Java Compartment.setConstant方法代码示例

import org.sbml.jsbml.Compartment; //导入方法依赖的package包/类
private void createCompartment(String strCompartName, String _Id,
		String _Constant, String _SpatialDimension, String _MetaId,
		String _SBOTermId, String _Size) {

	if (!foundCompartment(strCompartName)) {
		Compartment _compartment = model.createCompartment(_Id);
		_compartment.setName(strCompartName);
		_compartment.setConstant(Boolean.valueOf(_Constant));
		_compartment
				.setSpatialDimensions(Double.valueOf(_SpatialDimension));
		_compartment.setMetaId(_MetaId);
		_compartment.setSBOTerm(_SBOTermId);
		_compartment.setSize(Double.valueOf(_Size));

		_ListOfCompartments.add(strCompartName);
	}
}
 

import org.sbml.jsbml.Compartment; //导入方法依赖的package包/类
/**
   * Adds the domain types.
   */
public void addDomainTypes() {
	for (Entry<String, Integer> e : hashDomainTypes.entrySet()) {
		// DomainTypes
		DomainType dt = geometry.createDomainType();
		dt.setSpatialId(e.getKey());
		dt.setSpatialDimensions(e.getValue());
	
		// Compartment may need changes for name and id
		if(model.getListOfCompartments().get(e.getKey()) != null)
			continue;
		Compartment c = model.createCompartment();
		c.setSpatialDimensions(e.getValue());
		//c.setSpatialDimensions(3);
		c.setConstant(true);
		c.setId(e.getKey());
		c.setName(e.getKey());
		
		spatialcompplugin = (SpatialCompartmentPlugin) c.getPlugin("spatial");
		CompartmentMapping cm = new CompartmentMapping();
		cm.setSpatialId(e.getKey() + c.getId());
		cm.setDomainType(e.getKey());
		// TODO 
		//cm.setUnitSize(delta.x * delta.y * delta.z);
		cm.setUnitSize(1);

		spatialcompplugin.setCompartmentMapping(cm);
	}
}
 

import org.sbml.jsbml.Compartment; //导入方法依赖的package包/类
/**
 * Complete compartments.
 *
 * @param compartments
 *        the compartments
 * @return ListOf<Compartment>
 *         TODO
 */
public static ListOf<Compartment> completeCompartments(
  ListOf<Compartment> compartments) {
  int i = 0;
  for (Compartment c : compartments) {
    if (!c.isSetId()) {
      c.setId(c.getClass().getSimpleName() + i++);
    }
    if (!c.isSetConstant()) {
      c.setConstant(true);
    }
  }
  return compartments;
}
 

import org.sbml.jsbml.Compartment; //导入方法依赖的package包/类
public void createSBMLDocument(String modelId,boolean grid,boolean lema) {
	sbml = new SBMLDocument(GlobalConstants.SBML_LEVEL, GlobalConstants.SBML_VERSION);
	modelId = modelId.replaceAll("[\\W]|_", "_");
	if (Character.isDigit(modelId.charAt(0))) modelId = "m" + modelId;
	Model m = sbml.createModel(modelId);
	metaIDIndex = SBMLutilities.setDefaultMetaID(sbml, m, metaIDIndex); 
	sbmlFile = modelId + ".xml";
	createCompPlugin();
	createLayoutPlugin();
	createFBCPlugin();
	if (!lema) {
		Compartment c = m.createCompartment();
		if (grid) {
			if (!modelId.equals("Grid")) {
				c.setId("Grid");
			} else {
				c.setId("GridComp");
			}
			loadDefaultParameters();
		} else {
			if (!modelId.equals("Cell")) {
				c.setId("Cell");
			} else {
				c.setId("CellComp");
			}
			Port port = sbmlCompModel.createPort();
			port.setId(GlobalConstants.COMPARTMENT+"__"+c.getId());
			port.setIdRef(c.getId());
		}
		c.setSize(1);
		c.setSpatialDimensions(3);
		c.setConstant(true);
	}
}
 

import org.sbml.jsbml.Compartment; //导入方法依赖的package包/类
public String createCompartment(String id, float x, float y) {
	if (!checkCompartmentOverlap(id,x,y,
		GlobalConstants.DEFAULT_COMPARTMENT_WIDTH,GlobalConstants.DEFAULT_COMPARTMENT_HEIGHT)) {
		message.setErrorDialog("Compartment Overlap", "Compartments must not overlap.");
     this.notifyObservers(message);
		return "";
	}
	Compartment compartment = sbml.getModel().createCompartment();
	if (id == null) {
		do {
			creatingCompartmentID++;
			id = "Comp" + String.valueOf(creatingCompartmentID);
		}
		while ((SBMLutilities.getElementBySId(sbml, id)!=null)||(SBMLutilities.getElementByMetaId(sbml, id)!=null));
	}
	compartment.setId(id);
	// Set default promoter metaID
	metaIDIndex = SBMLutilities.setDefaultMetaID(sbml, compartment, metaIDIndex); 
	compartment.setConstant(true);
	compartment.setSize(1);
	compartment.setSpatialDimensions(3);

	if (!isGridEnabled()) {
		Layout layout = getLayout();
		CompartmentGlyph compartmentGlyph = null;
		if (layout.getCompartmentGlyph(GlobalConstants.GLYPH+"__"+id)!=null) {
			compartmentGlyph = layout.getCompartmentGlyph(GlobalConstants.GLYPH+"__"+id);
		} else {
			compartmentGlyph = layout.createCompartmentGlyph(GlobalConstants.GLYPH+"__"+id);
			compartmentGlyph.setCompartment(id);
			compartmentGlyph.createBoundingBox();
			compartmentGlyph.getBoundingBox().createDimensions();
			compartmentGlyph.getBoundingBox().createPosition();
		}
		compartmentGlyph.getBoundingBox().getPosition().setX(x);
		compartmentGlyph.getBoundingBox().getPosition().setY(y);
		compartmentGlyph.getBoundingBox().getDimensions().setWidth(GlobalConstants.DEFAULT_COMPARTMENT_WIDTH);
		compartmentGlyph.getBoundingBox().getDimensions().setHeight(GlobalConstants.DEFAULT_COMPARTMENT_HEIGHT);
		TextGlyph textGlyph = layout.createTextGlyph(GlobalConstants.TEXT_GLYPH+"__"+id);
		textGlyph.createBoundingBox();
		textGlyph.getBoundingBox().createDimensions();
		textGlyph.getBoundingBox().createPosition();
		textGlyph.setGraphicalObject(GlobalConstants.GLYPH+"__"+id);
		textGlyph.setText(SBMLutilities.getArrayId(sbml,id));
		textGlyph.setBoundingBox(compartmentGlyph.getBoundingBox().clone());
	}
	return id;
}