Java Species.getId方法代码示例

import org.sbml.jsbml.Species; //导入方法依赖的package包/类
/**
 * For each species that exist in an SBML model, this function will create a FunctionalComponent instance for the corresponding 
 * ComponentDefinition existing in the specified ModuleDefinition.
 * 
 * @param sbmlDoc - The SBML Document that contains the SBML species to be converted to SBOL FunctionalComponent. 
 * @param moduleDef - The SBOL ModuleDedfinition that the converted FunctionalComponent will be stored in.
 * @param compDef - The ComponentDefinition that the FunctionalComponent will reference from.
 * @param species - The SBML Species that will be converted to SBOL FunctionalComponent.
 * @return The FunctionalComponent that was created. 
 * @throws SBOLValidationException - SBOL validation exception while creating an SBOL object for SBML2SBOL conversion.
 */
private static FunctionalComponent setFunctionalComponent(SBMLDocument sbmlDoc, Model model, 
		ModuleDefinition moduleDef, ComponentDefinition compDef, Species species) throws SBOLValidationException
{
	AccessType access; 
	DirectionType direction;
	// create FunctionalComponents for these within the module
	String funcComp_identity =  species.getId();

	if (SBMLutilities.isInput(model,species.getId())) 
	{
		access    = AccessType.PUBLIC;
		direction = DirectionType.IN;
	} 
	else if (SBMLutilities.isOutput(model,species.getId())) 
	{
		access    = AccessType.PUBLIC;
		direction = DirectionType.OUT;
	} 
	else if (SBMLutilities.isOnPort(model,species.getId())) 
	{
		access    = AccessType.PUBLIC;
		direction = DirectionType.NONE;
	} 
	else 
	{
		access    = AccessType.PRIVATE; 
		direction = DirectionType.NONE;
	}
	FunctionalComponent fc = moduleDef.createFunctionalComponent(funcComp_identity, access, compDef.getIdentity(), direction);
	fc.setName(species.getId());
	return fc;
}
 

import org.sbml.jsbml.Species; //导入方法依赖的package包/类
/**
 * Gets the table model with species.
 *
 * @param los the los
 * @return the table model with species
 */
private MyTableModel getTableModelWithSpecies(ListOf<Species> los){
	int max = memberList.size();
	Object[][] data  = new Object[max][header.length];
	for(int i = 0; i < max; i++){
		Species s = (Species) memberList.get(i);
		data[i][0] = s.getId();
		if(s.isSetInitialAmount()){
			data[i][1] = "amount";
			data[i][2] = s.getInitialAmount();
		} else if(s.isSetInitialConcentration()){
			data[i][1] = "concentration";
			data[i][2] = s.getInitialConcentration();
		}
		data[i][3] = s.getCompartment();
		data[i][4] = s.getSubstanceUnits();
		data[i][5] = s.getHasOnlySubstanceUnits();
		data[i][6] = s.getBoundaryCondition();
		data[i][7] = s.getConstant();
	}
	
	MyTableModel tm = new MyTableModel(data, header) {
		private static final long serialVersionUID = 1L;

		@Override
		public Class<?> getColumnClass(int Column) {
			switch (Column) {
			case 0: // id
			case 1: // initial
				return String.class;
			case 2: // quantity
				return Double.class;
			case 3: // Compartment
			case 4: // substance unit
			case 5: // hasOnlySubstanceUnits
			case 6: // boundaryCondition
			case 7:	// constant
				return String.class;
			default:
				return String.class;
			}
		}};
	
	tm.setColumnIdentifiers(header);
		
