Java DataSourceTxt类代码示例

import org.bridgedb.bio.DataSourceTxt; //导入依赖的package包/类
public static void main(String args[]) throws ClassNotFoundException, IDMapperException
{
	// This example shows how to do a free text search for an identifier
	
	// first we have to load the driver
	// and initialize information about DataSources
	Class.forName("org.bridgedb.webservice.bridgerest.BridgeRest");
	DataSourceTxt.init();
	
	// now we connect to the driver and create a IDMapper instance.
	IDMapper mapper = BridgeDb.connect ("idmapper-bridgerest:http://webservice.bridgedb.org/Human");
	
	String query = "3643";
		
	// let's do a free search without specifying the input type:
	Set<Xref> hits = mapper.freeSearch(query, 100);
	
	// Now print the results.
	// with getURN we obtain valid MIRIAM urn's if possible.
	System.out.println (query + " search results:");
	for (Xref hit : hits)
		System.out.println("  " + hit.getURN());
}
 

import org.bridgedb.bio.DataSourceTxt; //导入依赖的package包/类
private void run() throws ClassNotFoundException, IDMapperException
{
	DataSourceTxt.init();		

	// Entrez gene id for INSR.
	String id = "3643";
	
	Class.forName ("org.bridgedb.webservice.cronos.IDMapperCronos");
	domapping ("idmapper-cronos:hsa", "3643", BioDataSource.ENTREZ_GENE,
			BioDataSource.ENSEMBL_HUMAN);

	Class.forName ("org.bridgedb.webservice.synergizer.IDMapperSynergizer");
	domapping ("idmapper-synergizer:?authority=ensembl&species=Homo sapiens",
			id, DataSource.getByFullName("entrezgene"),
			DataSource.getByFullName("ensembl_gene_id"));
}
 

import org.bridgedb.bio.DataSourceTxt; //导入依赖的package包/类
public static void main(String[] args) throws Exception {
    saveRegister();
    UriPattern.refreshUriPatterns();
    init();
    UriPattern.refreshUriPatterns();
    
    File mergedFile = new File("resources/IdentifiersOrgDataSource.ttl");
    BridgeDBRdfHandler.writeRdfToFile(mergedFile);
    BridgeDBRdfHandler.parseRdfFile(mergedFile);  
    
    File textFile = new File("resources/IdentifiersOrgDataSource.txt");
    BufferedWriter writer = new BufferedWriter(new FileWriter(textFile));
    DataSourceTxt.writeToBuffer(writer);
    InputStream is = new FileInputStream(textFile);
    DataSourceTxt.loadInputStream(is);
}
 

import org.bridgedb.bio.DataSourceTxt; //导入依赖的package包/类
@Override
protected void setUp() throws Exception {
	PreferenceManager.init();
	DataSourceTxt.init();

	//Load the expression data
	gexMgr = new GexManager();
	gexMgr.setCurrentGex(DATASET_FILE.getAbsolutePath(), false);

	Class.forName("org.bridgedb.rdb.IDMapperRdb");
	idMapper = BridgeDb.connect("idmapper-pgdb:" + IDMAPPER_FILE.getAbsolutePath());
}
 

import org.bridgedb.bio.DataSourceTxt; //导入依赖的package包/类
public static void loadModelAsWPRDF(String gpmlFile, String wpid, String revision) throws ConverterException, FileNotFoundException, ClassNotFoundException, IOException, IDMapperException {
	DataSourceTxt.init();
	InputStream input = AbstractConvertorTest.class.getClassLoader().getResourceAsStream(gpmlFile);
	Pathway pathway = PathwayReader.readPathway(input);
	Assert.assertNotNull(pathway);
	model = GpmlConverter.convertWp(pathway, wpid, revision, Collections.<String>emptyList());
	Assert.assertNotNull(model);
	// System.out.println("===== " + gpmlFile + " =====");
	// String ttlContent = toString(model);
	// if (ttlContent.length() > 1000) ttlContent.substring(0,1000);
	// System.out.println(ttlContent);
}
 

import org.bridgedb.bio.DataSourceTxt; //导入依赖的package包/类
public PathwayGeneParser(String url, File bridgeDbFile, File outputNodes, File outputEdges) throws MalformedURLException, ClassNotFoundException, IDMapperException {
	client = new WikiPathwaysClient(new URL(url));
	
