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

Example 46 with MathException

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

the class MathVerifier method scanBioModels.

/**
 * Insert the method's description here.
 * Creation date: (2/2/01 3:40:29 PM)
 */
public void scanBioModels(boolean bUpdateDatabase, KeyValue[] bioModelKeys) throws MathException, MappingException, SQLException, DataAccessException, ModelException, ExpressionException {
    java.util.Calendar calendar = java.util.GregorianCalendar.getInstance();
    // calendar.set(2002,java.util.Calendar.MAY,7+1);
    calendar.set(2002, java.util.Calendar.JULY, 1);
    final java.util.Date fluxCorrectionOrDisablingBugFixDate = calendar.getTime();
    // calendar.set(2001,java.util.Calendar.JUNE,13+1);
    calendar.set(2002, java.util.Calendar.JANUARY, 1);
    final java.util.Date totalVolumeCorrectionFixDate = calendar.getTime();
    User user = new User(PropertyLoader.ADMINISTRATOR_ACCOUNT, new KeyValue(PropertyLoader.ADMINISTRATOR_ID));
    for (int i = 0; i < bioModelKeys.length; i++) {
        BioModelInfo bioModelInfo = dbServerImpl.getBioModelInfo(user, bioModelKeys[i]);
        if (lg.isTraceEnabled())
            lg.trace("Testing bioModel with key '" + bioModelKeys[i] + "'");
        java.sql.Connection con = null;
        java.sql.Statement stmt = null;
        try {
            // 
            // read in the BioModel from the database
            // 
            BigString bioModelXML = dbServerImpl.getBioModelXML(user, bioModelInfo.getVersion().getVersionKey());
            BioModel bioModelFromDB = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
            BioModel bioModelNewMath = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
            bioModelFromDB.refreshDependencies();
            bioModelNewMath.refreshDependencies();
            // 
            // get all Simulations for this model
            // 
            Simulation[] modelSimsFromDB = bioModelFromDB.getSimulations();
            // 
            // for each application, recompute mathDescription, and verify it is equivalent
            // then check each associated simulation to ensure math overrides are applied in an equivalent manner also.
            // 
            SimulationContext[] simContextsFromDB = bioModelFromDB.getSimulationContexts();
            SimulationContext[] simContextsNewMath = bioModelNewMath.getSimulationContexts();
            for (int k = 0; k < simContextsFromDB.length; k++) {
                SimulationContext simContextFromDB = simContextsFromDB[k];
                Simulation[] appSimsFromDB = simContextFromDB.getSimulations();
                SimulationContext simContextNewMath = simContextsNewMath[k];
                Simulation[] appSimsNewMath = simContextNewMath.getSimulations();
                MathCompareResults mathCompareResults = null;
                try {
                    MathDescription origMathDesc = simContextFromDB.getMathDescription();
                    // 
                    // find out if any simulation belonging to this Application has data
                    // 
                    boolean bApplicationHasData = false;
                    for (int l = 0; l < modelSimsFromDB.length; l++) {
                        SimulationStatusPersistent simulationStatus = dbServerImpl.getSimulationStatus(modelSimsFromDB[l].getKey());
                        if (simulationStatus != null && simulationStatus.getHasData()) {
                            bApplicationHasData = true;
                        }
                    }
                    // 
                    try {
                        if (simContextNewMath.getGeometry().getDimension() > 0 && simContextNewMath.getGeometry().getGeometrySurfaceDescription().getGeometricRegions() == null) {
                            simContextNewMath.getGeometry().getGeometrySurfaceDescription().updateAll();
                        }
                    } catch (Exception e) {
                        e.printStackTrace(System.out);
                    }
                    // 
                    // updated mathdescription loaded into copy of biomodel, then test for equivalence.
                    // 
                    cbit.vcell.mapping.MathMapping mathMapping = simContextNewMath.createNewMathMapping();
                    MathDescription newMathDesc = mathMapping.getMathDescription();
                    String issueString = null;
                    org.vcell.util.Issue[] issues = mathMapping.getIssues();
                    if (issues != null && issues.length > 0) {
                        StringBuffer buffer = new StringBuffer("Issues(" + issues.length + "):");
                        for (int l = 0; l < issues.length; l++) {
                            buffer.append(" <<" + issues[l].toString() + ">>");
                        }
                        issueString = buffer.toString();
                    }
                    simContextNewMath.setMathDescription(newMathDesc);