	return tm;
}
 

import org.sbml.jsbml.Species; //导入方法依赖的package包/类
/**
 * Convert species to CD.
 *
 * @param sgList
 *        the sg list
 */
public void convertSpeciesToCD(List<SpeciesGlyph> sgList) {
  HashMap<String, Integer> hashSpeciesCounter = new HashMap<String, Integer>();
  for (SpeciesGlyph sg : sgList) {
    if (sg.isSetSpecies()) {
      Species s = (Species) sg.getSpeciesInstance();
      SpeciesAliasWrapper saw = mWrapper.createSpeciesAliasWrapper(sg);
      String cid = s.getCompartment();
      String sid = s.getId() + "alias";
      if (hashSpeciesCounter.isEmpty()
          || !hashSpeciesCounter.containsKey(sid)) {
        hashSpeciesCounter.put(sid, 1);
      } else {
        hashSpeciesCounter.put(sid, hashSpeciesCounter.get(sid) + 1);
      }
      sid = sid + hashSpeciesCounter.get(sid);
      saw.setId(sid);
      if (!cid.equals("default")) {
        saw.setCompartmentAlias(cid + "alias");
        saw.setCompartmentAliasWrapper(cid + "alias");
      }
      int sboterm = SBMLUtil.intSBOTermForDEFAULT_SPECIES;
      if (sg.isSetSBOTerm()) {
        sboterm = sg.getSBOTerm();
      } else if (s.isSetSBOTerm()) {
        sboterm = s.getSBOTerm();
      }
      mWrapper.createSpeciesObjectFromSBOTerm(sg, sboterm);
      String clazz = SBMLUtil.SBOTermToCDSpecies(sboterm);
      SpeciesWrapper sw = mWrapper.getSpeciesWrapperById(s.getId());
      sw.setClazz(clazz);
      if (clazz.equals("PROTEIN")) {
        sw.getSpeciesIdentity().setProteinReference(
          mWrapper.getProteinBySpeciesId(s.getId()).getId());
      } else if (clazz.equals("GENE")) {
        sw.getSpeciesIdentity().setGeneReference(
          mWrapper.getGeneBySpeciesId(s.getId()).getId());
      } else if (clazz.equals("RNA")) {
        sw.getSpeciesIdentity().setRnaReference(
          mWrapper.getRNABySpeciesId(s.getId()).getId());
      } else if (clazz.equals("ANTISENSE_RNA")) {
        sw.getSpeciesIdentity().setAntisensernaReference(
          mWrapper.getAntisenseRNABySpeciesId(s.getId()).getId());
      } else {
        sw.getSpeciesIdentity().setName(sw.getId());
      }
      // CompartmentGlyph cg =
      // getCompartmentGlyphByCompartmentId(s.getCompartment());
      // if(cg != null)
      // sw.setPositionToCompartment(LayoutUtil.getPositionToCompartment(sg,
      // cg));
      // else
      sw.setPositionToCompartment("inside");
    } else {
      // species glyph with no reference
    }
  }
}
 

import org.sbml.jsbml.Species; //导入方法依赖的package包/类
public void createGridDegradationReaction(Species species) {
	
	String speciesID = species.getId();
	Boolean speciesDegrades = false;			
	//Reaction degradation = BioModel.getDegradationReaction(speciesID, compModel);
	
	//fix the sbo term/annotation stuff if it's not correct
	//if (degradation != null)
		speciesDegrades = true;
	
	//only make grid degradation reactions if the species is degradable
	if (speciesDegrades) {
	
		//create array of grid degradation reactions
		String decayString = GlobalConstants.KECDECAY_STRING;
		double decayRate = sbml.getModel().getParameter("kecd").getValue();
			
		String decayUnitString = "u_1_second_n1";
		
		if (sbml.getModel().getUnitDefinition(decayUnitString) == null) {
			
			UnitDefinition ud = sbml.getModel().createUnitDefinition();
			Unit unit = ud.createUnit();
			unit.setExponent(-1.0);
			unit.setKind(Unit.Kind.valueOf("second".toUpperCase()));
			unit.setScale(0);
			unit.setMultiplier(1);
			ud.setId(decayUnitString);
		}
		
		Reaction r = sbml.getModel().createReaction();
		r.setId(GlobalConstants.DEGRADATION + "_" + speciesID);
		SBMLutilities.setMetaId(r, r.getId());
		r.setCompartment(sbml.getModel().getCompartment(0).getId());
		SBMLutilities.cloneDimensionAddIndex(sbml.getModel().getCompartment(r.getCompartment()),r,"compartment");
		r.setReversible(false);
		//r.setFast(false);
		r.setSBOTerm(GlobalConstants.SBO_DEGRADATION);
		
