import org.sbml.jsbml.SBMLDocument; //导入依赖的package包/类
/**
 * Checks if is sets the SBO term.
 *
 * @param document the document
 * @return boolean
 * TODO
 */
public static boolean isSetSBOTerm(SBMLDocument document) {
  boolean species = checkSBOTermFromList(document.getModel().getListOfSpecies());
  boolean compartment = checkSBOTermFromList(document.getModel().getListOfCompartments());
  boolean reaction = checkSBOTermFromList(document.getModel().getListOfReactions());
  ListOf<Reaction> lor = document.getModel().getListOfReactions();
  boolean reactant = true;
  boolean product = true;
  boolean modifier = true;

  for (Reaction r: lor) {
    if (!checkSBOTermFromList(r.getListOfReactants())) {
      reactant = false;
    }
    if (!checkSBOTermFromList(r.getListOfProducts())) {
      product = false;
    }
    if (!checkSBOTermFromList(r.getListOfModifiers())) {
      modifier = false;
    }
  }

  return species && compartment && reaction && reactant && product && modifier;
}
 

import org.sbml.jsbml.SBMLDocument; //导入依赖的package包/类
public AssemblyGraph2(BioModel biomodel) throws XMLStreamException, IOException, BioSimException {
		assemblyNodes = new HashSet<AssemblyNode2>(); // Initialize map of SBML element meta IDs to assembly nodes they identify
		assemblyEdges = new HashMap<AssemblyNode2, Set<AssemblyNode2>>(); // Initialize map of assembly node IDs to sets of node IDs (node IDs are SBML meta IDs)
		SBMLDocument sbmlDoc = biomodel.getSBMLDocument();
		HashMap<String, AssemblyNode2> idToNode = new HashMap<String, AssemblyNode2>();
//		 Creates assembly nodes for submodels and connect them to nodes for species
		if (parseSubModelSBOL(sbmlDoc, biomodel.getPath(), idToNode)) {
			// Creates flattened assembly graph in case hierarchy of SBOL can't be preserved
			SBMLDocument flatDoc;
			try {
				flatDoc = biomodel.flattenModel(true);
			} catch (Exception e){
				e.printStackTrace();
				flatDoc = null;
			}
			// TODO: Hack to prevent null returned by flattenModel to crash assembly code
			if (flatDoc==null) {
				flatDoc = sbmlDoc;
			}
			flatAssemblyGraph = new AssemblyGraph2(flatDoc);
		}
		constructGraph(sbmlDoc, idToNode);
	}
 

import org.sbml.jsbml.SBMLDocument; //导入依赖的package包/类
private void constructGraph(SBMLDocument sbmlDoc, HashMap<String, AssemblyNode2> idToNode) {
	Model sbmlModel = sbmlDoc.getModel();

	// Creates assembly nodes for species and maps their metaIDs to the nodes
	parseSpeciesSBOL(sbmlModel, idToNode);
	
	// Creates assembly nodes for global parameters and maps their metaIDs to the nodes
	parseParameterSBOL(sbmlModel, idToNode);

	// Creates assembly nodes for reactions and connects them to nodes for species
	// Maps reaction parameters to reactions
	parseReactionSBOL(sbmlModel, idToNode);

	// Creates assembly nodes for rules and connects them to nodes for reactions and rules
	// on the basis of shared parameters
	parseRuleSBOL(sbmlModel, idToNode);
	
	parseEventSBOL(sbmlModel, idToNode);
	
	constructReverseEdges();
	selectStartNodes();
}
 

import org.sbml.jsbml.SBMLDocument; //导入依赖的package包/类
/**
 * Create check if species used in reaction
 */
public static boolean usedInReaction(SBMLDocument document, String id)
{
	for (int i = 0; i < document.getModel().getReactionCount(); i++)
	{
		for (int j = 0; j < document.getModel().getReaction(i).getReactantCount(); j++)
		{
			if (document.getModel().getReaction(i).getReactant(j).getSpecies().equals(id))
			{
				return true;
			}
		}
		for (int j = 0; j < document.getModel().getReaction(i).getProductCount(); j++)
		{
			if (document.getModel().getReaction(i).getProduct(j).getSpecies().equals(id))
			{
				return true;
			}
		}
	}
	return false;
}
 

