Java Compartment.getId方法代码示例

import org.sbml.jsbml.Compartment; //导入方法依赖的package包/类
/**
 * Instantiates a new compartment alias wrapper.
 *
 * @param cg
 *        the cg
 * @param modelWrapper
 *        the model wrapper
 */
public CompartmentAliasWrapper(CompartmentGlyph cg, ModelWrapper modelWrapper) {
  this.compartmentAlias = new CompartmentAlias();
  modelWrapper.addCompartmentAlias(compartmentAlias);
  compartmentAliased = (Compartment) cg.getCompartmentInstance();
  this.id = compartmentAliased.getId() + "alias";
  compartmentAlias.setId(id);
  this.compartment = compartmentAliased.getId();
  compartmentAlias.setCompartment(compartmentAliased.getId());
  bounds = new Bounds();
  setH(cg.getBoundingBox().getDimensions().getHeight());
  setW(cg.getBoundingBox().getDimensions().getWidth());
  setX(cg.getBoundingBox().getPosition().getX());
  setY(cg.getBoundingBox().getPosition().getY());
  compartmentAlias.setBounds(bounds);
  this.clazz = "SQUARE";
  compartmentAlias.setClazz(clazz);
  doubleLine = new DoubleLine();
  doubleLine.setInnerWidth(new BigDecimal(DEFAULT_COMPARTMENT_INNER_WIDTH));
  doubleLine.setOuterWidth(new BigDecimal(DEFAULT_COMPARTMENT_OUTER_WIDTH));
  doubleLine.setThickness(new BigDecimal(DEFAULT_COMPARTMENT_WIDTH));
  compartmentAlias.setDoubleLine(doubleLine);
  info = new Info();
  info.setAngle(new BigDecimal(0d));
  info.setState("empty");
  compartmentAlias.setInfo(info);
  namePoint = new Point();
  compartmentAlias.setNamePoint(namePoint);
  paint = new Paint();
  paint.setColor("ffcccc00");
  paint.setScheme("Color");
  compartmentAlias.setPaint(paint);
  point = new Point();
  compartmentAlias.setPoint(new Point());
}
 

import org.sbml.jsbml.Compartment; //导入方法依赖的package包/类
/**
 * Refresh compartment panel
 */
public void refreshCompartmentPanel(BioModel gcm) {
	String selectedCompartment = "";
	if (!compartments.isSelectionEmpty()) {
		selectedCompartment = ((String) compartments.getSelectedValue()).split("\\[| ")[0];
	}
	this.bioModel = gcm;
	Model model = gcm.getSBMLDocument().getModel();
	ListOf<Compartment> listOfCompartments = model.getListOfCompartments();
	String[] comparts = new String[model.getCompartmentCount()];
	for (int i = 0; i < model.getCompartmentCount(); i++) {
		Compartment compartment = listOfCompartments.get(i);
		comparts[i] = compartment.getId() + SBMLutilities.getDimensionString(compartment);
		comparts[i] += " " + compartment.getSize();
		if (paramsOnly) {
			for (int j = 0; j < parameterChanges.size(); j++) {
				String[] splits = parameterChanges.get(j).split(" ");
				if (splits[0].equals(comparts[i].split(" ")[0])) {
					parameterChanges.set(j,	comparts[i] + " " + splits[splits.length-2] + " " + 
							splits[splits.length-1]);
					comparts[i] = parameterChanges.get(j);
				}
			}
		}
	}
	edu.utah.ece.async.ibiosim.dataModels.biomodel.util.Utility.sort(comparts);
	int selected = 0;
	for (int i = 0; i < comparts.length; i++) {
		if (comparts[i].split("\\[| ")[0].equals(selectedCompartment)) {
			selected = i;
		}
	}
	compartments.setListData(comparts);
	compartments.setSelectedIndex(selected);
}
 

import org.sbml.jsbml.Compartment; //导入方法依赖的package包/类
private static void setupCompartments(HierarchicalSimulation sim, ModelContainer container, VectorWrapper wrapper)
{
  Model model = container.getModel();
  HierarchicalModel modelstate = container.getHierarchicalModel();
  VariableNode node;
  for (Compartment compartment : model.getListOfCompartments())
  {
    ReplacementSetup.setupReplacement(sim, compartment, wrapper,VariableType.VARIABLE, container);

    String printVariable = container.getPrefix() + compartment.getId();
    String compartmentID = compartment.getId();
    node = modelstate.getNode(compartmentID);
    if(node == null)
    {
      node = new VariableNode(compartmentID);
      modelstate.addMappingNode(compartmentID, node);
    }
    if(sim.getInterestingSpecies() != null && sim.getInterestingSpecies().contains(printVariable))
    {
      sim.addPrintVariable(printVariable, node, modelstate.getIndex(), false);
    }
    if (modelstate.isDeletedBySId(compartmentID))
    {
      continue;
    }
    if (compartment.getConstant())
    {
      node.createState(StateType.SCALAR, wrapper);

    }
    else
    {
      int index = modelstate.getIndex();
      node.createState(sim.getAtomicType(), wrapper);
      modelstate.addVariable(node);
      node.getState().addState(index, 0);
      if(sim.getInterestingSpecies() == null)
      {
        sim.addPrintVariable(printVariable, node, modelstate.getIndex(), false);
      }
    }

    if (Double.isNaN(compartment.getSize()))
    {
      node.setValue(modelstate.getIndex(), 1);
    }
    else
    {
      node.setValue(modelstate.getIndex(), compartment.getSize());
      node.setIsSetInitialValue(true);
    }
  }
}
 

import org.sbml.jsbml.Compartment; //导入方法依赖的package包/类
/**
 * puts parameter-related information into data structures
 */
protected void setupParameters()
{

	// add local parameters
	for (Reaction reaction : model.getListOfReactions())
	{

		if (!reaction.isSetKineticLaw())
		{
			continue;
		}
		KineticLaw kineticLaw = reaction.getKineticLaw();
		setupLocalParameters(kineticLaw, reaction);
	}

	// add values to hashmap for easy access to global parameter values
	// NOTE: the IDs for the parameters and species must be unique, so
	// putting them in the
	// same hashmap is okay
	for (Parameter parameter : model.getListOfParameters())
	{

		setupSingleParameter(parameter);
	}

	// add compartment sizes in
	for (Compartment compartment : model.getListOfCompartments())
	{

		String compartmentID = compartment.getId();

		compartmentIDSet.add(compartmentID);
		variableToValueMap.put(compartmentID, compartment.getSize());

		if (Double.isNaN(compartment.getSize()))
		{
			variableToValueMap.put(compartmentID, 1.0);
		}

		variableToIsConstantMap.put(compartmentID, compartment.getConstant());

		if (numRules > 0)
		{
			variableToIsInAssignmentRuleMap.put(compartmentID, false);
		}

		if (numConstraints > 0)
		{
			variableToIsInConstraintMap.put(compartmentID, false);
		}
	}
}