                    MathCompareResults testIfSameResults = cbit.vcell.math.MathUtilities.testIfSame(SimulationSymbolTable.createMathSymbolTableFactory(), origMathDesc, newMathDesc);
                    mathCompareResults = MathDescription.testEquivalency(SimulationSymbolTable.createMathSymbolTableFactory(), origMathDesc, newMathDesc);
                    StringBuffer buffer = new StringBuffer();
                    buffer.append(">>>BioModel(" + bioModelFromDB.getVersion().getVersionKey() + ") '" + bioModelFromDB.getName() + "':" + bioModelFromDB.getVersion().getDate() + ", Application(" + simContextFromDB.getKey() + ") '" + simContextFromDB.getName() + "' <<EQUIV=" + mathCompareResults.isEquivalent() + ">>: " + mathCompareResults.toDatabaseStatus());
                    // 
                    if (bUpdateDatabase) {
                        con = null;
                        stmt = null;
                        try {
                            con = conFactory.getConnection(new Object());
                            stmt = con.createStatement();
                            // KeyValue mathKey = origMathDesc.getKey();
                            String UPDATESTATUS = "UPDATE " + SimContextStat2Table.table.getTableName() + " SET " + SimContextStat2Table.table.hasData.getUnqualifiedColName() + " = " + ((bApplicationHasData) ? (1) : (0)) + ", " + SimContextStat2Table.table.equiv.getUnqualifiedColName() + " = " + (mathCompareResults.isEquivalent() ? (1) : (0)) + ", " + SimContextStat2Table.table.status.getUnqualifiedColName() + " = '" + org.vcell.util.TokenMangler.getSQLEscapedString(mathCompareResults.toDatabaseStatus()) + "'" + ((issueString != null) ? (", " + SimContextStat2Table.table.comments.getUnqualifiedColName() + " = '" + org.vcell.util.TokenMangler.getSQLEscapedString(issueString, 255) + "'") : ("")) + " WHERE " + SimContextStat2Table.table.simContextRef.getUnqualifiedColName() + " = " + simContextFromDB.getKey();
                            int numRowsChanged = stmt.executeUpdate(UPDATESTATUS);
                            if (numRowsChanged != 1) {
                                System.out.println("failed to update status");
                            }
                            con.commit();
                            if (lg.isTraceEnabled())
                                lg.trace("-------------- Update=true, saved 'newMath' for Application '" + simContextFromDB.getName() + "'");
                        } catch (SQLException e) {
                            lg.error(e.getMessage(), e);
                            if (lg.isWarnEnabled())
                                lg.warn("*&*&*&*&*&*&*& Update=true, FAILED TO UPDATE MATH for Application '" + simContextFromDB.getName() + "'");
                        } finally {
                            if (stmt != null) {
                                stmt.close();
                            }
                            con.close();
                        }
                    }
                } catch (Throwable e) {
                    // exception in SimContext
                    lg.error(e.getMessage(), e);
                    if (bUpdateDatabase) {
                        con = null;
                        stmt = null;
                        try {
                            con = conFactory.getConnection(new Object());
                            stmt = con.createStatement();
                            String status = "'EXCEPTION: " + org.vcell.util.TokenMangler.getSQLEscapedString(e.toString()) + "'";
                            if (status.length() > 255)
                                status = status.substring(0, 254) + "'";
                            String UPDATESTATUS = "UPDATE " + SimContextStat2Table.table.getTableName() + " SET " + SimContextStat2Table.table.status.getUnqualifiedColName() + " = " + status + " WHERE " + SimContextStat2Table.table.simContextRef.getUnqualifiedColName() + " = " + simContextFromDB.getKey();
                            int numRowsChanged = stmt.executeUpdate(UPDATESTATUS);
                            if (numRowsChanged != 1) {
                                System.out.println("failed to update status with exception");
                            }
                            con.commit();
                            if (lg.isTraceEnabled())
                                lg.trace("-------------- Update=true, saved exception for Application '" + simContextFromDB.getName() + "'");
                        } catch (SQLException e2) {
                            lg.error(e2.getMessage(), e2);
                            if (lg.isWarnEnabled())
                                lg.warn("*&*&*&*&*&*&*& Update=true, FAILED TO save exception status for Application '" + simContextFromDB.getName() + "'");
                        } finally {
                            if (stmt != null) {
                                stmt.close();
                            }
                            con.close();
                        }
