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

Example 21 with ReactionStep

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

the class TransformMassActionTableModel method saveTransformedReactions.

public void saveTransformedReactions() throws Exception {
    // isTransformable and TransformedREactions are stored according to the indexes in model reaction steps.
    boolean[] isTransformable = getTransformMassActions().getIsTransformable();
    TransformMassActions.TransformedReaction[] trs = getTransformMassActions().getTransformedReactionSteps();
    ReactionStep[] origReactions = getModel().getReactionSteps();
    // names of those who can be transformed and will be transformed
    String okTransReacNames = "";
    // names of those who can be transformed and will not be transformed
    String noTransReacNames = "";
    // names of those who can not be transformed
    String errReacNames = "";
    for (int i = 0; i < isTransformable.length; i++) {
        if (trs[i].getTransformType() == TransformMassActions.TransformedReaction.TRANSFORMABLE && getIsSelected(i)) {
            okTransReacNames = okTransReacNames + origReactions[i].getName() + ",";
        } else if (trs[i].getTransformType() == TransformMassActions.TransformedReaction.TRANSFORMABLE && !getIsSelected(i)) {
            noTransReacNames = noTransReacNames + origReactions[i].getName() + ",";
        } else if (!isTransformable[i]) {
            errReacNames = errReacNames + origReactions[i].getName() + ",";
        }
    }
    // set transformed Mass Action kinetics to model reactions
    for (int i = 0; i < origReactions.length; i++) {
        if (getIsSelected(i)) {
            // for simple reaction, we replace the original kinetics with MassActionKinetics if it wasn't MassActionKinetics
            if (origReactions[i] instanceof SimpleReaction) {
                if (!(origReactions[i].getKinetics() instanceof MassActionKinetics)) {
                    // ***Below we will physically change the simple reaction***
                    // put all kinetic parameters together into array newKps
                    Vector<Kinetics.KineticsParameter> newKps = new Vector<Kinetics.KineticsParameter>();
                    // get original kinetic parameters which are not current density and reaction rate.
                    // those parameters are basically the symbols in rate expression.
                    Vector<Kinetics.KineticsParameter> origKps = new Vector<Kinetics.KineticsParameter>();
                    Kinetics.KineticsParameter[] Kps = origReactions[i].getKinetics().getKineticsParameters();
                    for (int j = 0; j < Kps.length; j++) {
                        if (!(Kps[j].getRole() == Kinetics.ROLE_CurrentDensity || Kps[j].getRole() == Kinetics.ROLE_ReactionRate)) {
                            origKps.add(Kps[j]);
                        }
                    }
                    // create mass action kinetics for the original reaction step
                    MassActionKinetics maKinetics = new MassActionKinetics(origReactions[i]);
                    maKinetics.getKineticsParameterFromRole(Kinetics.ROLE_KForward).setExpression(trs[i].getMassActionFunction().getForwardRate());
                    maKinetics.getKineticsParameterFromRole(Kinetics.ROLE_KReverse).setExpression(trs[i].getMassActionFunction().getReverseRate());
                    // Kinetics)
                    for (int j = 0; j < maKinetics.getKineticsParameters().length; j++) {
                        newKps.add(maKinetics.getKineticsParameters(j));
                    }
                    // copy other kinetic parameters from original kinetics
                    for (int j = 0; j < origKps.size(); j++) {
                        newKps.add(origKps.elementAt(j));
                    }
                    // add parameters to mass action kinetics
                    KineticsParameter[] newParameters = new KineticsParameter[newKps.size()];
                    newParameters = (KineticsParameter[]) newKps.toArray(newParameters);
                    maKinetics.addKineticsParameters(newParameters);
                    // after adding all the parameters, we bind the forward/reverse rate expression with symbol table (the reaction step itself)
                    origReactions[i].getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_KForward).getExpression().bindExpression(origReactions[i]);
                    origReactions[i].getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_KReverse).getExpression().bindExpression(origReactions[i]);
                }
            }
        // for flux, we set the flux reaction back, coz we will parse it to mass action form in stochastic math mapping.
        // However, we don't physically change it.
        }
    }
    String msg = "";
    if (!okTransReacNames.equals("")) {
        msg = msg + okTransReacNames + " have been transformed.\n";
    }
    // message to be displayed in popupdialog of DocumentWindow
    if (!msg.equals("")) {
        throw new Exception(msg);
    }
}

Example 22 with ReactionStep

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

the class ParameterTableModel method setReactionStep.

/**
 * Sets the geometry property (cbit.vcell.geometry.Geometry) value.
 * @param geometry The new value for the property.
 * @see #getGeometry
 */
public void setReactionStep(ReactionStep newValue) {
    ReactionStep oldValue = reactionStep;
    reactionStep = newValue;
    firePropertyChange("reactionStep", oldValue, newValue);
}

Example 23 with ReactionStep

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

the class ParameterTableModel method propertyChange.

