import org.sbml.jsbml.ModifierSpeciesReference; //导入依赖的package包/类
public static boolean isPromoter(ModifierSpeciesReference mod) {
	if (AnnotationUtility.checkObsoleteAnnotation(mod,"promoter")) {
		mod.setSBOTerm(GlobalConstants.SBO_PROMOTER_MODIFIER);
		AnnotationUtility.removeObsoleteAnnotation(mod);
		return true;
	} else if (mod.isSetSBOTerm()) {
		if (mod.getSBOTerm() == GlobalConstants.SBO_PROMOTER) {
			mod.setSBOTerm(GlobalConstants.SBO_PROMOTER_MODIFIER);
			return true;
		} else if (mod.getSBOTerm() == GlobalConstants.SBO_PROMOTER_MODIFIER) {
			return true;
		}
	} else if (isPromoterSpecies(mod.getSpeciesInstance())) {
		mod.setSBOTerm(GlobalConstants.SBO_PROMOTER_MODIFIER);
		return true;
	}
	return false;
}
 

import org.sbml.jsbml.ModifierSpeciesReference; //导入依赖的package包/类
public static boolean isRegulator(ModifierSpeciesReference modifier) {
	if (modifier!=null) {
		if (modifier.isSetSBOTerm()) {
			if (modifier.getSBOTerm()==GlobalConstants.SBO_REGULATION) {
				modifier.setSBOTerm(GlobalConstants.SBO_DUAL_ACTIVITY);
				return true;
			} else if (modifier.getSBOTerm()==GlobalConstants.SBO_DUAL_ACTIVITY) {
				return true;
			}
		}
		if (AnnotationUtility.checkObsoleteAnnotation(modifier,GlobalConstants.REGULATION)) {
			modifier.setSBOTerm(GlobalConstants.SBO_DUAL_ACTIVITY);
			AnnotationUtility.removeObsoleteAnnotation(modifier);
			return true;
		} else if (AnnotationUtility.checkObsoleteAnnotation(modifier,"promoter")) {
			AnnotationUtility.removeObsoleteAnnotation(modifier);
			return false;
		}
	}
	return false;
}
 

import org.sbml.jsbml.ModifierSpeciesReference; //导入依赖的package包/类
private static boolean modifierSpeciesReferenceMatch(ModifierSpeciesReference ref,String refStr) {
	String[] split = refStr.split(" ");
	String id = "";
	String dim = "";
	String species = "";
	String index = "";
	int offset = 0;
	if (refStr.contains(":")) {
		id = split[0].split("\\[")[0];
		if (split[0].contains("["))
			dim = split[0].substring(split[0].indexOf("["));
		offset = 2;
	}
	species = split[offset].split("\\[")[0];
	if (split[offset].contains("["))
		index = split[offset].substring(split[offset].indexOf("["));
	if (ref.isSetId() && !ref.getId().equals(id)) return false;
	if (!ref.getSpecies().equals(species)) return false;
	String refDim = SBMLutilities.getDimensionString(ref);
	if (!refDim.equals(dim)) return false;
	String refIndex = SBMLutilities.getIndicesString(ref, "species");
	if (!refIndex.equals(index)) return false;
	return true;
}
 

import org.sbml.jsbml.ModifierSpeciesReference; //导入依赖的package包/类
/**
 * Bool species in modifier S reference.
 *
 * @param los the los
 * @param losr the losr
 * @return the boolean[]
 */
private boolean[] boolSpeciesInModifierSReference(ListOf<Species> los, ListOf<ModifierSpeciesReference> losr){
	boolean[] bool = new boolean[(int)los.size()];
	
	for(int i = 0; i < los.size(); i++)
		for(int j = 0; j < losr.size(); j++)
			if(los.get(i).getId().equals(losr.get(j).getSpecies()))
				bool[i] = true;
		
	return bool;
}
 

import org.sbml.jsbml.ModifierSpeciesReference; //导入依赖的package包/类
/**
 * Complete modifier species reference.
 *
 * @param modifierSpeciesReference
 *        the modifier species reference
 * @return ListOf<ModifierSpeciesReference>
 *         TODO
 */
public static ListOf<ModifierSpeciesReference> completeModifierSpeciesReference(
  ListOf<ModifierSpeciesReference> modifierSpeciesReference) {
  for (ModifierSpeciesReference sr : modifierSpeciesReference) {
    if (!sr.isSetSpecies()){
      Species s = model.getSpecies(sr.getId());
      if(s == null) {
        sr.setSpecies(model.getSpecies(0));
      } else {
        sr.setSpecies(s);
      }
    }
  }
  return modifierSpeciesReference;
}
 

