Java Species.setHasOnlySubstanceUnits方法代码示例

import org.sbml.jsbml.Species; //导入方法依赖的package包/类
/**
 * Complete species.
 *
 * @param species
 *        the species
 * @return ListOf<Species>
 *         TODO
 */
public static ListOf<Species> completeSpecies(ListOf<Species> species) {
  int i = 0;
  for (Species s : species) {
    if (!s.isSetId()) {
      s.setId(s.getClass().getSimpleName() + i++);
    }
    if (!s.isSetCompartment()) {
      s.setCompartment(model.getCompartment(0));
    }
    if (!s.isSetHasOnlySubstanceUnits()) {
      s.setHasOnlySubstanceUnits(true);
    }
    if (!s.isSetBoundaryCondition()) {
      s.setBoundaryCondition(true);
    }
    if (!s.isSetConstant()) {
      s.setConstant(true);
    }
  }
  return species;
}
 

import org.sbml.jsbml.Species; //导入方法依赖的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.Species; //导入方法依赖的package包/类
@Override
public void visitSpasticSpecies(SpasticSpecies specie) {
	loadValues(specie);
	String compartment = checkCompartments(specie.getId());
	Species s = Utility.makeSpecies(specie.getId(), compartment, amount, concentration);
	s.setName(specie.getName());
	s.setHasOnlySubstanceUnits(true);
	Utility.addSpecies(document, s);
	
	r = new org.sbml.jsbml.Reaction(GlobalConstants.SBML_LEVEL, GlobalConstants.SBML_VERSION);
	r.setId("Constitutive_production_" + s.getId());
	r.setCompartment(compartment);
	r.addProduct(Utility.SpeciesReference(s.getId(), specie.getnp()));
	
	r.setReversible(false);
	//r.setFast(false);
	kl = r.createKineticLaw();
	Utility.Parameter(kl, "kp", specie.getKo());
	kl.setMath(SBMLutilities.myParseFormula("kp"));
	Utility.addReaction(document, r);		
}
 

import org.sbml.jsbml.Species; //导入方法依赖的package包/类
@Override
public void visitDiffusibleConstitutiveSpecies(DiffusibleConstitutiveSpecies specie) {
	
	loadValues(specie);
	String compartment = checkCompartments(specie.getId());
	Species s = Utility.makeSpecies(specie.getId(), compartment, amount, concentration);
	s.setName(specie.getName());
	s.setHasOnlySubstanceUnits(true);
	Utility.addSpecies(document, s);
	
	r = new org.sbml.jsbml.Reaction(GlobalConstants.SBML_LEVEL, GlobalConstants.SBML_VERSION);
	r.setId("Constitutive_production_" + s.getId());
	r.setCompartment(compartment);
	r.addProduct(Utility.SpeciesReference(s.getId(), Double.parseDouble(parameters.getParameter(GlobalConstants.STOICHIOMETRY_STRING))));
	
	r.setReversible(false);
	//r.setFast(false);
	kl = r.createKineticLaw();
	Utility.Parameter(kl, "kp", Double.parseDouble(parameters
				.getParameter((GlobalConstants.OCR_STRING))));	
	kl.setMath(SBMLutilities.myParseFormula("kp"));
	Utility.addReaction(document, r);	
}
 

import org.sbml.jsbml.Species; //导入方法依赖的package包/类
/**
 * Copy contents of Species from src to dst.
 * @param src
 * @param dst
 * @return
 */
public static Species copySpeciesContents(Species src, Species dst) {
	if (src.isSetInitialAmount()) dst.setInitialAmount(src.getInitialAmount());
	if (src.isSetInitialConcentration()) dst.setInitialConcentration(src.getInitialConcentration());
	dst.setCompartment(src.getCompartment());
	dst.setUnits(src.getUnits());
	dst.setBoundaryCondition(src.getBoundaryCondition());
	dst.setConstant(src.getConstant());
	dst.setHasOnlySubstanceUnits(src.getHasOnlySubstanceUnits());
  return dst;
}
 

