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

Example 1 with Unit

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

the class SBMLUnitTranslator method getSBMLUnitDefinition.

public static UnitDefinition getSBMLUnitDefinition(VCUnitDefinition vcUnitDefn, int level, int version, VCUnitSystem vcUnitSystem) throws SbmlException {
    final UnitDefinition sbmlUnitDefn = new UnitDefinition(3, 1);
    if (vcUnitDefn.isCompatible(vcUnitSystem.getInstance_DIMENSIONLESS())) {
        double multiplier = Double.parseDouble(vcUnitDefn.getSymbol());
        sbmlUnitDefn.addUnit(new Unit(multiplier, 0, Kind.DIMENSIONLESS, 1.0, 3, 1));
        return sbmlUnitDefn;
    }
    String vcSymbol = vcUnitDefn.getSymbol();
    double overallMultiplier = 1.0;
    if (vcSymbol.contains(" ")) {
        String[] unitParts = vcSymbol.split(" ");
        overallMultiplier = Double.parseDouble(unitParts[0]);
        vcSymbol = unitParts[1];
    }
    // String sbmlUnitSymbol = TokenMangler.mangleToSName(vcSymbol);
    String[] symbols = vcSymbol.split("\\.");
    if (symbols.length == 0) {
        symbols = new String[] { vcSymbol };
    }
    for (int i = 0; i < symbols.length; i++) {
        double multiplier = 1.0;
        if (i == 0) {
            multiplier *= overallMultiplier;
        }
        double exponent = 1.0;
        int scale = 0;
        String symbol = symbols[i];
        // }
        if (symbol.contains("-")) {
            String[] symbolAndExp = symbol.split("\\-");
            symbol = symbolAndExp[0];
            exponent = -1 * Integer.parseInt(symbolAndExp[1]);
        } else if (Character.isDigit(symbol.charAt(symbol.length() - 1))) {
            exponent = Integer.parseInt(symbol.substring(symbol.length() - 1));
            symbol = symbol.substring(0, symbol.length() - 1);
        }
        VCUnitDefinition vcUnit = vcUnitSystem.getInstance(symbol);
        boolean bFoundMatch = false;
        // check sbml builtin units (base SI and supported derived units) first.
        for (Kind kind : Kind.values()) {
            String kindSymbol = kind.getSymbol();
            if (kind == Kind.AVOGADRO || kind == Kind.CELSIUS || kind == Kind.INVALID || kind == Kind.BECQUEREL || kind == Kind.HERTZ) {
                continue;
            }
            if (kind == Kind.OHM) {
                kindSymbol = "Ohm";
            }
            if (kind == Kind.ITEM) {
                kindSymbol = "molecules";
            }
            VCUnitDefinition kindVcUnit = vcUnitSystem.getInstance(kindSymbol);
            if (kindVcUnit.isCompatible(vcUnit)) {
                if (kindVcUnit.isEquivalent(vcUnit)) {
                    sbmlUnitDefn.addUnit(new Unit(multiplier, scale, kind, exponent, 3, 1));
                } else {
                    double factor = vcUnit.convertTo(1.0, kindVcUnit);
                    double logFactor = Math.log10(factor);
                    if (logFactor == (int) logFactor) {
                        scale = (int) logFactor;
                    } else {
                        scale = 0;
                        multiplier = multiplier * factor;
                    }
                    Unit sbmlUnit = new Unit(multiplier, scale, kind, exponent, 3, 1);
                    sbmlUnitDefn.addUnit(sbmlUnit);
                    System.err.println("kind = " + kind.name() + " is equivalent to vcUnit = " + vcUnit.getSymbol() + ",  SBML unit is " + sbmlUnit);
                }
                bFoundMatch = true;
                break;
            }
        }
        if (!bFoundMatch) {
            // check for molar, kind of crazy that this one is missing.
            VCUnitDefinition kindVcUnit = vcUnitSystem.getInstance("molar");
            if (kindVcUnit.isCompatible(vcUnit)) {
                if (kindVcUnit.isEquivalent(vcUnit)) {
                    sbmlUnitDefn.addUnit(new Unit(multiplier, scale, Kind.MOLE, exponent, 3, 1));
                    sbmlUnitDefn.addUnit(new Unit(1, 0, Kind.LITRE, -exponent, 3, 1));