                    }
                }
                // 
                for (int l = 0; l < appSimsFromDB.length; l++) {
                    try {
                        boolean bSimEquivalent = Simulation.testEquivalency(appSimsNewMath[l], appSimsFromDB[l], mathCompareResults);
                        if (lg.isTraceEnabled())
                            lg.trace("Application(" + simContextFromDB.getKey() + ") '" + simContextFromDB.getName() + "', " + "Simulation(" + modelSimsFromDB[l].getKey() + ") '" + modelSimsFromDB[l].getName() + "':" + modelSimsFromDB[l].getVersion().getDate() + "mathEquivalency=" + mathCompareResults.isEquivalent() + ", simEquivalency=" + bSimEquivalent);
                        // 
                        if (bUpdateDatabase) {
                            con = null;
                            stmt = null;
                            try {
                                con = conFactory.getConnection(new Object());
                                stmt = con.createStatement();
                                String UPDATESTATUS = "UPDATE " + SimStatTable.table.getTableName() + " SET " + SimStatTable.table.equiv.getUnqualifiedColName() + " = " + ((bSimEquivalent) ? (1) : (0)) + ", " + SimStatTable.table.status.getUnqualifiedColName() + " = '" + org.vcell.util.TokenMangler.getSQLEscapedString(mathCompareResults.decision.description) + "'" + " WHERE " + SimStatTable.table.simRef.getUnqualifiedColName() + " = " + appSimsFromDB[l].getKey();
                                int numRowsChanged = stmt.executeUpdate(UPDATESTATUS);
                                if (numRowsChanged != 1) {
                                    System.out.println("failed to update status");
                                }
                                con.commit();
                                if (lg.isTraceEnabled())
                                    lg.trace("-------------- Update=true, saved 'simulation status for simulation '" + appSimsFromDB[l].getName() + "'");
                            } catch (SQLException e) {
                                lg.error(e.getMessage(), e);
                                if (lg.isWarnEnabled())
                                    lg.warn("*&*&*&*&*&*&*& Update=true, FAILED TO UPDATE status for simulation '" + appSimsFromDB[l].getName() + "'");
                            } finally {
                                if (stmt != null) {
                                    stmt.close();
                                }
                                con.close();
                            }
                        }
                    } catch (Throwable e) {
                        // exception in SimContext
                        lg.error(e.getMessage(), e);
                        if (bUpdateDatabase) {
                            con = null;
                            stmt = null;
                            try {
                                con = conFactory.getConnection(new Object());
                                stmt = con.createStatement();
                                String status = "'EXCEPTION: " + org.vcell.util.TokenMangler.getSQLEscapedString(e.toString()) + "'";
                                if (status.length() > 255)
                                    status = status.substring(0, 254) + "'";
                                String UPDATESTATUS = "UPDATE " + SimStatTable.table.getTableName() + " SET " + SimStatTable.table.status.getUnqualifiedColName() + " = " + status + " WHERE " + SimStatTable.table.simRef.getUnqualifiedColName() + " = " + appSimsFromDB[l].getKey();
                                int numRowsChanged = stmt.executeUpdate(UPDATESTATUS);
                                if (numRowsChanged != 1) {
                                    System.out.println("failed to update status with exception");
                                }
                                con.commit();
                                if (lg.isTraceEnabled())
                                    lg.trace("-------------- Update=true, saved exception for Simulation '" + appSimsFromDB[l].getName() + "'");
                            } catch (SQLException e2) {
                                lg.error(e2.getMessage(), e2);
                                if (lg.isWarnEnabled())
                                    lg.warn("*&*&*&*&*&*&*& Update=true, FAILED TO save exception status for simulation '" + appSimsFromDB[l].getName() + "'");
                            } finally {
                                if (stmt != null) {
                                    stmt.close();
                                }
                                con.close();
                            }
                        }
                    }
                }
            }
        } catch (Throwable e) {
            // exception in whole BioModel
            lg.error(e.getMessage(), e);
        // can't update anything in database, since we don't know what simcontexts are involved
        }
    }
}

