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

Example 11 with Catalyst

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

the class ReactionCartoonTool method mouseReleased.

@Override
public void mouseReleased(MouseEvent event) {
    if (getReactionCartoon() == null) {
        return;
    }
    try {
        if (dragStructTimer != null) {
            dragStructTimer.stop();
        }
        endPointWorld = getReactionCartoon().getResizeManager().unzoom(event.getPoint());
        Shape endShape = getReactionCartoon().pickWorld(endPointWorld);
        if (event.isPopupTrigger() && mode == Mode.SELECT) {
            // win, linux popup
            popupMenu(getReactionCartoon().getSelectedShape(), event.getX(), event.getY());
            return;
        }
        if (mode == Mode.SELECT && bStartRxContainerLabel) {
            resetDropTargets(null, mode == Mode.STRUCTURE);
            if (endShape != null && endShape instanceof ReactionContainerShape) {
                Rectangle labelOutlineRectangle = ((ReactionContainerShape) endShape).getLabelOutline(endShape.getAbsX(), endShape.getAbsY());
                boolean bLabel = labelOutlineRectangle.contains(startPointWorld.x, startPointWorld.y);
                getGraphPane().setCursor((bLabel ? Cursor.getPredefinedCursor(Cursor.HAND_CURSOR) : Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)));
            }
            bStartRxContainerLabel = false;
            RXContainerDropTargetInfo trueRXContainerDropTargetInfo = getSelectedContainerDropTargetInfo();
            lastRXContainerDropTargetInfoMap = null;
            if (trueRXContainerDropTargetInfo == null) {
                // turn off rxDropTargetRectangles
                getGraphPane().repaint();
                return;
            }
            StructureSuite structureSuite = null;
            structureSuite = getReactionCartoon().getStructureSuite();
            if (structureSuite != null) {
                Structure[] originalOrderedStructArr = structureSuite.getStructures().toArray(new Structure[0]);
                // find where user wants to put the structure
                try {
                    if (trueRXContainerDropTargetInfo != null) {
                        ArrayList<Structure> newStructOrderList = new ArrayList<Structure>(Arrays.asList(originalOrderedStructArr));
                        newStructOrderList.remove(((ReactionContainerShape) startShape).getStructure());
                        int indexEnd = newStructOrderList.indexOf(((ReactionContainerShape) trueRXContainerDropTargetInfo.dropShape).getStructure());
                        int indexClosestNeighbor = (trueRXContainerDropTargetInfo.closestNeighborShape == null ? (trueRXContainerDropTargetInfo.insertFlag == RXContainerDropTargetInfo.INSERT_BEGINNING ? 0 : newStructOrderList.size()) : newStructOrderList.indexOf(((ReactionContainerShape) trueRXContainerDropTargetInfo.closestNeighborShape).getStructure()));
                        if (indexClosestNeighbor < indexEnd) {
                            newStructOrderList.add(indexEnd, ((ReactionContainerShape) startShape).getStructure());
                        } else {
                            newStructOrderList.add(indexClosestNeighbor, ((ReactionContainerShape) startShape).getStructure());
                        }
                        if (structureSuite instanceof AllStructureSuite) {
                            ((AllStructureSuite) structureSuite).setModelStructureOrder(true);
                        }
                        ArrayList<Diagram> newDiagramOrderList = new ArrayList<Diagram>();
                        for (Structure structure : newStructOrderList) {
                            newDiagramOrderList.add(getModel().getDiagram(structure));
                        }
                        getModel().setDiagrams(newDiagramOrderList.toArray(new Diagram[0]));
                    }
                } catch (Exception e) {
                    e.printStackTrace();
                }
            }
            return;
        }
        // else do select and move
        switch(mode) {
            case SELECT:
                {
                    getGraphPane().setCursor(Cursor.getDefaultCursor());
                    if (bMoving) {
                        getGraphPane().invalidate();
                        ((JViewport) getGraphPane().getParent()).revalidate();
                        getGraphPane().repaint();
                        saveDiagram();
                    } else if (bRectStretch) {
                        Point absLoc = rectShape.getSpaceManager().getRelPos();
                        Dimension size = rectShape.getSpaceManager().getSize();
                        // remove temporary rectangle
                        getReactionCartoon().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;
                }
            case LINEDIRECTED:
                {
                    getGraphPane().setCursor(Cursor.getDefaultCursor());
                    if (bLineStretch && getDragDistanceSquared() >= MIN_DRAG_DISTANCE_TO_CREATE_NEW_ELEMENTS_SQUARED) {
                        bLineStretch = false;
                        // set label and color for line depending on which shape the edge started.
                        // (rather than attachment area on ReactionStepShape)
                        LineType lineType = getLineTypeFromDirection(startShape, endPointWorld);
                        if (endShape instanceof SimpleReactionShape) {
                            SimpleReaction simpleReaction = (SimpleReaction) endShape.getModelObject();
                            Object startShapeObject = null;
                            if (startShape != null) {
                                startShapeObject = startShape.getModelObject();
                            }
                            if (startShapeObject instanceof SpeciesContext) {
                                SpeciesContext speciesContext = (SpeciesContext) startShapeObject;
                                lineAction(speciesContext, simpleReaction);
                            } else if (startShapeObject instanceof Structure) {
                                Structure structure = (Structure) startShapeObject;
                                lineActon(structure, simpleReaction);
                            }
                        } else if (endShape instanceof SpeciesContextShape) {
                            SpeciesContext speciesContextEnd = (SpeciesContext) endShape.getModelObject();
                            Object startShapeObject = null;
                            if (startShape != null) {
                                startShapeObject = startShape.getModelObject();
                            }
                            if (startShapeObject instanceof SimpleReaction) {
                                SimpleReaction simpleReaction = (SimpleReaction) startShapeObject;
                                lineAction(simpleReaction, speciesContextEnd);
                            } else if (startShapeObject instanceof FluxReaction) {
                                FluxReaction fluxReaction = (FluxReaction) startShapeObject;
                                lineAction(fluxReaction, speciesContextEnd);
                            } else if (startShapeObject instanceof SpeciesContext) {
                                SpeciesContext speciesContextStart = (SpeciesContext) startShapeObject;
                                if (!speciesContextStart.equals(speciesContextEnd)) {
                                    lineAction(speciesContextStart, speciesContextEnd);
                                }
                            } else if (startShapeObject instanceof Structure) {
                                Structure startStructure = (Structure) startShapeObject;
                                lineAction(startStructure, speciesContextEnd);
                            }
                        } else if (endShape instanceof FluxReactionShape) {
                            FluxReaction fluxReaction = (FluxReaction) endShape.getModelObject();
                            fluxReaction.setModel(getModel());
                            Object startShapeObject = null;
                            if (startShape != null) {
                                startShapeObject = startShape.getModelObject();
                            }
                            if (startShapeObject instanceof SpeciesContext) {
                                SpeciesContext speciesContext = (SpeciesContext) startShapeObject;
                                lineAction(speciesContext, fluxReaction);
                            } else if (startShapeObject instanceof Structure) {
                                Structure structure = (Structure) startShapeObject;
                                lineActon(structure, fluxReaction);
                            }
                            // remove temporary edge
                            getReactionCartoon().removeShape(edgeShape);
                            edgeShape = null;
                        } else if (endShape instanceof ReactionContainerShape) {
