Examples with SymbolTableEntry cbit.vcell.parser.SymbolTableEntry used on opensource projects

Example 16 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class AbstractMathMapping method getDefaultGeometryClass.

protected GeometryClass getDefaultGeometryClass(Expression expr) throws ExpressionException, MappingException {
    GeometryClass geometryClass = null;
    if (simContext.getGeometry().getDimension() == 0) {
        return null;
    }
    String[] symbols = expr.getSymbols();
    // if expr has no symbols, model param cannot be localized to a domain (its a const).
    if (symbols == null) {
        return null;
    } else {
        Expression modelParamExpr = substituteGlobalParameters(expr);
        symbols = modelParamExpr.getSymbols();
        for (int k = 0; symbols != null && k < symbols.length; k++) {
            Structure symbolStructure = null;
            SymbolTableEntry ste = modelParamExpr.getSymbolBinding(symbols[k]);
            if (ste instanceof SpeciesContext) {
                symbolStructure = ((SpeciesContext) ste).getStructure();
            } else if (ste instanceof StructureSize) {
                symbolStructure = ((StructureSize) ste).getStructure();
            } else if (ste instanceof MembraneVoltage) {
                symbolStructure = ((MembraneVoltage) ste).getMembrane();
            }
            if (symbolStructure != null) {
                StructureMapping sm = simContext.getGeometryContext().getStructureMapping(symbolStructure);
                GeometryClass symbolGeomClass = sm.getGeometryClass();
                if (geometryClass == null) {
                    geometryClass = symbolGeomClass;
                } else {
                    if (geometryClass != symbolGeomClass) {
                        if (geometryClass instanceof SurfaceClass) {
                            if (symbolGeomClass instanceof SurfaceClass) {
                                throw new MappingException("The expression '" + expr.infix() + "' references variables in surface domain '" + geometryClass.getName() + "' & surface domain '" + symbolGeomClass.getName() + "' that cannot be evaluated.");
                            } else if (symbolGeomClass instanceof SubVolume) {
                                // geomClass : surfaceClass; symbolGeomClass : subVol
                                if (!((SurfaceClass) geometryClass).isAdjacentTo((SubVolume) symbolGeomClass)) {
                                    throw new MappingException("The expression '" + expr.infix() + "' references variables in surface domain '" + geometryClass.getName() + "' & volume domain '" + symbolGeomClass.getName() + "' that cannot be evaluated.");
                                }
                            } else {
                                throw new MappingException("unexpected geometry class : " + symbolGeomClass.getClass());
                            }
                        } else if (geometryClass instanceof SubVolume) {
                            // geometryClass is a SubVolume
                            if (symbolGeomClass instanceof SubVolume) {
                                // check if adjacent; if so, choose separating membrane.
                                SurfaceClass surfaceClass = simContext.getGeometry().getGeometrySurfaceDescription().getSurfaceClass((SubVolume) symbolGeomClass, (SubVolume) geometryClass);
                                if (surfaceClass != null) {
                                    geometryClass = surfaceClass;
                                } else {
                                    throw new MappingException("The expression '" + expr.infix() + "' references variables in volume domain '" + geometryClass.getName() + "' & volume domain '" + symbolGeomClass.getName() + "' that cannot be evaluated.");
                                }
                            } else {
                                // geomClass : subVol; symbolGeomClass = surfaceClass
                                SurfaceClass surfaceSymbolGeomClass = (SurfaceClass) symbolGeomClass;
                                if (!surfaceSymbolGeomClass.isAdjacentTo((SubVolume) geometryClass)) {
                                    throw new MappingException("The expression '" + expr.infix() + "' references variables in surface domain '" + surfaceSymbolGeomClass.getName() + "' & volume domain '" + geometryClass.getName() + "' that cannot be evaluated.");
                                } else {
                                    geometryClass = symbolGeomClass;
                                }
                            }
                        } else {
                            throw new MappingException("unexpected geometry class : " + geometryClass.getClass());
                        }
                    }
                }
            }
        }
    }
    return geometryClass;
}

