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

Example 11 with Compartment

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

the class SBMLImporter method checkIdentifiersNameLength.

private void checkIdentifiersNameLength() throws Exception {
    // Check compartment name lengths
    ListOf listofIds = sbmlModel.getListOfCompartments();
    boolean bLongCompartmentName = false;
    SBase issueSource = null;
    for (int i = 0; i < sbmlModel.getNumCompartments(); i++) {
        Compartment compartment = (Compartment) listofIds.get(i);
        String compartmentName = compartment.getId();
        if (compartmentName.length() > 64) {
            bLongCompartmentName = true;
            issueSource = compartment;
        }
    }
    // Check species name lengths
    listofIds = sbmlModel.getListOfSpecies();
    boolean bLongSpeciesName = false;
    for (int i = 0; i < sbmlModel.getNumSpecies(); i++) {
        org.sbml.jsbml.Species species = (org.sbml.jsbml.Species) listofIds.get(i);
        String speciesName = species.getId();
        if (speciesName.length() > 64) {
            bLongSpeciesName = true;
            issueSource = species;
        }
    }
    // Check parameter name lengths
    listofIds = sbmlModel.getListOfParameters();
    boolean bLongParameterName = false;
    for (int i = 0; i < sbmlModel.getNumParameters(); i++) {
        Parameter param = (Parameter) listofIds.get(i);
        String paramName = param.getId();
        if (paramName.length() > 64) {
            bLongParameterName = true;
            issueSource = param;
        }
    }
    // Check reaction name lengths
    listofIds = sbmlModel.getListOfReactions();
    boolean bLongReactionName = false;
    for (int i = 0; i < sbmlModel.getNumReactions(); i++) {
        Reaction rxn = (Reaction) listofIds.get(i);
        String rxnName = rxn.getId();
        if (rxnName.length() > 64) {
            bLongReactionName = true;
            issueSource = rxn;
        }
    }
    if (bLongCompartmentName || bLongSpeciesName || bLongParameterName || bLongReactionName) {
        String warningMsg = "WARNING: The imported model has one or more ";
        if (bLongCompartmentName) {
            warningMsg = warningMsg + "compartments, ";
        }
        if (bLongSpeciesName) {
            warningMsg = warningMsg + "species, ";
        }
        if (bLongParameterName) {
            warningMsg = warningMsg + "global parameters, ";
        }
        if (bLongReactionName) {
            warningMsg = warningMsg + "reactions ";
        }
        warningMsg = warningMsg + "that have ids/names that are longer than 64 characters. \n\nUser is STRONGLY recommeded to shorten " + "the names to avoid problems with the length of expressions these names might be used in.";
        localIssueList.add(new Issue(new SBMLIssueSource(issueSource), issueContext, IssueCategory.SBMLImport_UnsupportedAttributeOrElement, warningMsg, Issue.SEVERITY_WARNING));
    // logger.sendMessage(VCLogger.Priority.MediumPriority,
    // VCLogger.ErrorType.UnsupportedConstruct, warningMsg);
    }
}

Example 12 with Compartment

use of org.sbml.jsbml.Compartment 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);
    }
}