Examples with LocalParameter cbit.vcell.mapping.ParameterContext.LocalParameter used on opensource projects

Example 41 with LocalParameter

use of cbit.vcell.mapping.ParameterContext.LocalParameter in project vcell by virtualcell.

the class RbmKineticLaw method clone.

public static void clone(RbmKineticLaw toKineticLaw, ReactionRule fromRule, ReactionRule toRule) {
    RbmKineticLaw fromKineticLaw = fromRule.getKineticLaw();
    Model toModel = toRule.getModel();
    Model fromModel = fromRule.getModel();
    try {
        for (LocalParameter fromLocalParameter : fromKineticLaw.parameterContext.getLocalParameters()) {
            if (fromLocalParameter.getRole() != RbmKineticLawParameterType.UserDefined) {
                // find built-in parameter with same role and copy expression.
                // copy name also in case it was changed.
                LocalParameter toLocalParameter = toKineticLaw.parameterContext.getLocalParameterFromRole(fromLocalParameter.getRole());
                String toName = new String(fromLocalParameter.getName());
                if (!toName.equals(toLocalParameter.getName())) {
                    // new name must be different from existing name, no point to rename otherwise
                    toLocalParameter.setName(toName);
                }
                Expression fromExpression = fromLocalParameter.getExpression();
                if (fromExpression != null) {
                    Expression toExpression = new Expression(fromExpression);
                    toKineticLaw.setParameterValue(toLocalParameter, toExpression, true);
                }
            // TODO: units are not updated!
            }
        }
        for (LocalParameter fromLocalParameter : fromKineticLaw.parameterContext.getLocalParameters()) {
            if (fromLocalParameter.getRole() == RbmKineticLawParameterType.UserDefined) {
                LocalParameter toLocalParameter = toKineticLaw.getLocalParameter(fromLocalParameter.getName());
                if (toLocalParameter == null) {
                    // 
                    // after lazy parameter creation we didn't find a user-defined rule parameter with this same name.
                    // 
                    // there must be a global symbol with the same name, that the local reaction parameter has overridden.
                    // 
                    ParameterContext.LocalProxyParameter rule_proxy_parameter = null;
                    for (ProxyParameter proxyParameter : fromKineticLaw.getProxyParameters()) {
                        if (proxyParameter.getName().equals(fromLocalParameter.getName())) {
                            rule_proxy_parameter = (LocalProxyParameter) proxyParameter;
                        }
                    }
                    if (rule_proxy_parameter != null) {
                        // we want to convert to local
                        boolean bConvertToGlobal = false;
                        toKineticLaw.convertParameterType(rule_proxy_parameter, bConvertToGlobal);
                    } else {
                        // could find neither local parameter nor proxy parameter
                        throw new RuntimeException("user defined parameter " + fromLocalParameter.getName() + " from reactionRule " + fromRule.getName() + " didn't map to a reactionRule parameter");
                    }
                } else if (toLocalParameter.getRole() == RbmKineticLawParameterType.UserDefined) {
                    Expression expression = fromLocalParameter.getExpression();
                    if (expression != null) {
                        toKineticLaw.setParameterValue(toLocalParameter, expression, true);
                    }
                // TODO: make copy constructor for VCUnitDefinition
                // VCUnitDefinition toUnitDefinition = new VCUnitDefinition(fromLocalParameter.getUnitDefinition());
                // toLocalParameter.setUnitDefinition(toUnitDefinition);
                } else {
                    throw new RuntimeException("user defined parameter " + fromLocalParameter.getName() + " from reactionRule " + fromRule.getName() + " mapped to a reactionRule parameter with unexpected role " + toLocalParameter.getRole().getDescription());
                }
            }
        }
    // TODO: some params were assumed to be local but they are global in the 'from'
    // need to find if we have a global with same name, rename at need and make it global
    } catch (PropertyVetoException | ExpressionException e) {
        e.printStackTrace();
        throw new RuntimeException("Problem attempting to set RbmKineticLaw expression: " + e.getMessage());
    }
}

