Examples with SimpleReactionShape cbit.vcell.graph.SimpleReactionShape used on opensource projects

Example 6 with SimpleReactionShape

use of cbit.vcell.graph.SimpleReactionShape in project vcell by virtualcell.

the class ReactionCartoonTool method mouseClicked.

@Override
public void mouseClicked(MouseEvent event) {
    Point screenPoint = new Point(event.getX(), event.getY());
    Point worldPoint = screenToWorld(screenPoint);
    try {
        if (event.getButton() != MouseEvent.BUTTON1) {
            return;
        }
        switch(mode) {
            case SELECT:
                {
                    if (event.getClickCount() == 2) {
                        final Shape selectedShape = getReactionCartoon().getSelectedShape();
                        if (selectedShape instanceof ReactionContainerShape || selectedShape instanceof SpeciesContextShape || selectedShape instanceof SimpleReactionShape || selectedShape instanceof FluxReactionShape || selectedShape instanceof ReactionRuleDiagramShape || selectedShape instanceof RuleParticipantSignatureDiagramShape) {
                            editInPlace(selectedShape, worldPoint);
                        }
                        if (selectedShape != null) {
                            menuAction(selectedShape, CartoonToolMiscActions.Properties.MENU_ACTION);
                        }
                    }
                    break;
                }
            case STEP:
                {
                    Shape pickedShape = getReactionCartoon().pickWorld(worldPoint);
                    if (pickedShape instanceof ReactionContainerShape) {
                        Structure structure = ((ReactionContainerShape) pickedShape).getStructure();
                        if (getReactionCartoon().getStructureSuite().areReactionsShownFor(structure)) {
                            ReactionStep reactionStep = getReactionCartoon().getModel().createSimpleReaction(structure);
                            positionShapeForObject(structure, reactionStep, worldPoint);
                            saveDiagram();
                        }
                    }
                    break;
                }
            case FLUX:
                {
                    Shape pickedShape = getReactionCartoon().pickWorld(worldPoint);
                    if (pickedShape instanceof ReactionContainerShape) {
                        Structure structure = ((ReactionContainerShape) pickedShape).getStructure();
                        if (structure instanceof Membrane) {
                            Membrane membrane = (Membrane) structure;
                            FluxReaction fluxReaction = getReactionCartoon().getModel().createFluxReaction(membrane);
                            ReactionStepShape frShape = (ReactionStepShape) getReactionCartoon().getShapeFromModelObject(fluxReaction);
                            Point parentLocation = frShape.getParent().getSpaceManager().getAbsLoc();
                            frShape.getSpaceManager().setRelPos(worldPoint.x - parentLocation.x, worldPoint.y - parentLocation.y);
                            saveDiagram();
                        // setMode(SELECT_MODE);
                        } else {
                        // setMode(SELECT_MODE);
                        // throw new Exception("fluxes only applicable to membranes");
                        }
                    }
                    break;
                }
            case SPECIES:
                {
                    Shape pickedShape = getReactionCartoon().pickWorld(worldPoint);
                    if (pickedShape instanceof ReactionContainerShape) {
                        SpeciesContext speciesContext = getReactionCartoon().getModel().createSpeciesContext(((ReactionContainerShape) pickedShape).getStructure());
                        reactionCartoon.clearSelection();
                        getGraphModel().select(speciesContext);
                        positionShapeForObject(speciesContext.getStructure(), speciesContext, worldPoint);
                        // showCreateSpeciesContextDialog(getGraphPane(), getReactionCartoon().getModel(), ((ReactionContainerShape) pickedShape).getStructure(), scShapeLocation);
                        saveDiagram();
                    }
                }
            default:
                break;
        }
    } catch (Exception e) {
        System.out.println("CartoonTool.mouseClicked: uncaught exception");
        e.printStackTrace(System.out);
        Point canvasLoc = getGraphPane().getLocationOnScreen();
        canvasLoc.x += screenPoint.x;
        canvasLoc.y += screenPoint.y;
        DialogUtils.showErrorDialog(getGraphPane(), e.getMessage(), e);
    }
}

Example 7 with SimpleReactionShape

use of cbit.vcell.graph.SimpleReactionShape in project vcell by virtualcell.

the class ReactionCartoonTool method lineAction.