/**
 * This method gets called when a bound property is changed.
 * @param evt A PropertyChangeEvent object describing the event source
 *   and the property that has changed.
 */
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    if (evt.getSource() == this && evt.getPropertyName().equals("reactionStep")) {
        ReactionStep oldValue = (ReactionStep) evt.getOldValue();
        if (oldValue != null) {
            oldValue.removePropertyChangeListener(this);
            oldValue.getKinetics().removePropertyChangeListener(this);
            for (int i = 0; i < oldValue.getKinetics().getKineticsParameters().length; i++) {
                oldValue.getKinetics().getKineticsParameters()[i].removePropertyChangeListener(this);
            }
            for (int i = 0; i < oldValue.getKinetics().getProxyParameters().length; i++) {
                oldValue.getKinetics().getProxyParameters()[i].removePropertyChangeListener(this);
            }
        }
        ReactionStep newValue = (ReactionStep) evt.getNewValue();
        if (newValue != null) {
            newValue.addPropertyChangeListener(this);
            newValue.getKinetics().addPropertyChangeListener(this);
            for (int i = 0; i < newValue.getKinetics().getKineticsParameters().length; i++) {
                newValue.getKinetics().getKineticsParameters()[i].removePropertyChangeListener(this);
                newValue.getKinetics().getKineticsParameters()[i].addPropertyChangeListener(this);
            }
            for (int i = 0; i < newValue.getKinetics().getProxyParameters().length; i++) {
                newValue.getKinetics().getProxyParameters()[i].removePropertyChangeListener(this);
                newValue.getKinetics().getProxyParameters()[i].addPropertyChangeListener(this);
            }
            autoCompleteSymbolFilter = reactionStep.getAutoCompleteSymbolFilter();
        }
        refreshData();
    }
    if (evt.getSource() == reactionStep && evt.getPropertyName().equals(ReactionStep.PROPERTY_NAME_KINETICS)) {
        Kinetics oldValue = (Kinetics) evt.getOldValue();
        if (oldValue != null) {
            oldValue.removePropertyChangeListener(this);
            for (int i = 0; i < oldValue.getKineticsParameters().length; i++) {
                oldValue.getKineticsParameters()[i].removePropertyChangeListener(this);
            }
            for (int i = 0; i < oldValue.getProxyParameters().length; i++) {
                oldValue.getProxyParameters()[i].removePropertyChangeListener(this);
            }
        }
        Kinetics newValue = (Kinetics) evt.getNewValue();
        if (newValue != null) {
            newValue.addPropertyChangeListener(this);
            for (int i = 0; i < newValue.getKineticsParameters().length; i++) {
                newValue.getKineticsParameters()[i].removePropertyChangeListener(this);
                newValue.getKineticsParameters()[i].addPropertyChangeListener(this);
            }
            for (int i = 0; i < newValue.getProxyParameters().length; i++) {
                newValue.getProxyParameters()[i].removePropertyChangeListener(this);
                newValue.getProxyParameters()[i].addPropertyChangeListener(this);
            }
        }
        // get rid of all Catalysts when changing kynetic type
        if (reactionStep != null && reactionStep.hasCatalyst() && newValue != null && newValue != oldValue) {
            List<ReactionParticipant> rpList = new ArrayList<>(Arrays.asList(reactionStep.getReactionParticipants()));
            for (ReactionParticipant rp : rpList) {
                if (rp instanceof Catalyst) {
                    try {
                        reactionStep.removeReactionParticipant(rp);
                    } catch (PropertyVetoException | ExpressionException | ModelException e) {
                        // do nothing if it fails
                        e.printStackTrace();
                    }
                }
            }
        }
        refreshData();
    }
    if (evt.getSource() instanceof Kinetics && (evt.getPropertyName().equals("kineticsParameters") || evt.getPropertyName().equals("proxyParameters"))) {
        Parameter[] oldParams = (Parameter[]) evt.getOldValue();
        Parameter[] newParams = (Parameter[]) evt.getNewValue();
        for (int i = 0; oldParams != null && i < oldParams.length; i++) {
            oldParams[i].removePropertyChangeListener(this);
        }
        for (int i = 0; newParams != null && i < newParams.length; i++) {
            newParams[i].removePropertyChangeListener(this);
            newParams[i].addPropertyChangeListener(this);
        }
        if (evt.getPropertyName().equals("proxyParameters")) {
            List<Parameter> addedList = new ArrayList<>(Arrays.asList(newParams));
            addedList.removeAll(Arrays.asList(oldParams));
            List<Parameter> removedList = new ArrayList<>(Arrays.asList(oldParams));
            removedList.removeAll(Arrays.asList(newParams));
            if (reactionStep != null) {
                for (Parameter removed : removedList) {
                    if (removed instanceof ProxyParameter && ((ProxyParameter) removed).getTarget() instanceof SpeciesContext) {
                        SpeciesContext sc = (SpeciesContext) ((ProxyParameter) removed).getTarget();
                        if (reactionStep.getReactant(sc.getName()) == null && reactionStep.getProduct(sc.getName()) == null && reactionStep.getCatalyst(sc.getName()) != null) {
                            try {
                                reactionStep.removeReactionParticipant(reactionStep.getCatalyst(sc.getName()));
                            } catch (PropertyVetoException | ExpressionException | ModelException e) {
                                // we do nothing
                                e.printStackTrace();
                            }
                        }
                    }
                }
                for (Parameter added : addedList) {
                    if (added instanceof ProxyParameter && ((ProxyParameter) added).getTarget() instanceof SpeciesContext) {
                        SpeciesContext sc = (SpeciesContext) ((ProxyParameter) added).getTarget();
                        if (reactionStep.getReactant(sc.getName()) == null && reactionStep.getProduct(sc.getName()) == null && reactionStep.getCatalyst(sc.getName()) == null) {
                            try {
                                reactionStep.addCatalyst(sc);
                            } catch (PropertyVetoException | ModelException e) {
                                // we do nothing
                                e.printStackTrace();
                            }
                        }
                    }
                }
            }
        }
        refreshData();
    }
    if (evt.getSource() instanceof Parameter) {
        fireTableRowsUpdated(0, getRowCount() - 1);
    }
}

