Examples with EdgeShape cbit.gui.graph.EdgeShape used on opensource projects

Example 1 with EdgeShape

use of cbit.gui.graph.EdgeShape in project vcell by virtualcell.

the class WorkflowCartoonTool method layout.

public void layout(String layoutName) throws Exception {
    Blackboard bb = new Blackboard();
    HashMap<String, Shape> nodeShapeMap = new HashMap<String, Shape>();
    // add nodes
    boolean bHasSelections = getGraphModel().getSelectedShape() != null;
    ArrayList<Shape> vcellShapeList = new ArrayList<Shape>();
    for (Shape shape : getGraphModel().getShapes()) {
        vcellShapeList.add(shape);
        edu.rpi.graphdrawing.Node newNode = null;
        if (ShapeUtil.isMovable(shape)) {
            if (!bHasSelections || shape.isSelected()) {
                String shapeIndexStr = "node" + Integer.toString(vcellShapeList.indexOf(shape));
                newNode = bb.addNode(shapeIndexStr);
            }
        }
        // initialize node location to current absolute position
        if (newNode != null) {
            newNode.XY(shape.getSpaceManager().getAbsLoc().x, shape.getSpaceManager().getAbsLoc().y);
            nodeShapeMap.put(newNode.label(), shape);
        }
    }
    for (Shape shape : getGraphModel().getShapes()) {
        if (shape instanceof EdgeShape) {
            EdgeShape eShape = (EdgeShape) shape;
            Shape node1Shape = eShape.getStartShape();
            Shape node2Shape = eShape.getEndShape();
            if (!bHasSelections || (node1Shape.isSelected() && node2Shape.isSelected())) {
                String node1IndexStr = "node" + Integer.toString(vcellShapeList.indexOf(node1Shape));
                String node2IndexStr = "node" + Integer.toString(vcellShapeList.indexOf(node2Shape));
                bb.addEdge(node1IndexStr, node2IndexStr);
            }
        }
    }
    bb.setArea(0, 0, getGraphPane().getWidth(), getGraphPane().getHeight());
    bb.globals.D(20);
    bb.addEmbedder(GraphLayoutManager.OldLayouts.ANNEALER, new Annealer(bb));
    bb.addEmbedder(GraphLayoutManager.OldLayouts.CIRCULARIZER, new Circularizer(bb));
    bb.addEmbedder(GraphLayoutManager.OldLayouts.CYCLEIZER, new Cycleizer(bb));
    bb.addEmbedder(GraphLayoutManager.OldLayouts.FORCEDIRECT, new ForceDirect(bb));
    bb.addEmbedder(GraphLayoutManager.OldLayouts.LEVELLER, new Leveller(bb));
    bb.addEmbedder(GraphLayoutManager.OldLayouts.RANDOMIZER, new Randomizer(bb));
    bb.addEmbedder(GraphLayoutManager.OldLayouts.RELAXER, new Relaxer(bb));
    bb.addEmbedder(GraphLayoutManager.OldLayouts.STABILIZER, new Stabilizer(bb));
    bb.setEmbedding(layoutName);
    @SuppressWarnings("unchecked") List<Node> nodeList = bb.nodes();
    for (int i = 0; i < nodeList.size(); i++) {
        Node node = nodeList.get(i);
        System.out.println("Node " + node.label() + " @ (" + node.x() + "," + node.y() + ")");
    }
    bb.PreprocessNodes();
    Embedder embedder = bb.embedder();
    embedder.Init();
    for (int i = 0; i < 1000; i++) {
        embedder.Embed();
    }
    bb.removeDummies();
    @SuppressWarnings("unchecked") Vector<Node> nodes = bb.nodes();
    nodeList = nodes;
    // 
    // calculate offset and scaling so that resulting graph fits on canvas
    // 
    double lowX = 100000;
    double highX = -100000;
    double lowY = 100000;
    double highY = -100000;
    for (int i = 0; i < nodeList.size(); i++) {
        Node node = nodeList.get(i);
        lowX = Math.min(lowX, node.x());
        highX = Math.max(highX, node.x());
        lowY = Math.min(lowY, node.y());
        highY = Math.max(highY, node.y());
    }
    double scaleX = getGraphPane().getWidth() / (1.5 * (highX - lowX));
    double scaleY = getGraphPane().getHeight() / (1.5 * (highY - lowY));
    int offsetX = getGraphPane().getWidth() / 6;
    int offsetY = getGraphPane().getHeight() / 6;
    for (int i = 0; i < nodeList.size(); i++) {
        Node node = nodeList.get(i);
        Shape shape = nodeShapeMap.get(node.label());
        Point parentLoc = shape.getParent().getSpaceManager().getAbsLoc();
        shape.getSpaceManager().setAbsLoc(new Point((int) (scaleX * (node.x() - lowX)) + offsetX + parentLoc.x, (int) ((scaleY * (node.y() - lowY)) + offsetY + parentLoc.y)));
        System.out.println("Shape " + shape.getLabel() + " @ " + shape.getSpaceManager().getAbsLoc());
    }
    getGraphPane().repaint();
}