import org.sbml.jsbml.Species; //导入方法依赖的package包/类
public void createPromoterFromGCM(String s,Properties property) {
	Species promoter = sbml.getModel().getSpecies(s);
	if (promoter==null) {
		promoter = sbml.getModel().createSpecies();
		promoter.setId(s);
	}
	if (property != null && property.containsKey(GlobalConstants.PROMOTER_COUNT_STRING)) {
		promoter.setInitialAmount(Double.parseDouble(property.getProperty(GlobalConstants.PROMOTER_COUNT_STRING)));
	} else {
		promoter.setInitialAmount(sbml.getModel().getParameter(GlobalConstants.PROMOTER_COUNT_STRING).getValue());
	} 
	promoter.setCompartment(getDefaultCompartment());
	promoter.setBoundaryCondition(false);
	promoter.setConstant(false);
	promoter.setHasOnlySubstanceUnits(true);
	promoter.setSBOTerm(GlobalConstants.SBO_PROMOTER_BINDING_REGION);
	if (property==null) {
		createProductionReaction(s,GlobalConstants.ACTIVATED_STRING,
				GlobalConstants.STOICHIOMETRY_STRING,
				GlobalConstants.OCR_STRING,
				GlobalConstants.KBASAL_STRING,
				GlobalConstants.RNAP_BINDING_STRING,
				GlobalConstants.ACTIVATED_RNAP_BINDING_STRING,false,null);
	} else {
		createProductionReaction(s,property.getProperty(GlobalConstants.ACTIVATED_STRING),
				property.getProperty(GlobalConstants.STOICHIOMETRY_STRING),
				property.getProperty(GlobalConstants.OCR_STRING),
				property.getProperty(GlobalConstants.KBASAL_STRING),
				property.getProperty(GlobalConstants.RNAP_BINDING_STRING),
				property.getProperty(GlobalConstants.ACTIVATED_RNAP_BINDING_STRING),false,null);
	}
}
 

import org.sbml.jsbml.Species; //导入方法依赖的package包/类
/**
 * Prints the promoters in the network
 * 
 * @param document
 *            the SBML document
 */
private void printOnlyPromoters(SBMLDocument document) {

	for (Promoter p : promoters.values()) {
		Species s = Utility.makeSpecies(p.getId(), document.getModel().getCompartment(0).getId(), p.getInitialAmount(), -1);
		s.setHasOnlySubstanceUnits(true);
		Utility.addSpecies(document, s);			
	}
}
 

import org.sbml.jsbml.Species; //导入方法依赖的package包/类
@Override
	public void visitComplex(ComplexSpecies specie) {
		if (!complexAbstraction || (!specie.isAbstractable() && !specie.isSequesterAbstractable())) {
			loadValues(specie);
			String compartment = checkCompartments(specie.getId());
			Species s = Utility.makeSpecies(specie.getId(), compartment, amount, concentration);
//			s.setName(specie.getName()); this causes things to break...specie lacks name for some reason
			s.setHasOnlySubstanceUnits(true);
			Utility.addSpecies(document, s);
		} else
			 document.getModel().removeSpecies(specie.getId());

	}
 

import org.sbml.jsbml.Species; //导入方法依赖的package包/类
@Override
public void visitBaseSpecies(BaseSpecies specie) {
	loadValues(specie);
	String compartment = checkCompartments(specie.getId());
	Species s = Utility.makeSpecies(specie.getId(), compartment, amount, concentration);
	s.setName(specie.getName());
	s.setHasOnlySubstanceUnits(true);
	Utility.addSpecies(document, s);
}
 

import org.sbml.jsbml.Species; //导入方法依赖的package包/类
@Override
public void visitConstantSpecies(ConstantSpecies specie) {
	loadValues(specie);
	String compartment = checkCompartments(specie.getId());
	Species s = Utility.makeSpecies(specie.getId(), compartment, amount, concentration);
	s.setName(specie.getName());
	s.setHasOnlySubstanceUnits(true);
	s.setBoundaryCondition(true);
	//s.setConstant(true);
	Utility.addSpecies(document, s);
}
 

import org.sbml.jsbml.Species; //导入方法依赖的package包/类
@Override
public void visitDiffusibleSpecies(DiffusibleSpecies species) {
	
	loadValues(species);
	String compartment = checkCompartments(species.getId());
	Species s = Utility.makeSpecies(species.getId(), compartment, amount, concentration);
	s.setName(species.getName());
	s.setHasOnlySubstanceUnits(true);
	Utility.addSpecies(document, s);
}
 

import org.sbml.jsbml.Species; //导入方法依赖的package包/类
public static Species makeSpecies(String id, String compartment, double amount, double concentration) {
	Species specie = new Species(GlobalConstants.SBML_LEVEL, GlobalConstants.SBML_VERSION);
	specie.setId(id);
	specie.setName(id);
	specie.setCompartment(compartment);
	if (amount < 0) {
		specie.setInitialConcentration(concentration);
	} else{
		specie.setInitialAmount(amount);	
	}
	specie.setHasOnlySubstanceUnits(true);
	specie.setConstant(false);
	specie.setBoundaryCondition(false);
	return specie;
}
 