                } else {
                    double factor = vcUnit.convertTo(1.0, kindVcUnit);
                    double logFactor = Math.log10(factor);
                    if (logFactor == (int) logFactor) {
                        scale = (int) logFactor;
                    } else {
                        scale = 0;
                        multiplier = multiplier * factor;
                    }
                    sbmlUnitDefn.addUnit(new Unit(multiplier, scale, Kind.MOLE, exponent, 3, 1));
                    sbmlUnitDefn.addUnit(new Unit(1, 0, Kind.LITRE, -exponent, 3, 1));
                    System.err.println("matched to liter ... had to create a replacement for molar, vcUnit = " + vcUnit.getSymbol() + ",  SBML unit is " + sbmlUnitDefn);
                }
                bFoundMatch = true;
            }
        }
        if (!bFoundMatch) {
            throw new RuntimeException("didn't find a match for vcUnit " + vcUnit.getSymbol());
        // System.out.println("Still didn't find a match for vcUnit "+vcUnit.getSymbol());
        }
    // ucar.units_vcell.Unit ucarUnit = vcUnit.getUcarUnit();
    // if (ucarUnit instanceof ScaledUnit){
    // ScaledUnit scaledUnit = (ScaledUnit)ucarUnit;
    // double parsedScale = scaledUnit.getScale();
    // double logScale = Math.log10(parsedScale);
    // if (logScale == (int)logScale){
    // scale = (int)logScale;
    // }else{
    // scale = 0;
    // multiplier = multiplier*parsedScale;
    // }
    // ucar.units_vcell.Unit insideUnit = scaledUnit.getUnit();
    // boolean bFoundMatch = false;
    // for (Kind kind : Kind.values()){
    // String kindSymbol = kind.getSymbol();
    // if (kind==Kind.AVOGADRO){
    // continue;
    // }
    // if (kind==Kind.CELSIUS){
    // continue;
    // }
    // if (kind==Kind.INVALID){
    // continue;
    // }
    // if (kind==Kind.OHM){
    // kindSymbol = "Ohm";
    // }
    // String sym = insideUnit.toString();
    // if (vcUnitSystem.getInstance(kindSymbol).isEquivalent(vcUnitSystem.getInstance(sym))){
    // sbmlUnitDefn.addUnit(new Unit(multiplier, scale, kind, exponent, 3, 1));
    // bFoundMatch = true;
    // break;
    // }
    // }
    // if (!bFoundMatch){
    // System.err.println("couldn't find an SBML unit for vcUnit "+vcUnit.getSymbol());
    // System.err.println("couldn't find an SBML unit for vcUnit "+vcUnit.getSymbol());
    // }
    // }
    // System.err.println("vcUnit is "+symbols[i]+",  ucarUnit is "+ucarUnit.getSymbol());
    }
    sbmlUnitDefn.setId(TokenMangler.mangleToSName(vcSymbol));
    return sbmlUnitDefn;
// 
// // If VC unit is DIMENSIONLESS ...
// if (vcUnitDefn.isTBD()) {
// throw new RuntimeException("TBD unit has no SBML equivalent");
// } else if (vcUnitDefn.isCompatible(vcUnitSystem.getInstance_DIMENSIONLESS())) {
// double multiplier = 1.0;
// multiplier = vcUnitDefn.convertTo(multiplier, vcUnitSystem.getInstance_DIMENSIONLESS());
// sbmlUnitDefn = new UnitDefinition(level, version);
// sbmlUnitDefn.setId(TokenMangler.mangleToSName(TokenMangler.mangleToSName(vcSymbol)));
// Unit dimensionlessUnit = new UnitD(level, version);
// dimensionlessUnit.setMultiplier(multiplier);
// sbmlUnitDefn.addUnit(dimensionlessUnit);
// } else {
// // Translate the VCUnitDef into libSBML UnitDef : convert the units of VCUnitDef into libSBML units and add them to sbmlUnitDefn
// 
// sbmlUnitDefn = new UnitDefinition(level, version);
// sbmlUnitDefn.setId(TokenMangler.mangleToSName(TokenMangler.mangleToSName(sbmlUnitSymbol)));
// ucar.units_vcell.Unit vcUcarUnit = vcUnitDefn.getUcarUnit();
// //ArrayList<Unit> sbmlUnitsList = convertVCUnitsToSbmlUnits(1.0, vcUcarUnit, new ArrayList<Unit>(), level, version);
// List<Unit> sbmlUnitsList = convert(vcUcarUnit, level, version);
// 
// for (int i = 0; i < sbmlUnitsList.size(); i++){
// Unit sbmlUnit = sbmlUnitsList.get(i);
// sbmlUnitDefn.addUnit(sbmlUnit);
// }
// }
// 
// return sbmlUnitDefn;
}

