Examples with Event org.sbml.jsbml.Event used on opensource projects

Example 1 with Event

use of org.sbml.jsbml.Event in project vcell by virtualcell.

the class SBMLExporter method addEvents.

/**
 * Export events
 */
protected void addEvents() {
    BioEvent[] vcBioevents = getSelectedSimContext().getBioEvents();
    if (vcBioevents != null) {
        for (BioEvent vcEvent : vcBioevents) {
            Event sbmlEvent = sbmlModel.createEvent();
            sbmlEvent.setId(vcEvent.getName());
            sbmlEvent.setUseValuesFromTriggerTime(vcEvent.getUseValuesFromTriggerTime());
            // create trigger
            Trigger trigger = sbmlEvent.createTrigger();
            trigger.setPersistent(true);
            // NOTE: VCell solver behavior is to fire if trigger is true at timepoint 0
            // solver does work correctly if there is a non-zero delay
            // BUT - solver does not correctly simulate when the delay is 0 and when it also fires at 0
            // ----> will need a fix in solver
            // HOWEVER - the correct SBML translation requires to set the initial value to false
            trigger.setInitialValue(false);
            // get the math for the trigger in terms of variables and globals only
            try {
                Expression triggerExpr = vcEvent.generateTriggerExpression();
                Expression flattenedTrigger = MathUtilities.substituteModelParameters(triggerExpr, vcSelectedSimContext);
                // TODO - we will need to add event parameter info into VCell notes so we can recover the semantic of trigger type on roundtrip and transform back a flattened expression
                ASTNode math = getFormulaFromExpression(flattenedTrigger, MathType.BOOLEAN);
                trigger.setMath(math);
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("failed to generate trigger expression for event " + vcEvent.getName() + ": " + e.getMessage());
            }
            // create delay
            LocalParameter delayParam = vcEvent.getParameter(BioEventParameterType.TriggerDelay);
            if (delayParam != null && delayParam.getExpression() != null && !delayParam.getExpression().isZero()) {
                Delay delay = sbmlEvent.createDelay();
                Expression delayExpr = delayParam.getExpression();
                ASTNode math = getFormulaFromExpression(delayExpr);
                delay.setMath(math);
                sbmlEvent.setUseValuesFromTriggerTime(vcEvent.getUseValuesFromTriggerTime());
            }
            // create eventAssignments
            ArrayList<EventAssignment> vcEventAssgns = vcEvent.getEventAssignments();
            for (int j = 0; j < vcEventAssgns.size(); j++) {
                org.sbml.jsbml.EventAssignment sbmlEA = sbmlEvent.createEventAssignment();
                SymbolTableEntry target = vcEventAssgns.get(j).getTarget();
                sbmlEA.setVariable(target.getName());
                Expression eventAssgnExpr = new Expression(vcEventAssgns.get(j).getAssignmentExpression());
                ASTNode eaMath = getFormulaFromExpression(eventAssgnExpr);
                sbmlEA.setMath(eaMath);
            }
        }
    }
}

Example 2 with Event

use of org.sbml.jsbml.Event in project vcell by virtualcell.

the class SBMLImporter method addEvents.