import org.sbml.jsbml.Species; //导入方法依赖的package包/类
public void createSpeciesFromGCM(String s,Properties property) {
	Species species = sbml.getModel().getSpecies(s);
	if (species==null) {
		species = sbml.getModel().createSpecies();
		species.setId(s);
		species.setCompartment(getDefaultCompartment());
		species.setBoundaryCondition(false);
		species.setConstant(false);
		species.setInitialAmount(0);
		species.setHasOnlySubstanceUnits(true);
	}
	if (property.containsKey(GlobalConstants.INITIAL_STRING)) {
		String initialString = property.getProperty(GlobalConstants.INITIAL_STRING);
		if (Utility.isValid(initialString, Utility.NUMstring)) {
			species.setInitialAmount(Double.parseDouble(initialString));
		} 
		else if (Utility.isValid(initialString, Utility.CONCstring)) {
			species.setInitialConcentration(Double.parseDouble(initialString.substring(1,initialString.length()-1)));
		} 
	}
	boolean onPort = false;
	if (property.containsKey(GlobalConstants.TYPE)) {
		String type = property.getProperty(GlobalConstants.TYPE).replace("diffusible","").replace("constitutive","");
		createDirPort(species.getId(),type);
		if (type.equals(GlobalConstants.INPUT)) {
			species.setBoundaryCondition(true);
		}
		onPort = (type.equals(GlobalConstants.INPUT)||type.equals(GlobalConstants.OUTPUT));
	} 
	double kd = -1;
	if (property.containsKey(GlobalConstants.KDECAY_STRING)) {
		kd = Double.parseDouble(property.getProperty(GlobalConstants.KDECAY_STRING));
	} 
	if (kd != 0) {
		createDegradationReaction(s,kd,null,onPort,null);
	} 
	if (property.containsKey(GlobalConstants.TYPE) && 
		property.getProperty(GlobalConstants.TYPE).contains("diffusible")) {
		createDiffusionReaction(s,property.getProperty(GlobalConstants.MEMDIFF_STRING),onPort,null);
	}
	if (property.containsKey(GlobalConstants.TYPE) && 
			property.getProperty(GlobalConstants.TYPE).contains("constitutive")) {
		createConstitutiveReaction(s,null, null, onPort, null);
	}
}
 

import org.sbml.jsbml.Species; //导入方法依赖的package包/类
public String createSpecies(String id, float x, float y) {
	String compartment;
	if (x >= 0 && y >= 0) {
		compartment = getCompartmentByLocation(x,y, GlobalConstants.DEFAULT_SPECIES_WIDTH, 
				GlobalConstants.DEFAULT_SPECIES_HEIGHT);
		if (compartment.equals("")) {
			message.setErrorDialog("Compartment Required", "Species must be placed within a compartment.");
	    this.notifyObservers(message);
			return null;
		}
	} else {
		if (sbml.getModel().getCompartmentCount()==0) {
			message.setErrorDialog("Compartment Required", "Species must be placed within a compartment.");
       this.notifyObservers(message);
			return null;
		}
		compartment = sbml.getModel().getCompartment(0).getId();
	}
	if (id == null) {
		do {
			creatingSpeciesID++;
			id = "S" + String.valueOf(creatingSpeciesID);
		} while (SBMLutilities.getElementBySId(sbml, id)!=null);
	}
	if (sbml != null && sbml.getModel().getSpecies(id)==null) {
		Model m = sbml.getModel();
		Species species = m.createSpecies();
		species.setId(id);
		// Set default species metaID
		metaIDIndex = SBMLutilities.setDefaultMetaID(sbml, species, metaIDIndex); 
		species.setCompartment(compartment);
		SBMLutilities.cloneDimensionAddIndex(sbml.getModel().getCompartment(compartment),species,"compartment");
		species.setBoundaryCondition(false);
		species.setConstant(false);
		species.setInitialAmount(0);
		species.setHasOnlySubstanceUnits(true);
		if (x >= 0 && y >= 0) {
			Layout layout = getLayout();
			SpeciesGlyph speciesGlyph = null;
			if (layout.getSpeciesGlyph(GlobalConstants.GLYPH+"__"+id)!=null) {
				speciesGlyph = layout.getSpeciesGlyph(GlobalConstants.GLYPH+"__"+id);
			} else {
				speciesGlyph = layout.createSpeciesGlyph(GlobalConstants.GLYPH+"__"+id);
				speciesGlyph.createBoundingBox();
				speciesGlyph.getBoundingBox().createDimensions();
				speciesGlyph.getBoundingBox().createPosition();
				speciesGlyph.setSpecies(id);
			}
			speciesGlyph.getBoundingBox().getPosition().setX(x);
			speciesGlyph.getBoundingBox().getPosition().setY(y);
			speciesGlyph.getBoundingBox().getDimensions().setWidth(GlobalConstants.DEFAULT_SPECIES_WIDTH);
			speciesGlyph.getBoundingBox().getDimensions().setHeight(GlobalConstants.DEFAULT_SPECIES_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(speciesGlyph.getBoundingBox().clone());
		}
	}
	return id;
}
 