Example 2 with Unit

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

the class SBMLUnitTranslator method getVCUnitDefinition.

public static VCUnitDefinition getVCUnitDefinition(org.sbml.jsbml.UnitDefinition sbmlUnitDefn, VCUnitSystem vcUnitSystem) {
    // Each SBML UnitDefinition contains a list of Units, the total unit (VC unit) as represented by
    // an SBML UnitDefinition is the product of the list of units it contains.
    VCUnitDefinition vcUnitDefn = null;
    for (Unit sbmlUnit : sbmlUnitDefn.getListOfUnits()) {
        VCUnitDefinition vcUnit = getVCUnit(sbmlUnit, vcUnitSystem);
        if (vcUnitDefn == null) {
            vcUnitDefn = vcUnit;
        } else {
            vcUnitDefn = vcUnitDefn.multiplyBy(vcUnit);
        }
    }
    String originalSymbol = vcUnitDefn.getSymbol();
    String symbol = "." + originalSymbol + ".";
    final String[] moleSymbols = new String[] { "umol", "nmol", "mol", "mmol", "pmol" };
    final String[] molarSymbols = new String[] { "uM", "nM", "M", "mM", "pM" };
    for (int i = 0; i < moleSymbols.length; i++) {
        String mol = moleSymbols[i];
        String M = molarSymbols[i];
        if (symbol.contains(mol)) {
            symbol = symbol.replace("." + mol + ".l-1.", "." + M + ".");
            symbol = symbol.replace(".l-1." + mol + ".", "." + M + ".");
            symbol = symbol.replace("." + mol + "-1.l.", "." + M + "-1.");
            symbol = symbol.replace(".l." + mol + "-1.", "." + M + "-1.");
            symbol = symbol.replace("." + mol + "2.l-2.", "." + M + "2.");
            symbol = symbol.replace(".l-2." + mol + "2.", "." + M + "2.");
            symbol = symbol.replace("." + mol + "-2.l2.", "." + M + "-2.");
            symbol = symbol.replace(".l2." + mol + "-2.", "." + M + "-2.");
        }
    }
    symbol = symbol.substring(1, symbol.length() - 1);
    if (!symbol.equals(vcUnitDefn.getSymbol())) {
        System.err.println("new symbol is " + symbol + ",   old symbol is " + vcUnitDefn.getSymbol());
        VCUnitDefinition new_vcUnitDefn = vcUnitSystem.getInstance(symbol);
        if (!new_vcUnitDefn.isEquivalent(vcUnitDefn)) {
            throw new RuntimeException("failed to simplify unit " + vcUnitDefn.getSymbol() + ", created wrong symbol " + symbol);
        }
        return new_vcUnitDefn;
    } else {
        return vcUnitDefn;
    }
}

Example 3 with Unit

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

the class SBMLUnitTranslator method convertVCUnitsToSbmlUnits_NOT_USED.

