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

Example 6 with SymbolTableEntry

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

the class RbmUtils method toBnglString.

public static String toBnglString(Parameter parameter, boolean bFunction) {
    if (!bFunction) {
        // parameter
        String str = parameter.getName() + " ";
        if (parameter.getExpression() != null) {
            str += parameter.getExpression().infixBng();
        } else {
            str = "# " + str + "(expression undefined)";
        }
        return str;
    } else {
        // function
        String str = parameter.getName() + "()\t=\t";
        if (parameter.getExpression() != null) {
            String[] symbols = parameter.getExpression().getSymbols();
            for (String s : symbols) {
                SymbolTableEntry ste = parameter.getExpression().getSymbolBinding(s);
                if (ste instanceof SpeciesContext) {
                    System.out.println("SpeciesContext '" + s + "' found in expression of function, not exporting");
                    str = "# " + str;
                    break;
                }
            }
            str += parameter.getExpression().infixBng();
        } else {
            str = "# " + str + "(expression undefined)";
        }
        return str;
    }
}

Example 7 with SymbolTableEntry

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

the class RbmUtils method getBoundExpression.

public static Expression getBoundExpression(String expressionString, final SymbolTable symbolTable) throws ExpressionException {
    Expression exp = null;
    if (expressionString == null || expressionString.equals("")) {
        exp = new Expression(0);
    } else {
        exp = new Expression(expressionString);
    }
    // 
    // look for function invocations of unsupported but known functions
    // 
    FunctionInvocation[] invocations = exp.getFunctionInvocations(new FunctionFilter() {

        @Override
        public boolean accept(String functionName, FunctionType functionType) {
            if (functionName.equalsIgnoreCase("if")) {
                return true;
            }
            return false;
        }
    });
    if (invocations != null && invocations.length > 0) {
        for (FunctionInvocation invocation : invocations) {
            if (invocation.getFunctionName().equalsIgnoreCase("if")) {
                // build new expression
                // if (testExp, trueExp, falseExp)
                // 
                Expression testExp = invocation.getArguments()[0];
                Expression trueExp = invocation.getArguments()[1];
                Expression falseExp = invocation.getArguments()[2];
                Expression testPassed = Expression.relational("!=", testExp, new Expression(0.0));
                Expression testFailed = Expression.relational("==", testExp, new Expression(0.0));
                Expression newExp = Expression.add(Expression.mult(testPassed, trueExp), Expression.mult(testFailed, falseExp));
                // substitute new expression replacing if()
                exp.substituteInPlace(invocation.getFunctionExpression(), newExp);
            }
        }
        System.out.println(invocations.toString());
    }
    // 
    // "if()" functions are goine ... but lets look for BNGL function invocations
    // 1) if they have no arguments, drop the "()".
    // 2) if they have arguments, have to substitute the arguments in the expression ... flatten it.
    // 
    invocations = exp.getFunctionInvocations(new FunctionFilter() {

        @Override
        public boolean accept(String functionName, FunctionType functionType) {
            return true;
        }
    });
    if (invocations != null && invocations.length > 0) {
        for (FunctionInvocation invocation : invocations) {
            if (invocation.getArguments().length == 0) {
                // 
                // no arguments, look for existing parameter by name (parameter name is function name).
                // 
                // look up "identifier()" as "identifier" to find a model parameter generated earlier when processing functions (or prior functions)
                // 
                SymbolTableEntry parameter = symbolTable.getEntry(invocation.getFunctionName());
                if (parameter != null) {
                    exp.substituteInPlace(invocation.getFunctionExpression(), new Expression(parameter, parameter.getNameScope()));
                } else {
                    // 
                    // didn't find a parameter, may be a built-in function with zero arguments built into VCell. (none exists right now).
                    // 
                    SymbolTableFunctionEntry vcellFunction = (SymbolTableFunctionEntry) symbolTable.getEntry(invocation.getFormalDefinition());
                    if (vcellFunction != null) {
                    // 
                    // nothing to do, vcell will parse and interpret this correctly
                    // 
                    } else {
                        throw new RuntimeException("function \"" + invocation.getFunctionExpression().infix() + "\" not found as a bngl function or as a vcell built-in function");
                    }
                }
            } else {
                // 
                // should be a build-in vcell function with arguments ... user defined functions with arguments not supported yet in bngl import.
                // 
                FunctionType builtinFunctionType = cbit.vcell.parser.ASTFuncNode.FunctionType.fromFunctionName(invocation.getFunctionName());
                if (builtinFunctionType == null) {
                    throw new RuntimeException("function \"" + invocation.getFunctionExpression().infix() + "\" not found as a built-in VCell function (and bngl functions with arguments are not yet supported");
                } else {
                    if (invocation.getArguments().length != builtinFunctionType.getArgTypes().length) {
                        throw new RuntimeException("built-in function \"" + invocation.getFunctionExpression().infix() + "\" expects " + builtinFunctionType.getArgTypes().length + " arguments");
                    }
                }
            }
            System.out.println(invocations.toString());
        }
    }
    exp.bindExpression(symbolTable);
    return exp;
}

Example 8 with SymbolTableEntry

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

the class BioModelParametersTableModel method computeData.