import org.sbml.jsbml.SBMLDocument; //导入依赖的package包/类
/**
 * Prints the RNAP molecule to the document
 * 
 * @param document
 *            the SBML document
 */
private void printRNAP(SBMLDocument document) {
	double rnap = 30;
	if (properties != null) {
		rnap = Double.parseDouble(properties.getParameter(GlobalConstants.RNAP_STRING));
	}
	Species s = Utility.makeSpecies("RNAP", document.getModel().getCompartment(0).getId(), rnap, -1);		
	s.setHasOnlySubstanceUnits(true);
	Utility.addSpecies(document, s);
	//Adds RNA polymerase for compartments other than default
	this.compartments = new HashMap<String,Properties>(); 
	for (int i=0; i < document.getModel().getCompartmentCount(); i++) {
		compartments.put(document.getModel().getCompartment(i).getId(), null);
	}
	for (String compartment : compartments.keySet()) {
		Properties prop = compartments.get(compartment);
		if (prop != null && prop.containsKey(GlobalConstants.RNAP_STRING)) {
			rnap = Double.parseDouble((String)prop.get(GlobalConstants.RNAP_STRING));
		}
		Species sc = Utility.makeSpecies(compartment + "__RNAP", compartment, rnap, -1);
		sc.setHasOnlySubstanceUnits(true);
		Utility.addSpecies(document, sc);
	}
}
 

import org.sbml.jsbml.SBMLDocument; //导入依赖的package包/类
public static void updatePortDimensionsIndices(Submodel submodel, Port port, SBaseRef sbaseRef, Port subPort,
		SBMLDocument subDocument,SBMLDocument document)
{
	ArraysSBasePlugin sBasePlugin = getArraysSBasePlugin(submodel);
	ArraysSBasePlugin sBasePluginPort = getArraysSBasePlugin(port);
	ArraysSBasePlugin sBasePluginSBaseRef = getArraysSBasePlugin(sbaseRef);
	ArraysSBasePlugin sBasePluginSubPort = getArraysSBasePlugin(subPort);
	for (Dimension dim : sBasePluginSubPort.getListOfDimensions()) {
		Dimension dimClone = dim.clone();
		dimClone.setArrayDimension(dim.getArrayDimension()+sBasePlugin.getListOfDimensions().size());
		dimClone.setId("d"+dimClone.getArrayDimension());
		sBasePluginPort.addDimension(dimClone);
		Parameter p = subDocument.getModel().getParameter(dim.getSize()).clone();
		p.setId(submodel.getId()+"__"+p.getId());
		p.setMetaId(submodel.getId()+"__"+p.getMetaId());
		if (document.getModel().getParameter(p.getId())==null) {
			document.getModel().addParameter(p);
		}
		dimClone.setSize(p.getId());
		Index index = sBasePluginSBaseRef.createIndex();
		index.setArrayDimension(dim.getArrayDimension());
		index.setReferencedAttribute("comp:portRef");
		index.setMath(SBMLutilities.myParseFormula(dimClone.getId()));
	}
}
 

import org.sbml.jsbml.SBMLDocument; //导入依赖的package包/类
/**
 * Checks if species is a reactant in a non-degradation reaction
 */
public static boolean usedInNonDegradationReaction(SBMLDocument document, String id)
{
	for (int i = 0; i < document.getModel().getReactionCount(); i++)
	{
		for (int j = 0; j < document.getModel().getReaction(i).getReactantCount(); j++)
		{
			if (document.getModel().getReaction(i).getReactant(j).getSpecies().equals(id)
					&& (document.getModel().getReaction(i).getProductCount() > 0 || document.getModel().getReaction(i).getReactantCount() > 1))
			{
				return true;
			}
		}
	}
	return false;
}
 

import org.sbml.jsbml.SBMLDocument; //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.SBMLDocument; //导入依赖的package包/类
public static boolean checkUnitsInAssignmentRule(SBMLDocument document, Rule rule)
{
	UnitDefinition unitDef = rule.getDerivedUnitDefinition();
	UnitDefinition unitDefVar;
	Species species = document.getModel().getSpecies(getVariable(rule));
	Compartment compartment = document.getModel().getCompartment(getVariable(rule));
	Parameter parameter = document.getModel().getParameter(getVariable(rule));
	if (species != null)
	{
		unitDefVar = species.getDerivedUnitDefinition();
	}
	else if (compartment != null)
	{
		unitDefVar = compartment.getDerivedUnitDefinition();
	}
	else
	{
		unitDefVar = parameter.getDerivedUnitDefinition();
	}
	if (!UnitDefinition.areEquivalent(unitDef, unitDefVar))
	{
		return true;
	}
	return false;
}
 