import org.sbml.jsbml.Species; //导入方法依赖的package包/类
public String createPromoter(String promoterId, float x, float y, boolean isExplicit, 
		boolean createProduction, String reactionId) {
	createProductionDefaultParameters();
	String compartment;
	compartment = getCompartmentByLocation(x,y,GlobalConstants.DEFAULT_SPECIES_WIDTH,GlobalConstants.DEFAULT_SPECIES_HEIGHT);
	if (compartment.equals("")) {
		if (sbml.getModel().getCompartmentCount()==0) {
		  message.setErrorDialog("Compartment Required", "Species must be placed within a compartment.");
       this.notifyObservers(message);
			return "";
		}
		compartment = sbml.getModel().getCompartment(0).getId();
	} 
	Species promoter = sbml.getModel().createSpecies();
	// Set default species ID
	if (promoterId == null) {
		do {
			creatingPromoterID++;
			promoterId = "P" + String.valueOf(creatingPromoterID);
		}
		while (SBMLutilities.getElementBySId(sbml, promoterId)!=null);
	}
	promoter.setId(promoterId);
	// Set default promoter metaID
	metaIDIndex = SBMLutilities.setDefaultMetaID(sbml, promoter, metaIDIndex); 
	
	promoter.setSBOTerm(GlobalConstants.SBO_PROMOTER_BINDING_REGION);
	promoter.setInitialAmount(sbml.getModel().getParameter(GlobalConstants.PROMOTER_COUNT_STRING).getValue());

	promoter.setCompartment(compartment);
	SBMLutilities.cloneDimensionAddIndex(sbml.getModel().getCompartment(compartment),promoter,"compartment");
	promoter.setBoundaryCondition(false);
	promoter.setConstant(false);
	promoter.setHasOnlySubstanceUnits(true);
	if (createProduction)
		createProductionReaction(promoterId, reactionId, null, null, null, null, null, null, false, null);
	if (isExplicit) {
		Layout layout = getLayout();
		SpeciesGlyph speciesGlyph = null;
		if (layout.getSpeciesGlyph(GlobalConstants.GLYPH+"__"+promoterId)!=null) {
			speciesGlyph = layout.getSpeciesGlyph(GlobalConstants.GLYPH+"__"+promoterId);
		} else {
			speciesGlyph = layout.createSpeciesGlyph(GlobalConstants.GLYPH+"__"+promoterId);
			speciesGlyph.createBoundingBox();
			speciesGlyph.getBoundingBox().createDimensions();
			speciesGlyph.getBoundingBox().createPosition();
			speciesGlyph.setSpecies(promoterId);
		}
		speciesGlyph.getBoundingBox().getPosition().setX(x);
		speciesGlyph.getBoundingBox().getPosition().setY(y);
		speciesGlyph.getBoundingBox().getDimensions().setWidth(GlobalConstants.DEFAULT_SPECIES_WIDTH);
		speciesGlyph.getBoundingBox().getDimensions().setHeight(GlobalConstants.DEFAULT_SPECIES_HEIGHT);
		TextGlyph textGlyph = layout.createTextGlyph(GlobalConstants.TEXT_GLYPH+"__"+promoterId);
		textGlyph.createBoundingBox();
		textGlyph.getBoundingBox().createDimensions();
		textGlyph.getBoundingBox().createPosition();
		textGlyph.setGraphicalObject(GlobalConstants.GLYPH+"__"+promoterId);
		textGlyph.setText(SBMLutilities.getArrayId(sbml,promoterId));
		textGlyph.setBoundingBox(speciesGlyph.getBoundingBox().clone());
	}

	return promoterId;
}