Examples with Model cbit.vcell.model.Model used on opensource projects

Example 96 with Model

use of cbit.vcell.model.Model in project vcell by virtualcell.

the class SBMLImporter method addSpecies.

protected void addSpecies(VCMetaData metaData) {
    if (sbmlModel == null) {
        throw new SBMLImportException("SBML model is NULL");
    }
    ListOf listOfSpecies = sbmlModel.getListOfSpecies();
    if (listOfSpecies == null) {
        System.out.println("No Spcecies");
        return;
    }
    HashMap<String, Species> vcSpeciesHash = new HashMap<String, Species>();
    HashMap<Species, org.sbml.jsbml.Species> vc_sbmlSpeciesHash = new HashMap<Species, org.sbml.jsbml.Species>();
    SpeciesContext[] vcSpeciesContexts = new SpeciesContext[(int) sbmlModel.getNumSpecies()];
    // Get species from SBMLmodel; Add/get speciesContext
    try {
        // First pass - add the speciesContexts
        for (int i = 0; i < sbmlModel.getNumSpecies(); i++) {
            org.sbml.jsbml.Species sbmlSpecies = (org.sbml.jsbml.Species) listOfSpecies.get(i);
            // Sometimes, the species name can be null or a blank string; in
            // that case, use species id as the name.
            String speciesName = sbmlSpecies.getId();
            Species vcSpecies = null;
            // create a species with speciesName as commonName. If it is
            // different in the annotation, can change it later
            Element sbmlImportRelatedElement = sbmlAnnotationUtil.readVCellSpecificAnnotation(sbmlSpecies);
            if (sbmlImportRelatedElement != null) {
                Element embeddedElement = getEmbeddedElementInAnnotation(sbmlImportRelatedElement, SPECIES_NAME);
                if (embeddedElement != null) {
                    // species.
                    if (embeddedElement.getName().equals(XMLTags.SpeciesTag)) {
                        String vcSpeciesName = embeddedElement.getAttributeValue(XMLTags.NameAttrTag);
                        vcSpecies = vcSpeciesHash.get(vcSpeciesName);
                        if (vcSpecies == null) {
                            vcSpecies = new Species(vcSpeciesName, vcSpeciesName);
                            vcSpeciesHash.put(vcSpeciesName, vcSpecies);
                        }
                    }
                // if embedded element is not speciesTag, do I have to
                // do something?
                } else {
                    // Annotation element is present, but doesn't contain
                    // the species element.
                    vcSpecies = new Species(speciesName, speciesName);
                    vcSpeciesHash.put(speciesName, vcSpecies);
                }
            } else {
                vcSpecies = new Species(speciesName, speciesName);
                vcSpeciesHash.put(speciesName, vcSpecies);
            }
            // store vc & sbml species in hash to read in annotation later
            vc_sbmlSpeciesHash.put(vcSpecies, sbmlSpecies);
            // Get matching compartment name (of sbmlSpecies[i]) from
            // feature list
            String compartmentId = sbmlSpecies.getCompartment();
            Structure spStructure = vcBioModel.getSimulationContext(0).getModel().getStructure(compartmentId);
            vcSpeciesContexts[i] = new SpeciesContext(vcSpecies, spStructure);
            vcSpeciesContexts[i].setName(speciesName);
            // Adjust units of species, convert to VC units.
            // Units in SBML, compute this using some of the attributes of
            // sbmlSpecies
            Compartment sbmlCompartment = sbmlModel.getCompartment(sbmlSpecies.getCompartment());
            int dimension = 3;
            if (sbmlCompartment.isSetSpatialDimensions()) {
                dimension = (int) sbmlCompartment.getSpatialDimensions();
            }
            if (dimension == 0 || dimension == 1) {
                logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.UnitError, dimension + " dimensional compartment " + compartmentId + " not supported");
            }
        }
        // end - for sbmlSpecies
        // set the species & speciesContexts on model
        Model vcModel = vcBioModel.getSimulationContext(0).getModel();
        vcModel.setSpecies(vcSpeciesHash.values().toArray(new Species[0]));
        vcModel.setSpeciesContexts(vcSpeciesContexts);
        // Set annotations and notes from SBML to VCMetadata
        Species[] vcSpeciesArray = vc_sbmlSpeciesHash.keySet().toArray(new Species[0]);
        for (Species vcSpecies : vcSpeciesArray) {
            org.sbml.jsbml.Species sbmlSpecies = vc_sbmlSpeciesHash.get(vcSpecies);
            sbmlAnnotationUtil.readAnnotation(vcSpecies, sbmlSpecies);
            sbmlAnnotationUtil.readNotes(vcSpecies, sbmlSpecies);
        }
    } catch (ModelPropertyVetoException e) {
        throw new SBMLImportException("Error adding species context; " + e.getMessage(), e);
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new SBMLImportException("Error adding species context; " + e.getMessage(), e);
    }
}

