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

Example 91 with Structure

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

the class ReactionCartoonTool method resetDropTargets.

private void resetDropTargets(Boolean bDropTargetFlag, Boolean bStructureMode) {
    Structure[] structures = getModel().getStructures();
    for (int i = 0; i < structures.length; i++) {
        ((ReactionContainerShape) getGraphModel().getShapeFromModelObject(structures[i])).setDropTargetEnableLow(bDropTargetFlag, bStructureMode);
        ((ReactionContainerShape) getGraphModel().getShapeFromModelObject(structures[i])).setDropTargetEnableHigh(bDropTargetFlag, bStructureMode);
    }
}

Example 92 with Structure

use of cbit.vcell.model.Structure 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 93 with Structure

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

the class ReactionCartoonTool method lineAction.

private void lineAction(SpeciesContext speciesContextStart, ReactionStep reactionEnd) throws Exception {
    Structure endStructure = reactionEnd.getStructure();
    Structure startStructure = speciesContextStart.getStructure();
    if (StructureUtil.reactionHereCanHaveParticipantThere(endStructure, startStructure)) {
        int stoichiometry = 1;
        Reactant reactant = null;
        for (ReactionParticipant participant : reactionEnd.getReactionParticipants()) {
            if (participant instanceof Reactant && participant.getSpeciesContext().equals(speciesContextStart)) {
                reactant = (Reactant) participant;
            }
        }
        if (reactant != null) {
            // only increase stoichiometry if reaction is SimpleReaction
            if (reactionEnd instanceof SimpleReaction) {
                reactant.setStoichiometry(reactant.getStoichiometry() + 1);
            }
            Shape shape = getReactionCartoon().getShapeFromModelObject(reactant);
            if (shape != null) {
                shape.refreshLabel();
            }
        } else {
            // add speciesContextEnd as pdt to reactionStart only if reactionStart is a SimpleRxn or if it is a FluxRxn and doesn't have a pdt.
            if (reactionEnd instanceof SimpleReaction || ((reactionEnd instanceof FluxReaction) && !(reactionEnd.hasReactant()))) {
                reactionEnd.addReactant(speciesContextStart, stoichiometry);
            }
        }
        if (((startStructure instanceof Feature && endStructure instanceof Feature) || (startStructure instanceof Membrane && endStructure instanceof Membrane)) && startStructure != endStructure) {
        // ============ change kinetics to lumped or warn user ?????????
        // simpleReactionEnd.setKinetics(new GeneralLumpedKinetics(simpleReactionEnd));
        }
        getReactionCartoon().notifyChangeEvent();
    }
}

Example 94 with Structure

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

the class ElectricalStimulusPanel method newStimulus.

