Examples with SymbolTableEntry cbit.vcell.parser.SymbolTableEntry used on opensource projects

Example 76 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class StructureAnalyzer method refreshTotalDependancies.

/**
 * This method was created by a SmartGuide.
 * @param b cbit.vcell.math.Matrix
 * @param vars java.lang.String[]
 */
static StructureAnalyzer.Dependency[] refreshTotalDependancies(RationalMatrix nullSpaceMatrix, SpeciesContextMapping[] speciesContextMappings, MathMapping_4_8 argMathMapping, boolean bFast) throws Exception {
    // System.out.println("StructureAnalyzer.refreshTotalDependancies()");
    SimulationContext argSimContext = argMathMapping.getSimulationContext();
    if (nullSpaceMatrix == null) {
        // System.out.println("the matrix has full rank, there are no dependencies");
        return new StructureAnalyzer.Dependency[0];
    }
    if (speciesContextMappings.length != nullSpaceMatrix.getNumCols()) {
        // throw new Exception("varName array not same dimension as b matrix");
        System.out.println("varName array not same dimension as b matrix");
        nullSpaceMatrix.show();
        for (int i = 0; i < speciesContextMappings.length; i++) {
            System.out.println("scm[" + i + "] is " + speciesContextMappings[i].getSpeciesContext().getName());
        }
    }
    // System.out.println("there are "+nullSpaceMatrix.rows+" dependencies");
    Vector<Dependency> dependencyList = new Vector<Dependency>();
    for (int i = 0; i < nullSpaceMatrix.getNumRows(); i++) {
        // 
        // find first variable
        // 
        Expression exp = null;
        Expression constantExp = null;
        String constantName = null;
        SpeciesContextMapping firstSCM = null;
        boolean bFirst = true;
        for (int j = 0; j < nullSpaceMatrix.getNumCols(); j++) {
            RationalNumber coeff = nullSpaceMatrix.get_elem(i, j);
            if (coeff.doubleValue() != 0.0) {
                if (bFirst) {
                    if (coeff.doubleValue() != 1.0) {
                        System.out.println("i=" + i + " j=" + j);
                        nullSpaceMatrix.show();
                        throw new Exception("expecting a coefficient of 1.0, instead coeff = " + coeff.infix());
                    }
                    firstSCM = speciesContextMappings[j];
                    // 
                    // first term of dependancy expression   ("K_CalciumCyt")
                    // 
                    SpeciesContext firstSC = firstSCM.getSpeciesContext();
                    constantName = "K_" + firstSC.getName() + "_total";
                    exp = new Expression(constantName);
                    // 
                    // first term of K expression
                    // 
                    StructureMapping firstSM = argSimContext.getGeometryContext().getStructureMapping(firstSC.getStructure());
                    SpeciesContextSpec firstSCS = argSimContext.getReactionContext().getSpeciesContextSpec(firstSC);
                    SymbolTableEntry scSTE = null;
                    if (bFast) {
                        scSTE = firstSCS.getSpeciesContext();
                    } else {
                        scSTE = firstSCS.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
                    }
                    constantExp = Expression.mult(new Expression(coeff), firstSM.getNormalizedConcentrationCorrection(argSimContext, argMathMapping), new Expression(scSTE, argMathMapping.getNameScope()));
                    bFirst = false;
                } else {
                    // 
                    // add term to dependancy expression     (" - 2*IP3Cyt ")
                    // 
                    SpeciesContextMapping scm = speciesContextMappings[j];
                    SpeciesContext sc = scm.getSpeciesContext();
                    StructureMapping sm = argSimContext.getGeometryContext().getStructureMapping(sc.getStructure());
                    SpeciesContextSpec scs = argSimContext.getReactionContext().getSpeciesContextSpec(sc);
                    exp = Expression.add(exp, Expression.negate(Expression.mult(new Expression(coeff), sm.getNormalizedConcentrationCorrection(argSimContext, argMathMapping), new Expression(sc, argMathMapping.getNameScope()))));
                    // 
                    // add term to K expression
                    // 
                    SymbolTableEntry scSTE = null;
                    if (bFast) {
                        scSTE = sc;
                    } else {
                        scSTE = scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
                    }
                    constantExp = Expression.add(constantExp, Expression.mult(new Expression(coeff), sm.getNormalizedConcentrationCorrection(argSimContext, argMathMapping), new Expression(scSTE, argMathMapping.getNameScope())));
                }
            }
        }
        if (firstSCM != null) {
            // 
            // store totalMass parameter (e.g. K_xyz_total = xyz_init + wzy_init)
            // 
            // MathMapping.MathMappingParameter totalMassParameter = mathMapping.addMathMappingParameter(constantName,constantExp.flatten(),MathMapping.PARAMETER_ROLE_TOTALMASS,cbit.vcell.units.VCUnitDefinition.UNIT_uM);
            // 
            // store dependency parameter (e.g. xyz = K_xyz_total - wzy)
            // 
            StructureMapping sm = argSimContext.getGeometryContext().getStructureMapping(firstSCM.getSpeciesContext().getStructure());
            exp = Expression.mult(exp, Expression.invert(sm.getNormalizedConcentrationCorrection(argSimContext, argMathMapping)));
            exp = exp.flatten();
            // exp.bindExpression(mathMapping_temp);
            // firstSCM.setDependencyExpression(exp);
            Dependency dependency = new Dependency();
            dependency.dependencyExpression = exp;
            dependency.speciesContextMapping = firstSCM;
            dependency.invariantSymbolName = constantName;
            dependency.conservedMoietyExpression = constantExp.flatten();
            dependencyList.add(dependency);
        }
    }
    return (StructureAnalyzer.Dependency[]) BeanUtils.getArray(dependencyList, StructureAnalyzer.Dependency.class);
}