/**
 *   BaseUnit definitions copied from ucar.units_vcell.SI (as modified for Virtual Cell and SBML ... including item and molecules)
 *
 *   (PRIMARY BASE SI UNITS)
 *   AMPERE = 		bu("ampere",    "A",   BaseQuantity.ELECTRIC_CURRENT)
 *   CANDELA = 		bu("candela",   "cd",  BaseQuantity.LUMINOUS_INTENSITY)
 *   KELVIN = 		bu("kelvin",    "K",   BaseQuantity.THERMODYNAMIC_TEMPERATURE)
 *   KILOGRAM = 	bu("kilogram",  "kg",  BaseQuantity.MASS)
 *   METER = 		bu("metre",     "m",   BaseQuantity.LENGTH)	// NIST
 *   METRE = 		bu("metre",     "m",   BaseQuantity.LENGTH)	// ISO
 *   MOLE = 		bu("mole",      "mol", BaseQuantity.AMOUNT_OF_SUBSTANCE)
 *   SECOND = 		bu("second",    "s",   BaseQuantity.TIME)
 *
 *   (SUPPLEMENTARY BASE SI UNITS ... DIMENSIONLESS DERIVED UNITS) ... note that BaseUnit
 *   RADIAN = 		bu("radian",    "rad", BaseQuantity.PLANE_ANGLE)
 *   STERADIAN = 	bu("steradian", "sr",  BaseQuantity.SOLID_ANGLE)
 *
 *   (VCELL/SBML introduced base SI unit for items/molecules)
 *   ITEM =			bu("item",      "item", BaseQuantity.ITEM)
 */
/**
 * @param unitMultiplier
 * @param vcUcarUnit
 * @param allSbmlUnitsList
 * @param level
 * @param version
 * @return
 */
/*
 *  convertVCUnitsToSbmlUnits :
 *  --------- !!!! Ignoring OFFSET for UNITS, since SBML L2V2 gets rid of the offset field. !!!! ---------
 */
private static ArrayList<Unit> convertVCUnitsToSbmlUnits_NOT_USED(double unitMultiplier, ucar.units_vcell.Unit vcUcarUnit, ArrayList<Unit> allSbmlUnitsList, int level, int version) {
    int unitScale = 0;
    if (vcUcarUnit instanceof ucar.units_vcell.UnitImpl) {
        ucar.units_vcell.UnitImpl unitImpl = (ucar.units_vcell.UnitImpl) vcUcarUnit;
        if (unitImpl instanceof ucar.units_vcell.DerivedUnitImpl) {
            ucar.units_vcell.DerivedUnitImpl baseUnit = (ucar.units_vcell.DerivedUnitImpl) unitImpl;
            ucar.units_vcell.Factor[] factors = baseUnit.getDimension().getFactors();
            for (int i = 0; i < factors.length; i++) {
                ucar.units_vcell.RationalNumber exponent = factors[i].getExponent();
                String baseName = ((ucar.units_vcell.BaseUnit) factors[i].getBase()).getName();
                Unit sbmlUnit = null;
                if (factors.length > 1) {
                    // To avoid that, add a dimensionless unit.
                    if (i == 0) {
                        Unit dimensionlessUnit = new Unit(level, version);
                        dimensionlessUnit.setKind(Kind.DIMENSIONLESS);
                        dimensionlessUnit.setExponent(1);
                        dimensionlessUnit.setScale(unitScale);
                        dimensionlessUnit.setMultiplier(unitMultiplier);
                        allSbmlUnitsList.add(dimensionlessUnit);
                    }
                    sbmlUnit = new Unit(level, version);
                    Kind kind = Kind.valueOf(baseName);
                    sbmlUnit.setKind(kind);
                    sbmlUnit.setExponent(exponent.intValue());
                    sbmlUnit.setScale(unitScale);
                    sbmlUnit.setMultiplier(1.0);
                    allSbmlUnitsList.add(sbmlUnit);
                } else {
                    sbmlUnit = new Unit(level, version);
                    Kind kind = Kind.valueOf(baseName);
                    sbmlUnit.setKind(kind);
                    sbmlUnit.setExponent(exponent.intValue());
                    sbmlUnit.setScale(unitScale);
                    sbmlUnit.setMultiplier(Math.pow(unitMultiplier, exponent.inverse().doubleValue()));
                    allSbmlUnitsList.add(sbmlUnit);
                }
            }
            return allSbmlUnitsList;
        } else if (unitImpl instanceof ucar.units_vcell.ScaledUnit) {
            ucar.units_vcell.ScaledUnit multdUnit = (ucar.units_vcell.ScaledUnit) unitImpl;
            unitMultiplier *= multdUnit.getScale();
            if (multdUnit.getUnit() != multdUnit.getDerivedUnit()) {
                return convertVCUnitsToSbmlUnits_NOT_USED(unitMultiplier, multdUnit.getUnit(), allSbmlUnitsList, level, version);
            }
        }
        /**
         *** COMMENTED OUT SINCE OFFSET IS NOT GOING TO BE USED FROM SBML L2 V2 ... ****
         *		  else if (unitImpl instanceof ucar.units_vcell.OffsetUnit) {
         *			ucar.units_vcell.OffsetUnit offsetUnit = (ucar.units_vcell.OffsetUnit)unitImpl;
         *			unitOffset += offsetUnit.getOffset();
         *			if (offsetUnit.getUnit() != offsetUnit.getDerivedUnit()){
         *				return convertVCUnitsToSbmlUnits(unitMultiplier, offsetUnit.getUnit(), allSbmlUnitsList);
         *			}
         *		}
         */
        if (unitImpl.getDerivedUnit() != vcUcarUnit) {
            // i.e. we have not reached the base unit, yet
            return convertVCUnitsToSbmlUnits_NOT_USED(unitMultiplier, unitImpl.getDerivedUnit(), allSbmlUnitsList, level, version);
        }
    } else {
        System.err.println("Unable to process unit translation: " + " " + vcUcarUnit.getSymbol());
    }
    throw new RuntimeException("unexpected vcell unit during transformation to sbml units: " + vcUcarUnit);
// return null;
}