import org.sbml.jsbml.SBMLDocument; //导入依赖的package包/类
public static boolean checkUnitsInInitialAssignment(SBMLDocument document, InitialAssignment init)
{
	UnitDefinition unitDef = init.getDerivedUnitDefinition();
	UnitDefinition unitDefVar;
	Species species = document.getModel().getSpecies(init.getVariable());
	Compartment compartment = document.getModel().getCompartment(init.getVariable());
	Parameter parameter = document.getModel().getParameter(init.getVariable());
	if (species != null)
	{
		unitDefVar = species.getDerivedUnitDefinition();
	}
	else if (compartment != null)
	{
		unitDefVar = compartment.getDerivedUnitDefinition();
	}
	else
	{
		unitDefVar = parameter.getDerivedUnitDefinition();
	}
	if (!UnitDefinition.areEquivalent(unitDef, unitDefVar))
	{
		return true;
	}
	return false;
}
 

import org.sbml.jsbml.SBMLDocument; //导入依赖的package包/类
public static boolean checkUnitsInEventAssignment(SBMLDocument document, EventAssignment assign)
{
	UnitDefinition unitDef = assign.getDerivedUnitDefinition();
	UnitDefinition unitDefVar;
	Species species = document.getModel().getSpecies(assign.getVariable());
	Compartment compartment = document.getModel().getCompartment(assign.getVariable());
	Parameter parameter = document.getModel().getParameter(assign.getVariable());
	if (species != null)
	{
		unitDefVar = species.getDerivedUnitDefinition();
	}
	else if (compartment != null)
	{
		unitDefVar = compartment.getDerivedUnitDefinition();
	}
	else
	{
		unitDefVar = parameter.getDerivedUnitDefinition();
	}
	if (unitDef != null && unitDefVar != null && !UnitDefinition.areEquivalent(unitDef, unitDefVar))
	{
		return true;
	}
	return false;
}
 

import org.sbml.jsbml.SBMLDocument; //导入依赖的package包/类
public static void addRandomFunctions(SBMLDocument document)
{
	Model model = document.getModel();
	createFunction(model, "uniform", "Uniform distribution", "lambda(a,b,(a+b)/2)");
	createFunction(model, "normal", "Normal distribution", "lambda(m,s,m)");
	createFunction(model, "exponential", "Exponential distribution", "lambda(l,1/l)");
	createFunction(model, "gamma", "Gamma distribution", "lambda(a,b,a*b)");
	createFunction(model, "poisson", "Poisson distribution", "lambda(mu,mu)");
	createFunction(model, "lognormal", "Lognormal distribution", "lambda(z,s,exp(z+s^2/2))");
	createFunction(model, "chisq", "Chi-squared distribution", "lambda(nu,nu)");
	createFunction(model, "laplace", "Laplace distribution", "lambda(a,0)");
	createFunction(model, "cauchy", "Cauchy distribution", "lambda(a,a)");
	createFunction(model, "rayleigh", "Rayleigh distribution", "lambda(s,s*sqrt(pi/2))");
	createFunction(model, "binomial", "Binomial distribution", "lambda(p,n,p*n)");
	createFunction(model, "bernoulli", "Bernoulli distribution", "lambda(p,p)");
}
 

import org.sbml.jsbml.SBMLDocument; //导入依赖的package包/类
private static boolean checkFluxBound(SBMLDocument document,String boundStr, String attribute,
		String[] dimensionIds,String[] idDims) 
{
	if (boundStr.contains("[")) {
		String id = boundStr.substring(0,boundStr.indexOf("["));
		if (document.getModel().getParameter(id)==null) return false;
		String index = boundStr.substring(boundStr.indexOf("["));
		SBase variable = SBMLutilities.getElementBySId(document, id);
		String[] dex = Utils.checkIndices(index, variable, document, dimensionIds, attribute, 
				idDims, null, null);
		if (dex==null) return false;
	} else {
		return (document.getModel().getParameter(boundStr)!=null);
	}
	return true;
}
 

import org.sbml.jsbml.SBMLDocument; //导入依赖的package包/类
/**
 * Gets the document.
 *
 * @return the document
 * @throws NullPointerException the null pointer exception
 * @throws XMLStreamException the XML stream exception
 */
protected SBMLDocument getDocument() throws NullPointerException, XMLStreamException{
	JFileChooser chooser = new JFileChooser(OpenDialog.getLastDirectory());
	chooser.setFileSelectionMode(JFileChooser.FILES_AND_DIRECTORIES);
	chooser.setMultiSelectionEnabled(false);
	chooser.setFileFilter(new FileNameExtensionFilter("SBML File(*.xml)", "xml"));
	int returnVal = chooser.showOpenDialog(null);