Example 77 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class MathDescription method getEntry.

/**
 * This method was created by a SmartGuide.
 * @return cbit.vcell.parser.SymbolTableEntry
 * @param id java.lang.String
 * @param qualifier java.lang.String
 * @exception java.lang.Exception The exception description.
 */
public SymbolTableEntry getEntry(String id) {
    SymbolTableEntry entry = null;
    entry = ReservedMathSymbolEntries.getEntry(id, false);
    if (entry != null) {
        if (entry instanceof SymbolTableFunctionEntry) {
            if (entry.equals(MathFunctionDefinitions.Function_regionArea_current) || entry.equals(MathFunctionDefinitions.Function_regionArea_indexed) || entry.equals(MathFunctionDefinitions.Function_regionVolume_current) || entry.equals(MathFunctionDefinitions.Function_regionVolume_indexed)) {
                bRegionSizeFunctionsUsed = true;
            }
        }
        return entry;
    }
    entry = getVariable(id);
    if (entry != null) {
        return entry;
    }
    return null;
}

Example 78 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class MathSymbolMapping method reconcileVarNames.

/**
 * Insert the method's description here.
 * Creation date: (5/3/2006 4:03:51 PM)
 * @param mathDesc cbit.vcell.math.MathDescription
 */
public void reconcileVarNames(MathDescription mathDesc) {
    // 
    // clear secondary hashmaps in case called multiple times.
    // 
    biologicalToMathHash.clear();
    mathToBiologicalHash.clear();
    java.util.Set<SymbolTableEntry> keyset = biologicalToMathSymbolNameHash.keySet();
    java.util.Iterator<SymbolTableEntry> keysetIter = keyset.iterator();
    while (keysetIter.hasNext()) {
        SymbolTableEntry biologicalSymbol = keysetIter.next();
        String mathVarName = (String) biologicalToMathSymbolNameHash.get(biologicalSymbol);
        Variable var = mathDesc.getVariable(mathVarName);
        if (var != null) {
            biologicalToMathHash.put(biologicalSymbol, var);
            SymbolTableEntry[] previousBiologicalSymbolArr = (SymbolTableEntry[]) mathToBiologicalHash.put(var, new SymbolTableEntry[] { biologicalSymbol });
            if (previousBiologicalSymbolArr != null) {
                SymbolTableEntry[] steArr = (SymbolTableEntry[]) BeanUtils.addElement(previousBiologicalSymbolArr, biologicalSymbol);
                mathToBiologicalHash.put(var, steArr);
            }
        }
    }
}

Example 79 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class ParameterContext method getEntry.

/**
 * getEntry method comment.
 */
public SymbolTableEntry getEntry(String identifierString) {
    SymbolTableEntry localSTE = getLocalEntry(identifierString);
    if (localSTE != null && !(localSTE instanceof UnresolvedParameter)) {
        return localSTE;
    }
    // may be null.
    UnresolvedParameter unresolvedParameter = (UnresolvedParameter) localSTE;
    SymbolTableEntry externalSTE = getNameScope().getExternalEntry(identifierString, this);
    if (externalSTE instanceof SymbolTableFunctionEntry) {
        return externalSTE;
    }
    // 
    if (externalSTE != null) {
        if (unresolvedParameter != null) {
            removeUnresolvedParameters(this);
        }
        return addProxyParameter(externalSTE);
    } else if (unresolvedParameter != null) {
        return unresolvedParameter;
    }
    return null;
}

Example 80 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class ParameterContext method getLocalEntry.

/**
 * Insert the method's description here.
 * Creation date: (12/8/2003 11:46:37 AM)
 * @return SymbolTableEntry
 * @param identifier java.lang.String
 */
public SymbolTableEntry getLocalEntry(java.lang.String identifier) {
    SymbolTableEntry ste = getLocalParameterFromName(identifier);
    if (ste != null) {
        return ste;
    }
    ste = getProxyParameter(identifier);
    if (ste != null) {
        return ste;
    }
    return null;
}