Example 42 with LocalParameter

use of cbit.vcell.mapping.ParameterContext.LocalParameter in project vcell by virtualcell.

the class RbmKineticLaw method duplicate.

public static void duplicate(RbmKineticLaw to, ReactionRule fromRule) {
    RbmKineticLaw from = fromRule.getKineticLaw();
    try {
        for (LocalParameter fromLocalParameter : from.parameterContext.getLocalParameters()) {
            if (fromLocalParameter.getRole() != RbmKineticLawParameterType.UserDefined) {
                // find built-in parameter with same role and copy expression.
                // copy name also in case it was changed.
                LocalParameter toLocalParameter = to.parameterContext.getLocalParameterFromRole(fromLocalParameter.getRole());
                toLocalParameter.setName(fromLocalParameter.getName());
                Expression expression = fromLocalParameter.getExpression();
                if (expression != null) {
                    to.setParameterValue(toLocalParameter, new Expression(expression), true);
                }
            }
        }
        for (LocalParameter fromLocalParameter : from.parameterContext.getLocalParameters()) {
            if (fromLocalParameter.getRole() == RbmKineticLawParameterType.UserDefined) {
                LocalParameter toLocalParameter = to.getLocalParameter(fromLocalParameter.getName());
                if (toLocalParameter == null) {
                    // 
                    // after lazy parameter creation we didn't find a user-defined rule parameter with this same name.
                    // 
                    // there must be a global symbol with the same name, that the local reaction parameter has overridden.
                    // 
                    ParameterContext.LocalProxyParameter rule_proxy_parameter = null;
                    for (ProxyParameter proxyParameter : from.getProxyParameters()) {
                        if (proxyParameter.getName().equals(fromLocalParameter.getName())) {
                            rule_proxy_parameter = (LocalProxyParameter) proxyParameter;
                        }
                    }
                    if (rule_proxy_parameter != null) {
                        // we want to convert to local
                        boolean bConvertToGlobal = false;
                        to.convertParameterType(rule_proxy_parameter, bConvertToGlobal);
                    } else {
                        // could find neither local parameter nor proxy parameter
                        throw new RuntimeException("user defined parameter " + fromLocalParameter.getName() + " from reactionRule " + fromRule.getName() + " didn't map to a reactionRule parameter");
                    }
                } else if (toLocalParameter.getRole() == RbmKineticLawParameterType.UserDefined) {
                    Expression expression = fromLocalParameter.getExpression();
                    if (expression != null) {
                        to.setParameterValue(toLocalParameter, expression, true);
                    }
                    toLocalParameter.setUnitDefinition(fromLocalParameter.getUnitDefinition());
                } else {
                    throw new RuntimeException("user defined parameter " + fromLocalParameter.getName() + " from reactionRule " + fromRule.getName() + " mapped to a reactionRule parameter with unexpected role " + toLocalParameter.getRole().getDescription());
                }
            }
        }
    } catch (PropertyVetoException | ExpressionException e) {
        e.printStackTrace();
        throw new RuntimeException("Problem attempting to set RbmKineticLaw expression: " + e.getMessage());
    }
}

Example 43 with LocalParameter

use of cbit.vcell.mapping.ParameterContext.LocalParameter in project vcell by virtualcell.

the class RbmKineticLaw method refreshUnits.

