Examples with AssignmentRule cbit.vcell.mapping.AssignmentRule used on opensource projects

Example 11 with AssignmentRule

use of cbit.vcell.mapping.AssignmentRule in project vcell by virtualcell.

the class SimulationWorkspaceModelInfo method addAssignmentRuleParametersToMetaData.

private static void addAssignmentRuleParametersToMetaData(SimulationContext simulationContext, HashMap<String, DataSymbolMetadata> metaDataMap) {
    if (metaDataMap != null && simulationContext.getAssignmentRules() != null) {
        for (AssignmentRule ar : simulationContext.getAssignmentRules()) {
            if (ar.getAssignmentRuleVar() instanceof Model.ModelParameter) {
                Model.ModelParameter mp = (Model.ModelParameter) ar.getAssignmentRuleVar();
                VCUnitDefinition unit = mp.getUnitDefinition();
                String tooltip = "Assignment Rule Variable (ModelParameter), Function";
                DataSymbolMetadata dsmd = new DataSymbolMetadata(BioModelCategoryType.Other, unit, tooltip);
                metaDataMap.put(mp.getName(), dsmd);
            }
        }
    }
}

Example 12 with AssignmentRule

use of cbit.vcell.mapping.AssignmentRule in project vcell by virtualcell.

the class SpeciesContextSpecsTableModel method isCellEditable.

/**
 * Insert the method's description here.
 * Creation date: (2/24/01 12:27:46 AM)
 * @return boolean
 * @param rowIndex int
 * @param columnIndex int
 */
public boolean isCellEditable(int rowIndex, int columnIndex) {
    SpeciesContextSpec speciesContextSpec = getValueAt(rowIndex);
    ColumnType columnType = columns.get(columnIndex);
    switch(columnType) {
        case COLUMN_SPECIESCONTEXT:
            {
                return false;
            }
        case COLUMN_STRUCTURE:
            {
                return false;
            }
        case COLUMN_DEPICTION:
            {
                return false;
            }
        case COLUMN_CLAMPED:
            {
                return true;
            }
        case COLUMN_RULES:
            {
                return false;
            }
        case COLUMN_WELLMIXED:
            {
                return !speciesContextSpec.isConstant() && !getSimulationContext().isStoch();
            }
        case COLUMN_FORCECONTINUOUS:
            {
                return !speciesContextSpec.isConstant() && getSimulationContext().isStoch();
            }
        case COLUMN_INITIAL:
            {
                // RateRule rr = fieldSimulationContext.getRateRule(speciesContextSpec.getSpeciesContext());
                AssignmentRule ar = fieldSimulationContext.getAssignmentRule(speciesContextSpec.getSpeciesContext());
                if (/*rr != null || */
                ar != null) {
                    return false;
                }
                return true;
            }
        case COLUMN_DIFFUSION:
            {
                return !speciesContextSpec.isConstant() && (!speciesContextSpec.isWellMixed() || getSimulationContext().isStoch());
            }
        default:
            {
                return false;
            }
    }
}

Example 13 with AssignmentRule

use of cbit.vcell.mapping.AssignmentRule in project vcell by virtualcell.