Example 4 with Unit

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

the class SBMLSpatialTest method test.

// @Test
public void test() throws Exception {
    // BioModel bioModel1 = BioModelTest.getExampleWithImage();
    URL vcmlURL = SBMLSpatialTest.class.getResource("Solver_Suite_6_2.vcml");
    File vcmlFile = new File(vcmlURL.toURI());
    BioModel bioModel1 = XmlHelper.XMLToBioModel(new XMLSource(vcmlFile));
    bioModel1.refreshDependencies();
    // for (int i = 0; i<bioModel1.getNumSimulationContexts(); i++){
    for (int i = 5; i == 5; i++) {
        SimulationContext sc1 = bioModel1.getSimulationContext(i);
        if (sc1.getApplicationType() != Application.NETWORK_DETERMINISTIC) {
            System.err.println(sc1.getName() + " is not a network determistic application");
            continue;
        }
        boolean isSpatial = sc1.getGeometry().getDimension() > 0;
        SBMLExporter exporter = new SBMLExporter(bioModel1, 3, 1, isSpatial);
        sc1.refreshMathDescription(null, NetworkGenerationRequirements.ComputeFullNoTimeout);
        // sc1.setMathDescription(sc1.createNewMathMapping(null, NetworkGenerationRequirements.ComputeFullNoTimeout).getMathDescription());
        exporter.setSelectedSimContext(sc1);
        VCellSBMLDoc sbmlDoc = exporter.convertToSBML();
        for (UnitDefinition unitDefn : sbmlDoc.model.getListOfUnitDefinitions()) {
            for (Unit unit : unitDefn.getListOfUnits()) {
                System.out.println(unit.getKind());
                if (!unit.isSetKind()) {
                    throw new RuntimeException("kind of unit " + unit.printUnit() + " of UnitDefn " + UnitDefinition.printUnits(unitDefn) + " is not set");
                }
            }
        }
        // sbmlDoc.document.setConsistencyChecks(CHECK_CATEGORY.UNITS_CONSISTENCY, false);
        // int numErrors = sbmlDoc.document.checkConsistency();
        // System.out.println("consistency check, num errors = "+numErrors);
        // if (numErrors>0){
        // SBMLErrorLog errorLog = sbmlDoc.document.getListOfErrors();
        // for (int err=0; err<errorLog.getErrorCount(); err++){
        // System.err.println("ERROR IN EXPORTED SBML: "+errorLog.getError(err).getMessage());
        // }
        // //Assert.fail("generated SBML document was found to be inconsistent");
        // }
        String sbmlString = sbmlDoc.xmlString;
        File tempFile = File.createTempFile("sbmlSpatialTest_SBML_", ".sbml.xml");
        FileUtils.write(tempFile, sbmlString);
        System.out.println(tempFile);
        try {
            VCLogger argVCLogger = new TLogger();
            SBMLImporter importer = new SBMLImporter(tempFile.getAbsolutePath(), argVCLogger, isSpatial);
            BioModel bioModel2 = importer.getBioModel();
            File tempFile2 = File.createTempFile("sbmlSpatialTest_Biomodel_", ".vcml.xml");
            FileUtils.write(tempFile2, XmlHelper.bioModelToXML(bioModel2));
            System.out.println(tempFile2);
            // if (true) { throw new RuntimeException("stop"); }
            bioModel2.refreshDependencies();
            SimulationContext sc2 = bioModel2.getSimulationContext(0);
            // sc2.refreshMathDescription(null, NetworkGenerationRequirements.ComputeFullNoTimeout);
            sc2.setMathDescription(sc2.createNewMathMapping(null, NetworkGenerationRequirements.ComputeFullNoTimeout).getMathDescription());