Example 97 with Model

use of cbit.vcell.model.Model in project vcell by virtualcell.

the class SBMLImporter method getReactionStructure.

/**
 * getReactionStructure :
 */
private Structure getReactionStructure(org.sbml.jsbml.Reaction sbmlRxn, SpeciesContext[] speciesContexts, Element sbmlImportElement) throws Exception {
    Structure struct = null;
    String structName = null;
    Model vcModel = vcBioModel.getSimulationContext(0).getModel();
    // return structure from vcmodel, if present.
    if (bSpatial) {
        structName = sbmlRxn.getCompartment();
        if (structName != null && structName.length() > 0) {
            struct = vcModel.getStructure(structName);
            if (struct != null) {
                return struct;
            }
        }
    }
    // If annotation has structure name, return the corresponding structure.
    if (sbmlImportElement != null) {
        // Get the embedded element in the annotation str (fluxStep or
        // simpleReaction), and the structure attribute from the element.
        Element embeddedElement = getEmbeddedElementInAnnotation(sbmlImportElement, REACTION);
        if (embeddedElement != null) {
            structName = embeddedElement.getAttributeValue(XMLTags.StructureAttrTag);
            // Using the structName, get the structure from the structures
            // (compartments) list.
            struct = vcModel.getStructure(structName);
            return struct;
        }
    }
    if (sbmlRxn.isSetKineticLaw()) {
        // String rxnName = sbmlRxn.getId();
        KineticLaw kLaw = sbmlRxn.getKineticLaw();
        Expression kRateExp = getExpressionFromFormula(kLaw.getMath());
        String[] symbols = kRateExp.getSymbols();
        if (symbols != null) {
            for (String symbol : symbols) {
                Compartment sbmlCompartment = sbmlModel.getCompartment(symbol);
                if (sbmlCompartment != null) {
                    return vcBioModel.getSimulationContext(0).getModel().getStructure(sbmlCompartment.getId());
                }
            }
        }
    }
    HashSet<String> refSpeciesNameHash = new HashSet<String>();
    getReferencedSpecies(sbmlRxn, refSpeciesNameHash);
    java.util.Iterator<String> refSpIterator = refSpeciesNameHash.iterator();
    HashSet<String> compartmentNamesHash = new HashSet<String>();
    while (refSpIterator.hasNext()) {
        String spName = refSpIterator.next();
        String rxnCompartmentName = sbmlModel.getSpecies(spName).getCompartment();
        compartmentNamesHash.add(rxnCompartmentName);
    }
    if (compartmentNamesHash.size() == 1) {
        struct = vcModel.getStructure(compartmentNamesHash.iterator().next());
        return struct;
    } else if (compartmentNamesHash.size() == 0) {
        struct = vcModel.getStructures()[0];
        return struct;
    } else {
        // more than one structure in reaction participants, try to figure
        // out which one to choose
        HashMap<String, Integer> structureFrequencyHash = new HashMap<String, Integer>();
        for (String structureName : compartmentNamesHash) {
            if (structureFrequencyHash.containsKey(structureName)) {
                structureFrequencyHash.put(structureName, structureFrequencyHash.get(structName) + 1);
            } else {
                structureFrequencyHash.put(structureName, 1);
            }
        }
        Iterator<Entry<String, Integer>> iterator = structureFrequencyHash.entrySet().iterator();
        Entry<String, Integer> mostUsedStructureEntry = iterator.next();
        while (iterator.hasNext()) {
            Entry<String, Integer> currentStructureEntry = iterator.next();
            if (currentStructureEntry.getValue() > mostUsedStructureEntry.getValue()) {
                mostUsedStructureEntry = currentStructureEntry;
            }
        }
        String mostUsedStructureName = mostUsedStructureEntry.getKey();
        struct = vcModel.getStructure(mostUsedStructureName);
        return struct;
    }
}

