Java Model.getReactionCount方法代码示例

import org.sbml.jsbml.Model; //导入方法依赖的package包/类
private Set<SynthesisNode> constructGraph(Model sbmlModel, SBOLFileManager fileManager) throws SBOLException {
	HashMap<String, SynthesisNode> idToNode = new HashMap<String, SynthesisNode>();
	edges = new HashMap<SynthesisNode, List<SynthesisNode>>();
	nucleotideCount = 0;
	compURIs = new HashSet<URI>();
	signals = new HashSet<String>();
	for (int i = 0; i < sbmlModel.getReactionCount(); i++) 
	{
		Reaction sbmlReaction = sbmlModel.getReaction(i);
		if (sbmlReaction.getProductCount() > 0) 
			if (BioModel.isProductionReaction(sbmlReaction)) 
			{
				constructTranscriptionMotif(sbmlReaction, idToNode, sbmlModel, fileManager);
			} 
			else if ((BioModel.isComplexReaction(sbmlReaction))) 
			{
				constructComplexationMotif(sbmlReaction, idToNode, sbmlModel, fileManager);
			}
	}
	//TODO: why return the value of idToNode and ignore the key?
	//NOTE: create a table of all the values in idToNode which contains transcription and complex formation reaction
	return new HashSet<SynthesisNode>(idToNode.values());
}
 

import org.sbml.jsbml.Model; //导入方法依赖的package包/类
public static Reaction getDegradationReaction(String speciesId, Model sbmlModel) {
	String componentId = "";
	String shortSpeciesId = speciesId;
	if (speciesId.contains("__")) {
		componentId = speciesId.substring(0,speciesId.lastIndexOf("__")+2);
		shortSpeciesId = speciesId.substring(speciesId.lastIndexOf("__")+2);
	}
	Reaction degradation = sbmlModel.getReaction(componentId + GlobalConstants.DEGRADATION + "_" + shortSpeciesId);
	if (degradation == null) {
		for (int i = 0; i < sbmlModel.getReactionCount(); i++) {
			Reaction r = sbmlModel.getReaction(i);
			if (BioModel.isDegradationReaction(r) && r.hasReactant(new Species(speciesId)))
				return r;
		}
	} else if (BioModel.isDegradationReaction(degradation))
		return degradation;
	return null;
}
 

import org.sbml.jsbml.Model; //导入方法依赖的package包/类
public static Reaction getProductionReaction(String promoterId, Model sbmlModel) {
	String componentId = "";
	String shortPromoterId = promoterId;
	if (promoterId.contains("__")) {
		componentId = promoterId.substring(0, promoterId.lastIndexOf("__") + 2);
		shortPromoterId = promoterId.substring(promoterId.lastIndexOf("__") + 2);
	}
	Reaction production = sbmlModel.getReaction(componentId + GlobalConstants.PRODUCTION + "_" + shortPromoterId);
	if (production == null)
		for (int i = 0; i < sbmlModel.getReactionCount(); i++) {
			Reaction r = sbmlModel.getReaction(i);
			if (BioModel.isProductionReaction(r) && r.hasModifier(new Species(promoterId)))
				return r;
		}
	else if (BioModel.isProductionReaction(production))
		return production;
	return null;
}
 

import org.sbml.jsbml.Model; //导入方法依赖的package包/类
public static Reaction getComplexReaction(String speciesId, Model sbmlModel) {
	String componentId = "";
	String shortSpeciesId = speciesId;
	if (speciesId.contains("__")) {
		componentId = speciesId.substring(0,speciesId.lastIndexOf("__")+2);
		shortSpeciesId = speciesId.substring(speciesId.lastIndexOf("__")+2);
	}
	Reaction complexation = sbmlModel.getReaction(componentId + GlobalConstants.COMPLEXATION 
			+ "_" + shortSpeciesId);
	if (complexation == null) {
		for (int i = 0; i < sbmlModel.getReactionCount(); i++) {
			Reaction r = sbmlModel.getReaction(i);
			if (BioModel.isComplexReaction(r) && r.hasProduct(new Species(speciesId)))
				return r;
		}
	} else if (BioModel.isComplexReaction(complexation))
		return complexation;
	return null;
}
 