protected void addEvents() {
    if (sbmlModel.getNumEvents() > 0) {
        // VCell does not support events in spatial model
        if (bSpatial) {
            throw new SBMLImportException("Events are not supported in a spatial VCell model.");
        }
        ListOf<Event> listofEvents = sbmlModel.getListOfEvents();
        Model vcModel = vcBioModel.getSimulationContext(0).getModel();
        for (int i = 0; i < sbmlModel.getNumEvents(); i++) {
            try {
                Event event = listofEvents.get(i);
                // trigger - adjust for species context and time conversion
                // factors if necessary
                Expression triggerExpr = null;
                if (event.isSetTrigger()) {
                    triggerExpr = getExpressionFromFormula(event.getTrigger().getMath());
                    triggerExpr = adjustExpression(triggerExpr, vcModel);
                }
                // create bioevent
                String eventName = event.getId();
                if (eventName == null || eventName.length() == 0) {
                    eventName = TokenMangler.mangleToSName(event.getName());
                    // vcBioModel.getSimulationContext(0).
                    if (eventName == null || eventName.length() == 0) {
                        eventName = vcBioModel.getSimulationContext(0).getFreeEventName(null);
                    }
                }
                // delay
                BioEvent vcEvent = new BioEvent(eventName, TriggerType.GeneralTrigger, true, vcBioModel.getSimulationContext(0));
                if (event.isSetDelay()) {
                    Expression durationExpr = null;
                    durationExpr = getExpressionFromFormula(event.getDelay().getMath());
                    durationExpr = adjustExpression(durationExpr, vcModel);
                    boolean bUseValsFromTriggerTime = true;
                    if (event.isSetUseValuesFromTriggerTime()) {
                        bUseValsFromTriggerTime = event.isSetUseValuesFromTriggerTime();
                    } else {
                        if (durationExpr != null && !durationExpr.isZero()) {
                            bUseValsFromTriggerTime = false;
                        }
                    }
                    if (durationExpr != null && !durationExpr.isZero()) {
                        bUseValsFromTriggerTime = false;
                    }
                    vcEvent.setUseValuesFromTriggerTime(bUseValsFromTriggerTime);
                    vcEvent.getParameter(BioEventParameterType.TriggerDelay).setExpression(durationExpr);
                }
                // event assignments
                ArrayList<EventAssignment> vcEvntAssgnList = new ArrayList<EventAssignment>();
                for (int j = 0; j < event.getNumEventAssignments(); j++) {
                    org.sbml.jsbml.EventAssignment sbmlEvntAssgn = event.getEventAssignment(j);
                    String varName = sbmlEvntAssgn.getVariable();
                    SymbolTableEntry varSTE = vcBioModel.getSimulationContext(0).getEntry(varName);
                    if (varSTE != null) {
                        Expression evntAssgnExpr = getExpressionFromFormula(sbmlEvntAssgn.getMath());
                        evntAssgnExpr = adjustExpression(evntAssgnExpr, vcModel);
                        EventAssignment vcEvntAssgn = vcEvent.new EventAssignment(varSTE, evntAssgnExpr);
                        vcEvntAssgnList.add(vcEvntAssgn);
                    } else {
                        logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.UnsupportedConstruct, "No symbolTableEntry for '" + varName + "'; Cannot add event assignment.");
                    }
                }
                vcEvent.setEventAssignmentsList(vcEvntAssgnList);
                vcEvent.bind();
                vcBioModel.getSimulationContext(0).addBioEvent(vcEvent);
            } catch (Exception e) {
                e.printStackTrace(System.out);
                throw new SBMLImportException(e.getMessage(), e);
            }
        // end - try/catch
        }
    // end - for(sbmlEvents)
    }
// end - if numEvents > 0)
}

Example 3 with Event

use of org.sbml.jsbml.Event in project vcell by virtualcell.

the class SBMLImporter method addEvents.