Example 17 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class BioEvent method gatherIssues.

public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    // check all event assignment symbols
    if (eventAssignmentList != null) {
        for (EventAssignment ea : eventAssignmentList) {
            // the target of the event assignment
            SymbolTableEntry ste = simulationContext.getEntry(ea.getTarget().getName());
            // SymbolTableEntry ste = parameterContext.getEntry(ea.getTarget().getName());
            if (ste == null) {
                String msg = "Missing Parameter '" + ea.getTarget().getName() + "' used in BioEvent '" + name + "'.";
                String tip = "Remove the Action containing the missing parameter from the BioEvent '" + name + "'.";
                issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, tip, Issue.Severity.ERROR));
                // found one issue on this event assignment, we show it and go to next
                break;
            }
            // the expression of the event assignment
            Expression exp = ea.assignmentExpression;
            String[] symbols = exp.getSymbols();
            if (symbols != null) {
                boolean found = false;
                for (String symbol : symbols) {
                    ste = simulationContext.getEntry(symbol);
                    if (ste == null) {
                        String msg = "Missing Symbol '" + symbol + "' in Assignment Expression for BioEvent '" + name + "'.";
                        String tip = "Remove the Action containing the missing Symbol from the Assignment Expression of the BioEvent '" + name + "'.";
                        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, tip, Issue.Severity.ERROR));
                        found = true;
                        break;
                    }
                }
                if (found == true) {
                    // found one issue on this event assignment, we show it and go to next
                    break;
                }
            }
        }
    } else {
        String msg = "No Action assigned to BioEvent '" + name + "'.";
        String tip = "Please assign an Action to the BioEvent '" + name + "'.";
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, tip, Issue.Severity.WARNING));
    }
    // check all trigger condition symbols
    for (LocalParameter lp : getEventParameters()) {
        if (lp.getExpression() != null && lp.getExpression().getSymbols() != null) {
            String[] symbols = lp.getExpression().getSymbols();
            boolean found = false;
            for (String symbol : symbols) {
                SymbolTableEntry ste = simulationContext.getEntry(symbol);
                if (ste == null) {
                    String msg = "Missing Symbol '" + symbol + "' in the Trigger Condition for BioEvent '" + name + "'.";
                    String tip = "Remove the Action containing the missing Symbol from the Trigger Condition of the BioEvent '" + name + "'.";
                    issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, tip, Issue.Severity.ERROR));
                    found = true;
                    break;
                }
            }
            if (found == true) {
                // found one issue with a parameter on this trigger condition, we show it and stop
                break;
            }
        }
    }
}

Example 18 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class BioEvent method generateTriggerExpression.