protected void refreshUnits() {
    if (bRefreshingUnits) {
        return;
    }
    try {
        bRefreshingUnits = true;
        ModelUnitSystem modelUnitSystem = reactionRule.getModel().getUnitSystem();
        LocalParameter rateParm = getLocalParameter(RbmKineticLawParameterType.RuleRate);
        if (reactionRule.getStructure() instanceof Feature) {
            rateParm.setUnitDefinition(modelUnitSystem.getVolumeReactionRateUnit());
        } else if (reactionRule.getStructure() instanceof Membrane) {
            rateParm.setUnitDefinition(modelUnitSystem.getMembraneReactionRateUnit());
        }
        switch(this.rateLawType) {
            case MassAction:
                {
                    LocalParameter forwardRateParm = getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate);
                    LocalParameter reverseRateParm = getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate);
                    // since units for kinetic parameters are set from model's unit system, if model is null (possible when model is not yet set on reactionStep when reading from XML)
                    // don't worry about setting units on kinetic parameters. Call this method when model is set on reactionStep (rebindToModel()).
                    Model model = reactionRule.getModel();
                    if (model != null) {
                        // if (reactionRule.getStructure() instanceof Membrane){
                        // rateParm.setUnitDefinition(modelUnitSystem.getMembraneReactionRateUnit());
                        // if (currentDensityParm!=null){
                        // currentDensityParm.setUnitDefinition(modelUnitSystem.getCurrentDensityUnit());
                        // }
                        // KineticsParameter chargeValenceParm = getChargeValenceParameter();
                        // if (chargeValenceParm!=null){
                        // chargeValenceParm.setUnitDefinition(modelUnitSystem.getInstance_DIMENSIONLESS());
                        // }
                        // }else if (getReactionStep().getStructure() instanceof Feature){
                        // rateParm.setUnitDefinition(modelUnitSystem.getVolumeReactionRateUnit());
                        // }else{
                        // throw new RuntimeException("unexpected structure type "+getReactionStep().getStructure()+" in MassActionKinetics.refreshUnits()");
                        // }
                        cbit.vcell.units.VCUnitDefinition kfUnits = rateParm.getUnitDefinition();
                        cbit.vcell.units.VCUnitDefinition krUnits = rateParm.getUnitDefinition();
                        for (ReactantPattern reactantPattern : reactionRule.getReactantPatterns()) {
                            VCUnitDefinition reactantUnit = modelUnitSystem.getConcentrationUnit(reactantPattern.getStructure());
                            kfUnits = kfUnits.divideBy(reactantUnit);
                        }
                        for (ProductPattern productPattern : reactionRule.getProductPatterns()) {
                            VCUnitDefinition productUnit = modelUnitSystem.getConcentrationUnit(productPattern.getStructure());
                            krUnits = krUnits.divideBy(productUnit);
                        }
                        if (forwardRateParm != null && !kfUnits.compareEqual(forwardRateParm.getUnitDefinition())) {
                            forwardRateParm.setUnitDefinition(kfUnits);
                        }
                        if (reverseRateParm != null && !krUnits.compareEqual(reverseRateParm.getUnitDefinition())) {
                            reverseRateParm.setUnitDefinition(krUnits);
                        }
                    }
                    break;
                }
        }
    // end switch (rateLawType)
    } finally {
        bRefreshingUnits = false;
    }
}

Example 44 with LocalParameter

use of cbit.vcell.mapping.ParameterContext.LocalParameter in project vcell by virtualcell.

the class ReactionRule method deriveInverseRule.

// returns a new rule consisting of the "inverse" part of the reversible old rule
public static ReactionRule deriveInverseRule(ReactionRule oldRule) throws ExpressionBindingException, PropertyVetoException {
    Model m = oldRule.getModel();
    Structure s = oldRule.getStructure();
    boolean bR = false;
    String newName = oldRule.getDisplayName() + InverseHalf;
    ReactionRule newRule = new ReactionRule(m, newName, s, bR);
    RbmKineticLaw oldLaw = oldRule.getKineticLaw();
    RateLawType rateLawType = oldLaw.getRateLawType();
    if (rateLawType != RateLawType.MassAction) {
        throw new RuntimeException("Only Mass Action Kinetics supported at this time, " + ReactionRule.typeName + " \"" + oldRule.getName() + "\" uses kinetic law type \"" + rateLawType.toString() + "\"");
    }
    RbmKineticLaw newLaw = new RbmKineticLaw(newRule, rateLawType);
    newRule.setKineticLaw(newLaw);
    LocalParameter oldfr = oldLaw.getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate);
    Expression exp = oldfr.getExpression();
    newLaw.setLocalParameterValue(RbmKineticLawParameterType.MassActionForwardRate, exp);
    for (ReactantPattern oldrp : oldRule.getReactantPatterns()) {
        SpeciesPattern newsp = new SpeciesPattern(m, oldrp.getSpeciesPattern());
        ProductPattern newrp = new ProductPattern(newsp, oldrp.getStructure());
        newRule.addProduct(newrp, false, false);
    }
    for (ProductPattern oldpp : oldRule.getProductPatterns()) {
        SpeciesPattern newsp = new SpeciesPattern(m, oldpp.getSpeciesPattern());
        ReactantPattern newpp = new ReactantPattern(newsp, oldpp.getStructure());
        newRule.addReactant(newpp, false, false);
    }
    newLaw.bind(newRule);
    return newRule;
}