                            Structure endStructure = (Structure) endShape.getModelObject();
                            Object startObject = null;
                            if (startShape != null) {
                                startObject = startShape.getModelObject();
                            }
                            if (startObject instanceof SimpleReaction) {
                                SimpleReaction reaction = (SimpleReaction) startObject;
                                lineAction(reaction, endStructure);
                            } else if (startObject instanceof FluxReaction) {
                                FluxReaction reaction = (FluxReaction) startObject;
                                lineAction(reaction, endStructure);
                            } else if (startObject instanceof SpeciesContext) {
                                SpeciesContext speciesContextStart = (SpeciesContext) startObject;
                                lineAction(speciesContextStart, endStructure);
                            } else if (startObject instanceof Structure) {
                                Structure startStructure = (Structure) startObject;
                                lineAction(startStructure, endStructure, endShape);
                            }
                        }
                    }
                    saveDiagram();
                    break;
                }
            case LINECATALYST:
                {
                    getGraphPane().setCursor(Cursor.getDefaultCursor());
                    if (bLineStretch && getDragDistanceSquared() >= MIN_DRAG_DISTANCE_TO_CREATE_NEW_ELEMENTS_SQUARED) {
                        bLineStretch = false;
                        // set label and color for line depending on which shape the edge started.
                        // (rather than attachment area on ReactionStepShape)
                        Object startObject = startShape.getModelObject();
                        Object endObject = endShape.getModelObject();
                        ReactionStep reactionStep = null;
                        SpeciesContext speciesContext = null;
                        if (startObject instanceof ReactionStep) {
                            reactionStep = (ReactionStep) startObject;
                            if (endObject instanceof SpeciesContext) {
                                if (StructureUtil.reactionHereCanHaveParticipantThere(reactionStep.getStructure(), ((SpeciesContext) endObject).getStructure())) {
                                    speciesContext = (SpeciesContext) endObject;
                                }
                            } else if (endObject instanceof Structure) {
                                Structure endStructure = (Structure) endObject;
                                if (StructureUtil.reactionHereCanHaveParticipantThere(reactionStep.getStructure(), endStructure)) {
                                    speciesContext = getReactionCartoon().getModel().createSpeciesContext(endStructure);
                                    getReactionCartoon().notifyChangeEvent();
                                    Point endPos = edgeShape.getEnd();
                                    positionShapeForObject(endStructure, speciesContext, endPos);
                                }
                            }
                        } else if (startObject instanceof SpeciesContext) {
                            speciesContext = (SpeciesContext) startObject;
                            if (endObject instanceof ReactionStep) {
                                if (StructureUtil.reactionHereCanHaveParticipantThere(((ReactionStep) endObject).getStructure(), speciesContext.getStructure())) {
                                    reactionStep = (ReactionStep) endObject;
                                }
                            } else if (endObject instanceof Structure) {
                                Structure endStructure = (Structure) endObject;
                                if (StructureUtil.reactionHereCanHaveParticipantThere(endStructure, speciesContext.getStructure())) {
                                    reactionStep = getReactionCartoon().getModel().createSimpleReaction(endStructure);
                                    getReactionCartoon().notifyChangeEvent();
                                    Point endPos = edgeShape.getEnd();
                                    positionShapeForObject(endStructure, reactionStep, endPos);
                                }
                            }
                        } else if (startObject instanceof Structure) {
                            Structure startStructure = (Structure) startObject;
                            if (endObject instanceof ReactionStep) {
                                reactionStep = (ReactionStep) endObject;
                                if (StructureUtil.reactionHereCanHaveParticipantThere(reactionStep.getStructure(), startStructure)) {
                                    speciesContext = getReactionCartoon().getModel().createSpeciesContext(startStructure);
                                    getReactionCartoon().notifyChangeEvent();
                                    positionShapeForObject(startStructure, speciesContext, startPointWorld);
                                }
                            } else if (endObject instanceof SpeciesContext) {
                                speciesContext = (SpeciesContext) endObject;
                                if (StructureUtil.reactionHereCanHaveParticipantThere(startStructure, speciesContext.getStructure())) {
                                    reactionStep = getReactionCartoon().getModel().createSimpleReaction(startStructure);
                                    getReactionCartoon().notifyChangeEvent();
                                    positionShapeForObject(startStructure, reactionStep, startPointWorld);
                                }
                            } else if (endObject instanceof Structure) {
                                Structure endStructure = (Structure) endObject;
                                if (StructureUtil.reactionHereCanHaveParticipantThere(startStructure, endStructure)) {
                                    speciesContext = getReactionCartoon().getModel().createSpeciesContext(endStructure);
                                    reactionStep = getReactionCartoon().getModel().createSimpleReaction(startStructure);
                                    getReactionCartoon().notifyChangeEvent();
                                    Point endPos = edgeShape.getEnd();
                                    positionShapeForObject(endStructure, speciesContext, endPos);
                                    positionShapeForObject(startStructure, reactionStep, startPointWorld);
                                } else if (StructureUtil.reactionHereCanHaveParticipantThere(endStructure, startStructure)) {
                                    speciesContext = getReactionCartoon().getModel().createSpeciesContext(startStructure);
                                    reactionStep = getReactionCartoon().getModel().createSimpleReaction(endStructure);
                                    getReactionCartoon().notifyChangeEvent();
                                    positionShapeForObject(startStructure, speciesContext, startPointWorld);
                                    Point endPos = edgeShape.getEnd();
                                    positionShapeForObject(endStructure, reactionStep, endPos);
                                }
                            }
                        }
                        if (reactionStep != null && speciesContext != null) {
                            Catalyst catalyst = null;
                            for (ReactionParticipant participant : reactionStep.getReactionParticipants()) {
                                if (participant instanceof Catalyst && participant.getSpeciesContext().equals(speciesContext)) {
                                    catalyst = (Catalyst) participant;
                                }
                            }
                            if (catalyst == null) {
                                reactionStep.addCatalyst(speciesContext);
                                getReactionCartoon().notifyChangeEvent();
                            }
                        // add reactionParticipant to model
                        } else {
                            getGraphPane().repaint();
                        }
                    }
                    saveDiagram();
                    break;
                }
            default:
                {
                    break;
                }
        }
    } catch (Exception e) {
        System.out.println("CartoonTool.mouseReleased: uncaught exception");
        e.printStackTrace(System.out);
    }
    resetMouseActionHistory();
    getGraphPane().repaint();
}

Example 12 with Catalyst

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

the class DBReactionWizardPanel method parameterNameSelectionChanged.

