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

Example 81 with SymbolTableEntry

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

the class ReactionSpec method getEntry.

/**
 * getEntry method comment.
 */
public SymbolTableEntry getEntry(java.lang.String identifierString) {
    // 
    // look locally (in the ReactionSpec) to resolve identifier
    // 
    SymbolTableEntry ste = getLocalEntry(identifierString);
    if (ste != null) {
        return ste;
    }
    // 
    // travel in namespace
    // 
    ste = getNameScope().getExternalEntry(identifierString, this);
    return ste;
}

Example 82 with SymbolTableEntry

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

the class AbstractMathMapping method getIdentifierSubstitutions.

/**
 * Substitutes appropriate variables for speciesContext bindings
 *
 * @return cbit.vcell.parser.Expression
 * @param origExp cbit.vcell.parser.Expression
 * @param structureMapping cbit.vcell.mapping.StructureMapping
 */
protected Expression getIdentifierSubstitutions(Expression origExp, VCUnitDefinition desiredExpUnitDef, GeometryClass geometryClass) throws ExpressionException, MappingException {
    String[] symbols = origExp.getSymbols();
    if (symbols == null) {
        return origExp;
    }
    VCUnitDefinition expUnitDef = null;
    try {
        VCUnitEvaluator unitEvaluator = new VCUnitEvaluator(simContext.getModel().getUnitSystem());
        expUnitDef = unitEvaluator.getUnitDefinition(origExp);
        if (desiredExpUnitDef == null) {
            String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
            System.out.println("...........exp='" + expStr + "', desiredUnits are null");
            localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[null], observed=[" + expUnitDef.getSymbol() + "]", Issue.SEVERITY_WARNING));
        } else if (expUnitDef == null) {
            String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
            System.out.println("...........exp='" + expStr + "', evaluated Units are null");
            localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + desiredExpUnitDef.getSymbol() + "], observed=[null]", Issue.SEVERITY_WARNING));
        } else if (desiredExpUnitDef.isTBD()) {
            String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
            // System.out.println("...........exp='"+expStr+"', desiredUnits are ["+desiredExpUnitDef.getSymbol()+"] and expression units are ["+expUnitDef.getSymbol()+"]");
            localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + desiredExpUnitDef.getSymbol() + "], observed=[" + expUnitDef.getSymbol() + "] for exp = " + expStr, Issue.SEVERITY_WARNING));
        } else if (!desiredExpUnitDef.isEquivalent(expUnitDef) && !expUnitDef.isTBD()) {
            String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
            // System.out.println("...........exp='"+expStr+"', desiredUnits are ["+desiredExpUnitDef.getSymbol()+"] and expression units are ["+expUnitDef.getSymbol()+"]");
            localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + desiredExpUnitDef.getSymbol() + "], observed=[" + expUnitDef.getSymbol() + "] for exp = " + expStr, Issue.SEVERITY_WARNING));
        }
    } catch (VCUnitException e) {
        String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
        System.out.println(".........exp='" + expStr + "' exception='" + e.getMessage() + "'");
        localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + ((desiredExpUnitDef != null) ? (desiredExpUnitDef.getSymbol()) : ("null")) + "], exception=" + e.getMessage(), Issue.SEVERITY_WARNING));
    } catch (ExpressionException e) {
        String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
        System.out.println(".........exp='" + expStr + "' exception='" + e.getMessage() + "'");
        localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + ((desiredExpUnitDef != null) ? (desiredExpUnitDef.getSymbol()) : ("null")) + "], exception=" + e.getMessage(), Issue.SEVERITY_WARNING));
    } catch (Exception e) {
        e.printStackTrace(System.out);
        localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + ((desiredExpUnitDef != null) ? (desiredExpUnitDef.getSymbol()) : ("null")) + "], exception=" + e.getMessage(), Issue.SEVERITY_WARNING));
    }
    Expression newExp = new Expression(origExp);
    // 
    // flatten user-defined functions
    // 
    FunctionInvocation[] functionInvocations = newExp.getFunctionInvocations(new FunctionFilter() {

        @Override
        public boolean accept(String functionName, FunctionType functionType) {
            return functionType == FunctionType.USERDEFINED;
        }
    });
    for (FunctionInvocation functionInvocation : functionInvocations) {
        if (functionInvocation.getSymbolTableFunctionEntry() instanceof Model.ModelFunction) {
            ModelFunction modelFunction = (ModelFunction) functionInvocation.getSymbolTableFunctionEntry();
            newExp.substituteInPlace(functionInvocation.getFunctionExpression(), modelFunction.getFlattenedExpression(functionInvocation));
        }
    }
    // 
    // then substitute Math symbols for Biological symbols.
    // 
    newExp.bindExpression(null);
    for (int i = 0; i < symbols.length; i++) {
        SymbolTableEntry ste = origExp.getSymbolBinding(symbols[i]);
        if (ste == null) {
            throw new ExpressionBindingException("symbol '" + symbols[i] + "' not bound");
        // ste = simContext.getGeometryContext().getModel().getSpeciesContext(symbols[i]);
        }
        if (ste != null) {
            String newName = getMathSymbol(ste, geometryClass);
            if (!newName.equals(symbols[i])) {
                newExp.substituteInPlace(new Expression(symbols[i]), new Expression(newName));
            }
        }
    }
    return newExp;
}

Example 83 with SymbolTableEntry

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

the class AbstractMathMapping method getLocalEntry.