Example 47 with MathException

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

the class SimulationContextDbDriver method assignAnalysisTasksSQL.

/**
 * This method was created in VisualAge.
 * @param simContext cbit.vcell.mapping.SimulationContext
 */
private void assignAnalysisTasksSQL(Connection con, KeyValue simContextKey, SimulationContext simContext) throws SQLException, DataAccessException {
    String sql;
    AnalysisTaskXMLTable analysisTaskTable = AnalysisTaskXMLTable.table;
    sql = " SELECT " + analysisTaskTable.analysisTaskXML.toString() + " FROM " + analysisTaskTable.getTableName() + " WHERE " + analysisTaskTable.simContextRef + " = " + simContextKey + " ORDER BY " + // order-by to maintain order ... not really necessary
    analysisTaskTable.insertDate;
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        while (rset.next()) {
            String analysisXML = (String) getLOB(rset, analysisTaskTable.analysisTaskXML, dbSyntax);
            org.jdom.Element rootElement = XmlUtil.stringToXML(analysisXML, null).getRootElement();
            cbit.vcell.modelopt.ParameterEstimationTask parameterEstimationTask = cbit.vcell.modelopt.ParameterEstimationTaskXMLPersistence.getParameterEstimationTask(rootElement, simContext);
            simContext.addAnalysisTask(parameterEstimationTask);
        }
    } catch (MathException | MappingException | PropertyVetoException | ExpressionException e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException(e.getMessage());
    } finally {
        if (stmt != null) {
            stmt.close();
        }
    }
}

Example 48 with MathException

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

the class FastSystemAnalyzer method refreshInvarianceMatrix.