public Expression generateTriggerExpression() throws ExpressionException {
    SymbolTableEntry timeSymbolTableEntry = getSimulationContext().getModel().getTIME();
    Expression tExp = new Expression(timeSymbolTableEntry, getNameScope());
    switch(triggerType) {
        case GeneralTrigger:
            {
                return new Expression(getParameter(BioEventParameterType.GeneralTriggerFunction), getNameScope());
            }
        case ListOfTimes:
            {
                ArrayList<LocalParameter> timeParams = new ArrayList<LocalParameter>();
                for (LocalParameter p : parameterContext.getLocalParameters()) {
                    if (p.getRole() == BioEventParameterType.TimeListItem) {
                        timeParams.add(p);
                    }
                }
                if (timeParams.size() == 0) {
                    throw new RuntimeException("no times found for BioEvent " + getName());
                }
                // 
                if (timeParams.size() == 1) {
                    Expression timeParamExp = new Expression(timeParams.get(0), getNameScope());
                    return Expression.relational(">=", tExp, timeParamExp);
                }
                // 
                // if more than one, flatten time expressions to get list of doubles for event triggers.
                // these numbers are sorted to find the minimum distance between adjacent times.
                // epsilon is 1/2 of this inter-trigger time interval (to insert a falling edge between events)
                // 
                ArrayList<Double> timeValues = new ArrayList<Double>();
                for (LocalParameter p : timeParams) {
                    timeValues.add(MathUtilities.substituteModelParameters(p.getExpression(), getScopedSymbolTable()).flatten().evaluateConstant());
                }
                Collections.sort(timeValues);
                double epsilon = Double.MAX_VALUE;
                for (int i = 0; i < timeValues.size() - 1; i++) {
                    double absdiff = Math.abs(timeValues.get(i) - timeValues.get(i + 1));
                    epsilon = Math.min(epsilon, absdiff);
                }
                epsilon /= 2.0;
                // 
                // construct (((t >= t0) && (t <= t0+epsilon)) || ((t >= t1) && (t <= t1+epsilon)) || ((t >= t2) && (t <= t2+epsilon)))
                // 
                ArrayList<Expression> timeClauses = new ArrayList<Expression>();
                for (LocalParameter timeParam : timeParams) {
                    Expression timeParamExp = new Expression(timeParam, getNameScope());
                    Expression timeParamExpPlusEpsilon = Expression.add(timeParamExp, new Expression(epsilon));
                    timeClauses.add(Expression.and(Expression.relational(">=", tExp, timeParamExp), Expression.relational("<=", tExp, timeParamExpPlusEpsilon)));
                }
                if (timeClauses.size() == 1) {
                    return timeClauses.get(0);
                } else {
                    // put all individual time clauses together
                    return Expression.or(timeClauses.toArray(new Expression[timeClauses.size()]));
                }
            }
        case LinearRangeTimes:
        case LogRangeTimes:
            {
                // 
                // if more than one, flatten time expressions to get list of doubles for event triggers.
                // these numbers are sorted to find the minimum distance between adjacent times.
                // epsilon is 1/2 of this inter-trigger time interval (to insert a falling edge between events)
                // 
                LocalParameter firstTimeParam = getParameter(BioEventParameterType.RangeMinTime);
                LocalParameter lastTimeParam = getParameter(BioEventParameterType.RangeMaxTime);
                LocalParameter numTimesParam = getParameter(BioEventParameterType.RangeNumTimes);
                double firstTime = MathUtilities.substituteModelParameters(firstTimeParam.getExpression(), getScopedSymbolTable()).flatten().evaluateConstant();
                double lastTime = MathUtilities.substituteModelParameters(lastTimeParam.getExpression(), getScopedSymbolTable()).flatten().evaluateConstant();
                double numTimes = MathUtilities.substituteModelParameters(numTimesParam.getExpression(), getScopedSymbolTable()).flatten().evaluateConstant();
                Expression first = new Expression(firstTimeParam, getNameScope());
                Expression last = new Expression(lastTimeParam, getNameScope());
                Expression num = new Expression(numTimesParam, getNameScope());
                ArrayList<Expression> timeExps = new ArrayList<Expression>();
                ArrayList<Double> timeValues = new ArrayList<Double>();
                timeValues.add(firstTime);
                timeExps.add(first);
                if (getTriggerType() == TriggerType.LinearRangeTimes) {
                    double delta = (lastTime - firstTime) / (numTimes - 1);
                    Expression deltaExp = Expression.div(Expression.add(last, Expression.negate(first)), Expression.add(num, new Expression(-1)));
                    for (int i = 1; i < numTimes; i++) {
                        timeValues.add(firstTime + delta * i);
                        Expression eventTime = Expression.add(first, Expression.mult(deltaExp, new Expression(i)));
                        timeExps.add(eventTime);
                    }
                } else if (getTriggerType() == TriggerType.LogRangeTimes) {
                    double ratio = lastTime / firstTime;
                    Expression ratioExp = Expression.div(last, first);
                    double n_minus_1 = numTimes - 1;
                    Expression n_minus_1_exp = Expression.add(num, new Expression(-1));
                    for (int i = 1; i < numTimes; i++) {
                        timeValues.add(firstTime * Math.pow(ratio, i / n_minus_1));
                        timeExps.add(Expression.mult(first, Expression.power(ratioExp, Expression.div(new Expression(i), n_minus_1_exp))));
                    }
                }
                double epsilon = Double.MAX_VALUE;
                for (int i = 0; i < timeValues.size() - 1; i++) {
                    double absdiff = Math.abs(timeValues.get(i) - timeValues.get(i + 1));
                    epsilon = Math.min(epsilon, absdiff);
                }
                epsilon /= 2.0;
                // 
                // construct (((t >= t0) && (t <= t0+epsilon)) || ((t >= t1) && (t <= t1+epsilon)) || ((t >= t2) && (t <= t2+epsilon)))
                // 
                ArrayList<Expression> timeClauses = new ArrayList<Expression>();
                for (Expression timeExp : timeExps) {
                    Expression timeExpPlusEpsilon = Expression.add(timeExp, new Expression(epsilon));
                    timeClauses.add(Expression.and(Expression.relational(">=", tExp, timeExp), Expression.relational("<=", tExp, timeExpPlusEpsilon)));
                }
                if (timeClauses.size() == 1) {
                    return timeClauses.get(0);
                } else {
                    // put all individual time clauses together
                    return Expression.or(timeClauses.toArray(new Expression[timeClauses.size()]));
                }
            }
        case ObservableAboveThreshold:
            {
                Expression highTrigger = Expression.relational(">=", new Expression(getParameter(BioEventParameterType.Observable), getNameScope()), new Expression(getParameter(BioEventParameterType.Threshold), getNameScope()));
                return highTrigger;
            }
        case ObservableBelowThreshold:
            {
                Expression lowTrigger = Expression.relational("<=", new Expression(getParameter(BioEventParameterType.Observable), getNameScope()), new Expression(getParameter(BioEventParameterType.Threshold), getNameScope()));
                return lowTrigger;
            }
        case SingleTriggerTime:
            {
                SymbolTableEntry time = getSimulationContext().getModel().getTIME();
                return Expression.relational(">=", new Expression(time, getNameScope()), new Expression(getParameter(BioEventParameterType.SingleTriggerTime), getNameScope()));
            }
        default:
            {
                throw new RuntimeException("unexpected triggerType " + getTriggerType());
            }
    }
}