/**
 * Comment
 */
private void parameterNameSelectionChanged() {
    try {
        javax.swing.DefaultListModel dlm = (javax.swing.DefaultListModel) getParameterValuesJList().getModel();
        dlm.removeAllElements();
        // 
        if (getParameterNamesJList().getSelectedValue() != null) {
            // final cbit.vcell.clientdb.DocumentManager docManager = getDocumentManager();
            // final javax.swing.JList jlist = getReactionsJList();
            final MapStringToObject parameNameMSO = (MapStringToObject) getParameterNamesJList().getSelectedValue();
            final KeyValue reactionStepKey = ((ReactionStepInfo) parameNameMSO.getToObject()).getReactionKey();
            // 
            final String RXSTEP_HASH_VALUE_KEY = "rxStep";
            AsynchClientTask searchReactions = new AsynchClientTask("Getting Full Reaction", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                public void run(Hashtable<String, Object> hash) throws Exception {
                    Model reactionModel = getDocumentManager().getReactionStepAsModel(reactionStepKey);
                    ReactionStep rStep = reactionModel.getReactionStep(((ReactionStepInfo) parameNameMSO.getToObject()).getReactionName());
                    if (rStep != null) {
                        rStep.rebindAllToModel(reactionModel);
                        hash.put(RXSTEP_HASH_VALUE_KEY, rStep);
                    }
                }
            };
            // 
            AsynchClientTask updateRXParams = new AsynchClientTask("updateRXParams", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

                public void run(Hashtable<String, Object> hash) throws DataAccessException {
                    ReactionStep rStep = (ReactionStep) hash.get(RXSTEP_HASH_VALUE_KEY);
                    if (rStep != null) {
                        Kinetics.KineticsParameter[] kpArr = rStep.getKinetics().getKineticsParameters();
                        ReactionParticipant[] rpArr = rStep.getReactionParticipants();
                        // 
                        javax.swing.DefaultListModel pvdlm = (javax.swing.DefaultListModel) getParameterValuesJList().getModel();
                        pvdlm.removeAllElements();
                        for (int i = 0; i < kpArr.length; i += 1) {
                            pvdlm.addElement("Parameter - " + kpArr[i].getName().toString() + " = " + kpArr[i].getExpression().infix());
                        }
                        pvdlm.addElement("PhysicsOption=" + rStep.getPhysicsOptions());
                        for (int i = 0; i < rpArr.length; i += 1) {
                            String role = "Unknown";
                            if (rpArr[i] instanceof Reactant) {
                                role = "Reactant";
                            } else if (rpArr[i] instanceof Product) {
                                role = "Product";
                            } else if (rpArr[i] instanceof Catalyst) {
                                role = "Catalyst";
                            }
                            String fluxFlag = "";
                            // if(rStep instanceof FluxReaction){
                            // Membrane rStepStruct = (Membrane)rStep.getStructure();
                            // if(rpArr[i] instanceof Flux){
                            // if(rpArr[i].getStructure().equals(getModel().getStructureTopology().getOutsideFeature(rStepStruct))){
                            // fluxFlag = "Outside";
                            // }else{
                            // fluxFlag = "Inside";
                            // }
                            // }
                            // }
                            pvdlm.addElement("RXParticipant(" + role + ") " + fluxFlag + " " + (rpArr[i].getSpecies().getDBSpecies() != null ? "*" : "-") + " " + rpArr[i].getSpeciesContext().getName());
                        }
                    }
                    setReactionStep(rStep);
                    configureBFN();
                }
            };
            // 
            Hashtable<String, Object> hashTemp = new Hashtable<String, Object>();
            ClientTaskDispatcher.dispatch(this, hashTemp, new AsynchClientTask[] { searchReactions, updateRXParams }, true);
        } else {
            setReactionStep(null);
        }
    } catch (Exception e) {
        PopupGenerator.showErrorDialog(this, e.getMessage(), e);
    }
    // 
    configureBFN();
}

Example 13 with Catalyst

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

the class ReactionCartoonFull method refreshAll.