the class SpeciesContextSpecsTableModel 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 ReactionContext && evt.getPropertyName().equals("speciesContextSpecs")) {
        updateListenersReactionContext((ReactionContext) evt.getSource(), true);
        updateListenersReactionContext((ReactionContext) evt.getSource(), false);
        refreshData();
    }
    if (evt.getSource() instanceof SpeciesContext && evt.getPropertyName().equals("name")) {
        fireTableRowsUpdated(0, getRowCount() - 1);
    }
    if (evt.getSource() == getSimulationContext() && evt.getPropertyName().equals(SimulationContext.PROPERTY_NAME_ASSIGNMENT_RULE_CHANGE)) {
        AssignmentRule oldRule = (AssignmentRule) evt.getOldValue();
        AssignmentRule newRule = (AssignmentRule) evt.getNewValue();
        onAssignmentRuleVariableChanged(oldRule, newRule);
    } else if (evt.getSource() == getSimulationContext() && evt.getPropertyName().equals(SimulationContext.PROPERTY_NAME_RATE_RULE_CHANGE)) {
        RateRule oldRule = (RateRule) evt.getOldValue();
        RateRule newRule = (RateRule) evt.getNewValue();
        onRateRuleVariableChanged(oldRule, newRule);
    } else if (evt.getSource() == getSimulationContext() && evt.getPropertyName().equals(SimulationContext.PROPERTY_NAME_ASSIGNMENTRULES)) {
        System.out.println(evt.getPropertyName());
        AssignmentRule[] oldRules = (AssignmentRule[]) evt.getOldValue();
        AssignmentRule[] newRules = (AssignmentRule[]) evt.getNewValue();
        if (oldRules != null && newRules != null && oldRules.length > newRules.length) {
            onAssignmentRuleDelete(oldRules, newRules);
        }
    } else if (evt.getSource() == getSimulationContext() && evt.getPropertyName().equals(SimulationContext.PROPERTY_NAME_RATERULES)) {
        System.out.println(evt.getPropertyName());
        RateRule[] oldRules = (RateRule[]) evt.getOldValue();
        RateRule[] newRules = (RateRule[]) evt.getNewValue();
        if (oldRules != null && newRules != null && oldRules.length > newRules.length) {
            onRateRuleDelete(oldRules, newRules);
        }
    }
    if (evt.getSource() instanceof SpeciesContextSpec) {
        fireTableRowsUpdated(0, getRowCount() - 1);
    }
    if (evt.getSource() instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
        fireTableRowsUpdated(0, getRowCount() - 1);
    }
    if (evt.getSource() instanceof GeometryContext) {
        refreshColumns();
        fireTableStructureChanged();
    }
}

Example 14 with AssignmentRule

use of cbit.vcell.mapping.AssignmentRule in project vcell by virtualcell.

the class SpeciesContextSpecsTableModel method onAssignmentRuleDelete.

private void onAssignmentRuleDelete(AssignmentRule[] oldRules, AssignmentRule[] newRules) {
    System.out.println("old: " + oldRules.length + ", new: " + newRules.length);
    AssignmentRule deleted = null;
    for (AssignmentRule candidate : oldRules) {
        boolean found = false;
        for (AssignmentRule rule : newRules) {
            if (candidate.getName().equals(rule.getName())) {
                found = true;
                break;
            }
        }
        if (found == false) {
            deleted = candidate;
            break;
        }
    }
    if (deleted == null || deleted.getSimulationContext() != fieldSimulationContext) {
        return;
    }
    SymbolTableEntry ste = deleted.getAssignmentRuleVar();
    if (ste instanceof SpeciesContext) {
        SpeciesContext sc = (SpeciesContext) ste;
        removeRuleVariableMark(sc, true);
    }
}

Example 15 with AssignmentRule

use of cbit.vcell.mapping.AssignmentRule in project vcell by virtualcell.

the class ModelUnitConverter method createBioModelWithNewUnitSystem.

