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

Example 56 with Constant

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

the class MathOverrides method getVCML.

/**
 * Insert the method's description here.
 * Creation date: (10/24/00 12:41:09 PM)
 * @return java.lang.String
 */
public String getVCML() {
    // 
    // write format as follows:
    // 
    // MathOverrides {
    // Constant K1 200;
    // Constant K2 400;
    // Constant K3 494.0;
    // }
    // 
    // 
    StringBuffer buffer = new StringBuffer();
    buffer.append(VCML.MathOverrides + " " + VCML.BeginBlock + "\n");
    java.util.Enumeration<String> enum1 = getOverridesHash().keys();
    while (enum1.hasMoreElements()) {
        String name = enum1.nextElement();
        MathOverrides.Element element = (MathOverrides.Element) getOverridesHash().get(name);
        Expression exp = element.actualValue;
        if (exp != null) {
            // regular override
            Constant constant = new Constant(name, exp);
            buffer.append("   " + constant.getVCML());
        } else {
            // scan override
            buffer.append("   " + element.spec.getVCML());
        }
    }
    buffer.append("\n" + VCML.EndBlock + "\n");
    return buffer.toString();
}

Example 57 with Constant

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

the class MathOverrides method gatherIssues.

/**
 * This method was created in VisualAge.
 * @return boolean
 */
public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    MathDescription mathDescription = getSimulation().getMathDescription();
    // 
    // get list of names of constants in this math
    // 
    Enumeration<Constant> enumeration = mathDescription.getConstants();
    java.util.HashSet<String> mathDescriptionHash = new java.util.HashSet<String>();
    while (enumeration.hasMoreElements()) {
        Constant constant = enumeration.nextElement();
        mathDescriptionHash.add(constant.getName());
    }
    // 
    // for any elements in this MathOverrides but not in the new MathDescription, add an "error" issue
    // 
    Enumeration<String> mathOverrideNamesEnum = getOverridesHash().keys();
    while (mathOverrideNamesEnum.hasMoreElements()) {
        String name = mathOverrideNamesEnum.nextElement();
        if (!mathDescriptionHash.contains(name)) {
            Issue issue = new Issue(getSimulation(), issueContext, IssueCategory.Simulation_Override_NotFound, VCellErrorMessages.getErrorMessage(VCellErrorMessages.SIMULATION_OVERRIDE_NOTFOUND, name, getSimulation().getName()), Issue.SEVERITY_ERROR);
            issueList.add(issue);
        }
        Variable var = mathDescription.getVariable(name);
        if (getSimulation().getSimulationOwner() != null) {
            Issue issue = getSimulation().getSimulationOwner().gatherIssueForMathOverride(issueContext, getSimulation(), name);
            if (issue != null) {
                issueList.add(issue);
            }
        }
    }
}

Example 58 with Constant

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

the class OutputFunctionContext method getEntry.

public SymbolTableEntry getEntry(java.lang.String identifierString) {
    // 
    // use MathDescription as the primary SymbolTable, just replace the Constants with the overrides.
    // 
    SymbolTableEntry ste = null;
    MathDescription mathDescription = simulationOwner.getMathDescription();
    if (mathDescription != null) {
        ste = mathDescription.getEntry(identifierString);
        if (ste != null && !(ste instanceof PseudoConstant) && !(ste instanceof Constant)) {
            return ste;
        }
        ste = mathDescription.getPostProcessingBlock().getDataGenerator(identifierString);
        if (ste instanceof DataGenerator) {
            return ste;
        }
    }
    // see if it is an output function.
    ste = getOutputFunction(identifierString);
    return ste;
}

Example 59 with Constant

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

the class SimulationSymbolTable method getLocalConstant.

/**
 * Insert the method's description here.
 * Creation date: (6/6/2001 7:52:15 PM)
 * @return cbit.vcell.math.Function
 * @param functionName java.lang.String
 */
private Constant getLocalConstant(Constant referenceConstant) throws ExpressionException {
    if (localVariableHash == null) {
        localVariableHash = new HashMap<String, Variable>();
    }
    Variable var = localVariableHash.get(referenceConstant.getName());
    if (var instanceof Constant) {
        Constant localConstant = (Constant) var;
        // 
        // make sure expression for localConstant is still up to date with MathOverrides table
        // 
        Expression exp = simulation.getMathOverrides().getActualExpression(referenceConstant.getName(), index);
        if (exp.compareEqual(localConstant.getExpression())) {
            // localConstant.bind(this); // update bindings to latest mathOverrides
            return localConstant;
        } else {
            // 
            // MathOverride's Expression changed for this Constant, remove and create new one
            // 
            localVariableHash.remove(localConstant.getName());
        }
    } else if (var != null) {
        throw new RuntimeException("Variable " + var + " expected to be a Constant");
    }
    // 
    // if local Constant not found, create new one, bind it to the Simulation (which ensures MathOverrides), and add to list
    // 
    String name = referenceConstant.getName();
    Constant newLocalConstant = new Constant(name, simulation.getMathOverrides().getActualExpression(name, index));
    // newLocalConstant.bind(this);
    localVariableHash.put(newLocalConstant.getName(), newLocalConstant);
    return newLocalConstant;
}

Example 60 with Constant

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

the class SimulationSymbolTable method getVariables.

/**
 * Insert the method's description here.
 * Creation date: (5/25/01 11:34:08 AM)
 * @return cbit.vcell.math.Variable[]
 */
public Variable[] getVariables() {
    Vector<Variable> varList = new Vector<Variable>();
    // 
    // get all variables from MathDescription, but replace MathOverrides
    // 
    Enumeration<Variable> enum1 = simulation.getMathDescription().getVariables();
    while (enum1.hasMoreElements()) {
        Variable mathDescriptionVar = enum1.nextElement();
        // 
        if (mathDescriptionVar instanceof Constant) {
            try {
                Constant overriddenConstant = getLocalConstant((Constant) mathDescriptionVar);
                varList.addElement(overriddenConstant);
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("local Constant " + mathDescriptionVar.getName() + " not found for Simulation");
            }
        // 
        // replace all Functions with local Functions that are bound to this Simulation
        // 
        } else if (mathDescriptionVar instanceof Function) {
            try {
                Function overriddenFunction = getLocalFunction((Function) mathDescriptionVar);
                varList.addElement(overriddenFunction);
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("local Function " + mathDescriptionVar.getName() + " not found for Simulation");
            }
        // 
        // pass all other Variables through
        // 
        } else {
            varList.addElement(mathDescriptionVar);
        }
    }
    Variable[] variables = (Variable[]) BeanUtils.getArray(varList, Variable.class);
    return variables;
}