/**
 * Insert the method's description here.
 * Creation date: (9/23/2003 1:24:52 PM)
 * @return cbit.vcell.model.EditableSymbolTableEntry
 * @param row int
 */
protected List<EditableSymbolTableEntry> computeData() {
    ArrayList<EditableSymbolTableEntry> allEditableSymbolTableEntryList = new ArrayList<EditableSymbolTableEntry>();
    if (bioModel == null) {
        return null;
    }
    if (bGlobal) {
        Map<String, SymbolTableEntry> entryMap = new HashMap<String, SymbolTableEntry>();
        bioModel.getModel().getEntries(entryMap);
        for (SymbolTableEntry ste : entryMap.values()) {
            if (ste instanceof EditableSymbolTableEntry && !(ste instanceof ReservedSymbol)) {
                allEditableSymbolTableEntryList.add((EditableSymbolTableEntry) ste);
            }
        }
    }
    if (bReactions) {
        for (ReactionStep reactionStep : bioModel.getModel().getReactionSteps()) {
            allEditableSymbolTableEntryList.addAll(Arrays.asList(reactionStep.getKinetics().getUnresolvedParameters()));
            allEditableSymbolTableEntryList.addAll(Arrays.asList(reactionStep.getKinetics().getKineticsParameters()));
        }
        if (!bioModel.getModel().getRbmModelContainer().isEmpty()) {
            for (ReactionRule reactionRule : bioModel.getModel().getRbmModelContainer().getReactionRuleList()) {
                allEditableSymbolTableEntryList.addAll(Arrays.asList(reactionRule.getKineticLaw().getLocalParameters()));
                allEditableSymbolTableEntryList.addAll(Arrays.asList(reactionRule.getKineticLaw().getProxyParameters()));
                allEditableSymbolTableEntryList.addAll(Arrays.asList(reactionRule.getKineticLaw().getUnresolvedParameters()));
            }
        }
    }
    if (bApplications) {
        for (SimulationContext simContext : bioModel.getSimulationContexts()) {
            if (applicationSelection != null && (applicationSelection.isAll() || applicationSelection.getSimulationContext() == simContext)) {
                allEditableSymbolTableEntryList.addAll(getApplicationEditableSymbolTableEntryList(simContext));
            }
        }
    }
    boolean bSearchInactive = searchText == null || searchText.length() == 0;
    String lowerCaseSearchText = bSearchInactive ? null : searchText.toLowerCase();
    ArrayList<EditableSymbolTableEntry> parameterList = new ArrayList<EditableSymbolTableEntry>();
    for (EditableSymbolTableEntry parameter : allEditableSymbolTableEntryList) {
        boolean bNumeric = parameter.getExpression() == null || parameter.getExpression().isNumeric();
        if (bConstants && bNumeric || bFunctions && !bNumeric) {
            if (bSearchInactive || parameter.getNameScope().getPathDescription().toLowerCase().contains(lowerCaseSearchText) || parameter.getName().toLowerCase().contains(lowerCaseSearchText) || parameter.getExpression() != null && parameter.getExpression().infix().toLowerCase().contains(lowerCaseSearchText) || parameter.getDescription().toLowerCase().contains(lowerCaseSearchText)) {
                parameterList.add(parameter);
            }
        }
    }
    return parameterList;
}

Example 9 with SymbolTableEntry

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

the class SimulationContext method getLocalEntries.

public void getLocalEntries(Map<String, SymbolTableEntry> entryMap) {
    getModel().getEntries(entryMap);
    for (SymbolTableEntry ste : fieldSimulationContextParameters) {
        entryMap.put(ste.getName(), ste);
    }
    for (SymbolTableEntry ste : dataContext.getDataSymbols()) {
        entryMap.put(ste.getName(), ste);
    }
    for (SpatialObject spatialObject : spatialObjects) {
        for (SpatialQuantity spatialQuantity : spatialObject.getSpatialQuantities()) {
            if (spatialQuantity.isEnabled()) {
                entryMap.put(spatialQuantity.getName(), spatialQuantity);
            }
        }
    }
    entryMap.put(MathFunctionDefinitions.fieldFunctionDefinition.getName(), MathFunctionDefinitions.fieldFunctionDefinition);
}

Example 10 with SymbolTableEntry

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

the class SpeciesContextSpec method getEntry.

/**
 * getEntry method comment.
 */
public SymbolTableEntry getEntry(String identifierString) {
    SymbolTableEntry ste = getLocalEntry(identifierString);
    if (ste != null) {
        return ste;
    }
    ste = getNameScope().getExternalEntry(identifierString, this);
    if (ste instanceof SymbolTableFunctionEntry) {
        return ste;
    }
    if (ste != null) {
        if (ste instanceof SymbolTableFunctionEntry) {
            return ste;
        } else {
            return addProxyParameter(ste);
        }
    }
    return null;
}