Example 2 with EdgeShape

use of cbit.gui.graph.EdgeShape in project vcell by virtualcell.

the class ShapeGroupUtil method addEdgeBundleShapes.

public static void addEdgeBundleShapes(GraphModel graphModel, Shape groupShape, Shape groupParentShape) {
    Map<Shape, Set<EdgeShape>> connections = ShapeUtil.getExternalConnections(graphModel, groupShape);
    for (Map.Entry<Shape, Set<EdgeShape>> entry : connections.entrySet()) {
        Shape externalShape = entry.getKey();
        Set<EdgeShape> edgeShapes = entry.getValue();
        EdgeBundleShape edgeBundleShape = new EdgeBundleShape(graphModel, groupShape, externalShape, "", edgeShapes);
        groupParentShape.addChildShape(edgeBundleShape);
        graphModel.addShape(edgeBundleShape);
    }
}

Example 3 with EdgeShape

use of cbit.gui.graph.EdgeShape in project vcell by virtualcell.

the class PathwayGraphModel method refreshParticipant.

private void refreshParticipant(BioPaxInteractionShape interactionShape, InteractionParticipant participant) {
    BioPaxInteractionParticipantShape edgeShape = (BioPaxInteractionParticipantShape) getShapeFromModelObject(participant);
    PhysicalEntity physicalEntity = participant.getPhysicalEntity();
    BioPaxObject ancestorObject = pathwayModel.findTopLevelGroupAncestor(physicalEntity);
    if (edgeShape == null) {
        Shape shape = getShapeFromModelObject(physicalEntity);
        if (shape instanceof BioPaxPhysicalEntityShape) {
            BioPaxPhysicalEntityShape physicalEntityShape = (BioPaxPhysicalEntityShape) shape;
            edgeShape = new BioPaxInteractionParticipantShape(participant, interactionShape, physicalEntityShape, this);
            pathwayContainerShape.addChildShape(edgeShape);
            addShape(edgeShape);
        }
    } else {
        // edges without end objects will be removed
        if (ancestorObject != physicalEntity) {
            removeEdgeShape(edgeShape);
        }
    }
    unwantedShapes.remove(refreshGroup(pathwayContainerShape, ancestorObject, interactionShape, participant));
    unwantedShapes.remove(edgeShape);
}

Example 4 with EdgeShape

use of cbit.gui.graph.EdgeShape in project vcell by virtualcell.

the class PathwayGraphModel method refreshGroupInteraction.

private void refreshGroupInteraction(GroupObject groupObject, InteractionParticipant participant) {
    BioPaxGroupShape groupShape = (BioPaxGroupShape) getShapeFromModelObject(groupObject);
    PhysicalEntity physicalEntity = participant.getPhysicalEntity();
    GroupNeighbor groupNeighbor = new GroupNeighbor(groupObject, physicalEntity, participant.getType());
    BioPaxGroupNeighborShape edgeShape = (BioPaxGroupNeighborShape) getShapeFromModelObject(groupNeighbor);
    BioPaxObject ancestorObject = pathwayModel.findTopLevelGroupAncestor(physicalEntity);
    if (edgeShape == null) {
        Shape shape = getShapeFromModelObject(physicalEntity);
        if (shape instanceof BioPaxPhysicalEntityShape) {
            BioPaxPhysicalEntityShape physicalEntityShape = (BioPaxPhysicalEntityShape) shape;
            edgeShape = new BioPaxGroupNeighborShape(groupNeighbor, groupShape, physicalEntityShape, this);
            pathwayContainerShape.addChildShape(edgeShape);
            addShape(edgeShape);
        }
    } else {
        // edges without end objects will be removed
        if (ancestorObject != physicalEntity) {
            // for grouped objects
            removeEdgeShape(edgeShape);
        }
    }
    unwantedShapes.remove(refreshGroup(pathwayContainerShape, ancestorObject, groupShape, participant));
    unwantedShapes.remove(edgeShape);
}

Example 5 with EdgeShape

use of cbit.gui.graph.EdgeShape in project vcell by virtualcell.

the class ReactionContainerShape method randomize.

public void randomize() {
    // then draw in the reactionParticipant edges
    for (Shape child : childShapeList) {
        if (child instanceof SpeciesContextShape || child instanceof ReactionStepShape || child instanceof ReactionRuleDiagramShape || child instanceof RuleParticipantSignatureDiagramShape) {
            // position normally about the center
            child.getSpaceManager().setRelPos(getRandomPosition());
        }
    }
    // calculate locations and sizes of reactionParticipant edges
    for (Shape child : childShapeList) {
        if (child instanceof ReactionParticipantShape || child instanceof RuleParticipantEdgeDiagramShape) {
            EdgeShape reactionParticipantShape = (EdgeShape) child;
            reactionParticipantShape.refreshLayoutSelf();
        }
    }
    // position label
    int centerX = getSpaceManager().getSize().width / 2;
    int currentY = labelSize.height;
    labelPos.x = centerX - labelSize.width / 2;
    labelPos.y = currentY;
    currentY += labelSize.height;
}