/**
 */
private void refreshInvarianceMatrix() throws MathException, ExpressionException {
    // 
    // the invariance's are expressed in matrix form
    // 
    // |a a a a a -1  0  0|   |x1|   |0|
    // |a a a a a  0 -1  0| * |x2| = |0|
    // |a a a a a  0  0 -1|   |x3|   |0|
    // |x4|
    // |x5|
    // |c1|
    // |c2|
    // |c3|
    // 
    Variable[] vars = new Variable[fastVarList.size()];
    fastVarList.copyInto(vars);
    int numVars = fastVarList.size();
    int rows = fastSystem.getNumFastInvariants();
    int cols = numVars + fastSystem.getNumFastInvariants();
    RationalExpMatrix matrix = new RationalExpMatrix(rows, cols);
    Enumeration<FastInvariant> fastInvariantsEnum = fastSystem.getFastInvariants();
    for (int i = 0; i < rows && fastInvariantsEnum.hasMoreElements(); i++) {
        FastInvariant fi = (FastInvariant) fastInvariantsEnum.nextElement();
        Expression function = fi.getFunction();
        for (int j = 0; j < numVars; j++) {
            Variable var = (Variable) fastVarList.elementAt(j);
            Expression exp = function.differentiate(var.getName());
            exp.bindExpression(null);
            exp = exp.flatten();
            RationalExp coeffRationalExp = RationalExpUtils.getRationalExp(exp);
            matrix.set_elem(i, j, coeffRationalExp);
        }
        matrix.set_elem(i, numVars + i, -1);
    }
    // Print
    System.out.println("origMatrix");
    matrix.show();
    // 
    // gaussian elimination on the matrix give the following representation
    // note that some column pivoting (variable re-ordering) is sometimes required to
    // determine N-r dependent vars
    // 
    // |10i0iccc|
    // |01i0iccc|  where (c)'s are the coefficients for constants of invariances
    // |00i1iccc|        (i)'s are the coefficients for dependent vars in terms of independent vars
    // 
    // Print
    System.out.println("reducedMatrix");
    if (rows > 0) {
        try {
            matrix.gaussianElimination(new RationalExpMatrix(rows, rows));
        } catch (MatrixException e) {
            e.printStackTrace(System.out);
            throw new MathException(e.getMessage());
        }
    }
    matrix.show();
    for (int i = 0; i < vars.length; i++) {
        System.out.print(vars[i].getName() + "  ");
    }
    System.out.println("");
    // 
    for (int i = 0; i < rows; i++) {
        for (int j = 0; j < rows; j++) {
            RationalExp rexp = matrix.get(i, j).simplify();
            matrix.set_elem(i, j, rexp);
        }
    }
    for (int i = 0; i < rows; i++) {
        // 
        if (!matrix.get(i, i).isConstant() || matrix.get(i, i).getConstant().doubleValue() != 1) {
            for (int j = i + 1; j < numVars; j++) {
                if (matrix.get(i, j).isConstant() && matrix.get(i, j).getConstant().doubleValue() == 1.0) {
                    for (int ii = 0; ii < rows; ii++) {
                        RationalExp temp = matrix.get(ii, i);
                        matrix.set_elem(ii, i, matrix.get(ii, j));
                        matrix.set_elem(ii, j, temp);
                    }
                    Variable tempVar = vars[i];
                    vars[i] = vars[j];
                    vars[j] = tempVar;
                    break;
                }
            }
        }
    }
    // Print
    for (int i = 0; i < vars.length; i++) {
        System.out.print(vars[i].getName() + "  ");
    }
    System.out.println("");
    matrix.show();
    // 
    // separate into dependent and indepent variables, and chop off identity matrix (left N-r columns)
    // 
    // T       |iiccc|                   T
    // [x1 x2 x4] = -1 * |iiccc| * [x3 x5 c1 c2 c3]
    // |iiccc|
    // 
    // 
    int numInvariants = fastSystem.getNumFastInvariants();
    dependentVarList.removeAllElements();
    for (int i = 0; i < numInvariants; i++) {
        dependentVarList.addElement(vars[i]);
    }
    independentVarList.removeAllElements();
    for (int i = numInvariants; i < vars.length; i++) {
        independentVarList.addElement(vars[i]);
    }
    int new_cols = independentVarList.size() + numInvariants;
    dependencyMatrix = new RationalExpMatrix(rows, new_cols);
    for (int i = 0; i < rows; i++) {
        for (int j = 0; j < new_cols; j++) {
            RationalExp rexp = matrix.get(i, j + dependentVarList.size()).simplify().minus();
            dependencyMatrix.set_elem(i, j, rexp);
        }
    }
    // Print
    System.out.println("\n\nDEPENDENCY MATRIX");
    dependencyMatrix.show();
    System.out.print("dependent vars: ");
    for (int i = 0; i < dependentVarList.size(); i++) {
        System.out.print(((Variable) dependentVarList.elementAt(i)).getName() + "  ");
    }
    System.out.println("");
    System.out.print("independent vars: ");
    for (int i = 0; i < independentVarList.size(); i++) {
        System.out.print(((Variable) independentVarList.elementAt(i)).getName() + "  ");
    }
    System.out.println("");
}

Example 49 with MathException

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

the class FastSystemAnalyzer method refreshFastVarList.