            if (!sc1.getMathDescription().isValid()) {
                throw new RuntimeException("sc1.math is not valid");
            }
            if (!sc2.getMathDescription().isValid()) {
                throw new RuntimeException("sc2.math is not valid");
            }
            MathCompareResults mathCompareResults = MathDescription.testEquivalency(SimulationSymbolTable.createMathSymbolTableFactory(), sc1.getMathDescription(), sc2.getMathDescription());
            if (!mathCompareResults.isEquivalent()) {
                System.out.println("MATH DESCRIPTION 1 <UNCHANGED>");
                System.out.println(sc1.getMathDescription().getVCML_database());
                System.out.println("MATH DESCRIPTION 2 <UNCHANGED>");
                System.out.println(sc2.getMathDescription().getVCML_database());
                // if (mathCompareResults.decision  == Decision.MathDifferent_SUBDOMAINS_DONT_MATCH){
                // BioModel bioModel1_copy = XmlHelper.XMLToBioModel(new XMLSource(vcmlFile));
                // bioModel1_copy.refreshDependencies();
                // SimulationContext sc1_copy = bioModel1_copy.getSimulationContext(i);
                // VCImage image = sc1_copy.getGeometry().getGeometrySpec().getImage();
                // if (image!=null){
                // ArrayList<VCPixelClass> pcList = new ArrayList<VCPixelClass>();
                // for (VCPixelClass pc : image.getPixelClasses()){
                // pcList.add(new VCPixelClass(pc.getKey(),SBMLExporter.DOMAIN_TYPE_PREFIX+pc.getPixelClassName(),pc.getPixel()));
                // }
                // image.setPixelClasses(pcList.toArray(new VCPixelClass[0]));
                // }
                // for (GeometryClass gc : sc1_copy.getGeometry().getGeometryClasses()){
                // System.out.println("name before "+gc.getName());
                // gc.setName(SBMLExporter.DOMAIN_TYPE_PREFIX+gc.getName());
                // System.out.println("name after "+gc.getName());
                // }
                // sc1_copy.checkValidity();
                // bioModel1_copy.refreshDependencies();
                // sc1_copy.getGeometry().precomputeAll(new GeometryThumbnailImageFactoryAWT(), true, true);
                // sc1_copy.setMathDescription(sc1_copy.createNewMathMapping(null, NetworkGenerationRequirements.ComputeFullNoTimeout).getMathDescription());
                // MathCompareResults mathCompareResults_renamedSubdomains = MathDescription.testEquivalency(SimulationSymbolTable.createMathSymbolTableFactory(),sc1_copy.getMathDescription(), sc2.getMathDescription());
                // if (!mathCompareResults_renamedSubdomains.isEquivalent()){
                // System.out.println("MATH DESCRIPTION 1 <RENAMED>");
                // System.out.println(sc1_copy.getMathDescription().getVCML_database());
                // Assert.fail(mathCompareResults_renamedSubdomains.decision+" "+mathCompareResults_renamedSubdomains.details);
                // }
                // }else{
                System.err.println(mathCompareResults.decision + " " + mathCompareResults.details);
            // }
            } else {
                System.out.println("MATHS WERE EQUIVALENT");
            }
        } finally {
            tempFile.delete();
        }
    }
    // loop over determinstic applications
    System.out.println("done");
}