import org.sbml.jsbml.ModifierSpeciesReference; //导入依赖的package包/类
public Reaction addNoInfluenceToProductionReaction(String promoterId,String regulatorId,String productId) {
	Reaction r = getProductionReaction(promoterId);
	ModifierSpeciesReference modifier = r.getModifierForSpecies(regulatorId);
	if (!regulatorId.equals("none") && modifier==null) {
		modifier = r.createModifier();
		modifier.setSpecies(regulatorId);
		modifier.setSBOTerm(GlobalConstants.SBO_NEUTRAL);
	} else if (modifier != null) {
		return r;
	}
	if (modifier!=null) {
		SBMLutilities.copyDimensionsToEdgeIndex(r, sbml.getModel().getSpecies(regulatorId), modifier, "species");
	}
	if (!productId.equals("none") && r.getProductForSpecies(productId)==null) {
		SpeciesReference product = r.createProduct();
		product.setSpecies(productId);
		SBMLutilities.copyDimensionsToEdgeIndex(r, sbml.getModel().getSpecies(productId), product, "species");
		double np = sbml.getModel().getParameter(GlobalConstants.STOICHIOMETRY_STRING).getValue();
		product.setStoichiometry(np);
		product.setConstant(true);
		if (r.getProductForSpecies(promoterId + "_mRNA")!=null) {
			r.removeProduct(promoterId+"_mRNA");
		}
		if (sbml.getModel().getSpecies(promoterId + "_mRNA")!=null) {
			sbml.getModel().removeSpecies(promoterId+"_mRNA");
		}
	}
	r.getKineticLaw().setMath(SBMLutilities.myParseFormula(createProductionKineticLaw(r)));
	return r;
}
 

import org.sbml.jsbml.ModifierSpeciesReference; //导入依赖的package包/类
public static boolean isActivator(ModifierSpeciesReference modifier) {
	if (modifier.isSetSBOTerm()) {
		if (modifier.getSBOTerm()==GlobalConstants.SBO_ACTIVATION) return true;
	}
	if (AnnotationUtility.checkObsoleteAnnotation(modifier,GlobalConstants.ACTIVATION)) {
		modifier.setSBOTerm(GlobalConstants.SBO_ACTIVATION);
		AnnotationUtility.removeObsoleteAnnotation(modifier);
		return true;
	}
	return false;
}
 

import org.sbml.jsbml.ModifierSpeciesReference; //导入依赖的package包/类
public static boolean isRepressor(ModifierSpeciesReference modifier) {
	if (modifier.isSetSBOTerm()) {
		if (modifier.getSBOTerm()==GlobalConstants.SBO_REPRESSION) return true;
	}
	if (AnnotationUtility.checkObsoleteAnnotation(modifier,GlobalConstants.REPRESSION)) {
		modifier.setSBOTerm(GlobalConstants.SBO_REPRESSION);
		AnnotationUtility.removeObsoleteAnnotation(modifier);
		return true;
	}
	return false;
}
 

import org.sbml.jsbml.ModifierSpeciesReference; //导入依赖的package包/类
public static boolean isNeutral(ModifierSpeciesReference modifier) {
	if (modifier.isSetSBOTerm()) {
		if (modifier.getSBOTerm()==GlobalConstants.SBO_NEUTRAL) return true;
	}
	if (AnnotationUtility.checkObsoleteAnnotation(modifier,GlobalConstants.NOINFLUENCE)) {
		modifier.setSBOTerm(GlobalConstants.SBO_NEUTRAL);
		AnnotationUtility.removeObsoleteAnnotation(modifier);
		return true;
	}
	return false;
}
 

import org.sbml.jsbml.ModifierSpeciesReference; //导入依赖的package包/类
public static String getPromoterId(Reaction productionReaction)
{
	for (int i = 0; i < productionReaction.getModifierCount(); i++)
	{
		ModifierSpeciesReference modifier = productionReaction.getModifier(i);
		if (BioModel.isPromoter(modifier))
		{
			return modifier.getSpecies();
		}
	}
	return null;
}
 

import org.sbml.jsbml.ModifierSpeciesReference; //导入依赖的package包/类
public static ModifierSpeciesReference removeModifier(Reaction r, String species)
{
	if (r.getListOfModifiers() != null)
	{
		return r.removeModifier(species);
	}
	return null;
}
 

import org.sbml.jsbml.ModifierSpeciesReference; //导入依赖的package包/类
/**
 * Convert SBOL participation that takes on the role of activator into its equivalent SBML SpeciesReference.
 * 
 * @param activator - The SBOL participation to be annotated as SBML SpeciesReference.
 * @param promoter - The SBOL FunctionalComponent promoter of the activator.
 * @param moduleDef - The SBOL ModuleDefinition that contain the SBOL Participation.
 * @param productionRxn - The SBML reaction that will store the SpeciesReference created from the converted activator SBOL Participation.
 * @param targetModel - The SBML model to store the SBML Reaction and SpeciesReference created from the conversion.
 */
private static void generateActivatorReference(Participation activator, FunctionalComponent promoter, 
		ModuleDefinition moduleDef, Reaction productionRxn, BioModel targetModel) {
	FunctionalComponent tf = moduleDef.getFunctionalComponent(activator.getParticipantURI());

	targetModel.addActivatorToProductionReaction(getDisplayID(promoter),  
			getDisplayID(tf), "none", productionRxn, null, null, null);