	// setting up bridgedb
	DataSourceTxt.init();
	Class.forName("org.bridgedb.rdb.IDMapperRdb");
	mapper = BridgeDb.connect("idmapper-pgdb:" + bridgeDbFile.getAbsolutePath());
	
	this.outputEdges = outputEdges;
	this.outputNodes = outputNodes;
}
 

import org.bridgedb.bio.DataSourceTxt; //导入依赖的package包/类
public DrugbankTargetParser(File bridgeDbFile, File outputNodes, File outputEdges, File input) throws Exception {
	// setting up bridgedb
	DataSourceTxt.init();
	Class.forName("org.bridgedb.rdb.IDMapperRdb");
	mapper = BridgeDb.connect("idmapper-pgdb:" + bridgeDbFile.getAbsolutePath());
	
	this.input = input;
	this.outputEdges = outputEdges;
	this.outputNodes = outputNodes;
}
 

import org.bridgedb.bio.DataSourceTxt; //导入依赖的package包/类
public static void main(String args[]) throws ClassNotFoundException, IDMapperException
{
	// This example shows how to guess the type of an identifier
	
	// We have to initialize DataSource information,
	// but we don't need a driver
	DataSourceTxt.init();
	
	String query = "NP_036430";
	System.out.println ("Which patterns match " + query + "?");
	
	// DataSourcePatterns holds a registry of patterns
	Map<DataSource, Pattern> patterns = DataSourcePatterns.getPatterns();
	
	// loop over all patterns
	for (DataSource key : patterns.keySet())
	{
		// create a matcher for this pattern
		Matcher matcher = patterns.get(key).matcher(query);
		
		// see if the input matches, and print a message
		if (matcher.matches())
		{
			System.out.println (key.getFullName() + " matches!");
		}
	}		
}
 

import org.bridgedb.bio.DataSourceTxt; //导入依赖的package包/类
public static void main(String args[]) throws ClassNotFoundException, IDMapperException
{
	// This example shows how to map an identifier
	// using BridgeWebservice
	
	// first we have to load the driver
	// and initialize information about DataSources
	Class.forName("org.bridgedb.webservice.bridgerest.BridgeRest");
	DataSourceTxt.init();
	
	// now we connect to the driver and create a IDMapper instance.
	IDMapper mapper = BridgeDb.connect ("idmapper-bridgerest:http://webservice.bridgedb.org/Human");
	
	// We create an Xref instance for the identifier that we want to look up.
	// In this case we want to look up Entrez gene 3643.
	Xref src = new Xref ("3643", BioDataSource.ENTREZ_GENE);
	
	// let's see if there are cross-references to Ensembl Human
	Set<Xref> dests = mapper.mapID(src, DataSource.getBySystemCode("EnHs"));
	
	// and print the results.
	// with getURN we obtain valid MIRIAM urn's if possible.
	System.out.println (src.getURN() + " maps to:");
	for (Xref dest : dests)
		System.out.println("  " + dest.getURN());
	
}
 

import org.bridgedb.bio.DataSourceTxt; //导入依赖的package包/类
public static void main(String[] args) throws BridgeDBException, IOException, ClassNotFoundException{
   ConfigReader.logToConsole();

   //Load DataSources from BioDataSource and save that
   DataSourceTxt.init();
   File biofile = new File("resources/BioDataSource.ttl");
   BridgeDBRdfHandler.writeRdfToFile(biofile);
   BridgeDBRdfHandler.parseRdfFile(biofile);        
}
 

import org.bridgedb.bio.DataSourceTxt; //导入依赖的package包/类
public static void refreshUriPatterns() throws BridgeDBException{
    if (initialized){
        return;
    }
    DataSourceTxt.init();
    DataSourceMetaDataProvidor.assumeUnknownsAreBio();
    BridgeDBRdfHandler.init();
    IdentifersOrgReader.init();
    registerUriPatterns();
    initialized = true;
}
 

import org.bridgedb.bio.DataSourceTxt; //导入依赖的package包/类
/**
    * Test of init method, of class BridgeDBRdfHandler.
    */
@Ignore("Sensitive to test order")
   @Test
   public void testInit() throws Exception {
       Reporter.println("init");
       DataSourceTxt.init();
       BridgeDBRdfHandler.init();
       UriPattern.registerUriPatterns();
        