import org.sbml.jsbml.Model; //导入方法依赖的package包/类
/**
 * Convert the specified SBML model to its equivalent SBOL ModuleDefinition.
 * All SBML SBase referencing this SBML model will be converted to SBOL data object.
 * In this case, all SBML species will be converted to SBOL ComponentDefinition and FunctionalComponent.
 * All SBML reactions will be converted to SBOL Interactions. 
 * All SBML replacements will be converted to SBOL MapsTo.
 * 
 * @param source - reference to the source file for the given SBML model
 * @param externalSBMLPath - The full path of external SBML files to be referenced in the SBML2SBOL conversion
 * @param sbmlDoc - The SBML Document to be converted to SBOL
 * @param model - The SBML model to be converted to SBOL ModuleDefinition
 * @param sbolDoc - The SBOL document to store all SBOL objects converted from the SBML Document
 * @param sbol_Library - The global SBOL document that contains all SBOL objects referenced in conversion. 
 * @throws SBOLValidationException - SBOL Exception occurred when loading referenced SBOL files
 * @throws XMLStreamException - Invalid XML file.
 * @throws IOException - Input Exception occurred. 
 */
private static void parseSBMLModel(String source, String externalSBMLPath, SBMLDocument sbmlDoc, Model model, SBOLDocument sbolDoc, SBOLDocument sbol_Library) throws SBOLValidationException, XMLStreamException, IOException 
{
	//String modelId = model.getId();
	URI sourceURI  = URI.create(source);
	URI LANGUAGE  = EDAMOntology.SBML;
	URI FRAMEWORK = SystemsBiologyOntology.DISCRETE_FRAMEWORK;

	org.sbolstandard.core2.Model sbolModel = sbolDoc.getModel(model.getId() + "_model", VERSION);
	if (sbolModel!=null) {
		sbolDoc.removeModel(sbolModel);
	}
	
	sbolModel = sbolDoc.createModel(model.getId() + "_model", VERSION, sourceURI, LANGUAGE, FRAMEWORK);

	String identityStr  = model.getId() + "_md";
	ModuleDefinition moduleDef = sbolDoc.getModuleDefinition(identityStr, VERSION);
	if (moduleDef!=null) {
		sbolDoc.removeModuleDefinition(moduleDef);
	}
	moduleDef = sbolDoc.createModuleDefinition(identityStr, VERSION);
	moduleDef.addModel(sbolModel);

	for (int i = 0; i < model.getSpeciesCount(); i++) 
	{
		Species species = model.getSpecies(i);
		ComponentDefinition compDef = setComponentDefinition(sbol_Library, sbolDoc, model, species);
		setFunctionalComponent(sbmlDoc, model, moduleDef, compDef, species);
	}

	for (int i = 0; i < model.getReactionCount(); i++) 
	{
		Reaction reaction = model.getReaction(i);

		if(BioModel.isProductionReaction(reaction))
		{
			// if production reaction, then you want to examine the modifiers, and create interactions for 
			// each modifier that is a repressor from this species to the promoter
			parseProductionReaction(moduleDef, reaction);
		}
		else if(BioModel.isComplexReaction(reaction))
		{	
			// if complex reaction, then create on interaction
			parseComplexReaction(moduleDef, reaction);
		}
		else if(BioModel.isDegradationReaction(reaction))
		{
			// if degradation reaction, then create an interaction
			parseDegradationReaction(moduleDef, reaction);
		}
		else 
		{
			parseBiochemicalReaction(moduleDef, reaction);
		}
	}

	extractSubModels(source, externalSBMLPath, sbmlDoc, sbol_Library, sbolDoc, moduleDef, model);
}