public static BioModel createBioModelWithNewUnitSystem(BioModel oldBioModel, ModelUnitSystem newUnitSystem) throws ExpressionException, XmlParseException {
    // new BioModel has new unit system applied to all built-in units ... but expressions still need to be corrected (see below).
    String biomodelXMLString = XmlHelper.bioModelToXML(oldBioModel);
    XMLSource newXMLSource = new XMLSource(biomodelXMLString);
    BioModel newBioModel = XmlHelper.XMLToBioModel(newXMLSource, true, newUnitSystem);
    Model newModel = newBioModel.getModel();
    Model oldModel = oldBioModel.getModel();
    for (Parameter p : newBioModel.getModel().getModelParameters()) {
        convertVarsWithUnitFactors(oldBioModel.getModel(), newBioModel.getModel(), p);
    }
    for (ReactionStep reactionStep : newBioModel.getModel().getReactionSteps()) {
        SymbolTable oldSymbolTable = oldBioModel.getModel().getReactionStep(reactionStep.getName());
        SymbolTable newSymbolTable = reactionStep;
        for (Parameter p : reactionStep.getKinetics().getUnresolvedParameters()) {
            convertVarsWithUnitFactors(oldSymbolTable, newSymbolTable, p);
        }
        for (Parameter p : reactionStep.getKinetics().getKineticsParameters()) {
            convertVarsWithUnitFactors(oldSymbolTable, newSymbolTable, p);
        }
        Kinetics kinetics = reactionStep.getKinetics();
        KineticsParameter kineticsParameter = null;
        if (kinetics.getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate) != null) {
            kineticsParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate);
        } else if (kinetics.getKineticsParameterFromRole(Kinetics.ROLE_LumpedReactionRate) != null) {
            kineticsParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_LumpedReactionRate);
        } else {
            throw new RuntimeException("Role 'reaction rate' or role 'lumped reaction rate' expected");
        }
        Expression rateExpression = kineticsParameter.getExpression();
        jscl.math.Expression jsclExpression = null;
        String jsclExpressionString = rateExpression.infix_JSCL();
        try {
            jsclExpression = jscl.math.Expression.valueOf(jsclExpressionString);
        } catch (jscl.text.ParseException e) {
            e.printStackTrace(System.out);
            System.out.println("JSCL couldn't parse \"" + jsclExpressionString + "\"");
            return null;
        }
        jscl.math.Generic g1 = jsclExpression.expand().simplify();
        Expression newRate = new Expression(SymbolUtils.getRestoredStringJSCL(g1.toString()));
        newRate.bindExpression(reactionStep);
        // reactionStep.getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate).setExpression(newRate.flatten());
        if (reactionStep.getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate) != null) {
            reactionStep.getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate).setExpression(newRate.flatten());
        }
    }
    for (ReactionRule reactionRule : newBioModel.getModel().getRbmModelContainer().getReactionRuleList()) {
        SymbolTable oldSymbolTable = oldBioModel.getModel().getRbmModelContainer().getReactionRule(reactionRule.getName()).getKineticLaw().getScopedSymbolTable();
        SymbolTable newSymbolTable = reactionRule.getKineticLaw().getScopedSymbolTable();
        for (Parameter p : reactionRule.getKineticLaw().getUnresolvedParameters()) {
            convertVarsWithUnitFactors(oldSymbolTable, newSymbolTable, p);
        }
        for (Parameter p : reactionRule.getKineticLaw().getLocalParameters()) {
            convertVarsWithUnitFactors(oldSymbolTable, newSymbolTable, p);
        }
    }
    for (SimulationContext simContext : newBioModel.getSimulationContexts()) {
        SimulationContext oldSimContext = oldBioModel.getSimulationContext(simContext.getName());
        // ArrayList<Parameter> parameterList = new ArrayList<Parameter>();
        for (StructureMapping mapping : simContext.getGeometryContext().getStructureMappings()) {
            Structure oldStructure = oldModel.getStructure(mapping.getStructure().getName());
            StructureMapping oldMapping = oldSimContext.getGeometryContext().getStructureMapping(oldStructure);
            for (Parameter p : mapping.computeApplicableParameterList()) {
                convertVarsWithUnitFactors(oldMapping, mapping, p);
            }
        }
        for (SpeciesContextSpec spec : simContext.getReactionContext().getSpeciesContextSpecs()) {