       SortedSet<UriPattern> result = UriPattern.byCodeAndType("M", UriPatternType.mainUrlPattern);
       UriPattern expected = UriPattern.byPattern("http://www.informatics.jax.org/marker/$id");
       assertThat(result, hasItem(expected));
       assertEquals(1, result.size());
       
       result = UriPattern.byCodeAndType("M", UriPatternType.identifiersOrgPatternSimple);
       expected = UriPattern.byPattern("http://identifiers.org/mgd/$id");
       assertThat(result, hasItem(expected));
       assertEquals(1, result.size());
       
       result = UriPattern.byCodeAndType("M", UriPatternType.codeMapperPattern);
       expected = UriPattern.byPattern("http://purl.uniprot.org/mgi/$id");
       assertThat(result, hasItem(expected));
       assertThat(result.size(), greaterThanOrEqualTo(1));
       
       File file = File.createTempFile("GeneratedDataSource", ".ttl");
       Reporter.println("writing to " + file.getAbsolutePath());
       BridgeDBRdfHandler.writeRdfToFile(file);
       
       Reporter.println("Reading back in " + file.getAbsolutePath());
       BridgeDBRdfHandler.parseRdfFile(file);
   }
 

import org.bridgedb.bio.DataSourceTxt; //导入依赖的package包/类
public static IDMapper setUpIDMapper(File file) throws IDMapperException, ClassNotFoundException {
	Class.forName("org.bridgedb.rdb.IDMapperRdb");  
	DataSourceTxt.init();
	IDMapper mapper = BridgeDb.connect("idmapper-pgdb:" + file.getAbsolutePath());
	return mapper;
}
 

import org.bridgedb.bio.DataSourceTxt; //导入依赖的package包/类
@Before
public void setUp() throws Exception {
	client = ConnectionSettings.createClient();
	DataSourceTxt.init();
}
 

import org.bridgedb.bio.DataSourceTxt; //导入依赖的package包/类
public static void main(String[] args) throws Exception {
	if (args.length < 7) {
		// printUsage();
		System.err
				.println("Please provide the following parameters in order: dbhost dbName dbUser dbPwd dbPort outputDir species");
		System.exit(1);
	}

	MySQLAdaptor adaptor = new MySQLAdaptor(args[0], args[1], args[2],
			args[3], Integer.parseInt(args[4]));

	File dir = new File(args[5]);
	String species = args[6];
	String version = args[7];
	
	dir.mkdirs();
	
	// Initialize BridgeDb datasources file
	// Only have to do it once
	DataSourceTxt.init();
	
	CLIConverter converter = new CLIConverter(adaptor);
	/*
	 * Boolean true to save ATXML files
	 */
	/*
	 * Abacavir transport (Test pathway)
	 */
	// converter.convertReactomeToGPMLByID((long) 264876, dir, true);
	// converter.convertReactomeToGPMLByID((long) 5602358, dir, false);
	// converter.convertReactomeToGPMLByID((long) 73857, dir, false);
	// converter.convertReactomeToGPMLByID((long) 5602358, dir, false);
	System.out.println("Converter Started");
	converter.convertPathwayDiagrams(dir, species, false, version);
	System.out.println("Converter Stopped");
	// converter.convertReactomeToGPMLByID((long) 975155, dir, false);
	// converter.convertReactomeToGPMLByID((long) 5602358, dir, false);
	// converter.convertPlantPathwayDiagrams(dir, false);
	// converter.getSpeciesDbID();
	// converter.getReactomeDbID(species);
}