 1 with LNode

use of org.ivis.layout.LNode in project cytoscape-impl by cytoscape.

the class SbgnPDLayout method calculateBounds.

/**
 * This method returns the bounding rectangle of the given set of nodes with
 * or without the margins
 */
protected RectangleD calculateBounds(boolean isMarginIncluded, ArrayList<SbgnPDNode> nodes) {
    int boundLeft = Integer.MAX_VALUE;
    int boundRight = Integer.MIN_VALUE;
    int boundTop = Integer.MAX_VALUE;
    int boundBottom = Integer.MIN_VALUE;
    int nodeLeft;
    int nodeRight;
    int nodeTop;
    int nodeBottom;
    Iterator<SbgnPDNode> itr = nodes.iterator();
    while (itr.hasNext()) {
        LNode lNode = itr.next();
        nodeLeft = (int) (lNode.getLeft());
        nodeRight = (int) (lNode.getRight());
        nodeTop = (int) (lNode.getTop());
        nodeBottom = (int) (lNode.getBottom());
        if (boundLeft > nodeLeft)
            boundLeft = nodeLeft;
        if (boundRight < nodeRight)
            boundRight = nodeRight;
        if (boundTop > nodeTop)
            boundTop = nodeTop;
        if (boundBottom < nodeBottom)
            boundBottom = nodeBottom;
    }
    if (isMarginIncluded) {
        return new RectangleD(boundLeft - SbgnPDConstants.COMPLEX_MEM_MARGIN, boundTop - SbgnPDConstants.COMPLEX_MEM_MARGIN, boundRight - boundLeft + 2 * SbgnPDConstants.COMPLEX_MEM_MARGIN, boundBottom - boundTop + 2 * SbgnPDConstants.COMPLEX_MEM_MARGIN);
    } else {
        return new RectangleD(boundLeft, boundTop, boundRight - boundLeft, boundBottom - boundTop);
    }
}

Example 2 with LNode

use of org.ivis.layout.LNode in project cytoscape-impl by cytoscape.

the class GraphMLWriter method mapNodes.

/**
 * A recursive function for writing nodes of the specified LGraphManager
 * into the specified file
 *
 * @param root
 * @param level
 * @param parentStr
 */
private void mapNodes(LGraph root, short level, String parentStr) {
    String currNodeStr;
    LNode node;
    // for each node of the root graph...
    for (int i = 0; i < root.getNodes().size(); i++) {
        node = (LNode) root.getNodes().get(i);
        // check if the current root graph is the root graph of the LGraphManager
        if (level != 0)
            currNodeStr = parentStr + ":n" + i;
        else
            currNodeStr = "n" + i;
        // add new node to the node-string map
        this.map.put(node, currNodeStr);
        // then make a recursive call with current node's child graph
        if (node.getChild() != null) {
            this.mapNodes(node.getChild(), (short) (level + 1), currNodeStr);
        }
    }
}

Example 3 with LNode

use of org.ivis.layout.LNode in project cytoscape-impl by cytoscape.

the class CoSELayoutAlgorithmTask method createLEdge.

private LEdge createLEdge(final LayoutEdge layoutEdge, final CoSELayout cose, final Map<CyNode, LNode> lNodeMap, final Map<CyEdge, LEdge> lEdgeMap) {
    final LNode ln1 = lNodeMap.get(layoutEdge.getSource().getNode());
    final LNode ln2 = lNodeMap.get(layoutEdge.getTarget().getNode());
    if (ln1 != null && ln2 != null) {
        final VEdge ve = new VEdge(layoutEdge);
        final LEdge le = cose.getGraphManager().add(cose.newEdge(ve), ln1, ln2);
        lEdgeMap.put(layoutEdge.getEdge(), le);
        return le;
    }
    return null;
}

Example 4 with LNode

use of org.ivis.layout.LNode in project cytoscape-impl by cytoscape.

the class GraphMLWriter method writeNodes.

/**
 * A recursive function that writes the nodes of the specified LGraphManager
 *
 * @param root
 * @param level
 * @param parentStr
 */
private void writeNodes(LGraph root, short level, String parentStr) {
    short currIndentation = (short) (this.INITIAL_INDENTATION + (level * 2));
    LNode node;
    LNode parent = root.getParent();
    int x, y;
    String currNodeStr;
    try {
        this.writeSpaces((short) (currIndentation - 2));
        if (level == 0)
            out.write("<graph id=\"\" edgedefault=\"undirected\">\n");
        else
            out.write("  <graph id=\"" + parentStr + ":\" edgedefault=\"undirected\">\n");
        for (int i = 0; i < root.getNodes().size(); i++) {
            node = (LNode) root.getNodes().get(i);
            // if it is the root graph
            if (parent == null) {
                x = (int) node.getRect().x;
                y = (int) node.getRect().y;
            } else {
                x = (int) (node.getRect().x - parent.getRect().x);
                y = (int) (node.getRect().y - parent.getRect().y);
            }
            // write the node data
            this.writeSpaces(currIndentation);
            out.write("<node id=\"");
            currNodeStr = (String) this.map.get(node);
            out.write(currNodeStr + "\">\n");
            this.writeSpaces((short) (currIndentation + 2));
            out.write("<data key=\"x\">" + x + "</data>\n");
            this.writeSpaces((short) (currIndentation + 2));
            out.write("<data key=\"y\">" + y + "</data>\n");
            this.writeSpaces((short) (currIndentation + 2));
            out.write("<data key=\"height\">" + (int) node.getRect().height + "</data>\n");
            this.writeSpaces((short) (currIndentation + 2));
            out.write("<data key=\"width\">" + (int) node.getRect().width + "</data>\n");
            this.writeToFile(NODE_DATA_1, (short) (currIndentation + 2));
            this.writeSpaces((short) (currIndentation + 2));
            out.write("<data key=\"text\">" + currNodeStr + "</data>\n");
            this.writeToFile(NODE_DATA_2, (short) (currIndentation + 2));
            // if current node is a compound, then make a recursive call
            if (node.getChild() != null) {
                this.writeNodes(node.getChild(), (short) (level + 1), currNodeStr);
            } else {
                this.writeSpaces((short) (currIndentation + 2));
                out.write("<data key=\"shape\">Rectangle</data>\n");
            }
            this.writeSpaces(currIndentation);
            out.write("</node>\n");
        }
        if (level != 0) {
            this.writeSpaces(currIndentation);
            out.write("<data key=\"margin\">10</data>\n");
            this.writeSpaces((short) (currIndentation - 2));
            out.write("</graph>\n");
        }
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 5 with LNode

use of org.ivis.layout.LNode 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);
}