@Override
protected void refreshAll(boolean reallocateShapes) {
    try {
        if (getModel() == null || getStructureSuite() == null) {
            return;
        }
        System.out.println("ReactionCartoonFull, RefreshAll()");
        for (Structure structure : structureSuite.getStructures()) {
            Diagram diagram = getModel().getDiagram(structure);
            if (diagram != null) {
                // Maintain consistency between rule participant nodes, signatures and
                // species pattern when a molecule is being modified.
                rebindAll(diagram);
            }
        }
        // calculate species context weight (number of reactions for which it's a participant)
        Map<SpeciesContext, Integer> scWeightMap = new HashMap<>();
        // all the species contexts that are catalysts
        Set<SpeciesContext> scCatalystSet = new HashSet<>();
        // calculate species context length (number of species patterns it contains, 1 if has no species patterns)
        for (ReactionStep rs : getModel().getReactionSteps()) {
            ReactionParticipant[] rpList = rs.getReactionParticipants();
            for (int i = 0; i < rpList.length; i++) {
                ReactionParticipant rp = rpList[i];
                SpeciesContext sc = rp.getSpeciesContext();
                // int increment = rp.getStoichiometry();
                int increment = 1;
                if (rp instanceof Catalyst) {
                    scCatalystSet.add(sc);
                }
                if (scWeightMap.containsKey(sc)) {
                    int weight = scWeightMap.get(sc);
                    weight += increment;
                    scWeightMap.put(sc, weight);
                } else {
                    scWeightMap.put(sc, increment);
                }
            }
        }
        Set<Shape> unwantedShapes = new HashSet<Shape>();
        Set<RuleParticipantSignature> unwantedSignatures = new HashSet<RuleParticipantSignature>();
        unwantedShapes.addAll(getShapes());
        unwantedSignatures.addAll(ruleParticipantSignatures);
        ContainerContainerShape containerShape = (ContainerContainerShape) getShapeFromModelObject(getModel());
        List<ReactionContainerShape> reactionContainerShapeList = new ArrayList<ReactionContainerShape>();
        List<Structure> structureList = new ArrayList<Structure>(getStructureSuite().getStructures());
        // create all ReactionContainerShapes (one for each Structure)
        for (Structure structure : structureList) {
            if (structure instanceof Membrane) {
                Membrane membrane = (Membrane) structure;
                ReactionContainerShape membraneShape = (ReactionContainerShape) getShapeFromModelObject(membrane);
                if (membraneShape == null) {
                    membraneShape = new ReactionContainerShape(membrane, structureSuite, this);
                    addShape(membraneShape);
                    membrane.getMembraneVoltage().removePropertyChangeListener(this);
                    membrane.getMembraneVoltage().addPropertyChangeListener(this);
                } else {
                    membraneShape.setStructureSuite(structureSuite);
                }
                membrane.removePropertyChangeListener(this);
                membrane.addPropertyChangeListener(this);
                membraneShape.refreshLabel();
                unwantedShapes.remove(membraneShape);
                reactionContainerShapeList.add(membraneShape);
            } else if (structure instanceof Feature) {
                Feature feature = (Feature) structure;
                ReactionContainerShape featureShape = (ReactionContainerShape) getShapeFromModelObject(feature);
                if (featureShape == null) {
                    featureShape = new ReactionContainerShape(feature, structureSuite, this);
                    addShape(featureShape);
                } else {
                    featureShape.setStructureSuite(structureSuite);
                }
                feature.removePropertyChangeListener(this);
                feature.addPropertyChangeListener(this);
                featureShape.refreshLabel();
                unwantedShapes.remove(featureShape);
                reactionContainerShapeList.add(featureShape);
            }
        }
        if (containerShape == null) {
            containerShape = new ContainerContainerShape(this, getModel(), reactionContainerShapeList);
            addShape(containerShape);
        } else {
            containerShape.setReactionContainerShapeList(reactionContainerShapeList);
        }
        containerShape.refreshLabel();
        unwantedShapes.remove(containerShape);
        // add all species context shapes within the structures
        for (Structure structure : getStructureSuite().getStructures()) {
            ReactionContainerShape reactionContainerShape = (ReactionContainerShape) getShapeFromModelObject(structure);
            structure.removePropertyChangeListener(this);
            structure.addPropertyChangeListener(this);
            for (SpeciesContext structSpeciesContext : getModel().getSpeciesContexts(structure)) {
                SpeciesContextShape ss = (SpeciesContextShape) getShapeFromModelObject(structSpeciesContext);
                if (ss == null) {
                    ss = new SpeciesContextShape(structSpeciesContext, this);
                    ss.truncateLabelName(false);
                    structSpeciesContext.getSpecies().removePropertyChangeListener(this);
                    structSpeciesContext.getSpecies().addPropertyChangeListener(this);
                    reactionContainerShape.addChildShape(ss);
                    addShape(ss);
                    ss.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                }
                if (speciesSizeOption == SpeciesSizeOptions.weight) {
                    // this number sets the diameter of the shape
                    Integer weight = scWeightMap.get(structSpeciesContext);
                    if (weight != null) {
                        // we cap the diameter of the shape to something reasonable
                        weight = Math.min(weight, 16);
                    }
                    ss.setFilters(highlightCatalystOption ? scCatalystSet.contains(structSpeciesContext) : false, weight);
                } else if (speciesSizeOption == SpeciesSizeOptions.length) {
                    Integer length = null;
                    if (structSpeciesContext.getSpeciesPattern() != null && !structSpeciesContext.getSpeciesPattern().getMolecularTypePatterns().isEmpty()) {
                        length = structSpeciesContext.getSpeciesPattern().getMolecularTypePatterns().size() * 2;
                        length = Math.min(length, 16);
                    }
                    ss.setFilters(highlightCatalystOption ? scCatalystSet.contains(structSpeciesContext) : false, length);
                } else {
                    ss.setFilters(highlightCatalystOption ? scCatalystSet.contains(structSpeciesContext) : false, null);
                }
                structSpeciesContext.removePropertyChangeListener(this);
                structSpeciesContext.addPropertyChangeListener(this);
                ss.refreshLabel();
                unwantedShapes.remove(ss);
            }
        }
        // add all reactionSteps that are in this structure (ReactionContainerShape), and draw the lines
        getModel().removePropertyChangeListener(this);
        getModel().addPropertyChangeListener(this);
        // 
        for (ReactionRule rr : getModel().getRbmModelContainer().getReactionRuleList()) {
            rr.removePropertyChangeListener(this);
            rr.addPropertyChangeListener(this);
            Structure structure = rr.getStructure();
            if (getStructureSuite().areReactionsShownFor(structure)) {
                ReactionContainerShape reactionContainerShape = (ReactionContainerShape) getShapeFromModelObject(structure);
                ReactionRuleFullDiagramShape rrShape = (ReactionRuleFullDiagramShape) getShapeFromModelObject(rr);
                if (rrShape == null) {
                    rrShape = new ReactionRuleFullDiagramShape(rr, this);
                    addShape(rrShape);
                    rrShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                    reactionContainerShape.addChildShape(rrShape);
                    rrShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                }
                rrShape.refreshLabel();
                unwantedShapes.remove(rrShape);
                // 
                // add reaction participants as edges and SignatureShapes as needed
                // 
                List<ReactionRuleParticipant> participants = rr.getReactionRuleParticipants();
                List<RuleParticipantEdgeDiagramShape> ruleEdges = new ArrayList<>();
                for (ReactionRuleParticipant participant : participants) {
                    participant.getSpeciesPattern().removePropertyChangeListener(this);
                    participant.getSpeciesPattern().addPropertyChangeListener(this);
                    Structure speciesStructure = participant.getStructure();
                    Structure reactionStructure = rr.getStructure();
                    if (getStructureSuite().getStructures().contains(speciesStructure) && getStructureSuite().areReactionsShownFor(reactionStructure)) {
                        // 
                        // find existing RuleParticipantSignatureShape in cartoon
                        // 
                        RuleParticipantLongSignature ruleParticipantLongSignature = null;
                        for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                            if (signature instanceof RuleParticipantLongSignature && signature.getStructure() == participant.getStructure() && signature.compareByCriteria(participant.getSpeciesPattern(), GroupingCriteria.full)) {
                                ruleParticipantLongSignature = (RuleParticipantLongSignature) signature;
                                break;
                            }
                        }