Example 45 with LocalParameter

use of cbit.vcell.mapping.ParameterContext.LocalParameter in project vcell by virtualcell.

the class StimulusTable method getSQLValueList.

/**
 * This method was created in VisualAge.
 * @return java.lang.String
 * @param key KeyValue
 * @param modelName java.lang.String
 */
public String getSQLValueList(InsertHashtable hash, KeyValue Key, KeyValue simContextKey, ElectricalStimulus stimulus) throws DataAccessException {
    KeyValue structureKey = hash.getDatabaseKey(stimulus.getElectrode().getFeature());
    if (structureKey == null) {
        structureKey = stimulus.getElectrode().getFeature().getKey();
        if (structureKey == null) {
            throw new DataAccessException("no key for structure " + stimulus.getElectrode().getFeature());
        }
    }
    Expression exp = null;
    int stimulusType = UNKNOWN_STIMULUS;
    if (stimulus instanceof CurrentDensityClampStimulus) {
        stimulusType = CURRENTDENSITY_CLAMP_STIMULUS;
        LocalParameter currentDensityParameter = ((CurrentDensityClampStimulus) stimulus).getCurrentDensityParameter();
        exp = currentDensityParameter.getExpression();
    } else if (stimulus instanceof TotalCurrentClampStimulus) {
        stimulusType = TOTALCURRENT_CLAMP_STIMULUS;
        LocalParameter totalCurrentParameter = ((TotalCurrentClampStimulus) stimulus).getCurrentParameter();
        exp = totalCurrentParameter.getExpression();
    } else if (stimulus instanceof VoltageClampStimulus) {
        stimulusType = VOLTAGE_CLAMP_STIMULUS;
        LocalParameter voltageParameter = ((VoltageClampStimulus) stimulus).getVoltageParameter();
        exp = voltageParameter.getExpression();
    } else {
        throw new DataAccessException("storage for Stimulus type " + stimulus.getClass().getName() + " not yet supported");
    }
    java.io.StringWriter esParameterWriter = new java.io.StringWriter();
    java.io.PrintWriter pw = new java.io.PrintWriter(esParameterWriter);
    stimulus.parameterVCMLWrite(pw);
    pw.flush();
    pw.close();
    StringBuffer buffer = new StringBuffer();
    buffer.append("(");
    buffer.append(Key + ",");
    buffer.append(structureKey + ",");
    buffer.append(simContextKey + ",");
    buffer.append("'" + stimulus.getName() + "',");
    buffer.append(stimulusType + ",");
    buffer.append("'" + TokenMangler.getSQLEscapedString(exp.infix()) + "',");
    buffer.append(stimulus.getElectrode().getPosition().getX() + ",");
    buffer.append(stimulus.getElectrode().getPosition().getY() + ",");
    buffer.append(stimulus.getElectrode().getPosition().getZ() + ",");
    buffer.append("'" + TokenMangler.getSQLEscapedString(esParameterWriter.getBuffer().toString()) + "'");
    buffer.append(")");
    return buffer.toString();
}