Example 5 with Unit

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

the class SBMLUnitTranslatorTest method testSBMLtoVCell.

@Test
public void testSBMLtoVCell() throws XMLStreamException, IOException, SbmlException {
    File[] sbmlFiles = getBiomodelsCuratedSBMLFiles();
    // };
    for (File sbmlFile : sbmlFiles) {
        if (sbmlFile.getName().equals("BIOMD0000000539.xml")) {
            System.err.println("skipping this model, seems like a bug in jsbml  RenderParser.processEndDocument() ... line 403 ... wrong constant for extension name");
            continue;
        }
        SBMLDocument doc = SBMLReader.read(sbmlFile);
        BioModel bioModel = new BioModel(null);
        VCUnitSystem unitSystem = bioModel.getModel().getUnitSystem();
        Model sbmlModel = doc.getModel();
        ListOf<UnitDefinition> listOfUnitDefinitions = sbmlModel.getListOfUnitDefinitions();
        for (UnitDefinition sbmlUnitDef : listOfUnitDefinitions) {
            VCUnitDefinition vcUnit = SBMLUnitTranslator.getVCUnitDefinition(sbmlUnitDef, unitSystem);
            UnitDefinition new_sbmlUnitDef = SBMLUnitTranslator.getSBMLUnitDefinition(vcUnit, 3, 1, unitSystem);
            VCUnitDefinition new_vcUnit = SBMLUnitTranslator.getVCUnitDefinition(new_sbmlUnitDef, unitSystem);
            if (!vcUnit.getSymbol().equals(new_vcUnit.getSymbol())) {
                System.err.println("orig vcUnit '" + vcUnit.getSymbol() + "' doesn't match new vcUnit '" + new_vcUnit.getSymbol() + "'");
            }
            // System.out.println("sbmlUnit = "+sbmlUnitDef.toString()+", vcUnit = "+vcUnit.getSymbol());
            System.out.println("sbmlUnit(" + sbmlUnitDef.getClass().getName() + ", builtin=" + sbmlUnitDef.isVariantOfSubstance() + ") = " + sbmlUnitDef.toString() + ", id=" + sbmlUnitDef.getId() + ",  name=" + sbmlUnitDef.getName() + ",   vcUnit = " + vcUnit.getSymbol());
            if (sbmlUnitDef.getNumUnits() > 1) {
                System.out.println("vcUnit = " + vcUnit.getSymbol());
                for (Unit unit : sbmlUnitDef.getListOfUnits()) {
                    try {
                        // VCUnitDefinition vcUnit = unitSystem.getInstance(unit.getKind().getName());
                        System.out.println("    vcUnit = " + unit);
                    } catch (Exception e) {
                        e.printStackTrace();
                    }
                }
                System.out.println("found bigger unit, " + sbmlUnitDef);
            }
        }
        if (sbmlFile == sbmlFiles[0]) {
            System.out.println("sbml length unit = " + sbmlModel.getLengthUnitsInstance() + ", idref=" + sbmlModel.getLengthUnits());
            System.out.println("sbml area unit = " + sbmlModel.getAreaUnitsInstance() + ", idref=" + sbmlModel.getAreaUnits());
            System.out.println("sbml volume unit = " + sbmlModel.getVolumeUnitsInstance() + ", idref=" + sbmlModel.getVolumeUnits());
            System.out.println("sbml time unit = " + sbmlModel.getTimeUnitsInstance() + ", idref=" + sbmlModel.getTimeUnits());
            System.out.println("sbml extent unit = " + sbmlModel.getExtentUnitsInstance() + ", idref=" + sbmlModel.getExtentUnits());
            System.out.println("sbml substance unit = " + sbmlModel.getSubstanceUnitsInstance() + ", idref=" + sbmlModel.getSubstanceUnits());
            for (UnitDefinition sbmlUnitDef : sbmlModel.getListOfPredefinedUnitDefinitions()) {
                if (sbmlUnitDef.getNumUnits() == 1 && sbmlUnitDef.getUnit(0).isAvogadro()) {
                    continue;
                }
                if (sbmlUnitDef.getNumUnits() == 1 && sbmlUnitDef.getUnit(0).isKatal()) {
                    continue;
                }
                VCUnitDefinition vcUnit = SBMLUnitTranslator.getVCUnitDefinition(sbmlUnitDef, unitSystem);
                // System.out.println("sbmlUnit = "+sbmlUnitDef.toString()+", vcUnit = "+vcUnit.getSymbol());
                System.out.println("sbmlUnit(" + sbmlUnitDef.getClass().getName() + ", builtin=" + sbmlUnitDef.isVariantOfSubstance() + ") = " + sbmlUnitDef.toString() + ", id=" + sbmlUnitDef.getId() + ",  name=" + sbmlUnitDef.getName() + ",   vcUnit = " + vcUnit.getSymbol());
            // for (Unit unit : sbmlUnitDef.getListOfUnits()){
            // try {
            // VCUnitDefinition vcUnit = unitSystem.getInstance(unit.getKind().getName());
            // System.out.println("    vcUnit = "+vcUnit.getSymbol());
            // }catch (Exception e){
            // e.printStackTrace();
            // }
            // }
            }
        }
    }
}