protected void addEvents(Map<String, String> sbmlToVcNameMap) {
    if (sbmlModel.getNumEvents() > 0) {
        // VCell does not support events in spatial model
        if (bSpatial) {
            throw new SBMLImportException("Events are not supported in a spatial VCell model.");
        }
        ListOf<Event> listofEvents = sbmlModel.getListOfEvents();
        SimulationContext simContext = vcBioModel.getSimulationContext(0);
        Model vcModel = simContext.getModel();
        Map<String, SymbolTableEntry> entryMap = new HashMap<String, SymbolTableEntry>();
        simContext.getEntries(entryMap);
        for (int i = 0; i < sbmlModel.getNumEvents(); i++) {
            try {
                Event event = listofEvents.get(i);
                // trigger - adjust for species context and time conversion factors if necessary
                Expression triggerExpr = null;
                if (event.isSetTrigger()) {
                    triggerExpr = getExpressionFromFormula(event.getTrigger().getMath());
                    triggerExpr = adjustExpression(triggerExpr, vcModel);
                }
                // convert reserved symbols, if any
                if (!sbmlToVcNameMap.isEmpty() && triggerExpr != null && triggerExpr.getSymbols() != null && triggerExpr.getSymbols().length > 0) {
                    String[] symbols = triggerExpr.getSymbols();
                    for (String oldSymbol : symbols) {
                        String newSymbol = sbmlToVcNameMap.get(oldSymbol);
                        if (newSymbol != null) {
                            triggerExpr.substituteInPlace(new Expression(oldSymbol), new Expression(newSymbol));
                        }
                    }
                }
                // create bioevent
                String eventName = event.getId();
                if (eventName == null || eventName.length() == 0) {
                    eventName = TokenMangler.mangleToSName(event.getName());
                    // vcBioModel.getSimulationContext(0).
                    if (eventName == null || eventName.length() == 0) {
                        eventName = vcBioModel.getSimulationContext(0).getFreeEventName(null);
                    }
                }
                // delay
                BioEvent vcEvent = new BioEvent(eventName, TriggerType.GeneralTrigger, true, vcBioModel.getSimulationContext(0));
                if (event.isSetDelay()) {
                    Expression durationExpr = null;
                    durationExpr = getExpressionFromFormula(event.getDelay().getMath());
                    durationExpr = adjustExpression(durationExpr, vcModel);
                    // convert reserved symbols, if any
                    if (!sbmlToVcNameMap.isEmpty() && durationExpr != null && durationExpr.getSymbols() != null && durationExpr.getSymbols().length > 0) {
                        String[] symbols = durationExpr.getSymbols();
                        for (String oldSymbol : symbols) {
                            String newSymbol = sbmlToVcNameMap.get(oldSymbol);
                            if (newSymbol != null) {
                                durationExpr.substituteInPlace(new Expression(oldSymbol), new Expression(newSymbol));
                            }
                        }
                    }
                    boolean bUseValsFromTriggerTime = true;
                    if (event.isSetUseValuesFromTriggerTime()) {
                        bUseValsFromTriggerTime = event.isSetUseValuesFromTriggerTime();
                    } else {
                        if (durationExpr != null && !durationExpr.isZero()) {
                            bUseValsFromTriggerTime = false;
                        }
                    }
                    if (durationExpr != null && !durationExpr.isZero()) {
                        bUseValsFromTriggerTime = false;
                    }
                    vcEvent.setUseValuesFromTriggerTime(bUseValsFromTriggerTime);
                    vcEvent.getParameter(BioEventParameterType.TriggerDelay).setExpression(durationExpr);
                }
                cbit.vcell.mapping.ParameterContext.LocalParameter triggerParameter = vcEvent.getParameter(BioEventParameterType.GeneralTriggerFunction);
                triggerParameter.setExpression(triggerExpr);
                // event assignments
                ArrayList<EventAssignment> vcEvntAssgnList = new ArrayList<EventAssignment>();
                for (int j = 0; j < event.getNumEventAssignments(); j++) {
                    org.sbml.jsbml.EventAssignment sbmlEvntAssgn = event.getEventAssignment(j);
                    String sbmlVarName = sbmlEvntAssgn.getVariable();
                    String vcVarName = sbmlVarName;
                    if (sbmlToVcNameMap.get(sbmlVarName) != null) {
                        // convert reserved symbols, if any
                        vcVarName = sbmlToVcNameMap.get(sbmlVarName);
                    }
                    SymbolTableEntry ste = simContext.getEntry(vcVarName);
                    if (ste != null) {
                        Expression evntAssgnExpr;
                        ASTNode node = sbmlEvntAssgn.getMath();
                        if (node == null) {
                            evntAssgnExpr = new Expression("0.0");
                            String msg = "Event assignment expression is null for event '" + eventName + "'.";
                            localIssueList.add(new Issue(vcBioModel, issueContext, IssueCategory.SBMLImport_UnsupportedAttributeOrElement, msg, Issue.Severity.WARNING));
                        } else {
                            evntAssgnExpr = getExpressionFromFormula(node);
                        }
                        evntAssgnExpr = adjustExpression(evntAssgnExpr, vcModel);
                        // convert reserved symbols, if any
                        if (!sbmlToVcNameMap.isEmpty() && evntAssgnExpr != null && evntAssgnExpr.getSymbols() != null && evntAssgnExpr.getSymbols().length > 0) {
                            String[] symbols = evntAssgnExpr.getSymbols();
                            for (String oldSymbol : symbols) {
                                String newSymbol = sbmlToVcNameMap.get(oldSymbol);
                                if (newSymbol != null) {
                                    evntAssgnExpr.substituteInPlace(new Expression(oldSymbol), new Expression(newSymbol));
                                }
                            }
                        }
                        EventAssignment vcEvntAssgn = vcEvent.new EventAssignment(ste, evntAssgnExpr);
                        vcEvntAssgnList.add(vcEvntAssgn);
                    } else {
                        logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.UnsupportedConstruct, "No symbolTableEntry for '" + vcVarName + "'; Cannot add event assignment.");
                    }
                }
                vcEvent.setEventAssignmentsList(vcEvntAssgnList);
                vcEvent.bind();
                vcBioModel.getSimulationContext(0).addBioEvent(vcEvent);
            } catch (Exception e) {
                e.printStackTrace(System.out);
                throw new SBMLImportException(e.getMessage(), e);
            }
        // end - try/catch
        }
    // end - for(sbmlEvents)
    }
// end - if numEvents > 0)
}