	// Annotate SBML activator species reference with SBOL activator participation
	ModifierSpeciesReference activatorRef = productionRxn.getModifierForSpecies(getDisplayID(tf));
	SBMLutilities.setDefaultMetaID(targetModel.getSBMLDocument(), activatorRef, 1);
	annotateSpeciesReference(activatorRef, activator);
}
 

import org.sbml.jsbml.ModifierSpeciesReference; //导入依赖的package包/类
/**
 * Convert SBOL participation that takes on the role of repressor into its equivalent SBML SpeciesReference.
 * 
 * @param repressor - The SBOL participation to be annotated as SBML SpeciesReference.
 * @param promoter - The SBOL FunctionalComponent promoter of the repressor.
 * @param moduleDef - The SBOL ModuleDefinition that contain the SBOL Participation.
 * @param productionRxn - The SBML reaction that will store the SpeciesReference created from the converted repressor SBOL Participation.
 * @param targetModel - The SBML model to store the SBML Reaction and SpeciesReference created from the conversion.
 */
private static void generateRepressorReference(Participation repressor, FunctionalComponent promoter, 
		ModuleDefinition moduleDef, Reaction productionRxn, BioModel targetModel) {
	FunctionalComponent tf = moduleDef.getFunctionalComponent(repressor.getParticipantURI());
	targetModel.addRepressorToProductionReaction(getDisplayID(promoter),  
			getDisplayID(tf), "none", productionRxn, null, null, null);

	// Annotate SBML repressor species reference with SBOL repressor participation
	ModifierSpeciesReference repressorRef = productionRxn.getModifierForSpecies(getDisplayID(tf));
	SBMLutilities.setDefaultMetaID(targetModel.getSBMLDocument(), repressorRef, 1);
	annotateSpeciesReference(repressorRef, repressor);
}
 

import org.sbml.jsbml.ModifierSpeciesReference; //导入依赖的package包/类
private void assignModifiers(ListOf<ModifierSpeciesReference> modifiers) {
    for (ModifierSpeciesReference reference : modifiers) {
        logger.debug("Assigning Chemical Entity {} as catalytic modifier.", reference.getSpecies());
        String identifier = reference.getSpecies();
        currentReaction.getKineticLaw().referenceChemicalEntityToParameter(identifier, entities.get(identifier));
        currentReaction.getCatalyticReactants().add(new CatalyticReactant(entities.get(identifier), ReactantRole.INCREASING));
    }
}
 

import org.sbml.jsbml.ModifierSpeciesReference; //导入依赖的package包/类
/**
 * Adds the default SBO term.
 *
 * @param node the node
 */
public static void addDefaultSBOTerm(TreeNode node) {
  for (int i = 0; i < node.getChildCount(); i++) {
    addDefaultSBOTerm(node.getChildAt(i));
  }

  if (!(node instanceof SBase) ) {
    return ;
  }

  SBase sbase = (SBase) node;
  if (sbase.isSetSBOTerm()) {
    return;
  }

  if (sbase instanceof Model) {
    sbase.setSBOTerm(intSBOTermForModel);
  } else if (sbase instanceof Species) {
    sbase.setSBOTerm(intSBOTermForGENERIC);
  } else if (sbase instanceof Compartment) {
    sbase.setSBOTerm(intSBOTermForCompartment);
  } else if (sbase instanceof Parameter) {
    sbase.setSBOTerm(intSBOTermForParameter);
  } else if (sbase instanceof Rule) {
    sbase.setSBOTerm(intSBOTermForRateRule);
  } else if (sbase instanceof Compartment) {
    sbase.setSBOTerm(intSBOTermForCompartment);
  } else if (sbase instanceof Reaction) {
    sbase.setSBOTerm(intSBOTermForReaction);
  } else if (sbase instanceof SpeciesReference) {
    Reaction r = (Reaction) ((SpeciesReference) sbase).getParentSBMLObject().getParentSBMLObject();
    if (r.getListOfReactants().contains(sbase)) {
      sbase.setSBOTerm(intSBOTermForReactant);
    } else {
      sbase.setSBOTerm(intSBOTermForProduct);
    }
  } else if (sbase instanceof ModifierSpeciesReference) {
    sbase.setSBOTerm(intSBOTermForModifierSpeciesReference);
  } else if (sbase instanceof KineticLaw) {
    sbase.setSBOTerm(intSBOTermForKineticLaw);
  }
}
 

import org.sbml.jsbml.ModifierSpeciesReference; //导入依赖的package包/类
public void addModifierToReaction(String modifierId,String reactionId) {
	Reaction r = sbml.getModel().getReaction(reactionId);
	ModifierSpeciesReference s = r.createModifier();
	s.setSpecies(modifierId);
	SBMLutilities.copyDimensionsToEdgeIndex(r, sbml.getModel().getSpecies(modifierId), s, "species");
}
 

import org.sbml.jsbml.ModifierSpeciesReference; //导入依赖的package包/类
public static ModifierSpeciesReference ModifierSpeciesReference(String id) {
	ModifierSpeciesReference sr = new ModifierSpeciesReference(GlobalConstants.SBML_LEVEL, GlobalConstants.SBML_VERSION);
	sr.setSpecies(id);
	return sr;
}