                        for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                            if (signature instanceof RuleParticipantShortSignature && signature.getStructure() == participant.getStructure()) {
                                System.out.println("ReactionCartoonFull, refreshAll(), RuleParticipantShortSignature");
                            }
                        }
                        // 
                        // if didn't find signature in cartoons list of signatures, then create one (and create a shape for it).
                        // 
                        RuleParticipantSignatureFullDiagramShape signatureShape = null;
                        if (ruleParticipantLongSignature == null) {
                            ruleParticipantLongSignature = RuleParticipantLongSignature.fromReactionRuleParticipant(participant, this);
                            ruleParticipantSignatures.add(ruleParticipantLongSignature);
                            signatureShape = new RuleParticipantSignatureFullDiagramShape(ruleParticipantLongSignature, this);
                            addShape(signatureShape);
                            ReactionContainerShape participantContainerShape = (ReactionContainerShape) getShapeFromModelObject(participant.getStructure());
                            signatureShape.getSpaceManager().setRelPos(participantContainerShape.getRandomPosition());
                            participantContainerShape.addChildShape(signatureShape);
                            signatureShape.getSpaceManager().setRelPos(participantContainerShape.getRandomPosition());
                        } else {
                            signatureShape = (RuleParticipantSignatureFullDiagramShape) getShapeFromModelObject(ruleParticipantLongSignature);
                        }
                        unwantedShapes.remove(signatureShape);
                        unwantedSignatures.remove(ruleParticipantLongSignature);
                        signatureShape.refreshLabel();
                        signatureShape.setVisible(true);
                        // 
                        // add edge for ReactionRuleParticipant if not already present.
                        // 
                        RuleParticipantEdgeDiagramShape ruleParticipantShape = (RuleParticipantEdgeDiagramShape) getShapeFromModelObject(participant);
                        if (ruleParticipantShape == null || ruleParticipantShape.getRuleParticipantSignatureShape() != signatureShape) {
                            if (participant instanceof ReactantPattern && signatureShape.isVisible()) {
                                ruleParticipantShape = new ReactantPatternEdgeDiagramShape((ReactantPattern) participant, rrShape, signatureShape, this);
                            } else if (participant instanceof ProductPattern && signatureShape.isVisible()) {
                                ruleParticipantShape = new ProductPatternEdgeDiagramShape((ProductPattern) participant, rrShape, signatureShape, this);
                            } else {
                                throw new RuntimeException("unsupported ReactionRuleParticipant " + participant.getClass());
                            }
                            addShape(ruleParticipantShape);
                        }
                        if (!containerShape.getChildren().contains(ruleParticipantShape)) {
                            containerShape.addChildShape(ruleParticipantShape);
                        }
                        unwantedShapes.remove(ruleParticipantShape);
                        ruleParticipantShape.refreshLabel();
                        // all the edges for this rule
                        ruleEdges.add(ruleParticipantShape);
                    }
                }
                // a product edge (a closed loop) between the rule diagram shape and the signature diagram shape
                for (RuleParticipantEdgeDiagramShape ours : ruleEdges) {
                    // reset them all
                    ours.setSibling(false);
                }
                for (RuleParticipantEdgeDiagramShape ours : ruleEdges) {
                    for (RuleParticipantEdgeDiagramShape theirs : ruleEdges) {
                        if (ours == theirs) {
                            // don't compare with self
                            continue;
                        }
                        if (ours.getRuleParticipantSignatureShape() == theirs.getRuleParticipantSignatureShape()) {
                            ours.setSibling(true);
                            theirs.setSibling(true);
                        }
                    }
                }
            }
        }
        ruleParticipantSignatures.removeAll(unwantedSignatures);
        for (ReactionStep reactionStep : getModel().getReactionSteps()) {
            reactionStep.removePropertyChangeListener(this);
            reactionStep.addPropertyChangeListener(this);
            Structure structure = reactionStep.getStructure();
            if (getStructureSuite().areReactionsShownFor(structure)) {
                ReactionContainerShape reactionContainerShape = (ReactionContainerShape) getShapeFromModelObject(structure);
                if (reactionContainerShape == null) {
                    System.out.println("Reaction container shape is null for structure " + structure + " for reaction step " + reactionStep);
                }
                ReactionStepShape reactionStepShape = (ReactionStepShape) getShapeFromModelObject(reactionStep);
                if (reactionStepShape == null) {
                    if (reactionStep instanceof SimpleReaction) {
                        reactionStepShape = new SimpleReactionShape((SimpleReaction) reactionStep, this);
                    } else if (reactionStep instanceof FluxReaction) {
                        reactionStepShape = new FluxReactionShape((FluxReaction) reactionStep, this);
                    } else {
                        throw new RuntimeException("unknown type of ReactionStep '" + reactionStep.getClass().toString());
                    }
                    addShape(reactionStepShape);
                    reactionStepShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                    reactionContainerShape.addChildShape(reactionStepShape);
                    reactionStepShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                }
                reactionStepShape.refreshLabel();
                unwantedShapes.remove(reactionStepShape);
                // add reaction participants as edges
                for (ReactionParticipant participant : reactionStep.getReactionParticipants()) {
                    participant.removePropertyChangeListener(this);
                    participant.addPropertyChangeListener(this);
                    Structure speciesStructure = participant.getStructure();
                    Structure reactionStructure = reactionStep.getStructure();
                    if (getStructureSuite().getStructures().contains(speciesStructure) && getStructureSuite().areReactionsShownFor(reactionStructure)) {
                        SpeciesContext speciesContext = getModel().getSpeciesContext(participant.getSpecies(), speciesStructure);
                        // add speciesContextShapes that are not in this structure, but are referenced from the reactionParticipants
                        // these are only when reactionParticipants are from features that are outside of the membrane being displayed
                        SpeciesContextShape speciesContextShape = (SpeciesContextShape) getShapeFromModelObject(speciesContext);
                        if (speciesContextShape == null) {
                            speciesContextShape = new SpeciesContextShape(speciesContext, this);
                            speciesContextShape.truncateLabelName(false);
                            reactionContainerShape.addChildShape(speciesContextShape);
                            addShape(speciesContextShape);
                            speciesContextShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                        }
                        speciesContextShape.refreshLabel();
                        unwantedShapes.remove(speciesContextShape);
                        ReactionParticipantShape reactionParticipantShape = (ReactionParticipantShape) getShapeFromModelObject(participant);
                        if (reactionParticipantShape == null) {
                            if (participant instanceof Reactant) {
                                reactionParticipantShape = new ReactantShape((Reactant) participant, reactionStepShape, speciesContextShape, this);
                            } else if (participant instanceof Product) {
                                reactionParticipantShape = new ProductShape((Product) participant, reactionStepShape, speciesContextShape, this);
                            } else if (participant instanceof Catalyst) {
                                reactionParticipantShape = new CatalystShape((Catalyst) participant, reactionStepShape, speciesContextShape, this);
                            } else {
                                throw new RuntimeException("unsupported ReactionParticipant " + participant.getClass());
                            }
                            addShape(reactionParticipantShape);
                        }
                        if (!containerShape.getChildren().contains(reactionParticipantShape)) {
                            containerShape.addChildShape(reactionParticipantShape);
                        }
                        unwantedShapes.remove(reactionParticipantShape);
                        reactionParticipantShape.refreshLabel();
                    }
                }
            }
        }
        for (Shape unwantedShape : unwantedShapes) {
            removeShape(unwantedShape);
        }
        // update diagrams
        for (Structure structure : structureSuite.getStructures()) {
            Diagram diagram = getModel().getDiagram(structure);
            if (diagram != null) {
                applyDefaults(diagram);
            }
        }
        fireGraphChanged(new GraphEvent(this));
    } catch (Throwable e) {
        handleException(e);
    }
}