/**
 * @return java.util.Vector
 */
private void refreshFastVarList() throws MathException, ExpressionException {
    fastVarList.clear();
    // 
    // get list of unique (VolVariables and MemVariables) in fastRate expressions
    // 
    Enumeration<FastRate> fastRatesEnum = fastSystem.getFastRates();
    while (fastRatesEnum.hasMoreElements()) {
        FastRate fr = fastRatesEnum.nextElement();
        Expression exp = fr.getFunction();
        Enumeration<Variable> enum1 = MathUtilities.getRequiredVariables(exp, this);
        while (enum1.hasMoreElements()) {
            Variable var = enum1.nextElement();
            if (var instanceof VolVariable || var instanceof MemVariable) {
                if (!fastVarList.contains(var)) {
                    fastVarList.addElement(var);
                // System.out.println("FastSystemImplicit.refreshFastVarList(), FAST RATE VARIABLE: "+var.getName());
                }
            }
        }
    }
    // 
    // get list of all variables used in invariant expressions that are not used in fast rates
    // 
    Enumeration<FastInvariant> fastInvariantsEnum = fastSystem.getFastInvariants();
    while (fastInvariantsEnum.hasMoreElements()) {
        FastInvariant fi = (FastInvariant) fastInvariantsEnum.nextElement();
        Expression exp = fi.getFunction();
        // System.out.println("FastSystemImplicit.refreshFastVarList(), ORIGINAL FAST INVARIANT: "+exp);
        Enumeration<Variable> enum1 = MathUtilities.getRequiredVariables(exp, this);
        while (enum1.hasMoreElements()) {
            Variable var = enum1.nextElement();
            if (var instanceof VolVariable || var instanceof MemVariable) {
                if (!fastVarList.contains(var)) {
                    fastVarList.addElement(var);
                }
            }
        }
    }
    // 
    // verify that there are N equations (rates+invariants) and N unknowns (fastVariables)
    // 
    int numBoundFunctions = fastSystem.getNumFastInvariants() + fastSystem.getNumFastRates();
    if (fastVarList.size() != numBoundFunctions) {
        throw new MathException("FastSystem.checkDimension(), there are " + fastVarList.size() + " variables and " + numBoundFunctions + " FastInvariant's & FastRates");
    }
}

Example 50 with MathException

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

the class XmlReader method getMathDescription.