Example 19 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry 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 20 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class MassActionSolver method substituteParameters.

public static Expression substituteParameters(Expression exp, boolean substituteConst) throws ExpressionException {
    Expression result = new Expression(exp);
    boolean bSubstituted = true;
    while (bSubstituted) {
        bSubstituted = false;
        String[] symbols = result.getSymbols();
        for (int k = 0; symbols != null && k < symbols.length; k++) {
            SymbolTableEntry ste = result.getSymbolBinding(symbols[k]);
            if (ste instanceof ProxyParameter) {
                ProxyParameter pp = (ProxyParameter) ste;
                result.substituteInPlace(new Expression(pp, pp.getNameScope()), new Expression(pp.getTarget(), pp.getTarget().getNameScope()));
                bSubstituted = true;
            } else if (ste instanceof Parameter) {
                Parameter kp = (Parameter) ste;
                try {
                    Expression expKP = kp.getExpression();
                    if (!expKP.flatten().isNumeric() || substituteConst) {
                        result.substituteInPlace(new Expression(symbols[k]), new Expression(kp.getExpression()));
                        bSubstituted = true;
                    }
                } catch (ExpressionException e1) {
                    e1.printStackTrace();
                    throw new ExpressionException(e1.getMessage());
                }
            } else if (substituteConst && ste instanceof Model.ReservedSymbol) {
                Model.ReservedSymbol rs = (Model.ReservedSymbol) ste;
                try {
                    if (rs.getExpression() != null) {
                        result.substituteInPlace(new Expression(symbols[k]), new Expression(rs.getExpression()));
                        bSubstituted = true;
                    }
                } catch (ExpressionException e1) {
                    e1.printStackTrace();
                    throw new ExpressionException(e1.getMessage());
                }
            }
        }
    }
    return result;
}