Examples with Event cbit.vcell.math.Event used on opensource projects

Example 6 with Event

use of cbit.vcell.math.Event in project vcell by virtualcell.

the class XmlReader method getEvent.

private Event getEvent(MathDescription mathdesc, Element eventElement) throws XmlParseException {
    String name = unMangle(eventElement.getAttributeValue(XMLTags.NameAttrTag));
    Element element = eventElement.getChild(XMLTags.TriggerTag, vcNamespace);
    Expression triggerExp = unMangleExpression(element.getText());
    element = eventElement.getChild(XMLTags.DelayTag, vcNamespace);
    Delay delay = null;
    if (element != null) {
        boolean useValuesFromTriggerTime = Boolean.valueOf(element.getAttributeValue(XMLTags.UseValuesFromTriggerTimeAttrTag)).booleanValue();
        Expression durationExp = unMangleExpression(element.getText());
        delay = new Delay(useValuesFromTriggerTime, durationExp);
    }
    ArrayList<EventAssignment> eventAssignmentList = new ArrayList<EventAssignment>();
    Iterator<Element> iter = eventElement.getChildren(XMLTags.EventAssignmentTag, vcNamespace).iterator();
    while (iter.hasNext()) {
        element = iter.next();
        String varname = element.getAttributeValue(XMLTags.EventAssignmentVariableAttrTag);
        Expression assignExp = unMangleExpression(element.getText());
        Variable var = mathdesc.getVariable(varname);
        EventAssignment eventAssignment = new EventAssignment(var, assignExp);
        eventAssignmentList.add(eventAssignment);
    }
    Event event = new Event(name, triggerExp, delay, eventAssignmentList);
    transcribeComments(eventElement, event);
    return event;
}

Example 7 with Event

use of cbit.vcell.math.Event in project vcell by virtualcell.

the class OdeFileWriter method writeEvents.

private String writeEvents(HashMap<Discontinuity, String> discontinuityNameMap) throws ExpressionException {
    Simulation simulation = simTask.getSimulation();
    StringBuffer sb = new StringBuffer();
    MathDescription mathDescription = simulation.getMathDescription();
    Iterator<Event> iter = mathDescription.getEvents();
    sb.append("EVENTS " + mathDescription.getNumEvents() + "\n");
    while (iter.hasNext()) {
        Event event = iter.next();
        sb.append("EVENT " + event.getName() + "\n");
        Expression triggerExpression = event.getTriggerExpression();
        triggerExpression = MathUtilities.substituteFunctions(triggerExpression, varsSymbolTable).flatten();
        Vector<Discontinuity> v = triggerExpression.getDiscontinuities();
        for (Discontinuity od : v) {
            od = getSubsitutedAndFlattened(od, varsSymbolTable);
            String dname = discontinuityNameMap.get(od);
            if (dname == null) {
                dname = ROOT_VARIABLE_PREFIX + discontinuityNameMap.size();
                discontinuityNameMap.put(od, dname);
            }
            triggerExpression.substituteInPlace(od.getDiscontinuityExp(), new Expression("(" + dname + "==1)"));
        }
        sb.append("TRIGGER " + triggerExpression.infix() + ";\n");
        Delay delay = event.getDelay();
        if (delay != null) {
            Expression durationExpression = delay.getDurationExpression();
            durationExpression = MathUtilities.substituteFunctions(durationExpression, varsSymbolTable).flatten();
            sb.append("DELAY " + delay.useValuesFromTriggerTime() + " " + durationExpression.infix() + ";\n");
        }
        sb.append("EVENTASSIGNMENTS " + event.getNumEventAssignments() + "\n");
        Iterator<EventAssignment> iter2 = event.getEventAssignments();
        while (iter2.hasNext()) {
            EventAssignment eventAssignment = iter2.next();
            Expression assignmentExpression = eventAssignment.getAssignmentExpression();
            assignmentExpression = MathUtilities.substituteFunctions(assignmentExpression, varsSymbolTable).flatten();
            Variable assignmentTarget = eventAssignment.getVariable();
            for (int i = 0; i < fieldStateVariables.size(); i++) {
                if (assignmentTarget.getName().equals(fieldStateVariables.get(i).getVariable().getName())) {
                    sb.append(i + " " + assignmentExpression.infix() + ";\n");
                    break;
                }
            }
        }
    }
    return sb.toString();
}

Example 8 with Event

use of cbit.vcell.math.Event in project vcell by virtualcell.

the class MathModel_SBMLExporter method addSbmlEvent.

protected static void addSbmlEvent(Model sbmlModel, Event vcellMathEvent) {
    org.sbml.jsbml.Event sbmlEvent = sbmlModel.createEvent();
    sbmlEvent.setId(vcellMathEvent.getName());
    // create trigger
    Trigger trigger = sbmlEvent.createTrigger();
    Expression triggerExpr = vcellMathEvent.getTriggerExpression();
    // 
    // if trigger expression is not already in "boolean" form, then new expression is (exp != 0.0) ...nonzero is true.
    // 
    ASTNode triggerMath = getFormulaFromExpression(triggerExpr, MathType.BOOLEAN);
    trigger.setMath(triggerMath);
    // create delay
    cbit.vcell.math.Event.Delay vcellMathDelay = vcellMathEvent.getDelay();
    if (vcellMathDelay != null && vcellMathDelay.getDurationExpression() != null && !vcellMathDelay.getDurationExpression().isZero()) {
        Delay delay = sbmlEvent.createDelay();
        Expression delayExpr = vcellMathDelay.getDurationExpression();
        ASTNode delayMath = getFormulaFromExpression(delayExpr, MathType.REAL);
        delay.setMath(delayMath);
        sbmlEvent.setUseValuesFromTriggerTime(vcellMathDelay.useValuesFromTriggerTime());
    }
    // create eventAssignments
    Iterator<EventAssignment> vcEventAssignments = vcellMathEvent.getEventAssignments();
    while (vcEventAssignments.hasNext()) {
        EventAssignment vcEventAssignment = vcEventAssignments.next();
        org.sbml.jsbml.EventAssignment sbmlEA = sbmlEvent.createEventAssignment();
        Variable target = vcEventAssignment.getVariable();
        sbmlEA.setVariable(target.getName());
        Expression eventAssgnExpr = new Expression(vcEventAssignment.getAssignmentExpression());
        ASTNode eaMath = getFormulaFromExpression(eventAssgnExpr, MathType.REAL);
        sbmlEA.setMath(eaMath);
    }
}