Example 24 with ReactionStep

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

the class BioModel method getVCID.

public VCID getVCID(Identifiable identifiable) {
    if (identifiable == null) {
        return null;
    }
    String localName;
    String className;
    if (identifiable instanceof SpeciesContext) {
        localName = ((SpeciesContext) identifiable).getName();
        className = VCID.CLASS_SPECIES_CONTEXT;
    } else if (identifiable instanceof Species) {
        localName = ((Species) identifiable).getCommonName();
        className = VCID.CLASS_SPECIES;
    } else if (identifiable instanceof Structure) {
        localName = ((Structure) identifiable).getName();
        className = VCID.CLASS_STRUCTURE;
    } else if (identifiable instanceof ReactionStep) {
        localName = ((ReactionStep) identifiable).getName();
        className = VCID.CLASS_REACTION_STEP;
    } else if (identifiable instanceof BioModel) {
        localName = ((BioModel) identifiable).getName();
        className = VCID.CLASS_BIOMODEL;
    } else if (identifiable instanceof BioPaxObject) {
        localName = ((BioPaxObject) identifiable).getID();
        className = VCID.CLASS_BIOPAX_OBJECT;
    } else if (identifiable instanceof MolecularType) {
        localName = ((MolecularType) identifiable).getName();
        className = VCID.CLASS_MOLECULE;
    } else if (identifiable instanceof ReactionRule) {
        localName = ((ReactionRule) identifiable).getName();
        className = VCID.CLASS_REACTION_RULE;
    } else if (identifiable instanceof RbmObservable) {
        localName = ((RbmObservable) identifiable).getName();
        className = VCID.CLASS_OBSERVABLE;
    } else if (identifiable instanceof Model.ModelParameter) {
        localName = ((Model.ModelParameter) identifiable).getName();
        className = VCID.CLASS_MODEL_PARAMETER;
    } else if (identifiable instanceof SimulationContext) {
        localName = ((SimulationContext) identifiable).getName();
        className = VCID.CLASS_APPLICATION;
    } else {
        throw new RuntimeException("unsupported Identifiable class");
    }
    localName = TokenMangler.mangleVCId(localName);
    VCID vcid;
    try {
        vcid = VCID.fromString(className + "(" + localName + ")");
    } catch (VCID.InvalidVCIDException e) {
        e.printStackTrace();
        throw new RuntimeException(e.getMessage());
    }
    return vcid;
}

Example 25 with ReactionStep

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

the class BioModel method propertyChange.