/**
 * This method returns a MathDescription from a XML element.
 * Creation date: (4/26/2001 12:11:14 PM)
 * @return cbit.vcell.math.MathDescription
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
MathDescription getMathDescription(Element param, Geometry geometry) throws XmlParseException {
    MathDescription mathdes = null;
    Element tempelement;
    // Retrieve Metadata(Version)
    Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    // Retrieve attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    // Create new MathDescription
    if (version != null) {
        mathdes = new MathDescription(version);
    } else {
        mathdes = new MathDescription(name);
    }
    try {
        // this step is needed!
        mathdes.setGeometry(geometry);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("a PropertyVetoException was fired when setting the Geometry to the Mathdescription in the simContext " + name, e);
    }
    // set attributes
    try {
        mathdes.setName(name);
        // String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag);
        // if (annotation!=null) {
        // mathdes.setDescription(unMangle(annotation));
        // }
        // add Annotation
        String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotationText != null && annotationText.length() > 0) {
            mathdes.setDescription(unMangle(annotationText));
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException was fired when setting the name " + name + ", to a new MathDescription!", e);
    }
    VariableHash varHash = new VariableHash();
    // Retrieve Constant
    Iterator<Element> iterator = param.getChildren(XMLTags.ConstantTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getConstant(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve FilamentRegionVariables
    iterator = param.getChildren(XMLTags.FilamentRegionVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getFilamentRegionVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve FilamentVariables
    iterator = param.getChildren(XMLTags.FilamentVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getFilamentVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // retrieve InsideVariables
    // **** This variables are for internal USE ******
    // Retrieve MembraneRegionVariable
    iterator = param.getChildren(XMLTags.MembraneRegionVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getMembraneRegionVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve MembraneVariable
    iterator = param.getChildren(XMLTags.MembraneVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getMemVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve PointVariable
    iterator = param.getChildren(XMLTags.PointVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getPointVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // retrieve OutsideVariables
    // **** This variables are for internal USE ******
    // Retrieve Volume Region variable
    iterator = param.getChildren(XMLTags.VolumeRegionVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getVolumeRegionVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve VolumeVariable
    iterator = param.getChildren(XMLTags.VolumeVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getVolVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve StochVolVariable
    iterator = param.getChildren(XMLTags.StochVolVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getStochVolVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve all the Functions //This needs to be processed before all the variables are read!
    iterator = param.getChildren(XMLTags.FunctionTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getFunction(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    iterator = param.getChildren(XMLTags.VolumeRandomVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getRandomVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    iterator = param.getChildren(XMLTags.MembraneRandomVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getRandomVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    iterator = param.getChildren(XMLTags.VolumeParticleVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getVolumeParticalVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    iterator = param.getChildren(XMLTags.MembraneParticleVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getMembraneParticalVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // ParticleMolecularTypeTag       getParticleMolecularTypes
    // has to be done before VolumeParticleSpeciesPattern and VolumeParticleObservable
    iterator = param.getChildren(XMLTags.ParticleMolecularTypeTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        mathdes.addParticleMolecularType(getParticleMolecularType(tempelement));
    }
    // VolumeParticleSpeciesPatternTag
    iterator = param.getChildren(XMLTags.VolumeParticleSpeciesPatternTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getVolumeParticleSpeciesPattern(tempelement, mathdes));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // VolumeParticleObservableTag    getParticleObservables
    iterator = param.getChildren(XMLTags.VolumeParticleObservableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getVolumeParticleObservable(tempelement, varHash));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // 
    try {
        mathdes.setAllVariables(varHash.getAlphabeticallyOrderedVariables());
    } catch (MathException e) {
        e.printStackTrace();
        throw new XmlParseException("Error adding the Function variables to the MathDescription " + name, e);
    } catch (ExpressionBindingException e) {
        e.printStackTrace();
        throw new XmlParseException("Error adding the Function variables to the MathDescription " + name, e);
    }
    // Retrieve CompartmentsSubdomains
    iterator = param.getChildren(XMLTags.CompartmentSubDomainTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            mathdes.addSubDomain(getCompartmentSubDomain(tempelement, mathdes));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("Error adding a new CompartmentSubDomain to the MathDescription " + name, e);
        }
    }
    // Retrieve MembraneSubdomains
    iterator = param.getChildren(XMLTags.MembraneSubDomainTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            mathdes.addSubDomain(getMembraneSubDomain(tempelement, mathdes));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("Error adding a new MembraneSubDomain to the MathDescription " + name, e);
        }
    }
    // Retrieve the FilamentSubdomain (if any)
    tempelement = param.getChild(XMLTags.FilamentSubDomainTag, vcNamespace);
    if (tempelement != null) {
        try {
            mathdes.addSubDomain(getFilamentSubDomain(tempelement, mathdes));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("Error adding a new FilamentSubDomain to the MathDescription " + name, e);
        }
    }
    // Retrieve the PointSubdomain (if any)
    tempelement = param.getChild(XMLTags.PointSubDomainTag, vcNamespace);
    if (tempelement != null) {
        try {
            mathdes.addSubDomain(getPointSubDomain(tempelement, mathdes));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("Error adding a new PointSubDomain to the MathDescription " + name, e);
        }
    }
    iterator = param.getChildren(XMLTags.EventTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        Event event = getEvent(mathdes, tempelement);
        try {
            mathdes.addEvent(event);
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException(e);
        }
    }
    iterator = param.getChildren(XMLTags.PostProcessingBlock, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        getPostProcessingBlock(mathdes, tempelement);
    }
    return mathdes;
}