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

Example 6 with LGraph

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

the class SbgnPDLayout method createPortNodes.

/**
 * This method creates two port nodes and a compound for each process nodes
 * and adds them to graph.
 */
private void createPortNodes() {
    for (Object o : this.getAllNodes()) {
        SbgnPDNode originalProcessNode = (SbgnPDNode) o;
        if (originalProcessNode.type.equals(SbgnPDConstants.PROCESS)) {
            LGraph ownerGraph = originalProcessNode.getOwner();
            // create new nodes and graphs
            SbgnProcessNode processNode = (SbgnProcessNode) newProcessNode(null);
            SbgnPDNode inputPort = (SbgnPDNode) newPortNode(null, SbgnPDConstants.INPUT_PORT);
            SbgnPDNode outputPort = (SbgnPDNode) newPortNode(null, SbgnPDConstants.OUTPUT_PORT);
            // create a dummy compound
            SbgnPDNode compoundNode = (SbgnPDNode) newNode(null);
            compoundNode.type = SbgnPDConstants.DUMMY_COMPOUND;
            // add labels
            compoundNode.label = "DummyCompound_" + originalProcessNode.label;
            inputPort.label = "InputPort_" + originalProcessNode.label;
            outputPort.label = "OutputPort_" + originalProcessNode.label;
            // create child graph (= 2port+process) to be set as child to
            // dummy compound
            LGraph childGraph = newGraph(null);
            ownerGraph.add(processNode);
            // convert the process node to SbgnProcessNode
            processNode.copyFromSBGNPDNode(originalProcessNode, this.getGraphManager());
            processNode.connectNodes(compoundNode, inputPort, outputPort);
            // create rigid edges, change edge connections
            processNode.reconnectEdges(idealEdgeLength);
            SbgnPDEdge rigidToProduction = (SbgnPDEdge) newRigidEdge(null);
            rigidToProduction.label = "" + (this.graphManager.getAllEdges().length + 1);
            SbgnPDEdge rigidToConsumption = (SbgnPDEdge) newRigidEdge(null);
            rigidToConsumption.label = "" + (this.graphManager.getAllEdges().length + 2);
            ownerGraph.remove(processNode);
            // organize child graph
            childGraph.add(processNode);
            childGraph.add(inputPort);
            childGraph.add(outputPort);
            childGraph.add(rigidToProduction, inputPort, processNode);
            childGraph.add(rigidToConsumption, outputPort, processNode);
            // organize the compound node
            compoundNode.setOwner(ownerGraph);
            compoundNode.setCenter(processNode.getCenterX(), processNode.getCenterY());
            ownerGraph.add(compoundNode);
            this.graphManager.add(childGraph, compoundNode);
            // remove the original process node
            ownerGraph.remove(originalProcessNode);
            this.processNodeList.add(processNode);
            this.graphManager.updateBounds();
        }
    }
    // reset the topology
    this.graphManager.resetAllNodes();
    this.graphManager.resetAllNodesToApplyGravitation();
    this.graphManager.resetAllEdges();
    this.calculateNodesToApplyGravitationTo();
}

Example 7 with LGraph

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

the class SbgnPDLayout method repopulateComplexes.

/**
 * Reassigns the complex content. The outermost complex is placed first.
 */
protected void repopulateComplexes() {
    for (SbgnPDNode comp : emptiedDummyComplexMap.keySet()) {
        LGraph chGr = emptiedDummyComplexMap.get(comp);
        comp.setChild(chGr);
        this.getGraphManager().getGraphs().add(chGr);
    }
    for (int i = complexOrder.size() - 1; i >= 0; i--) {
        SbgnPDNode comp = complexOrder.get(i);
        LGraph chGr = childGraphMap.get(comp);
        // repopulate the complex
        comp.setChild(chGr);
        // if the child graph is not null, adjust the positions of members
        if (chGr != null) {
            // adjust the positions of the members
            if (compactionMethod == DefaultCompactionAlgorithm.POLYOMINO_PACKING) {
                adjustLocation(comp, chGr);
                getGraphManager().getGraphs().add(chGr);
            } else if (compactionMethod == DefaultCompactionAlgorithm.TILING) {
                getGraphManager().getGraphs().add(chGr);
                MemberPack pack = memberPackMap.get(comp);
                pack.adjustLocations(comp.getLeft(), comp.getTop());
            }
        }
    }
    for (SbgnPDNode comp : emptiedDummyComplexMap.keySet()) {
        LGraph chGr = emptiedDummyComplexMap.get(comp);
        adjustLocation(comp, chGr);
    }
    removeDummyComplexes();
    // reset
    getGraphManager().resetAllNodes();
    getGraphManager().resetAllNodesToApplyGravitation();
    getGraphManager().resetAllEdges();
    this.calculateNodesToApplyGravitationTo();
}

Example 8 with LGraph

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

the class SbgnPDLayout method clearComplex.

// ********************* SECTION : TILING METHODS *********************
private void clearComplex(SbgnPDNode comp) {
    MemberPack pack = null;
    LGraph childGr = comp.getChild();
    childGraphMap.put(comp, childGr);
    if (childGr == null)
        return;
    if (compactionMethod == DefaultCompactionAlgorithm.POLYOMINO_PACKING) {
        applyPolyomino(comp);
    } else if (compactionMethod == DefaultCompactionAlgorithm.TILING) {
        pack = new MemberPack(childGr);
        memberPackMap.put(comp, pack);
    }
    if (dummyComplexList.contains(comp)) {
        for (Object o : comp.getChild().getNodes()) {
            clearDummyComplexGraphs((SbgnPDNode) o);
        }
    }
    getGraphManager().getGraphs().remove(childGr);
    comp.setChild(null);
    if (compactionMethod == DefaultCompactionAlgorithm.TILING) {
        comp.setWidth(pack.getWidth());
        comp.setHeight(pack.getHeight());
    }
    // Redirect the edges of complex members to the complex.
    if (childGr != null) {
        for (Object ch : childGr.getNodes()) {
            SbgnPDNode chNd = (SbgnPDNode) ch;
            for (Object obj : new ArrayList(chNd.getEdges())) {
                LEdge edge = (LEdge) obj;
                if (edge.getSource() == chNd) {
                    chNd.getEdges().remove(edge);
                    edge.setSource(comp);
                    comp.getEdges().add(edge);
                } else if (edge.getTarget() == chNd) {
                    chNd.getEdges().remove(edge);
                    edge.setTarget(comp);
                    comp.getEdges().add(edge);
                }
            }
        }
    }
}

Example 9 with LGraph

use of org.ivis.layout.LGraph 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 10 with LGraph

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