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

Example 1 with LGraph

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

the class SbgnPDLayout method groupZeroDegreeMembers.

/**
 * This method finds all the zero degree nodes in the graph which are not
 * owned by a complex node. Zero degree nodes at each level are grouped
 * together and placed inside a dummy complex to reduce bounds of root
 * graph.
 */
private void groupZeroDegreeMembers() {
    Map<SbgnPDNode, LGraph> childComplexMap = new HashMap<SbgnPDNode, LGraph>();
    for (Object graphObj : this.getGraphManager().getGraphs()) {
        ArrayList<SbgnPDNode> zeroDegreeNodes = new ArrayList<SbgnPDNode>();
        LGraph ownerGraph = (LGraph) graphObj;
        // do not process complex nodes (their members are already owned)
        if (ownerGraph.getParent().type != null && ((SbgnPDNode) ownerGraph.getParent()).isComplex())
            continue;
        for (Object nodeObj : ownerGraph.getNodes()) {
            SbgnPDNode node = (SbgnPDNode) nodeObj;
            if (calcGraphDegree(node) == 0) {
                zeroDegreeNodes.add(node);
            }
        }
        if (zeroDegreeNodes.size() > 1) {
            // create a new dummy complex
            SbgnPDNode complex = (SbgnPDNode) newNode(null);
            complex.type = SbgnPDConstants.COMPLEX;
            complex.label = "DummyComplex_" + ownerGraph.getParent().label;
            ownerGraph.add(complex);
            LGraph childGraph = newGraph(null);
            for (SbgnPDNode zeroNode : zeroDegreeNodes) {
                ownerGraph.remove(zeroNode);
                childGraph.add(zeroNode);
            }
            dummyComplexList.add(complex);
            childComplexMap.put(complex, childGraph);
        }
    }
    for (SbgnPDNode complex : dummyComplexList) this.graphManager.add(childComplexMap.get(complex), complex);
    this.getGraphManager().updateBounds();
    this.graphManager.resetAllNodes();
    this.graphManager.resetAllNodesToApplyGravitation();
    this.graphManager.resetAllEdges();
    this.calculateNodesToApplyGravitationTo();
}

Example 2 with LGraph

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

the class SbgnPDLayout method removeDummyComplexes.

/**
 * Dummy complexes (placed in the "dummyComplexList") are removed from the
 * graph.
 */
private void removeDummyComplexes() {
    // remove dummy complexes and connect children to original parent
    for (SbgnPDNode dummyComplex : dummyComplexList) {
        LGraph childGraph = dummyComplex.getChild();
        LGraph owner = dummyComplex.getOwner();
        getGraphManager().getGraphs().remove(childGraph);
        dummyComplex.setChild(null);
        owner.remove(dummyComplex);
        for (Object s : childGraph.getNodes()) owner.add((SbgnPDNode) s);
    }
}

Example 3 with LGraph

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

the class SbgnPDLayout method removeDummyCompounds.

/**
 * This method is used to remove the dummy compounds (previously created for
 * each process node) from the graph.
 */
private void removeDummyCompounds() {
    for (SbgnProcessNode processNode : this.processNodeList) {
        SbgnPDNode dummyNode = processNode.parentCompound;
        LGraph childGraph = dummyNode.getChild();
        LGraph owner = dummyNode.getOwner();
        // add children to original parent
        for (Object s : childGraph.getNodes()) owner.add((SbgnPDNode) s);
        for (Object e : childGraph.getEdges()) {
            SbgnPDEdge edge = (SbgnPDEdge) e;
            // childGraph.remove(edge);
            owner.add(edge, edge.getSource(), edge.getTarget());
        }
        // add effectors / remaining edges back to the process
        for (int i = 0; i < dummyNode.getEdges().size(); i++) {
            SbgnPDEdge edge = (SbgnPDEdge) dummyNode.getEdges().get(i);
            dummyNode.getEdges().remove(edge);
            edge.setTarget(processNode);
            processNode.getEdges().add(edge);
            i--;
        }
        // remove the graph
        getGraphManager().getGraphs().remove(childGraph);
        dummyNode.setChild(null);
        owner.remove(dummyNode);
    }
    getGraphManager().resetAllNodes();
    getGraphManager().resetAllNodesToApplyGravitation();
    getGraphManager().resetAllEdges();
    this.calculateNodesToApplyGravitationTo();
}

Example 4 with LGraph

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

the class SbgnPDLayout method applyPolyomino.

/**
 * This method tiles the given list of nodes by using polyomino packing
 * algorithm.
 */
private void applyPolyomino(SbgnPDNode parent) {
    RectangleD r;
    LGraph childGr = parent.getChild();
    if (childGr == null) {
        System.out.println("Child graph is empty (Polyomino)");
    } else {
        // packing takes the input as an array. put the members in an array.
        SbgnPDNode[] mpArray = new SbgnPDNode[childGr.getNodes().size()];
        for (int i = 0; i < childGr.getNodes().size(); i++) {
            SbgnPDNode s = (SbgnPDNode) childGr.getNodes().get(i);
            mpArray[i] = s;
        }
        // pack rectangles
        RectProc.packRectanglesMino(SbgnPDConstants.COMPLEX_MEM_HORIZONTAL_BUFFER, mpArray.length, mpArray);
        // apply compaction
        Compaction c = new Compaction((ArrayList<SbgnPDNode>) childGr.getNodes());
        c.perform();
        // get the resulting rectangle and set parent's (complex) width &
        // height
        r = calculateBounds(true, (ArrayList<SbgnPDNode>) childGr.getNodes());
        parent.setWidth(r.getWidth());
        parent.setHeight(r.getHeight());
    }
}

Example 5 with LGraph

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

the class SbgnPDNode method updateBounds.

/**
 * This method updates the bounds of this compound node. If the node is a
 * dummy compound, do not include label and extra margins.
 */
@Override
public void updateBounds() {
    assert this.getChild() != null;
    if (this.getChild().getNodes().size() != 0) {
        // wrap the children nodes by re-arranging the boundaries
        LGraph childGraph = this.getChild();
        childGraph.updateBounds(true);
        this.rect.x = childGraph.getLeft();
        this.rect.y = childGraph.getTop();
        if (this.type != null && this.type.equals(SbgnPDConstants.DUMMY_COMPOUND)) {
            this.setWidth(childGraph.getRight() - childGraph.getLeft());
            this.setHeight(childGraph.getBottom() - childGraph.getTop());
        } else {
            this.setWidth(childGraph.getRight() - childGraph.getLeft() + 2 * LayoutConstants.COMPOUND_NODE_MARGIN);
            this.setHeight(childGraph.getBottom() - childGraph.getTop() + 2 * LayoutConstants.COMPOUND_NODE_MARGIN + LayoutConstants.LABEL_HEIGHT);
        }
    }
}