smdb21 / java-miape-api Goto Github PK

public class createMiape(PersistenceManager databaseManager, ControlVocabularyManager cvManager) {
	// project
	ProjectBuilder projectBuilder = MiapeDocumentFactory.createProjectBuilder("my project")
		.date(new MiapeDate(new Date()));

	// User (if needed for persistence, like a database)
	UserBuilder userBuilder = MiapeDocumentFactory.createUserBuilder("myUserName", "myPassword", databaseManager);

	// Spectrometer	
	SpectrometerBuilder spectrometerBuilder = (SpectrometerBuilder) MiapeMSDocumentFactory
   		.createSpectrometerBuilder(SpectrometerName.LTQ_ORBITRAP_XL_NAME).manufacturer("Thermo Scientific")
		.version("version XL").catalogNumber("#12345").model("The new Orbitrap XL");

	// Analyzer	
	AnalyserBuilder analyserBuilder = MiapeMSDocumentFactory.createAnalyserBuilder("orbitrap")
		.description("Description of the orbitrap");

	// Ion source
	EsiBuilder esiBuilder = MiapeMSDocumentFactory.createEsiBuilder("nano-ESI").parameters("xx Volts")
		.supplyType("regular supply");

	// Instrument Configuration (analiser + esi)
	InstrumentConfigurationBuilder instrumentConfigurationBuilder = MiapeMSDocumentFactory
		.createInstrumentConfigurationBuilder("LTQ configuration").analyser(analyserBuilder.build())
		.esi(esiBuilder.build());

	// MIAPE MS document (user + miape project + spectrometer + instrument
	// configuration
	MiapeMSDocument miapeMS = (MiapeMSDocument) MiapeMSDocumentFactory
		.createMiapeMSDocumentBuilder(projectBuilder.build(), "my first miape document", userBuilder.build())
		.instrumentConfiguration(instrumentConfigurationBuilder.build())  
		.spectrometer(spectrometerBuilder.build()).cvManager(cvManager)  
		.dbManager(databaseManager) // needed for later use of .store()
		.build();

	// Save MIAPE MS to XML file
	MiapeXmlFile<MiapeMSDocument> miapeMSXML = MiapeMSXmlFactory.getFactory().toXml(miapeMS, cvManager);
	try {
		miapeMSXML.saveAs("/home/username/myFirstMiapeMS.xml");
		System.out.println("New file created at :" + miapeMSXML.getPath());
	} catch (IOException e1) {
		e1.printStackTrace();
	}

	// Store it in the database
	try {
		int identifier = miapeMS.store();
		System.out.println("Document stored in the database with identifier " + identifier);
	} catch (MiapeDatabaseException | MiapeSecurityException e) {
		e.printStackTrace();
	}
}

public void extractMIAPEInformationFromFiles(ControlVocabularyManager cvManager)
			throws MiapeDatabaseException, MiapeSecurityException {
	File prideXMLFile = new File("path_to_pride_xml");
	File xtandemXMLFile = new File("path_to_xtandem_xml");
	File mzIdentMLFile = new File("path_to_mzIdentML");
	File mzMLFile = new File("path_to_mzML");
	File tsvFile = new File("path_to_tsv_xml");
	File dtaSelectFile = new File("path_to_dtaSelect_xml");

	// PRIDE XML
	MiapeFullPrideXMLFile miapeFullPride = new MiapeFullPrideXMLFile(prideXMLFile);
	miapeFullPride.setCVManager(cvManager);
	// because all MIAPEs are under a project
	miapeFullPride.setProjectName("my project");
	MiapeMSDocument miapeMSFromPRIDEXML = miapeFullPride.toMiapeMS();
	MiapeMSIDocument miapeMSIromPRIDEXML = miapeFullPride.toMiapeMSI();
	printMiapeMS(miapeMSFromPRIDEXML);
	printMiapeMSI(miapeMSIromPRIDEXML);
    
	// XTANDEM XML
	MiapeXTandemFile miapeXTandemXMLFile = new MiapeXTandemFile(xtandemXMLFile);
	miapeXTandemXMLFile.setCvManager(cvManager);
	miapeXTandemXMLFile.setProjectName("my project");
	MiapeMSIDocument miapeMSIFromXTandem = miapeXTandemXMLFile.toDocument();
	printMiapeMSI(miapeMSIFromXTandem);

