Examples with PropertyVetoException java.beans.PropertyVetoException used on opensource projects

Example 41 with PropertyVetoException

use of java.beans.PropertyVetoException in project vcell by virtualcell.

the class Kinetics method setParameterValue.

/**
 * This method was created by a SmartGuide.
 * @param expressionString java.lang.String
 * @exception java.lang.Exception The exception description.
 */
public void setParameterValue(KineticsParameter parm, Expression exp) throws ExpressionException, PropertyVetoException {
    Parameter p = getKineticsParameter(parm.getName());
    if (p != parm) {
        throw new RuntimeException("parameter " + parm.getName() + " not found");
    }
    Expression oldExpression = parm.getExpression();
    boolean bBound = false;
    try {
        KineticsParameter[] newKineticsParameters = (KineticsParameter[]) fieldKineticsParameters.clone();
        // KineticsProxyParameter newProxyParameters[] = (KineticsProxyParameter[])fieldProxyParameters.clone();
        String[] symbols = exp.getSymbols();
        ModelUnitSystem modelUnitSystem = getReactionStep().getModel().getUnitSystem();
        for (int i = 0; symbols != null && i < symbols.length; i++) {
            SymbolTableEntry ste = reactionStep.getEntry(symbols[i]);
            if (ste == null) {
                newKineticsParameters = (KineticsParameter[]) BeanUtils.addElement(newKineticsParameters, new KineticsParameter(symbols[i], new Expression(0.0), ROLE_UserDefined, modelUnitSystem.getInstance_TBD()));
            }
        }
        parm.setExpression(exp);
        setKineticsParameters(newKineticsParameters);
        // setProxyParameters(newProxyParameters);
        exp.bindExpression(reactionStep);
        bBound = true;
    } finally {
        try {
            if (!bBound) {
                parm.setExpression(oldExpression);
            }
            cleanupParameters();
        } catch (ModelException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException(e.getMessage());
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException(e.getMessage());
        }
    }
}

Example 42 with PropertyVetoException

use of java.beans.PropertyVetoException in project vcell by virtualcell.

the class Model method createModelParameter.

public ModelParameter createModelParameter() {
    String globalParamName = null;
    int count = 0;
    while (true) {
        globalParamName = "g" + count;
        if (getModelParameter(globalParamName) == null) {
            break;
        }
        count++;
    }
    try {
        ModelParameter modelParameter = new ModelParameter(globalParamName, new Expression(0), Model.ROLE_UserDefined, unitSystem.getInstance_TBD());
        addModelParameter(modelParameter);
        return modelParameter;
    } catch (PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException(e.getMessage());
    }
}

Example 43 with PropertyVetoException

use of java.beans.PropertyVetoException in project vcell by virtualcell.

the class StochMathMapping_4_8 method refreshVariables.

/**
 * Map speciesContext to variable, used for structural analysis (slow reactions and fast reactions)
 * Creation date: (10/25/2006 8:59:43 AM)
 * @exception cbit.vcell.mapping.MappingException The exception description.
 */
private void refreshVariables() throws MappingException {
    // 
    // non-constant dependant variables(means rely on other contants/functions) require a function
    // 
    Enumeration<SpeciesContextMapping> enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = enum1.nextElement();
        SpeciesContextSpec scs = getSimulationContext().getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext());
        if (scm.getDependencyExpression() != null && !scs.isConstant()) {
            // scm.setVariable(new Function(scm.getSpeciesContext().getName(),scm.getDependencyExpression()));
            scm.setVariable(null);
        }
    }
    // 
    // non-constant independant variables require either a membrane or volume variable
    // 
    enum1 = getSpeciesContextMappings();
    // stochastic substance unit from modelUnitSystem
    ModelUnitSystem modelUnitSystem = getSimulationContext().getModel().getUnitSystem();
    VCUnitDefinition stochSubstanceUnit = modelUnitSystem.getStochasticSubstanceUnit();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
        SpeciesContextSpec scs = getSimulationContext().getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext());
        // stochastic variable is always a function of size.
        MathMapping_4_8.SpeciesCountParameter spCountParm = null;
        try {
            String countName = scs.getSpeciesContext().getName() + BIO_PARAM_SUFFIX_SPECIES_COUNT;
            Expression countExp = new Expression(0.0);
            spCountParm = addSpeciesCountParameter(countName, countExp, MathMapping_4_8.PARAMETER_ROLE_COUNT, stochSubstanceUnit, scs);
        } catch (PropertyVetoException pve) {
            pve.printStackTrace();
            throw new MappingException(pve.getMessage());
        }
        // add concentration of species as MathMappingParameter - this will map to species concentration function
        try {
            String concName = scs.getSpeciesContext().getName() + BIO_PARAM_SUFFIX_SPECIES_CONCENTRATION;
            Expression concExp = getExpressionAmtToConc(new Expression(spCountParm.getName()), scs.getSpeciesContext());
            concExp.bindExpression(this);
            addSpeciesConcentrationParameter(concName, concExp, MathMapping_4_8.PARAMETER_ROLE_CONCENRATION, scs.getSpeciesContext().getUnitDefinition(), scs);
        } catch (Exception e) {
            e.printStackTrace();
            throw new MappingException(e.getMessage());
        }
        if (scm.getDependencyExpression() == null && !scs.isConstant()) {
            scm.setVariable(new StochVolVariable(getMathSymbol(spCountParm, getSimulationContext().getGeometryContext().getStructureMapping(scs.getSpeciesContext().getStructure()))));
            mathSymbolMapping.put(scm.getSpeciesContext(), scm.getVariable().getName());
        }
    }
}

Example 44 with PropertyVetoException

use of java.beans.PropertyVetoException in project vcell by virtualcell.

the class OutputOptionsPanel method checkExplicitOutputTimes.

private boolean checkExplicitOutputTimes(ExplicitOutputTimeSpec ots) {
    boolean bValid = true;
    double startingTime = solverTaskDescription.getTimeBounds().getStartingTime();
    double endingTime = solverTaskDescription.getTimeBounds().getEndingTime();
    double[] times = ((ExplicitOutputTimeSpec) ots).getOutputTimes();
    if (times[0] < startingTime || times[times.length - 1] > endingTime) {
        bValid = false;
        String ret = PopupGenerator.showWarningDialog(OutputOptionsPanel.this, "Output times should be within [" + startingTime + "," + endingTime + "].\n\nChange ENDING TIME to " + times[times.length - 1] + "?", new String[] { UserMessage.OPTION_YES, UserMessage.OPTION_NO }, UserMessage.OPTION_YES);
        if (ret.equals(UserMessage.OPTION_YES)) {
            try {
                solverTaskDescription.setTimeBounds(new TimeBounds(startingTime, times[times.length - 1]));
                bValid = true;
            } catch (PropertyVetoException e) {
                e.printStackTrace(System.out);
                DialogUtils.showErrorDialog(OutputOptionsPanel.this, e.getMessage());
            }
        }
    }
    if (bValid) {
        getOutputTimesTextField().setBorder(UIManager.getBorder("TextField.border"));
    } else {
        getOutputTimesTextField().setBorder(GuiConstants.ProblematicTextFieldBorder);
        javax.swing.SwingUtilities.invokeLater(new Runnable() {

            public void run() {
                getOutputTimesTextField().requestFocus();
            }
        });
    }
    return bValid;
}

Example 45 with PropertyVetoException

use of java.beans.PropertyVetoException 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);
            }
        }
    }
}