Example 14 with Catalyst

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

the class ReactionCartoonMolecule method refreshAll.

@Override
protected void refreshAll(boolean reallocateShapes) {
    try {
        if (getModel() == null || getStructureSuite() == null) {
            return;
        }
        System.out.println("ReactionCartoonMolecule, RefreshAll()");
        for (Structure structure : structureSuite.getStructures()) {
            Diagram diagram = getModel().getDiagram(structure);
            if (diagram != null) {
                // Maintain consistency between rule participant nodes, signatures and
                // species pattern when a molecule is being modified.
                rebindAll(diagram);
            }
        }
        // calculate species context weight (number of reactions for which it's a participant)
        Map<SpeciesContext, Integer> scWeightMap = new HashMap<>();
        // all the species contexts that are catalysts
        Set<SpeciesContext> scCatalystSet = new HashSet<>();
        // calculate species context length (number of species patterns it contains, 1 if has no species patterns)
        for (ReactionStep rs : getModel().getReactionSteps()) {
            ReactionParticipant[] rpList = rs.getReactionParticipants();
            for (int i = 0; i < rpList.length; i++) {
                ReactionParticipant rp = rpList[i];
                SpeciesContext sc = rp.getSpeciesContext();
                int increment = 1;
                if (rp instanceof Catalyst) {
                    scCatalystSet.add(sc);
                }
                if (scWeightMap.containsKey(sc)) {
                    int weight = scWeightMap.get(sc);
                    weight += increment;
                    scWeightMap.put(sc, weight);
                } else {
                    scWeightMap.put(sc, increment);
                }
            }
        }
        Set<Shape> unwantedShapes = new HashSet<Shape>();
        Set<RuleParticipantSignature> unwantedSignatures = new HashSet<RuleParticipantSignature>();
        unwantedShapes.addAll(getShapes());
        unwantedSignatures.addAll(ruleParticipantSignatures);
        ContainerContainerShape containerShape = (ContainerContainerShape) getShapeFromModelObject(getModel());
        List<ReactionContainerShape> reactionContainerShapeList = new ArrayList<ReactionContainerShape>();
        List<Structure> structureList = new ArrayList<Structure>(getStructureSuite().getStructures());
        // create all ReactionContainerShapes (one for each Structure)
        for (Structure structure : structureList) {
            if (structure instanceof Membrane) {
                Membrane membrane = (Membrane) structure;
                ReactionContainerShape membraneShape = (ReactionContainerShape) getShapeFromModelObject(membrane);
                if (membraneShape == null) {
                    membraneShape = new ReactionContainerShape(membrane, structureSuite, this);
                    addShape(membraneShape);
                    membrane.getMembraneVoltage().removePropertyChangeListener(this);
                    membrane.getMembraneVoltage().addPropertyChangeListener(this);
                } else {
                    membraneShape.setStructureSuite(structureSuite);
                }
                membrane.removePropertyChangeListener(this);
                membrane.addPropertyChangeListener(this);
                membraneShape.refreshLabel();
                unwantedShapes.remove(membraneShape);
                reactionContainerShapeList.add(membraneShape);
            } else if (structure instanceof Feature) {
                Feature feature = (Feature) structure;
                ReactionContainerShape featureShape = (ReactionContainerShape) getShapeFromModelObject(feature);
                if (featureShape == null) {
                    featureShape = new ReactionContainerShape(feature, structureSuite, this);
                    addShape(featureShape);
                } else {
                    featureShape.setStructureSuite(structureSuite);
                }
                feature.removePropertyChangeListener(this);
                feature.addPropertyChangeListener(this);
                featureShape.refreshLabel();
                unwantedShapes.remove(featureShape);
                reactionContainerShapeList.add(featureShape);
            }
        }
        if (containerShape == null) {
            containerShape = new ContainerContainerShape(this, getModel(), reactionContainerShapeList);
            addShape(containerShape);
        } else {
            containerShape.setReactionContainerShapeList(reactionContainerShapeList);
        }
        containerShape.refreshLabel();
        unwantedShapes.remove(containerShape);
        // add all species context shapes within the structures
        for (Structure structure : getStructureSuite().getStructures()) {
            ReactionContainerShape reactionContainerShape = (ReactionContainerShape) getShapeFromModelObject(structure);
            structure.removePropertyChangeListener(this);
            structure.addPropertyChangeListener(this);
            for (SpeciesContext structSpeciesContext : getModel().getSpeciesContexts(structure)) {
                SpeciesContextShape ss = (SpeciesContextShape) getShapeFromModelObject(structSpeciesContext);
                if (ss == null) {
                    ss = new SpeciesContextShape(structSpeciesContext, this);
                    ss.truncateLabelName(false);
                    structSpeciesContext.getSpecies().removePropertyChangeListener(this);
                    structSpeciesContext.getSpecies().addPropertyChangeListener(this);
                    reactionContainerShape.addChildShape(ss);
                    addShape(ss);
                    ss.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                }
                if (speciesSizeOption == SpeciesSizeOptions.weight) {
                    // this number sets the diameter of the shape
                    Integer weight = scWeightMap.get(structSpeciesContext);
                    if (weight != null) {
                        // we cap the diameter of the shape to something reasonable
                        weight = Math.min(weight, 16);
                    }
                    ss.setFilters(highlightCatalystOption ? scCatalystSet.contains(structSpeciesContext) : false, weight);
                } else if (speciesSizeOption == SpeciesSizeOptions.length) {
                    Integer length = null;
                    if (structSpeciesContext.getSpeciesPattern() != null && !structSpeciesContext.getSpeciesPattern().getMolecularTypePatterns().isEmpty()) {
                        length = structSpeciesContext.getSpeciesPattern().getMolecularTypePatterns().size() * 2;
                        length = Math.min(length, 16);
                    }
                    ss.setFilters(highlightCatalystOption ? scCatalystSet.contains(structSpeciesContext) : false, length);
                } else {
                    ss.setFilters(highlightCatalystOption ? scCatalystSet.contains(structSpeciesContext) : false, null);
                }
                structSpeciesContext.removePropertyChangeListener(this);
                structSpeciesContext.addPropertyChangeListener(this);
                ss.refreshLabel();
                unwantedShapes.remove(ss);
            }
        }
        // add all reactionSteps that are in this structure (ReactionContainerShape), and draw the lines
        getModel().removePropertyChangeListener(this);
        getModel().addPropertyChangeListener(this);
        // 
        for (ReactionRule rr : getModel().getRbmModelContainer().getReactionRuleList()) {
            rr.removePropertyChangeListener(this);
            rr.addPropertyChangeListener(this);
            Structure structure = rr.getStructure();
            if (getStructureSuite().areReactionsShownFor(structure)) {
                ReactionContainerShape reactionContainerShape = (ReactionContainerShape) getShapeFromModelObject(structure);
                ReactionRuleFullDiagramShape rrShape = (ReactionRuleFullDiagramShape) getShapeFromModelObject(rr);
                if (rrShape == null) {
                    rrShape = new ReactionRuleFullDiagramShape(rr, this);
                    addShape(rrShape);
                    rrShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                    reactionContainerShape.addChildShape(rrShape);
                    rrShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                }
                rrShape.refreshLabel();
                unwantedShapes.remove(rrShape);
                // 
                // add reaction participants as edges and SignatureShapes as needed
                // 
                List<ReactionRuleParticipant> participants = rr.getReactionRuleParticipants();
                List<RuleParticipantEdgeDiagramShape> ruleEdges = new ArrayList<>();
                for (ReactionRuleParticipant participant : participants) {
                    participant.getSpeciesPattern().removePropertyChangeListener(this);
                    participant.getSpeciesPattern().addPropertyChangeListener(this);
                    Structure speciesStructure = participant.getStructure();
                    Structure reactionStructure = rr.getStructure();
                    if (getStructureSuite().getStructures().contains(speciesStructure) && getStructureSuite().areReactionsShownFor(reactionStructure)) {
                        // 
                        // find existing RuleParticipantSignatureShape in cartoon
                        // 
                        RuleParticipantShortSignature ruleParticipantShortSignature = null;
                        for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                            if (signature instanceof RuleParticipantLongSignature && signature.getStructure() == participant.getStructure()) {
                                System.out.println("ReactionCartoonMolecule, refreshAll(), RuleParticipantLongSignature");
                                break;
                            }
                        }