            SpeciesContext oldSpeciesContext = oldModel.getSpeciesContext(spec.getSpeciesContext().getName());
            SpeciesContextSpec oldSpec = oldSimContext.getReactionContext().getSpeciesContextSpec(oldSpeciesContext);
            for (Parameter p : spec.computeApplicableParameterList()) {
                convertVarsWithUnitFactors(oldSpec, spec, p);
            }
        }
        for (int i = 0; i < simContext.getElectricalStimuli().length; i++) {
            ElectricalStimulus newElectricalStimulus = simContext.getElectricalStimuli()[i];
            ElectricalStimulus oldElectricalStimulus = oldSimContext.getElectricalStimuli()[i];
            for (Parameter p : newElectricalStimulus.getParameters()) {
                convertVarsWithUnitFactors(oldElectricalStimulus.getNameScope().getScopedSymbolTable(), newElectricalStimulus.getNameScope().getScopedSymbolTable(), p);
            }
        }
        // convert events : trigger and delay parameters and event assignments
        for (int i = 0; simContext.getBioEvents() != null && oldSimContext.getBioEvents() != null && i < simContext.getBioEvents().length; i++) {
            BioEvent newBioEvent = simContext.getBioEvents()[i];
            BioEvent oldBioEvent = oldSimContext.getBioEvent(newBioEvent.getName());
            for (Parameter p : newBioEvent.getEventParameters()) {
                convertVarsWithUnitFactors(oldBioEvent.getNameScope().getScopedSymbolTable(), newBioEvent.getNameScope().getScopedSymbolTable(), p);
            }
            // for each event assignment expression
            for (int e = 0; e < newBioEvent.getEventAssignments().size(); e++) {
                ScopedSymbolTable newSymbolTable = newBioEvent.getNameScope().getScopedSymbolTable();
                ScopedSymbolTable oldSymbolTable = oldBioEvent.getNameScope().getScopedSymbolTable();
                EventAssignment newEventAssignment = newBioEvent.getEventAssignments().get(e);
                EventAssignment oldEventAssignment = oldBioEvent.getEventAssignments().get(e);
                VCUnitDefinition oldTargetUnit = oldEventAssignment.getTarget().getUnitDefinition();
                VCUnitDefinition newTargetUnit = newEventAssignment.getTarget().getUnitDefinition();
                Expression eventAssgnExpr = newEventAssignment.getAssignmentExpression();
                convertExprWithUnitFactors(oldSymbolTable, newSymbolTable, oldTargetUnit, newTargetUnit, eventAssgnExpr);
            }
        }
        /**
         * @TODO: If rate rule variable unit is TBD, we still need to handle the rate expression unit.
         */
        // convert rate rules
        RateRule[] rateRules = simContext.getRateRules();
        if (rateRules != null && rateRules.length > 0) {
            for (RateRule rateRule : rateRules) {
                RateRule oldRateRule = oldSimContext.getRateRule(rateRule.getName());
                ScopedSymbolTable oldSymbolTable = oldRateRule.getSimulationContext();
                ScopedSymbolTable newSymbolTable = rateRule.getSimulationContext();
                VCUnitDefinition oldTargetUnit = oldRateRule.getRateRuleVar().getUnitDefinition();
                VCUnitDefinition newTargetUnit = rateRule.getRateRuleVar().getUnitDefinition();
                Expression rateRuleExpr = rateRule.getRateRuleExpression();
                convertExprWithUnitFactors(oldSymbolTable, newSymbolTable, oldTargetUnit, newTargetUnit, rateRuleExpr);
            }
        }
        AssignmentRule[] assignmentRules = simContext.getAssignmentRules();
        if (assignmentRules != null && assignmentRules.length > 0) {
            for (AssignmentRule assignmentRule : assignmentRules) {
                AssignmentRule oldAssignRule = oldSimContext.getAssignmentRule(assignmentRule.getName());
                ScopedSymbolTable oldSymbolTable = oldAssignRule.getSimulationContext();
                ScopedSymbolTable newSymbolTable = assignmentRule.getSimulationContext();
                VCUnitDefinition oldTargetUnit = oldAssignRule.getAssignmentRuleVar().getUnitDefinition();
                VCUnitDefinition newTargetUnit = assignmentRule.getAssignmentRuleVar().getUnitDefinition();
                Expression assignmentRuleExpr = assignmentRule.getAssignmentRuleExpression();
                convertExprWithUnitFactors(oldSymbolTable, newSymbolTable, oldTargetUnit, newTargetUnit, assignmentRuleExpr);
            }
        }
    }
    // end  for - simulationContext
    return newBioModel;
}