/**
 * Comment
 */
private void newStimulus() {
    try {
        SimulationContext simContext = getSimulationContext();
        if (simContext == null) {
            return;
        }
        // 
        // When the voltage and current clamp radio buttons is deselected within the same simulation context (application),
        // display a warning saying that the present clamp settings will be lost (not applicable when the 'no clamp'
        // radiobutton is deselected.
        // 
        ElectricalStimulus currElectricalStimulus = null;
        if (simContext.getElectricalStimuli() != null && simContext.getElectricalStimuli().length > 0) {
            currElectricalStimulus = simContext.getElectricalStimuli()[0];
        }
        // 
        // ignore selection if already selected
        // warn upon deselect if about to loose edits
        // 
        Clamp selectedClamp = (Clamp) clampComboBox.getSelectedItem();
        if (currElectricalStimulus instanceof VoltageClampStimulus) {
            if (selectedClamp == Clamp.Voltage_Clamp) {
                return;
            }
            String response = PopupGenerator.showWarningDialog(this, "warning: the present voltage clamp settings will be lost", new String[] { UserMessage.OPTION_CONTINUE, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_CONTINUE);
            if (response == null || response.equals(UserMessage.OPTION_CANCEL)) {
                // revert back to Voltage Clamp
                clampComboBox.setSelectedItem(Clamp.Voltage_Clamp);
                return;
            }
        }
        if (currElectricalStimulus instanceof TotalCurrentClampStimulus) {
            if (selectedClamp == Clamp.Total_Current_Clamp) {
                return;
            }
            String response = PopupGenerator.showWarningDialog(this, "warning: the present current clamp settings will be lost", new String[] { UserMessage.OPTION_CONTINUE, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_CONTINUE);
            if (response == null || response.equals(UserMessage.OPTION_CANCEL)) {
                // revert back to Current Clamp
                clampComboBox.setSelectedItem(Clamp.Total_Current_Clamp);
                return;
            }
        }
        if (currElectricalStimulus instanceof CurrentDensityClampStimulus) {
            if (selectedClamp == Clamp.Current_Density_Clamp) {
                return;
            }
            String response = PopupGenerator.showWarningDialog(this, "warning: the present current clamp settings will be lost", new String[] { UserMessage.OPTION_CONTINUE, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_CONTINUE);
            if (response == null || response.equals(UserMessage.OPTION_CANCEL)) {
                // revert back to Current Clamp
                clampComboBox.setSelectedItem(Clamp.Current_Density_Clamp);
                return;
            }
        }
        if (currElectricalStimulus == null && selectedClamp == Clamp.No_Clamp) {
            return;
        }
        StructureTopology structTopology = getSimulationContext().getModel().getStructureTopology();
        Structure[] structures = getSimulationContext().getModel().getStructures();
        ArrayList<Feature> features = new ArrayList<Feature>();
        for (Structure structure : structures) {
            if (structure instanceof Feature) {
                features.add((Feature) structure);
            }
        }
        if (features.size() < 2) {
            PopupGenerator.showErrorDialog(this, "error: electrodes must be placed in distinct volumetric structures, found " + features.size() + " volumetric structures in model");
            return;
        }
        Feature groundFeature = features.get(0);
        Feature clampedFeature = features.get(1);
        // 
        if (selectedClamp == Clamp.Total_Current_Clamp) {
            if (simContext.getElectricalStimuli().length == 0 || !(simContext.getElectricalStimuli()[0] instanceof TotalCurrentClampStimulus)) {
                Electrode probeElectrode = new Electrode(clampedFeature, new Coordinate(0, 0, 0));
                TotalCurrentClampStimulus ccStimulus = new TotalCurrentClampStimulus(probeElectrode, "ccElectrode", new Expression(0.0), simContext);
                System.out.println(" Geo's dim = " + simContext.getGeometry().getDimension());
                simContext.setElectricalStimuli(new ElectricalStimulus[] { ccStimulus });
                simContext.setGroundElectrode(new Electrode(groundFeature, new Coordinate(0, 0, 0)));
            }
        }
        // 
        if (selectedClamp == Clamp.Current_Density_Clamp) {
            if (simContext.getElectricalStimuli().length == 0 || !(simContext.getElectricalStimuli()[0] instanceof CurrentDensityClampStimulus)) {
                Electrode probeElectrode = new Electrode(clampedFeature, new Coordinate(0, 0, 0));
                CurrentDensityClampStimulus ccStimulus = new CurrentDensityClampStimulus(probeElectrode, "ccElectrode", new Expression(0.0), simContext);
                System.out.println(" Geo's dim = " + simContext.getGeometry().getDimension());
                simContext.setElectricalStimuli(new ElectricalStimulus[] { ccStimulus });
                simContext.setGroundElectrode(new Electrode(groundFeature, new Coordinate(0, 0, 0)));
            }
        }
        // 
        if (selectedClamp == Clamp.No_Clamp) {
            if (simContext.getElectricalStimuli().length > 0) {
                simContext.setElectricalStimuli(new ElectricalStimulus[0]);
            }
        }
        // 
        if (selectedClamp == Clamp.Voltage_Clamp) {
            if (simContext.getElectricalStimuli().length == 0 || !(simContext.getElectricalStimuli()[0] instanceof VoltageClampStimulus)) {
                Electrode probeElectrode = new Electrode(clampedFeature, new Coordinate(0, 0, 0));
                VoltageClampStimulus vcStimulus = new VoltageClampStimulus(probeElectrode, "vcElectrode", new Expression(0.0), simContext);
                System.out.println(" Geo's dim = " + simContext.getGeometry().getDimension());
                simContext.setElectricalStimuli(new ElectricalStimulus[] { vcStimulus });
                simContext.setGroundElectrode(new Electrode(groundFeature, new Coordinate(0, 0, 0)));
            }
        }
    } catch (java.beans.PropertyVetoException e) {
        PopupGenerator.showErrorDialog(this, "Error setting electrical stimulus: " + e.getMessage());
    }
}

Example 95 with Structure

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

the class GeneratedReactionTableRow method deriveRule.