/**
 * This method gets called when a bound property is changed.
 * @param evt A PropertyChangeEvent object describing the event source
 *   	and the property that has changed.
 */
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    // 
    if (evt.getSource() instanceof SimulationContext && evt.getPropertyName().equals("mathDescription") && evt.getNewValue() != null) {
        if (fieldSimulations != null) {
            for (int i = 0; i < fieldSimulations.length; i++) {
                if (fieldSimulations[i].getMathDescription() == evt.getOldValue()) {
                    try {
                        fieldSimulations[i].setMathDescription((MathDescription) evt.getNewValue());
                    } catch (PropertyVetoException e) {
                        System.out.println("error propagating math from SimulationContext '" + ((SimulationContext) evt.getSource()).getName() + "' to Simulation '" + fieldSimulations[i].getName());
                        e.printStackTrace(System.out);
                    }
                }
            }
        }
    }
    // 
    if (evt.getSource() == this && evt.getPropertyName().equals(PropertyConstants.PROPERTY_NAME_SIMULATIONS) && evt.getNewValue() != null) {
        // 
        if (evt.getOldValue() != null) {
            Simulation[] simulations = (Simulation[]) evt.getOldValue();
            for (int i = 0; i < simulations.length; i++) {
                simulations[i].removeVetoableChangeListener(this);
                simulations[i].removePropertyChangeListener(this);
            }
        }
        // 
        if (evt.getOldValue() != null) {
            Simulation[] simulations = (Simulation[]) evt.getNewValue();
            for (int i = 0; i < simulations.length; i++) {
                simulations[i].addVetoableChangeListener(this);
                simulations[i].addPropertyChangeListener(this);
            }
        }
    }
    if (evt.getSource() == this && evt.getPropertyName().equals(PROPERTY_NAME_SIMULATION_CONTEXTS) && evt.getNewValue() != null) {
        // 
        if (evt.getOldValue() != null) {
            SimulationContext[] simulationContexts = (SimulationContext[]) evt.getOldValue();
            for (int i = 0; i < simulationContexts.length; i++) {
                simulationContexts[i].removeVetoableChangeListener(this);
                simulationContexts[i].removePropertyChangeListener(this);
            }
        }
        // 
        if (evt.getOldValue() != null) {
            SimulationContext[] simulationContexts = (SimulationContext[]) evt.getNewValue();
            for (int i = 0; i < simulationContexts.length; i++) {
                simulationContexts[i].addVetoableChangeListener(this);
                simulationContexts[i].addPropertyChangeListener(this);
            }
        }
    }
    if (evt.getSource() == fieldModel && (evt.getPropertyName().equals(Model.PROPERTY_NAME_SPECIES_CONTEXTS) || evt.getPropertyName().equals(Model.PROPERTY_NAME_REACTION_STEPS))) {
        // remove the relationship objects if the biomodelEntity objects were removed
        Set<BioModelEntityObject> removedObjects = relationshipModel.getBioModelEntityObjects();
        for (SpeciesContext sc : fieldModel.getSpeciesContexts()) {
            removedObjects.remove(sc);
        }
        for (ReactionStep rs : fieldModel.getReactionSteps()) {
            removedObjects.remove(rs);
        }
        for (MolecularType mt : fieldModel.getRbmModelContainer().getMolecularTypeList()) {
            removedObjects.remove(mt);
        }
        for (ReactionRule rr : fieldModel.getRbmModelContainer().getReactionRuleList()) {
            removedObjects.remove(rr);
        }
        relationshipModel.removeRelationshipObjects(removedObjects);
    }
    // adjust the relationship model when a molecule gets deleted
    if (evt.getSource() == fieldModel && (evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_MOLECULAR_TYPE_LIST))) {
        @SuppressWarnings("unchecked") List<MolecularType> oldListCopy = new ArrayList<MolecularType>((List<MolecularType>) evt.getOldValue());
        @SuppressWarnings("unchecked") List<MolecularType> newList = (List<MolecularType>) evt.getNewValue();
        if (newList != null && oldListCopy != null && oldListCopy.size() > newList.size()) {
            // something got deleted
            oldListCopy.removeAll(newList);
            for (MolecularType removedMt : oldListCopy) {
                relationshipModel.removeRelationshipObject(removedMt);
            }
        }
    }
    if (evt.getSource() == fieldModel && (evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_REACTION_RULE_LIST))) {
        @SuppressWarnings("unchecked") List<ReactionRule> oldListCopy = new ArrayList<ReactionRule>((List<ReactionRule>) evt.getOldValue());
        @SuppressWarnings("unchecked") List<ReactionRule> newList = (List<ReactionRule>) evt.getNewValue();
        if (newList != null && oldListCopy != null && oldListCopy.size() > newList.size()) {
            // something got deleted
            oldListCopy.removeAll(newList);
            for (ReactionRule removedRr : oldListCopy) {
                relationshipModel.removeRelationshipObject(removedRr);
            }
        }
    }
    if (evt.getSource() == fieldModel && (evt.getPropertyName().equals(Model.PROPERTY_NAME_MODEL_ENTITY_NAME))) {
        firePropertyChange(Model.PROPERTY_NAME_MODEL_ENTITY_NAME, evt.getOldValue(), evt.getNewValue());
    }
}