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

Example 11 with Shape

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

the class ReactionCartoonFull method setPositionsFromReactionCartoon.

public void setPositionsFromReactionCartoon(Diagram diagram) {
    List<NodeReference> nodeList = new ArrayList<NodeReference>();
    NodeReference.Mode mode = NodeReference.Mode.full;
    for (Shape shape : getShapes()) {
        if (shape instanceof FluxReactionShape) {
            nodeList.add(new NodeReference(mode, NodeReference.FLUX_REACTION_NODE, ((FluxReaction) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof SimpleReactionShape) {
            nodeList.add(new NodeReference(mode, NodeReference.SIMPLE_REACTION_NODE, ((ReactionStep) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof ReactionRuleDiagramShape) {
            nodeList.add(new NodeReference(mode, NodeReference.REACTION_RULE_NODE, ((ReactionRule) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof SpeciesContextShape) {
            nodeList.add(new NodeReference(mode, NodeReference.SPECIES_CONTEXT_NODE, ((SpeciesContext) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof RuleParticipantSignatureFullDiagramShape) {
            RuleParticipantSignature ruleParticipantSignature = (RuleParticipantSignature) shape.getModelObject();
            if (ruleParticipantSignature.getStructure() == diagram.getStructure()) {
                String spAsString = ruleParticipantSignature.getFirstSpeciesPatternAsString();
                NodeReference nr = new NodeReference(mode, NodeReference.RULE_PARTICIPANT_SIGNATURE_FULL_NODE, spAsString, shape.getSpaceManager().getRelPos());
                nr.speciesPattern = ruleParticipantSignature.getSpeciesPattern();
                nodeList.add(nr);
            }
        } else if (shape instanceof RuleParticipantSignatureShortDiagramShape) {
            System.out.println("ReactionCartoonFull, Invalid shape type 'RuleParticipantSignatureShortDiagramShape'");
            RuleParticipantSignature ruleParticipantSignature = (RuleParticipantSignature) shape.getModelObject();
            if (ruleParticipantSignature.getStructure() == diagram.getStructure()) {
                String spAsString = ruleParticipantSignature.getFirstSpeciesPatternAsString();
                NodeReference nr = new NodeReference(mode, NodeReference.RULE_PARTICIPANT_SIGNATURE_SHORT_NODE, spAsString, shape.getSpaceManager().getRelPos());
                nr.speciesPattern = ruleParticipantSignature.getSpeciesPattern();
                nodeList.add(nr);
            }
        }
    }
    diagram.setNodeReferences(mode, nodeList);
}

Example 12 with Shape

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

the class ReactionCartoonFull method applyDefaults.

public void applyDefaults(Diagram diagram) {
    List<NodeReference> nodeList = diagram.getNodeFullList();
    List<NodeReference> orphansList = new ArrayList<NodeReference>();
    for (int i = 0; i < nodeList.size(); i++) {
        NodeReference node = nodeList.get(i);
        Object obj = null;
        Structure struct = diagram.getStructure();
        boolean found = false;
        switch(node.nodeType) {
            case NodeReference.SIMPLE_REACTION_NODE:
                obj = getModel().getReactionStep(node.name);
                if (!(obj instanceof SimpleReaction)) {
                    System.out.println("ReactionCartoon.applyDefaults(), diagram reaction " + node.name + " type mismatch in model, using location anyway");
                }
                break;
            case NodeReference.FLUX_REACTION_NODE:
                obj = getModel().getReactionStep(node.name);
                if (!(obj instanceof FluxReaction)) {
                    System.out.println("ReactionCartoon.applyDefaults(), diagram flux " + node.name + " type mismatch in model, using location anyway");
                }
                break;
            case NodeReference.SPECIES_CONTEXT_NODE:
                obj = getModel().getSpeciesContext(node.name);
                break;
            case NodeReference.REACTION_RULE_NODE:
                obj = getModel().getRbmModelContainer().getReactionRule(node.name);
                break;
            case // obj is a RuleParticipantSignature
            NodeReference.RULE_PARTICIPANT_SIGNATURE_FULL_NODE:
                for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                    if (signature instanceof RuleParticipantLongSignature && signature.getStructure() == struct && signature.compareByCriteria(node.getName(), GroupingCriteria.full)) {
                        obj = signature;
                        found = true;
                        break;
                    }
                }
                if (!found) {
                    orphansList.add(node);
                }
                break;
            case NodeReference.RULE_PARTICIPANT_SIGNATURE_SHORT_NODE:
                System.out.println("ReactionCartoonFull, RULE_PARTICIPANT_SIGNATURE_SHORT_NODE detected");
                for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                    if (signature instanceof RuleParticipantShortSignature && signature.getStructure() == struct && signature.compareByCriteria(node.getName(), GroupingCriteria.full)) {
                        obj = signature;
                        found = true;
                        break;
                    }
                }
                if (!found) {
                    orphansList.add(node);
                }
                break;
        }
        // -- switch
        Shape shape = getShapeFromModelObject(obj);
        if (shape != null) {
            Point relPosOld = shape.getRelPos();
            Point relPosNew = node.location;
            // In old models, the same node can appear in multiple diagrams.
            // Now, we have only one diagram, so if a node has multiple positions,
            // some would overwrite others.
            // This attempts to prevent overwriting a position with a worse one.
            // if(relPosOld.x + relPosOld.y < relPosNew.x + relPosNew.y) {
            shape.setRelPos(relPosNew);
        // }
        }
    }
    if (!orphansList.isEmpty()) {
        diagram.removeNodeReferences(NodeReference.Mode.full, orphansList);
    }
}