/**
 * Insert the method's description here.
 * Creation date: (4/4/2004 1:01:22 AM)
 * @return cbit.vcell.parser.SymbolTableEntry
 * @param identifier java.lang.String
 */
public SymbolTableEntry getLocalEntry(java.lang.String identifier) {
    // 
    // the MathMapping "nameScope" is the union of the Model and SimContext namescopes (with the addition of any locally defined parameters)
    // 
    // 
    // try "truely" local first
    // 
    SymbolTableEntry localParamSTE = getMathMappingParameter(identifier);
    SymbolTableEntry localQuantitySTE = getMathMappingQuantity(identifier);
    // 
    // try "model" next
    // 
    SymbolTableEntry modelSTE = simContext.getModel().getLocalEntry(identifier);
    // 
    // try "simContext" next
    // 
    SymbolTableEntry simContextSTE = simContext.getLocalEntry(identifier);
    int resolutionCount = 0;
    SymbolTableEntry ste = null;
    if (localParamSTE != null) {
        resolutionCount++;
        ste = localParamSTE;
    }
    if (localQuantitySTE != null) {
        resolutionCount++;
        ste = localQuantitySTE;
    }
    if (modelSTE != null) {
        resolutionCount++;
        ste = modelSTE;
    }
    if (simContextSTE != null && simContextSTE != modelSTE) {
        resolutionCount++;
        ste = simContextSTE;
    }
    if (resolutionCount == 0 || resolutionCount == 1) {
        return ste;
    } else {
        StringBuffer buffer = new StringBuffer();
        buffer.append("identifier '" + identifier + "' ambiguous, resolved by [");
        if (localParamSTE != null) {
            buffer.append(" MathMappingParameter(" + localParamSTE + ")");
        }
        if (localQuantitySTE != null) {
            buffer.append(" MathMappingQuantity(" + localQuantitySTE + ")");
        }
        if (modelSTE != null) {
            buffer.append(" Model(" + modelSTE + ")");
        }
        if (simContextSTE != null && simContextSTE != modelSTE) {
            buffer.append(" Application(" + simContextSTE + ")");
        }
        buffer.append(" ]");
        throw new RuntimeException(buffer.toString());
    }
}

Example 84 with SymbolTableEntry

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

the class AbstractStochMathMapping method getSubstitutedExpr.

/**
 * @param expr
 * @param bConcentration
 * @return
 * @throws ExpressionException
 */
protected Expression getSubstitutedExpr(Expression expr, boolean bConcentration, boolean bIsInitialCondn) throws ExpressionException {
    expr = new Expression(expr);
    String[] symbols = expr.getSymbols();
    // Check if 'expr' has other speciesContexts in its expression, need to replace it with 'spContext_init'
    for (int j = 0; symbols != null && j < symbols.length; j++) {
        // if symbol is a speciesContext, replacing it with a reference to initial condition for that speciesContext.
        SpeciesContext spC = null;
        SymbolTableEntry ste = expr.getSymbolBinding(symbols[j]);
        if (ste instanceof ProxyParameter) {
            // if expression is for speciesContextSpec or Kinetics, ste will be a ProxyParameter instance.
            ProxyParameter spspp = (ProxyParameter) ste;
            if (spspp.getTarget() instanceof SpeciesContext) {
                spC = (SpeciesContext) spspp.getTarget();
            }
        } else if (ste instanceof SpeciesContext) {
            // if expression is for a global parameter, ste will be a SpeciesContext instance.
            spC = (SpeciesContext) ste;
        }
        if (spC != null) {
            SpeciesContextSpec spcspec = getSimulationContext().getReactionContext().getSpeciesContextSpec(spC);
            Parameter spCParm = null;
            if (bConcentration && bIsInitialCondn) {
                // speciesContext has initConcentration set, so need to replace 'spContext' in 'expr' 'spContext_init'
                spCParm = spcspec.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
            } else if (!bConcentration && bIsInitialCondn) {
                // speciesContext has initCount set, so need to replace 'spContext' in 'expr' 'spContext_initCount'
                spCParm = spcspec.getParameterFromRole(SpeciesContextSpec.ROLE_InitialCount);
            } else if (bConcentration && !bIsInitialCondn) {
                // need to replace 'spContext' in 'expr' 'spContext_Conc'
                spCParm = getSpeciesConcentrationParameter(spC);
            } else if (!bConcentration && !bIsInitialCondn) {
                // need to replace 'spContext' in 'expr' 'spContext_Count'
                spCParm = getSpeciesCountParameter(spC);
            }
            // need to get init condn expression, but can't get it from getMathSymbol() (mapping between bio and math), hence get it as below.
            Expression scsInitExpr = new Expression(spCParm, getNameScope());
            // scsInitExpr.bindExpression(this);
            expr.substituteInPlace(new Expression(spC.getName()), scsInitExpr);
        }
    }
    return expr;
}