private void deriveRule(String inputString, Model tempModel) {
    if (owner != null && owner.getSimulationContext() != null) {
        List<MolecularType> mtList = owner.getSimulationContext().getModel().getRbmModelContainer().getMolecularTypeList();
        try {
            tempModel.getRbmModelContainer().setMolecularTypeList(mtList);
        } catch (PropertyVetoException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Unexpected exception setting " + MolecularType.typeName + " list: " + e1.getMessage(), e1);
        }
    } else {
        // This should not be possible
        throw new RuntimeException("Owner or SimulationContext are null.");
    }
    int arrowIndex = inputString.indexOf("<->");
    boolean bReversible = true;
    if (arrowIndex < 0) {
        arrowIndex = inputString.indexOf("->");
        bReversible = false;
    }
    String left = inputString.substring(0, arrowIndex).trim();
    String right = inputString.substring(arrowIndex + (bReversible ? 3 : 2)).trim();
    if (left.length() == 0 && right.length() == 0) {
        return;
    }
    String name = reactionObject.getRuleName();
    if (name.contains(GeneratedReactionTableModel.reverse)) {
        name = name.substring(GeneratedReactionTableModel.reverse.length());
    }
    if (name.endsWith(ReactionRule.DirectHalf)) {
        name = name.substring(0, name.indexOf(ReactionRule.DirectHalf));
    }
    if (name.endsWith(ReactionRule.InverseHalf)) {
        name = name.substring(0, name.indexOf(ReactionRule.InverseHalf));
    }
    // try to get the name of the original structure from the original rule and make here another structure with the same name
    String strStructure = null;
    Structure ruleStructure;
    SimulationContext sc = owner.getSimulationContext();
    ReactionRule rr = sc.getModel().getRbmModelContainer().getReactionRule(name);
    if (rr != null && rr.getStructure() != null) {
        strStructure = rr.getStructure().getName();
    }
    if (strStructure != null) {
        if (tempModel.getStructure(strStructure) == null) {
            try {
                tempModel.addFeature(strStructure);
            } catch (ModelException | PropertyVetoException e) {
                e.printStackTrace();
            }
        }
        ruleStructure = tempModel.getStructure(strStructure);
    } else {
        throw new RuntimeException("Failed to recover a Structure name from the Reaction Rule: " + name);
    }
    // making the fake rules just for display purpose, actually they are the flattened reactions resulted from bngl
    // the name is probably not unique, it's likely that many flattened reactions are derived from the same rule
    reactionRule = tempModel.getRbmModelContainer().createReactionRule(name, ruleStructure, bReversible);
    String regex = "[^!]\\+";
    String[] patterns = left.split(regex);
    for (String spString : patterns) {
        try {
            spString = spString.trim();
            // if compartments are present, we're making some fake compartments in the tempModel just for compartment name display purposes
            SpeciesPattern speciesPattern = (SpeciesPattern) RbmUtils.parseSpeciesPattern(spString, tempModel);
            strStructure = RbmUtils.parseCompartment(spString, tempModel);
            speciesPattern.resolveBonds();
            Structure structure;
            if (strStructure != null) {
                if (tempModel.getStructure(strStructure) == null) {
                    tempModel.addFeature(strStructure);
                }
                structure = tempModel.getStructure(strStructure);
            } else {
                // if nothing explicit for a participant, we use by default the structure of the rule
                structure = ruleStructure;
            }
            reactionRule.addReactant(new ReactantPattern(speciesPattern, structure));
        } catch (Throwable ex) {
            ex.printStackTrace();
            return;
        }
    }
    patterns = right.split(regex);
    for (String spString : patterns) {
        try {
            spString = spString.trim();
            SpeciesPattern speciesPattern = (SpeciesPattern) RbmUtils.parseSpeciesPattern(spString, tempModel);
            strStructure = RbmUtils.parseCompartment(spString, tempModel);
            speciesPattern.resolveBonds();
            Structure structure;
            if (strStructure != null) {
                if (tempModel.getStructure(strStructure) == null) {
                    tempModel.addFeature(strStructure);
                }
                structure = tempModel.getStructure(strStructure);
            } else {
                structure = ruleStructure;
            }
            reactionRule.addProduct(new ProductPattern(speciesPattern, structure));
        } catch (Throwable ex) {
            ex.printStackTrace();
            return;
        }
    }
}