		AnnotationUtility.setGridAnnotation(r, gridTable.getNumRows(), gridTable.getNumCols());
		
		KineticLaw kl = r.createKineticLaw();
		
		if (decayRate > 0) {
			
			//this is the mathematical expression for the decay
			String decayExpression = decayString + "* get2DArrayElement(" + speciesID + ", i, j)";				
			
			SpeciesReference reactant = r.createReactant();
			reactant.setSpecies(speciesID);
			reactant.setStoichiometry(1);
			reactant.setConstant(false);
			
			LocalParameter i = kl.createLocalParameter();
			LocalParameter j = kl.createLocalParameter();
			
			AnnotationUtility.setArraySizeAnnotation(i, gridTable.getNumRows());
			AnnotationUtility.setArraySizeAnnotation(j, gridTable.getNumCols());

			i.setId("i");
			j.setId("j");
			
			//parameter: id="kecd" value=(usually 0.005) units="u_1_second_n1" (inverse seconds)
			Utility.Parameter(kl, decayString, decayRate, decayUnitString);
			
			//formula: kecd * species
			kl.setMath(SBMLutilities.myParseFormula(decayExpression));
			
			Utility.addReaction(sbml, r);
		}
	}		
}
 

import org.sbml.jsbml.Species; //导入方法依赖的package包/类
/**
 * puts species-related information into data structures
 * 
 */
private static void setupSpecies(HierarchicalSimulation sim, ModelContainer container, VectorWrapper wrapper)
{
  Model model = container.getModel();
  HierarchicalModel modelstate = container.getHierarchicalModel();
  SpeciesNode node;
  boolean isConcentration = false;
  for (Species species : model.getListOfSpecies())
  {

    ReplacementSetup.setupReplacement(sim, species, wrapper,VariableType.SPECIES, container);

    String printVariable = container.getPrefix() + species.getId();
    node = (SpeciesNode) modelstate.getNode(species.getId());

    if(sim.getPrintConcentrationSpecies().contains(printVariable))
    {
      isConcentration = true;
    }

    if(node == null)
    {
      node = new SpeciesNode(species.getId());

      node.createState(sim.getAtomicType(), wrapper);
      node.createSpeciesTemplate();
      modelstate.addMappingNode(species.getId(), node);
    }


    if(sim.getInterestingSpecies() != null && sim.getInterestingSpecies().contains(printVariable))
    {
      sim.addPrintVariable(printVariable, node, modelstate.getIndex(), isConcentration);
    }

    if(sim.getInterestingSpecies() == null)
    {
      sim.addPrintVariable(printVariable, node, modelstate.getIndex(), isConcentration);
    }

    if (modelstate.isDeletedBySId(species.getId()))
    {
      continue;
    }

    if(!species.getConstant())
    {
      modelstate.addVariable(node);

    }

    boolean isBoundary = species.getBoundaryCondition();
    boolean isOnlySubstance = species.getHasOnlySubstanceUnits();

    node.setBoundaryCondition(isBoundary);
    node.setHasOnlySubstance(isOnlySubstance);

    VariableNode compartment = modelstate.getNode(species.getCompartment());
    node.setCompartment(compartment);

    if (species.isSetInitialAmount())
    {
      node.setValue(modelstate.getIndex(), species.getInitialAmount());
      node.setIsSetInitialValue(true);
    }
    else if (species.isSetInitialConcentration())
    {
      HierarchicalNode initConcentration = new HierarchicalNode(Type.TIMES);
      initConcentration.addChild(new HierarchicalNode(species.getInitialConcentration()));
      initConcentration.addChild(compartment);
      FunctionNode functionNode = new FunctionNode(node, initConcentration);
      modelstate.addInitConcentration(functionNode);
      node.setHasAmountUnits(false);
      node.setIsSetInitialValue(true);
    }
  }
}