Example 13 with Shape

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

the class ReactionCartoonMolecule method setPositionsFromReactionCartoon.

public void setPositionsFromReactionCartoon(Diagram diagram) {
    List<NodeReference> nodeList = new ArrayList<NodeReference>();
    NodeReference.Mode mode = NodeReference.Mode.molecule;
    for (Shape shape : getShapes()) {
        if (shape instanceof FluxReactionShape) {
            nodeList.add(new NodeReference(mode, NodeReference.FLUX_REACTION_NODE, ((FluxReaction) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof SimpleReactionShape) {
            nodeList.add(new NodeReference(mode, NodeReference.SIMPLE_REACTION_NODE, ((ReactionStep) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof ReactionRuleDiagramShape) {
            nodeList.add(new NodeReference(mode, NodeReference.REACTION_RULE_NODE, ((ReactionRule) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof SpeciesContextShape) {
            nodeList.add(new NodeReference(mode, NodeReference.SPECIES_CONTEXT_NODE, ((SpeciesContext) shape.getModelObject()).getName(), shape.getSpaceManager().getRelPos()));
        } else if (shape instanceof RuleParticipantSignatureFullDiagramShape) {
            System.out.println("ReactionCartoonMolecule, Invalid shape type 'RuleParticipantSignatureFullDiagramShape'");
            RuleParticipantSignature ruleParticipantSignature = (RuleParticipantSignature) shape.getModelObject();
            if (ruleParticipantSignature.getStructure() == diagram.getStructure()) {
                String spAsString = ruleParticipantSignature.getFirstSpeciesPatternAsString();
                NodeReference nr = new NodeReference(mode, NodeReference.RULE_PARTICIPANT_SIGNATURE_FULL_NODE, spAsString, shape.getSpaceManager().getRelPos());
                nr.speciesPattern = ruleParticipantSignature.getSpeciesPattern();
                nodeList.add(nr);
            }
        } else if (shape instanceof RuleParticipantSignatureShortDiagramShape) {
            RuleParticipantSignature ruleParticipantSignature = (RuleParticipantSignature) shape.getModelObject();
            if (ruleParticipantSignature.getStructure() == diagram.getStructure()) {
                String spAsString = ruleParticipantSignature.getFirstSpeciesPatternAsString();
                NodeReference nr = new NodeReference(mode, NodeReference.RULE_PARTICIPANT_SIGNATURE_SHORT_NODE, spAsString, shape.getSpaceManager().getRelPos());
                nr.speciesPattern = ruleParticipantSignature.getSpeciesPattern();
                nodeList.add(nr);
            }
        }
    }
    diagram.setNodeReferences(mode, nodeList);
}

Example 14 with Shape

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

the class WorkflowCartoonTool method mouseReleased.

@Override
public void mouseReleased(MouseEvent event) {
    if (getGraphModel() == null) {
        return;
    }
    try {
        // Pick shape
        int eventX = event.getX();
        int eventY = event.getY();
        java.awt.Point worldPoint = new Point((int) (eventX * 100.0 / getGraphModel().getZoomPercent()), (int) (eventY * 100.0 / getGraphModel().getZoomPercent()));
        Shape pickedShape = getGraphModel().pickWorld(worldPoint);
        // if mouse popupMenu event, popup menu
        if (event.isPopupTrigger() && mode == Mode.SELECT) {
            if (pickedShape == getGraphModel().getSelectedShape()) {
                popupMenu(getGraphModel().getSelectedShape(), event.getX(), event.getY());
            }
            return;
        }
        if ((event.getModifiers() & (InputEvent.BUTTON2_MASK | InputEvent.BUTTON3_MASK)) != 0) {
            return;
        }
        // else do select and move
        switch(mode) {
            case SELECT:
                {
                    getGraphPane().setCursor(Cursor.getDefaultCursor());
                    if (bMoving) {
                        getGraphPane().invalidate();
                        ((JViewport) getGraphPane().getParent()).revalidate();
                        getGraphPane().repaint();
                    } else if (bRectStretch) {
                        Point absLoc = rectShape.getSpaceManager().getRelPos();
                        Dimension size = rectShape.getSpaceManager().getSize();
                        // remove temporary rectangle
                        getGraphModel().removeShape(rectShape);
                        rectShape = null;
                        Rectangle rect = new Rectangle(absLoc.x, absLoc.y, size.width, size.height);
                        boolean bShift = (event.getModifiers() & InputEvent.SHIFT_MASK) == InputEvent.SHIFT_MASK;
                        boolean bCntrl = (event.getModifiers() & InputEvent.CTRL_MASK) == InputEvent.CTRL_MASK;
                        selectEventFromWorld(rect, bShift, bCntrl);
                        getGraphPane().repaint();
                    }
                    bMoving = false;
                    movingShape = null;
                    bRectStretch = false;
                    rectShape = null;
                    break;
                }
            default:
                {
                    break;
                }
        }
    } catch (Exception e) {
        System.out.println("CartoonTool.mouseReleased: uncaught exception");
        e.printStackTrace(System.out);
    }
}

Example 15 with Shape

use of cbit.gui.graph.Shape 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();
}