Examples with SpeciesContext cbit.vcell.model.SpeciesContext used on opensource projects

Example 76 with SpeciesContext

use of cbit.vcell.model.SpeciesContext in project vcell by virtualcell.

the class ReactionCartoonTool method lineActon.

private void lineActon(Structure startStructure, ReactionStep reactionEnd) throws Exception {
    Structure endStructure = reactionEnd.getStructure();
    if (StructureUtil.reactionHereCanHaveParticipantThere(endStructure, startStructure)) {
        // if reactionStart is a SimpleRxn OR FluxRxn without a product, add speciesContext as reactant
        if ((reactionEnd instanceof SimpleReaction) || ((reactionEnd instanceof FluxReaction) && !reactionEnd.hasReactant())) {
            SpeciesContext speciesContext = getReactionCartoon().getModel().createSpeciesContext(startStructure);
            reactionEnd.addReactant(speciesContext, 1);
            positionShapeForObject(startStructure, speciesContext, edgeShape.getStart());
        }
        if (((startStructure instanceof Feature && endStructure instanceof Feature) || (startStructure instanceof Membrane && endStructure instanceof Membrane)) && startStructure != endStructure) {
        // ============ change kinetics to lumped or warn user ?????????
        // simpleReaction.setKinetics(new GeneralLumpedKinetics(simpleReaction));
        }
        getReactionCartoon().notifyChangeEvent();
    }
}

Example 77 with SpeciesContext

use of cbit.vcell.model.SpeciesContext in project vcell by virtualcell.

the class ReactionCartoonTool method getLineTypeFromDirection.

private LineType getLineTypeFromDirection(Shape startingShape, Point worldPoint) throws Exception {
    Shape mouseOverShape = getReactionCartoon().pickWorld(worldPoint);
    if (mouseOverShape instanceof ReactionStepShape) {
        if (startingShape instanceof SpeciesContextShape) {
            SpeciesContext speciesContext = (SpeciesContext) startingShape.getModelObject();
            // check if the ReactionStep already has a Product for this SpeciesContext
            ReactionStep reactionStep = (ReactionStep) mouseOverShape.getModelObject();
            ReactionParticipant[] rps = reactionStep.getReactionParticipants();
            if ((mouseOverShape instanceof SimpleReactionShape) || (mouseOverShape instanceof FluxReactionShape)) {
                for (int i = 0; i < rps.length; i++) {
                    if (rps[i] instanceof Reactant && rps[i].getSpeciesContext() == speciesContext) {
                        return LineType.NULL;
                    }
                }
                return LineType.REACTANT;
            }
        // else if (mouseOverShape instanceof FluxReactionShape){
        // for (int i = 0; i < rps.length; i++){
        // if ((rps[i] instanceof Reactant || rps[i] instanceof Product) && rps[i].getSpeciesContext() == speciesContext) {
        // return LineType.NULL;
        // }
        // }
        // return LineType.FLUX;
        // }
        }
    } else if (mouseOverShape instanceof SpeciesContextShape) {
        SpeciesContext speciesContext = (SpeciesContext) mouseOverShape.getModelObject();
        if (startingShape instanceof SpeciesContextShape) {
            // straight from one species to another ... will create a reaction upon release
            return LineType.PRODUCT;
        } else if (startingShape instanceof ReactionStepShape) {
            ReactionStep reactionStep = (ReactionStep) startingShape.getModelObject();
            ReactionParticipant[] rps = reactionStep.getReactionParticipants();
            // } else
            if (reactionStep instanceof SimpleReaction || reactionStep instanceof FluxReaction) {
                for (int i = 0; i < rps.length; i++) {
                    if (rps[i] instanceof Reactant && rps[i].getSpeciesContext() == speciesContext) {
                        return LineType.NULL;
                    }
                }
                return LineType.REACTANT;
            }
        }
    }
    return LineType.NULL;
}

Example 78 with SpeciesContext

use of cbit.vcell.model.SpeciesContext 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 79 with SpeciesContext

use of cbit.vcell.model.SpeciesContext in project vcell by virtualcell.

the class ReactionCartoonTool method deleteReactionsAndSpecies.