	// MZIDENTML
	MiapeMzIdentMLFile miapeMzIdentMLFile = new MiapeMzIdentMLFile(mzIdentMLFile);
	miapeMzIdentMLFile.setCvManager(cvManager);
	miapeMzIdentMLFile.setProjectName("my project");
	MiapeMSIDocument miapeMSIFromMzIdentML = miapeMzIdentMLFile.toDocument();
	printMiapeMSI(miapeMSIFromMzIdentML);

	// MZML
	MiapeMzMLFile miapeMzMLFile = new MiapeMzMLFile(mzMLFile);
	miapeMzMLFile.setCvManager(cvManager);
	miapeMzMLFile.setProjectName("my project");
	MiapeMSDocument miapeMSFromMzML = miapeMzMLFile.toDocument();
	printMiapeMS(miapeMSFromMzML);

	// TAB SEPARATED FILE
	MiapeTSVFile miapeTSVFile = new MiapeTSVFile(tsvFile, TableTextFileSeparator.TAB);
	miapeTSVFile.setCvManager(cvManager);
	miapeTSVFile.setProjectName("my project");
	MiapeMSIDocument miapeMSIFromTSV = miapeTSVFile.toDocument();
	printMiapeMSI(miapeMSIFromTSV);

	// DTASELECT
	MiapeDTASelectFile miapeDTASelectFile = new MiapeDTASelectFile(dtaSelectFile);
	miapeDTASelectFile.setCvManager(cvManager);
	miapeDTASelectFile.setProjectName("my project");
	MiapeMSIDocument miapeMSIFromDTASelect = miapeDTASelectFile.toDocument();
	printMiapeMSI(miapeMSIFromDTASelect);
}

private void printMiapeMSI(MiapeMSIDocument miapeMSI) {
	System.out.println("MIAPE MSI: ");
	System.out.println("Name: " + miapeMSI.getName());
	System.out.println("");
	System.out.println("Total number of PSMs: " + miapeMSI.getIdentifiedPeptides().size());
	for (IdentifiedProteinSet proteinSet : miapeMSI.getIdentifiedProteinSets()) {
		InputParameter ip = proteinSet.getInputParameter();
		System.out.println("Input parameters: " + ip.getName());
		System.out.println("Search engine: " + ip.getSoftware().getName());
		System.out.println("Parent tolerance: " + ip.getPrecursorMassTolerance() + " " + ip.getPrecursorMassToleranceUnit());
		System.out.println("Fragment tolerance: " + ip.getFragmentMassTolerance() + " " + ip.getFragmentMassToleranceUnit());
		System.out.println("Num miss-cleavages: " + ip.getMisscleavages());

		System.out.println("Number of proteins: " + proteinSet.getIdentifiedProteins().size());
		for (String proteinACC : proteinSet.getIdentifiedProteins().keySet()) {
			IdentifiedProtein protein = proteinSet.getIdentifiedProteins().get(proteinACC);
			System.out.println("Protein " + proteinACC + " contains " + protein.getIdentifiedPeptides().size() + " PSMs");
			for (IdentifiedPeptide peptide : protein.getIdentifiedPeptides()) {
				System.out.println("PSM " + peptide.getSpectrumRef() + " with sequence " + peptide.getSequence()
						+ " and charge " + peptide.getCharge());
			}
		}
	}
}

private void printMiapeMS(MiapeMSDocument miapeMS) {
	System.out.println("MIAPE MS: ");
	System.out.println("Name: " + miapeMS.getName());
	System.out.println("");
	for (InstrumentConfiguration ic : miapeMS.getInstrumentConfigurations()) {
		for (Analyser analyser : ic.getAnalyzers()) {
			System.out.println("Analyser: " + analyser.getName());
			System.out.println("Description: " + analyser.getDescription());
		}
		for (Esi esi : ic.getEsis()) {
			System.out.println("ESI: " + esi.getName());
			System.out.println("Parameters: " + esi.getParameters());
			System.out.println("Supply type: " + esi.getSupplyType());
		}
		for (ActivationDissociation ad : ic.getActivationDissociations()) {
			System.out.println("Name: " + ad.getName());
			System.out.println("Activation type: " + ad.getActivationType());
			System.out.println("Gas type: " + ad.getGasType());
			System.out.println("Gas pressure: " + ad.getGasPressure() + " " + ad.getPressureUnit());
		}
	}
}