Example 85 with SymbolTableEntry

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

the class PdeEquation method isDummy.

public boolean isDummy(MathSymbolTable simSymbolTable, CompartmentSubDomain thisCompartment) {
    if (!(getVariable() instanceof VolVariable)) {
        return false;
    }
    VolVariable volVar = (VolVariable) getVariable();
    // in any case the initial conditions will be respected.
    if (testZero(simSymbolTable, getRateExpression()) && testZero(simSymbolTable, velocityX) && testZero(simSymbolTable, velocityY) && testZero(simSymbolTable, velocityZ) && testZero(simSymbolTable, gradientX) && testZero(simSymbolTable, gradientY) && testZero(simSymbolTable, gradientZ)) {
        if (testZero(simSymbolTable, diffusionExp)) {
            // zero rate, velocity and diffusion
            return true;
        } else {
            // for non-zero diffusion, look for non zero fluxes or non-uniform initial conditions.
            if (testConstant(simSymbolTable, getInitialExpression()) && testZero(simSymbolTable, boundaryXm) && testZero(simSymbolTable, boundaryXp) && testZero(simSymbolTable, boundaryYm) && testZero(simSymbolTable, boundaryYp) && testZero(simSymbolTable, boundaryZm) && testZero(simSymbolTable, boundaryZp)) {
                // 1. get THIS compartment
                // 2. get all membranes that touch this compartment
                // 3. get jump condition for this variable
                // 4. check either influx or outflux
                Enumeration<SubDomain> subDomainEnum = simSymbolTable.getMathDescription().getSubDomains();
                while (subDomainEnum.hasMoreElements()) {
                    SubDomain subDomain = (SubDomain) subDomainEnum.nextElement();
                    if (subDomain instanceof MembraneSubDomain) {
                        MembraneSubDomain memSubDomain = (MembraneSubDomain) subDomain;
                        if (memSubDomain.getInsideCompartment() == thisCompartment) {
                            JumpCondition jump = memSubDomain.getJumpCondition(volVar);
                            if (jump != null && !testZero(simSymbolTable, jump.getInFluxExpression())) {
                                // non zero jump condition
                                return false;
                            }
                        } else if (memSubDomain.getOutsideCompartment() == thisCompartment) {
                            JumpCondition jump = memSubDomain.getJumpCondition(volVar);
                            if (jump != null && !testZero(simSymbolTable, jump.getOutFluxExpression())) {
                                // non zero jump condition
                                return false;
                            }
                        }
                        // check if BoundaryConditionValue is defined for var on membrane
                        try {
                            BoundaryConditionValue boundaryValue = getBoundaryConditionValue(memSubDomain.getName());
                            if (boundaryValue != null) {
                                Expression boundaryValExpr = boundaryValue.getBoundaryConditionExpression();
                                BoundaryConditionSpec boundarySpec = thisCompartment.getBoundaryConditionSpec(memSubDomain.getName());
                                if (boundarySpec != null) {
                                    boolean bZeroFlux = boundarySpec.getBoundaryConditionType().isNEUMANN() && testZero(simSymbolTable, boundaryValExpr);
                                    boolean bUniformDirichlet = boundarySpec.getBoundaryConditionType().isDIRICHLET() && testZero(simSymbolTable, Expression.add(boundaryValExpr, Expression.negate(getInitialExpression())));
                                    if (!bZeroFlux && !bUniformDirichlet) {
                                        return false;
                                    }
                                }
                            }
                        } catch (ExpressionException e) {
                            e.printStackTrace(System.out);
                        }
                    }
                }
                // check fast system if jump conditions are all zero
                FastSystem fastSystem = thisCompartment.getFastSystem();
                if (fastSystem != null) {
                    Enumeration<FastInvariant> fastInvariants = fastSystem.getFastInvariants();
                    while (fastInvariants.hasMoreElements()) {
                        FastInvariant fi = fastInvariants.nextElement();
                        try {
                            // look for fast invariants that involve only this variable
                            // which means this variable is not affected by fast system
                            Expression exp = new Expression(fi.getFunction());
                            exp.bindExpression(simSymbolTable);
                            exp = exp.flatten();
                            SymbolTableEntry ste = exp.getSymbolBinding(volVar.getName());
                            if (ste != null && exp.getSymbols().length == 1) {
                                return true;
                            }
                        } catch (ExpressionException ex) {
                            ex.printStackTrace(System.out);
                            throw new RuntimeException("PdeEquation::isDummy(), not expected: " + ex.getMessage());
                        }
                    }
                    // the variable is not found to be invariant in this fast system, might be changed by fast system
                    return false;
                }
                // not changed by jump conditions, boundary conditions and fast system even if diffusion rate is non zero
                return true;
            }
        }
    }
    // non zero rate or velocity
    return false;
}