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

Example 71 with SymbolTableEntry

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

the class MathMapping_4_8 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, StructureMapping structureMapping) 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);
    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, structureMapping);
            if (!newName.equals(symbols[i])) {
                newExp.substituteInPlace(new Expression(symbols[i]), new Expression(newName));
            }
        }
    }
    return newExp;
}

Example 72 with SymbolTableEntry

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

the class MathMapping_4_8 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 localSTE = getMathMappingParameter(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 (localSTE != null) {
        resolutionCount++;
        ste = localSTE;
    }
    if (modelSTE != null) {
        resolutionCount++;
        ste = modelSTE;
    }
    if (simContextSTE != null) {
        resolutionCount++;
        ste = simContextSTE;
    }
    if (resolutionCount == 0 || resolutionCount == 1) {
        return ste;
    } else if (resolutionCount == 2) {
        if (localSTE != null) {
            if (modelSTE != null) {
                // local and model
                throw new RuntimeException("identifier '" + identifier + "' ambiguous, resolved by MathMapping (" + localSTE + ") and Model (" + modelSTE + ")");
            } else {
                // local and simContext
                throw new RuntimeException("identifier '" + identifier + "' ambiguous, resolved by MathMapping (" + localSTE + ") and Application (" + simContextSTE + ")");
            }
        } else {
            // model and simContext
            if (!modelSTE.equals(simContextSTE)) {
                throw new RuntimeException("identifier '" + identifier + "' ambiguous, resolved by Model (" + modelSTE + ") and Application (" + simContextSTE + ")");
            } else {
                return ste;
            }
        }
    } else if (resolutionCount == 3) {
        // local and model and simContext
        throw new RuntimeException("identifier '" + identifier + "' ambiguous, resolved by MathMapping (" + localSTE + ") and Model (" + modelSTE + ") and Application (" + simContextSTE + ")");
    }
    return null;
}

Example 73 with SymbolTableEntry

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

the class MathMapping_4_8 method getLocalEntries.

public void getLocalEntries(Map<String, SymbolTableEntry> entryMap) {
    simContext.getModel().getLocalEntries(entryMap);
    simContext.getLocalEntries(entryMap);
    for (SymbolTableEntry ste : fieldMathMappingParameters) {
        entryMap.put(ste.getName(), ste);
    }
}

Example 74 with SymbolTableEntry

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

the class MathMapping_4_8 method getEntry.

/**
 * getEntry method comment.
 */
public SymbolTableEntry getEntry(java.lang.String identifierString) {
    SymbolTableEntry ste = getLocalEntry(identifierString);
    if (ste != null) {
        return ste;
    }
    ste = getNameScope().getExternalEntry(identifierString, this);
    if (ste == null) {
        System.out.println("MathMapping is unable to bind identifier '" + identifierString + "'");
    }
    return ste;
}

Example 75 with SymbolTableEntry

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

the class StochMathMapping_4_8 method getSubstitutedExpr.

/**
 * @param expr
 * @param bConcentration
 * @return
 * @throws ExpressionException
 */
private 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;
}