Example 98 with Model

use of cbit.vcell.model.Model 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 99 with Model

use of cbit.vcell.model.Model in project vcell by virtualcell.

the class SBMLImporter method addInitialAssignments.

protected void addInitialAssignments() {
    if (sbmlModel == null) {
        throw new SBMLImportException("SBML model is NULL");
    }
    ListOf listofInitialAssgns = sbmlModel.getListOfInitialAssignments();
    if (listofInitialAssgns == null) {
        System.out.println("No Initial Assignments specified");
        return;
    }
    Model vcModel = vcBioModel.getSimulationContext(0).getModel();
    for (int i = 0; i < sbmlModel.getNumInitialAssignments(); i++) {
        try {
            InitialAssignment initAssgn = (InitialAssignment) listofInitialAssgns.get(i);
            String initAssgnSymbol = initAssgn.getSymbol();
            Expression initAssignMathExpr = getExpressionFromFormula(initAssgn.getMath());
            // support compartmentSize expressions, warn and bail out.
            if (sbmlModel.getCompartment(initAssgnSymbol) != null) {
                if (!initAssignMathExpr.isNumeric()) {
                    logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.CompartmentError, "compartment '" + initAssgnSymbol + "' size has an initial assignment, cannot handle it at this time.");
                }
            // if init assgn for compartment is numeric, the numeric
            // value for size is set in addCompartments().
            }
            // or other species. Not allowed for species.
            if (!bSpatial && sbmlModel.getSpecies(initAssgnSymbol) != null) {
                if (initAssignMathExpr.hasSymbol(vcModel.getX().getName()) || initAssignMathExpr.hasSymbol(vcModel.getY().getName()) || initAssignMathExpr.hasSymbol(vcModel.getZ().getName())) {
                    logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.SpeciesError, "species '" + initAssgnSymbol + "' initial assignment expression cannot contain 'x', 'y', 'z'.");
                }
            }
            initAssignMathExpr = adjustExpression(initAssignMathExpr, vcModel);
            // set the init assgn expr on VCell species init condn or global
            // parameter expression
            SpeciesContextSpec scs = vcBioModel.getSimulationContext(0).getReactionContext().getSpeciesContextSpec(vcBioModel.getSimulationContext(0).getModel().getSpeciesContext(initAssgnSymbol));
            ModelParameter mp = vcBioModel.getSimulationContext(0).getModel().getModelParameter(initAssgnSymbol);
            if (scs != null) {
                scs.getInitialConditionParameter().setExpression(initAssignMathExpr);
            } else if (mp != null) {
                mp.setExpression(initAssignMathExpr);
            } else {
                localIssueList.add(new Issue(new SBMLIssueSource(initAssgn), issueContext, IssueCategory.SBMLImport_UnsupportedAttributeOrElement, "Symbol '" + initAssgnSymbol + "' not a species or global parameter in VCell; initial assignment ignored.", Issue.SEVERITY_WARNING));
            // logger.sendMessage(VCLogger.Priority.MediumPriority,
            // VCLogger.ErrorType.UnsupportedConstruct,
            // "Symbol '"+initAssgnSymbol+"' not a species or global parameter in VCell; initial assignment ignored..");
            }
        } catch (Exception e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error reading InitialAssignment : " + e.getMessage());
        }
    }
}

Example 100 with Model

use of cbit.vcell.model.Model in project vcell by virtualcell.

the class SBMLImporter method setSpeciesInitialConditions.