	if (returnVal != JFileChooser.APPROVE_OPTION)
		throw new NullPointerException();
	File f = chooser.getSelectedFile();
	return SBMLReader.read(f.getAbsolutePath());
}
 

import org.sbml.jsbml.SBMLDocument; //导入依赖的package包/类
/**
 * Check SBML document.
 *
 * @param document the document
 */
public void checkSBMLDocument(SBMLDocument document){
	if(document == null || document.getModel() == null) 
		throw new IllegalArgumentException("Non-supported format file");
	model = document.getModel();
	checkLevelAndVersion();
	checkExtension();
}
 

import org.sbml.jsbml.SBMLDocument; //导入依赖的package包/类
/**
 * Instantiates a new spatial SBML exporter.
 */
public SpatialSBMLExporter() {
	document = new SBMLDocument(3,1);
	document.setPackageRequired(SpatialConstants.namespaceURI, true);
	document.addDeclaredNamespace(PluginConstants.TAG_CELLDESIGNER_PREFIX, PluginConstants.CDNAMESPACE);
	model = document.createModel();

	SBasePlugin basePlugin = (model.getPlugin(SpatialConstants.namespaceURI));
	spatialplugin = (SpatialModelPlugin) basePlugin;
	if (spatialplugin == null) {
		System.exit(1);
	}
}
 

import org.sbml.jsbml.SBMLDocument; //导入依赖的package包/类
/**
 * Upgrade.
 *
 * @param document
 *        the document
 * @return SBMLDocument
 *         TODO
 */
public static SBMLDocument upgrade(SBMLDocument document) {
  if (document.getLevel() != SBMLUtil.DEFAULT_SBML_LEVEL
      || document.getVersion() != SBMLUtil.DEFAULT_SBML_VERSION) {
    document.setLevelAndVersion(SBMLUtil.DEFAULT_SBML_LEVEL,
      SBMLUtil.DEFAULT_SBML_VERSION);
  }
  document = SBMLModelCompleter.autoCompleteRequiredAttributes(document);
  return document;
}
 

import org.sbml.jsbml.SBMLDocument; //导入依赖的package包/类
/**
 * Downgrade.
 *
 * @param document
 *        the document
 * @return the SBML document
 */
public static SBMLDocument downgrade(SBMLDocument document) {
  if (document.getLevel() > SBMLUtil.DEFAULT_CELLDESIGNER_SBML_LEVEL
      || document.getVersion() != SBMLUtil.DEFAULT_CELLDESIGNER_SBML_VERSION) {
    document.setLevelAndVersion(SBMLUtil.DEFAULT_CELLDESIGNER_SBML_LEVEL,
      SBMLUtil.DEFAULT_CELLDESIGNER_SBML_VERSION);
  }
  document = SBMLModelCompleter.autoCompleteRequiredAttributes(document);
  return document;
}
 

import org.sbml.jsbml.SBMLDocument; //导入依赖的package包/类
/**
 * Adds the extension package layout.
 *
 * @param document the document
 * @return the SBML document
 */
public static SBMLDocument addExtensionPackageLayout(SBMLDocument document) {
  document.enablePackage(LayoutConstants.getNamespaceURI(SBMLUtil.DEFAULT_SBML_LEVEL, SBMLUtil.DEFAULT_SBML_VERSION), true);
  document.setPackageRequired(LayoutConstants.getNamespaceURI(SBMLUtil.DEFAULT_SBML_LEVEL, SBMLUtil.DEFAULT_SBML_VERSION), true);

  return document;
}
 

import org.sbml.jsbml.SBMLDocument; //导入依赖的package包/类
/**
 * Adds the extension package fbc.
 *
 * @param document the document
 * @return the SBML document
 */
public static SBMLDocument addExtensionPackageFBC(SBMLDocument document) {
  document.enablePackage(FBCConstants.getNamespaceURI(SBMLUtil.DEFAULT_SBML_LEVEL, SBMLUtil.DEFAULT_SBML_VERSION), true);
  document.setPackageRequired(FBCConstants.getNamespaceURI(SBMLUtil.DEFAULT_SBML_LEVEL, SBMLUtil.DEFAULT_SBML_VERSION), false);

  return document;
}