                        for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                            if (signature instanceof RuleParticipantShortSignature && signature.getStructure() == participant.getStructure() && signature.compareByCriteria(participant.getSpeciesPattern(), GroupingCriteria.molecule)) {
                                ruleParticipantShortSignature = (RuleParticipantShortSignature) signature;
                                break;
                            }
                        }
                        // 
                        // if didn't find signature in cartoons list of signatures, then create one (and create a shape for it).
                        // 
                        RuleParticipantSignatureShortDiagramShape signatureShape = null;
                        if (ruleParticipantShortSignature == null) {
                            ruleParticipantShortSignature = RuleParticipantShortSignature.fromReactionRuleParticipant(participant, this);
                            ruleParticipantSignatures.add(ruleParticipantShortSignature);
                            signatureShape = new RuleParticipantSignatureShortDiagramShape(ruleParticipantShortSignature, this);
                            addShape(signatureShape);
                            ReactionContainerShape participantContainerShape = (ReactionContainerShape) getShapeFromModelObject(participant.getStructure());
                            signatureShape.getSpaceManager().setRelPos(participantContainerShape.getRandomPosition());
                            participantContainerShape.addChildShape(signatureShape);
                            signatureShape.getSpaceManager().setRelPos(participantContainerShape.getRandomPosition());
                        } else {
                            signatureShape = (RuleParticipantSignatureShortDiagramShape) getShapeFromModelObject(ruleParticipantShortSignature);
                        }
                        unwantedShapes.remove(signatureShape);
                        unwantedSignatures.remove(ruleParticipantShortSignature);
                        signatureShape.refreshLabel();
                        signatureShape.setVisible(true);
                        // 
                        // add edge for ReactionRuleParticipant if not already present.
                        // 
                        RuleParticipantEdgeDiagramShape ruleParticipantShape = (RuleParticipantEdgeDiagramShape) getShapeFromModelObject(participant);
                        if (ruleParticipantShape == null || ruleParticipantShape.getRuleParticipantSignatureShape() != signatureShape) {
                            if (participant instanceof ReactantPattern && signatureShape.isVisible()) {
                                ruleParticipantShape = new ReactantPatternEdgeDiagramShape((ReactantPattern) participant, rrShape, signatureShape, this);
                            } else if (participant instanceof ProductPattern && signatureShape.isVisible()) {
                                ruleParticipantShape = new ProductPatternEdgeDiagramShape((ProductPattern) participant, rrShape, signatureShape, this);
                            } else {
                                throw new RuntimeException("unsupported ReactionRuleParticipant " + participant.getClass());
                            }
                            addShape(ruleParticipantShape);
                        }
                        if (!containerShape.getChildren().contains(ruleParticipantShape)) {
                            containerShape.addChildShape(ruleParticipantShape);
                        }
                        unwantedShapes.remove(ruleParticipantShape);
                        ruleParticipantShape.refreshLabel();
                        // all the edges for this rule
                        ruleEdges.add(ruleParticipantShape);
                    }
                }
                // a product edge (a closed loop) between the rule diagram shape and the signature diagram shape
                for (RuleParticipantEdgeDiagramShape ours : ruleEdges) {
                    // reset them all
                    ours.setSibling(false);
                }
                for (RuleParticipantEdgeDiagramShape ours : ruleEdges) {
                    for (RuleParticipantEdgeDiagramShape theirs : ruleEdges) {
                        if (ours == theirs) {
                            // don't compare with self
                            continue;
                        }
                        if (ours.getRuleParticipantSignatureShape() == theirs.getRuleParticipantSignatureShape()) {
                            ours.setSibling(true);
                            theirs.setSibling(true);
                        }
                    }
                }
            }
        }
        ruleParticipantSignatures.removeAll(unwantedSignatures);
        for (ReactionStep reactionStep : getModel().getReactionSteps()) {
            reactionStep.removePropertyChangeListener(this);
            reactionStep.addPropertyChangeListener(this);
            Structure structure = reactionStep.getStructure();
            if (getStructureSuite().areReactionsShownFor(structure)) {
                ReactionContainerShape reactionContainerShape = (ReactionContainerShape) getShapeFromModelObject(structure);
                if (reactionContainerShape == null) {
                    System.out.println("Reaction container shape is null for structure " + structure + " for reaction step " + reactionStep);
                }
                ReactionStepShape reactionStepShape = (ReactionStepShape) getShapeFromModelObject(reactionStep);
                if (reactionStepShape == null) {
                    if (reactionStep instanceof SimpleReaction) {
                        reactionStepShape = new SimpleReactionShape((SimpleReaction) reactionStep, this);
                    } else if (reactionStep instanceof FluxReaction) {
                        reactionStepShape = new FluxReactionShape((FluxReaction) reactionStep, this);
                    } else {
                        throw new RuntimeException("unknown type of ReactionStep '" + reactionStep.getClass().toString());
                    }
                    addShape(reactionStepShape);
                    reactionStepShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                    reactionContainerShape.addChildShape(reactionStepShape);
                    reactionStepShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                }
                reactionStepShape.refreshLabel();
                unwantedShapes.remove(reactionStepShape);
                // add reaction participants as edges
                for (ReactionParticipant participant : reactionStep.getReactionParticipants()) {
                    participant.removePropertyChangeListener(this);
                    participant.addPropertyChangeListener(this);
                    Structure speciesStructure = participant.getStructure();
                    Structure reactionStructure = reactionStep.getStructure();
                    if (getStructureSuite().getStructures().contains(speciesStructure) && getStructureSuite().areReactionsShownFor(reactionStructure)) {
                        SpeciesContext speciesContext = getModel().getSpeciesContext(participant.getSpecies(), speciesStructure);
                        // add speciesContextShapes that are not in this structure, but are referenced from the reactionParticipants
                        // these are only when reactionParticipants are from features that are outside of the membrane being displayed
                        SpeciesContextShape speciesContextShape = (SpeciesContextShape) getShapeFromModelObject(speciesContext);
                        if (speciesContextShape == null) {
                            speciesContextShape = new SpeciesContextShape(speciesContext, this);
                            speciesContextShape.truncateLabelName(false);
                            reactionContainerShape.addChildShape(speciesContextShape);
                            addShape(speciesContextShape);
                            speciesContextShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
                        }
                        speciesContextShape.refreshLabel();
                        unwantedShapes.remove(speciesContextShape);
                        ReactionParticipantShape reactionParticipantShape = (ReactionParticipantShape) getShapeFromModelObject(participant);
                        if (reactionParticipantShape == null) {
                            if (participant instanceof Reactant) {
                                reactionParticipantShape = new ReactantShape((Reactant) participant, reactionStepShape, speciesContextShape, this);
                            } else if (participant instanceof Product) {
                                reactionParticipantShape = new ProductShape((Product) participant, reactionStepShape, speciesContextShape, this);
                            } else if (participant instanceof Catalyst) {
                                reactionParticipantShape = new CatalystShape((Catalyst) participant, reactionStepShape, speciesContextShape, this);
                            } else {
                                throw new RuntimeException("unsupported ReactionParticipant " + participant.getClass());
                            }
                            addShape(reactionParticipantShape);
                        }
                        if (!containerShape.getChildren().contains(reactionParticipantShape)) {
                            containerShape.addChildShape(reactionParticipantShape);
                        }
                        unwantedShapes.remove(reactionParticipantShape);
                        reactionParticipantShape.refreshLabel();
                    }
                }
            }
        }
        for (Shape unwantedShape : unwantedShapes) {
            removeShape(unwantedShape);
        }
        // update diagrams
        for (Structure structure : structureSuite.getStructures()) {
            Diagram diagram = getModel().getDiagram(structure);
            if (diagram != null) {
                applyDefaults(diagram);
            }
        }
        fireGraphChanged(new GraphEvent(this));
    } catch (Throwable e) {
        handleException(e);
    }
}