/**
 * setSpeciesInitialConditions : called after speciesContexts and global
 * parameters have been set. Checks for init conditions set on species in
 * the Sbml model, and if it is set using an assignment rule, obtain the
 * corresponding expression. Obtain the sbml -> vc unit conversion factor
 * for species concentrations to adjust the species initial condition
 * units/factor.
 */
private void setSpeciesInitialConditions() {
    try {
        // fill in SpeciesContextSpec for each speciesContext
        Model vcModel = vcBioModel.getSimulationContext(0).getModel();
        SpeciesContext[] vcSpeciesContexts = vcModel.getSpeciesContexts();
        for (int i = 0; i < vcSpeciesContexts.length; i++) {
            org.sbml.jsbml.Species sbmlSpecies = (org.sbml.jsbml.Species) sbmlModel.getSpecies(vcSpeciesContexts[i].getName());
            // Sometimes, the species name can be null or a blank string; in
            // that case, use species id as the name.
            String speciesName = sbmlSpecies.getId();
            Compartment compartment = (Compartment) sbmlModel.getCompartment(sbmlSpecies.getCompartment());
            Expression initExpr = null;
            if (sbmlSpecies.isSetInitialConcentration()) {
                // If initial
                // Concentration
                // is set
                Expression initConcentration = new Expression(sbmlSpecies.getInitialConcentration());
                // check if initConc is set by a (assignment) rule. That
                // takes precedence over initConc value set on species.
                initExpr = getValueFromAssignmentRule(speciesName);
                if (initExpr == null) {
                    initExpr = new Expression(initConcentration);
                }
            } else if (sbmlSpecies.isSetInitialAmount()) {
                // If initial
                // amount is set
                double initAmount = sbmlSpecies.getInitialAmount();
                // initConcentration. Else, throw exception.
                if (compartment.isSetSize()) {
                    double compartmentSize = compartment.getSize();
                    Expression initConcentration = new Expression(0.0);
                    if (compartmentSize != 0.0) {
                        initConcentration = new Expression(initAmount / compartmentSize);
                    } else {
                        logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.UnitError, "compartment '" + compartment.getId() + "' has zero size, unable to determine initial concentration for species " + speciesName);
                    }
                    // check if initConc is set by a (assignment) rule. That
                    // takes precedence over initConc/initAmt value set on
                    // species.
                    initExpr = getValueFromAssignmentRule(speciesName);
                    if (initExpr == null) {
                        initExpr = new Expression(initConcentration);
                    }
                } else {
                    logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.SpeciesError, " Compartment '" + compartment.getId() + "' size not set or is defined by a rule; cannot calculate initConc.");
                }
            } else {
                // initConc/initAmt not set; check if species has a
                // (assignment) rule.
                initExpr = getValueFromAssignmentRule(speciesName);
                if (initExpr == null) {
                    // warning and set it to 0.0
                    if (sbmlModel.getInitialAssignment(speciesName) == null) {
                        localIssueList.add(new Issue(new SBMLIssueSource(sbmlModel.getSpecies(speciesName)), issueContext, IssueCategory.SBMLImport_MissingSpeciesInitCondition, "no initial condition for species " + speciesName + ", assuming 0.0", Issue.SEVERITY_WARNING));
                    // logger.sendMessage(VCLogger.Priority.MediumPriority,
                    // VCLogger.ErrorType.UnitError,
                    // "no initial condition for species "+speciesName+", assuming 0.0");
                    }
                    initExpr = new Expression(0.0);
                }
            }
            // similar to the conversion that is done in reactions.
            if (initExpr != null) {
                // initExpr will be changed
                initExpr = adjustExpression(initExpr, vcModel);
            }
            // If any of the symbols in the expression for speciesConc is a
            // rule, expand it.
            substituteGlobalParamRulesInPlace(initExpr, false);
            SpeciesContextSpec speciesContextSpec = vcBioModel.getSimulationContext(0).getReactionContext().getSpeciesContextSpec(vcSpeciesContexts[i]);
            speciesContextSpec.getInitialConditionParameter().setExpression(initExpr);
            speciesContextSpec.setConstant(sbmlSpecies.getBoundaryCondition() || sbmlSpecies.getConstant());
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
        throw new SBMLImportException("Error setting initial condition for species context; " + e.getMessage(), e);
    }
}