public static void deleteReactionsAndSpecies(Component requester, ReactionStep[] reactionStepArr, SpeciesContext[] speciesContextArr) throws Exception, UserCancelException {
    if ((speciesContextArr == null && reactionStepArr == null) || (reactionStepArr == null && speciesContextArr != null && speciesContextArr.length == 0) || (speciesContextArr == null && reactionStepArr != null && reactionStepArr.length == 0) || (speciesContextArr != null && speciesContextArr.length == 0 && reactionStepArr != null && reactionStepArr.length == 0)) {
        return;
    }
    int rxCount = (reactionStepArr != null ? reactionStepArr.length : 0);
    int speciesCount = (speciesContextArr != null ? speciesContextArr.length : 0);
    boolean bHasBoth = speciesCount > 0 && rxCount > 0;
    ReactionCartoon rxCartoon = null;
    if (requester instanceof GraphPane && ((GraphPane) requester).getGraphModel() instanceof ReactionCartoon) {
        rxCartoon = (ReactionCartoon) (((GraphPane) requester).getGraphModel());
    } else if (requester instanceof ReactionCartoonEditorPanel) {
        rxCartoon = ((ReactionCartoonEditorPanel) requester).getReactionCartoon();
    } else {
        throw new IllegalArgumentException("ReactionCartoonTool.deleteSpeciesContext not implemented for type '" + requester.getClass().getName() + "'");
    }
    DeleteSpeciesInfo deleteSpeciesInfo = null;
    final String DETAILS = "Details...";
    while (true) {
        String response = DialogUtils.showWarningDialog(requester, RXSPECIES_DELETE + " " + (bHasBoth ? "Reactions and Species." : (rxCount > 0 ? "Reactions." : (speciesCount > 0 ? "Species." : ""))), RXSPECIES_DELETE + " " + (bHasBoth ? rxCount + " Reactions and " + speciesCount + " Species." : (rxCount > 0 ? rxCount + " Reactions." : (speciesCount > 0 ? speciesCount + " Species." : ""))), new String[] { RXSPECIES_DELETE, DETAILS, RXSPECIES_CANCEL }, RXSPECIES_DELETE);
        if (response == null || response.equals(RXSPECIES_CANCEL)) {
            throw UserCancelException.CANCEL_GENERIC;
        }
        deleteSpeciesInfo = (deleteSpeciesInfo == null ? detailsDeleteSpecies(requester, speciesContextArr, reactionStepArr, rxCartoon) : deleteSpeciesInfo);
        if (response.equals(DETAILS)) {
            TableListResult tableListResult = showDeleteDetails(requester, deleteSpeciesInfo, reactionStepArr, false);
        // if(!tableListResult.selectedOption.equals(RXSPECIES_BACK)){
        // //if(!tableListResult.selectedOption.equals((bCut?RXSPECIES_CUT:RXSPECIES_DELETE))){
        // throw UserCancelException.CANCEL_GENERIC;
        // }
        } else {
            break;
        }
    }
    if (deleteSpeciesInfo != null) {
        for (Boolean errors : deleteSpeciesInfo.getbUnresolvableHashMap().values()) {
            if (errors) {
                while (true) {
                    String response = DialogUtils.showWarningDialog(requester, "Error warning.", "Warning: 1 or more SpeciesContexts have Model references that could cause Model corruption if " + RXSPECIES_DELETE + ".", new String[] { DETAILS, RXSPECIES_CANCEL }, DETAILS);
                    if (response == null || response.equals(RXSPECIES_CANCEL)) {
                        throw UserCancelException.CANCEL_GENERIC;
                    }
                    showDeleteDetails(requester, deleteSpeciesInfo, reactionStepArr, true);
                }
            }
        }
    }
    if (reactionStepArr != null) {
        for (int i = 0; i < reactionStepArr.length; i += 1) {
            rxCartoon.getModel().removeReactionStep(reactionStepArr[i]);
        }
    }
    if (deleteSpeciesInfo != null) {
        // remove all ReactionParticipants ("lines" between reaction and species in "Reaction Diagram") that have this speciesContext before deleting SpeciesContext
        for (SpeciesContext objSpeciesContext : deleteSpeciesInfo.getRxPartHashMap().keySet()) {
            if (deleteSpeciesInfo.getbUnresolvableHashMap().get(objSpeciesContext)) {
                continue;
            }
            Iterator<ReactionParticipant> iterRxPart = deleteSpeciesInfo.getRxPartHashMap().get(objSpeciesContext).iterator();
            while (iterRxPart.hasNext()) {
                ReactionParticipant objRxPart = iterRxPart.next();
                if (rxCartoon.getObjects().contains(objRxPart)) {
                    // Reaction delete may have already removed
                    objRxPart.getReactionStep().removeReactionParticipant(objRxPart);
                }
            }
        }
        // remove the SpeciesContext
        for (int i = 0; i < speciesContextArr.length; i++) {
            if (deleteSpeciesInfo.getbUnresolvableHashMap().get(speciesContextArr[i])) {
                continue;
            }
            if (rxCartoon.getObjects().contains(speciesContextArr[i])) {
                // Reaction delete may have already removed
                rxCartoon.getModel().removeSpeciesContext(speciesContextArr[i]);
            }
        }
    }
}

Example 80 with SpeciesContext

use of cbit.vcell.model.SpeciesContext 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);
        }
    }
}