private void lineAction(Structure startStructure, Structure endStructure, Shape endShape) throws Exception, PropertyVetoException, ExpressionException {
    Point startPos = edgeShape.getStart();
    Point endPos = edgeShape.getEnd();
    if (endStructure.equals(startStructure)) {
        SpeciesContext speciesContext1 = getReactionCartoon().getModel().createSpeciesContext(endStructure);
        SpeciesContext speciesContext2 = getReactionCartoon().getModel().createSpeciesContext(endStructure);
        SimpleReaction reaction = getReactionCartoon().getModel().createSimpleReaction(endStructure);
        reaction.addReactant(speciesContext1, 1);
        reaction.addProduct(speciesContext2, 1);
        getReactionCartoon().notifyChangeEvent();
        positionShapeForObject(endStructure, speciesContext1, startPos);
        positionShapeForObject(endStructure, speciesContext2, endPos);
        positionShapeForObject(endStructure, reaction, new Point((startPos.x + endPos.x) / 2, (startPos.y + endPos.y) / 2));
        getGraphModel().clearSelection();
        getGraphModel().select(reaction);
    } else {
        if (endStructure instanceof Membrane && startStructure instanceof Feature) {
            Membrane endMembrane = (Membrane) endStructure;
            Feature startFeature = (Feature) startStructure;
            // if(structTopology.getOutsideFeature(endMembrane).equals(startFeature) || structTopology.getInsideFeature(endMembrane).equals(startFeature))
            // {
            SpeciesContext speciesContext1 = getReactionCartoon().getModel().createSpeciesContext(startFeature);
            SpeciesContext speciesContext2 = getReactionCartoon().getModel().createSpeciesContext(endMembrane);
            SimpleReaction reaction = getReactionCartoon().getModel().createSimpleReaction(endMembrane);
            reaction.addReactant(speciesContext1, 1);
            reaction.addProduct(speciesContext2, 1);
            getReactionCartoon().notifyChangeEvent();
            positionShapeForObject(startFeature, speciesContext1, startPos);
            positionShapeForObject(endMembrane, speciesContext2, endPos);
            // finding correct insertion point for reaction, statements below should be put into a utility if used often
            int memAbsXmin = endShape.getSpaceManager().getAbsLoc().x;
            int memAbsXmax = memAbsXmin + endShape.getSpaceManager().getSize().width;
            int reactionWidth = new SimpleReactionShape(reaction, getReactionCartoon()).getSpaceManager().getSize().width;
            int reactionAbsX = (startPos.x + endPos.x) / 2;
            if ((memAbsXmax - memAbsXmin) <= reactionWidth) {
                reactionAbsX = memAbsXmin;
            } else {
                reactionAbsX = Math.max(reactionAbsX, memAbsXmin);
                reactionAbsX = Math.min(reactionAbsX, (memAbsXmax - reactionWidth));
            }
            positionShapeForObject(endMembrane, reaction, new Point(reactionAbsX, (startPos.y + endPos.y) / 2));
            getGraphModel().clearSelection();
            getGraphModel().select(reaction);
        // }
        } else if (endStructure instanceof Feature && startStructure instanceof Membrane) {
            Membrane startMembrane = (Membrane) startStructure;
            Feature endFeature = (Feature) endStructure;
            // if(structTopology.getOutsideFeature(startMembrane).equals(endFeature) || structTopology.getInsideFeature(startMembrane).equals(endFeature))
            // {
            SpeciesContext speciesContext1 = getReactionCartoon().getModel().createSpeciesContext(startMembrane);
            SpeciesContext speciesContext2 = getReactionCartoon().getModel().createSpeciesContext(endFeature);
            SimpleReaction reaction = getReactionCartoon().getModel().createSimpleReaction(startMembrane);
            reaction.addReactant(speciesContext1, 1);
            reaction.addProduct(speciesContext2, 1);
            getReactionCartoon().notifyChangeEvent();
            positionShapeForObject(startMembrane, speciesContext1, startPos);
            positionShapeForObject(endFeature, speciesContext2, endPos);
            // finding correct insertion point for reaction, statements below should be put into a utility if used often
            int memAbsXmin = startShape.getSpaceManager().getAbsLoc().x;
            int memAbsXmax = memAbsXmin + startShape.getSpaceManager().getSize().width;
            int reactionWidth = new SimpleReactionShape(reaction, getReactionCartoon()).getSpaceManager().getSize().width;
            int reactionAbsX = (startPos.x + endPos.x) / 2;
            if ((memAbsXmax - memAbsXmin) <= reactionWidth) {
                reactionAbsX = memAbsXmin;
            } else {
                reactionAbsX = Math.max(reactionAbsX, memAbsXmin);
                reactionAbsX = Math.min(reactionAbsX, (memAbsXmax - reactionWidth));
            }
            positionShapeForObject(startMembrane, reaction, new Point(reactionAbsX, (startPos.y + endPos.y) / 2));
            getGraphModel().clearSelection();
            getGraphModel().select(reaction);
        // }
        } else if (endStructure instanceof Feature && startStructure instanceof Feature) {
            Feature startFeature = (Feature) startStructure;
            Feature endFeature = (Feature) endStructure;
            SpeciesContext speciesContext1 = getReactionCartoon().getModel().createSpeciesContext(startStructure);
            SpeciesContext speciesContext2 = getReactionCartoon().getModel().createSpeciesContext(endStructure);
            SimpleReaction reaction = getReactionCartoon().getModel().createSimpleReaction(startStructure);
            reaction.addReactant(speciesContext1, 1);
            reaction.addProduct(speciesContext2, 1);
            reaction.setKinetics(new GeneralLumpedKinetics(reaction));
            getReactionCartoon().notifyChangeEvent();
            positionShapeForObject(startStructure, speciesContext1, startPos);
            positionShapeForObject(endStructure, speciesContext2, endPos);
            positionShapeForObject(startStructure, reaction, new Point((startPos.x + endPos.x) / 2, (startPos.y + endPos.y) / 2));
            getGraphModel().clearSelection();
            getGraphModel().select(reaction);
        } else if (endStructure instanceof Membrane && startStructure instanceof Membrane) {
            SpeciesContext speciesContext1 = getReactionCartoon().getModel().createSpeciesContext(startStructure);
            SpeciesContext speciesContext2 = getReactionCartoon().getModel().createSpeciesContext(endStructure);
            SimpleReaction reaction = getReactionCartoon().getModel().createSimpleReaction(startStructure);
            reaction.addReactant(speciesContext1, 1);
            reaction.addProduct(speciesContext2, 1);
            reaction.setKinetics(new GeneralLumpedKinetics(reaction));
            getReactionCartoon().notifyChangeEvent();
            positionShapeForObject(startStructure, speciesContext1, startPos);
            positionShapeForObject(endStructure, speciesContext2, endPos);
            positionShapeForObject(startStructure, reaction, new Point((startPos.x + endPos.x) / 2, (startPos.y + endPos.y) / 2));
            getGraphModel().clearSelection();
            getGraphModel().select(reaction);
        }
    }
}