Example 15 with Catalyst

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

the class Xmlproducer method getXML.

/**
 * This method returns a XML representation of a Flux Reaction object.
 * Creation date: (2/26/2001 12:30:13 PM)
 * @return Element
 * @param param cbit.vcell.model.FluxReaction
 */
private Element getXML(FluxReaction param) throws XmlParseException {
    Element fluxreaction = new Element(XMLTags.FluxStepTag);
    // get Attributes
    String versionName = (param.getName() != null) ? mangle(param.getName()) : "unnamed_fluxReaction";
    fluxreaction.setAttribute(XMLTags.NameAttrTag, versionName);
    fluxreaction.setAttribute(XMLTags.StructureAttrTag, mangle(param.getStructure().getName()));
    fluxreaction.setAttribute(XMLTags.ReversibleAttrTag, mangle(Boolean.valueOf(param.isReversible()).toString()));
    if (param.getPhysicsOptions() == FluxReaction.PHYSICS_ELECTRICAL_ONLY) {
        fluxreaction.setAttribute(XMLTags.FluxOptionAttrTag, XMLTags.FluxOptionElectricalOnly);
    } else if (param.getPhysicsOptions() == FluxReaction.PHYSICS_MOLECULAR_AND_ELECTRICAL) {
        fluxreaction.setAttribute(XMLTags.FluxOptionAttrTag, XMLTags.FluxOptionMolecularAndElectrical);
    } else if (param.getPhysicsOptions() == FluxReaction.PHYSICS_MOLECULAR_ONLY) {
        fluxreaction.setAttribute(XMLTags.FluxOptionAttrTag, XMLTags.FluxOptionMolecularOnly);
    }
    // If keyFlag is on print the Keyvalue
    if (param.getKey() != null && this.printKeysFlag) {
        fluxreaction.setAttribute(XMLTags.KeyValueAttrTag, param.getKey().toString());
    }
    // Add subelements: Reactants/Products/Catalysts
    // separate the order of the reactants, products, and modifiers.
    ReactionParticipant[] rpArray = param.getReactionParticipants();
    ArrayList<Element> products = new ArrayList<Element>();
    ArrayList<Element> modifiers = new ArrayList<Element>();
    for (int i = 0; i < rpArray.length; i++) {
        Element rp = getXML(rpArray[i]);
        if (rp != null) {
            if (rpArray[i] instanceof Reactant)
                fluxreaction.addContent(rp);
            else if (rpArray[i] instanceof Product)
                products.add(rp);
            else if (rpArray[i] instanceof Catalyst)
                modifiers.add(rp);
        }
    }
    for (int i = 0; i < products.size(); i++) fluxreaction.addContent((Element) products.get(i));
    for (int i = 0; i < modifiers.size(); i++) fluxreaction.addContent((Element) modifiers.get(i));
    // Add Kinetics
    fluxreaction.addContent(getXML(param.getKinetics()));
    return fluxreaction;
}