import org.sbml.jsbml.FunctionDefinition; //导入依赖的package包/类
/**
 * Check if a function is in use.
 * @param document
 * @param id
 * @param zeroDim
 * @param checkReactions
 * @param observable TODO
 * @param observer TODO
 * @return
 */

public static boolean functionInUse(SBMLDocument document, String id, boolean zeroDim, boolean checkReactions, BioObservable observable, BioObserver observer)
{
	if (variableInUse(document,id,zeroDim,checkReactions, observable, observer)) {
		return true;
	}
	Model model = document.getModel();
	for (int i = 0; i < model.getFunctionDefinitionCount(); i++)
	{
		FunctionDefinition funcDefn = model.getFunctionDefinition(i);
		String funcDefnStr = SBMLutilities.myFormulaToString(funcDefn.getMath());
		String[] vars = funcDefnStr.split(" |\\(|\\)|\\,");
		for (int j = 0; j < vars.length; j++)
		{
			if (vars[j].equals(id))
			{
				return true;
			}
		}
	}
	return false;
}
 

import org.sbml.jsbml.FunctionDefinition; //导入依赖的package包/类
public ArrayList<String> getFunctions() {
	ArrayList<String> functionSet = new ArrayList<String>();
	if (sbml!=null) {
		for (int i = 0; i < sbml.getModel().getFunctionDefinitionCount(); i++) {
			FunctionDefinition function = sbml.getModel().getFunctionDefinition(i);
			functionSet.add(function.getId());
		}
	}
	return functionSet;
}
 

import org.sbml.jsbml.FunctionDefinition; //导入依赖的package包/类
public static void createDistribution(FunctionDefinition f, String[] inputTypes, String[] inputs, String distribution)
{
	DistribFunctionDefinitionPlugin distrib = SBMLutilities.getDistribFunctionDefinitionPlugin(f);
	DrawFromDistribution draw = distrib.createDrawFromDistribution();
	for (int i = 0; i < inputs.length; i++)
	{
		DistribInput input = draw.createDistribInput();
		input.setId(inputs[i]);
		input.setIndex(i);
	}
	// UncertML element
	XMLNode xmlNode = new XMLNode(new XMLTriple("UncertML"), new XMLAttributes(), new XMLNamespaces());
	xmlNode.addNamespace("http://www.uncertml.org/3.0");

	// NormalDistribution element
	XMLNode distNode = new XMLNode(new XMLTriple(distribution), new XMLAttributes(), new XMLNamespaces());
	distNode.addAttr("definition", "http://www.uncertml.org/distributions");
	xmlNode.addChild(distNode);

	for (int i = 0; i < inputs.length; i++)
	{
		XMLNode inputNode = new XMLNode(new XMLTriple(inputTypes[i]), new XMLAttributes(), new XMLNamespaces());
		distNode.addChild(inputNode);
		XMLNode varNode = new XMLNode(new XMLTriple("var"), new XMLAttributes(), new XMLNamespaces());
		varNode.addAttr("varId", inputs[i]);
		inputNode.addChild(varNode);
	}
	draw.setUncertML(xmlNode);
}
 

import org.sbml.jsbml.FunctionDefinition; //导入依赖的package包/类
public static boolean isBoolean(SBMLDocument document, ASTNode node)
{
	if (node == null)
	{
		return false;
	}
	else if (node.isBoolean())
	{
		return true;
	}
	else if (node.getType() == ASTNode.Type.FUNCTION)
	{
		FunctionDefinition fd = document.getModel().getFunctionDefinition(node.getName());
		if (fd != null && fd.isSetMath())
		{
			return isBoolean(document, fd.getMath().getRightChild());
		}
		return false;
	}
	else if (node.getType() == ASTNode.Type.FUNCTION_PIECEWISE)
	{
		for (int c = 0; c < node.getChildCount(); c += 2)
		{
			if (!isBoolean(document, node.getChild(c)))
			{
				return false;
			}
		}
		return true;
	}
	return false;
}
 

import org.sbml.jsbml.FunctionDefinition; //导入依赖的package包/类
public static DistribFunctionDefinitionPlugin getDistribFunctionDefinitionPlugin(FunctionDefinition function)
{
	if (function.getExtension(DistribConstants.namespaceURI) != null)
	{
		return (DistribFunctionDefinitionPlugin) function.getExtension(DistribConstants.namespaceURI);
	}
	DistribFunctionDefinitionPlugin distrib = new DistribFunctionDefinitionPlugin(function);
	function.addExtension(DistribConstants.namespaceURI, distrib);
	return distrib;
}
 

import org.sbml.jsbml.FunctionDefinition; //导入依赖的package包/类
/**
 * Remove a function if not in use
 */
private void removeFunction() {
	int index = functions.getSelectedIndex();
	if (index != -1) {
		if (!SBMLutilities.variableInUse(bioModel.getSBMLDocument(), ((String) functions.getSelectedValue()).split(" ")[0], false, true, this, null)) {
			FunctionDefinition tempFunc = bioModel.getSBMLDocument().getModel().getFunctionDefinition(((String) functions.getSelectedValue()).split(" ")[0]);
			ListOf<FunctionDefinition> f = bioModel.getSBMLDocument().getModel().getListOfFunctionDefinitions();
			for (int i = 0; i < bioModel.getSBMLDocument().getModel().getFunctionDefinitionCount(); i++) {
				if (f.get(i).getId().equals(tempFunc.getId())) {
					f.remove(i);
				}
			}
			for (int i = 0; i < bioModel.getSBMLCompModel().getListOfPorts().size(); i++) {
				Port port = bioModel.getSBMLCompModel().getListOfPorts().get(i);
				if (port.isSetIdRef() && port.getIdRef().equals(tempFunc.getId())) {
					bioModel.getSBMLCompModel().getListOfPorts().remove(i);
					break;
				}
			}
			functions.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
			Utility.remove(functions);
			functions.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
			if (index < functions.getModel().getSize()) {
				functions.setSelectedIndex(index);
			}
			else {
				functions.setSelectedIndex(index - 1);
			}
			modelEditor.setDirty(true);
			modelEditor.makeUndoPoint();
		}
	}
}
 

import org.sbml.jsbml.FunctionDefinition; //导入依赖的package包/类
private ASTNode replaceFunctionDefinition(ASTNode equation, ListOf<FunctionDefinition> functions) {
	if (equation.getType() == ASTNode.Type.FUNCTION) {
		FunctionDefinition fd = functions.get(equation.getName());
		ASTNode newNode = fd.getBody();
		for (int i = 0; i < fd.getArgumentCount(); i++) {
			newNode = replace(fd.getArgument(i).getName(), equation.getChild(i), newNode);
		}
		return newNode;
	}
	for (int i = 0; i < equation.getChildCount(); i++) {
		equation.replaceChild(i, replaceFunctionDefinition(equation.getChild(i), functions));
	}
	return equation;
}
 

import org.sbml.jsbml.FunctionDefinition; //导入依赖的package包/类
private void replaceAllFunctionDefinitions(ListOf<FunctionDefinition> functions) {
	for (String key : odes.keySet()) {
		odes.put(key, replaceFunctionDefinition(odes.get(key), functions));
	}
}
 

import org.sbml.jsbml.FunctionDefinition; //导入依赖的package包/类
@Override
public ASTNodeValue function(FunctionDefinition functionDefinition, List<ASTNode> args) throws SBMLException {
	throw new UnsupportedOperationException("Method not supported by DoubleCompiler");
}