本文整理汇总了Java中org.bridgedb.bio.DataSourceTxt.init方法的典型用法代码示例。如果您正苦于以下问题:Java DataSourceTxt.init方法的具体用法?Java DataSourceTxt.init怎么用?Java DataSourceTxt.init使用的例子?那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类org.bridgedb.bio.DataSourceTxt
的用法示例。
在下文中一共展示了DataSourceTxt.init方法的15个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: main
import org.bridgedb.bio.DataSourceTxt; //导入方法依赖的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());
}
示例2: run
import org.bridgedb.bio.DataSourceTxt; //导入方法依赖的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"));
}
示例3: setUp
import org.bridgedb.bio.DataSourceTxt; //导入方法依赖的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());
}
示例4: loadModelAsWPRDF
import org.bridgedb.bio.DataSourceTxt; //导入方法依赖的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);
}
示例5: PathwayGeneParser
import org.bridgedb.bio.DataSourceTxt; //导入方法依赖的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;
}
示例6: DrugbankTargetParser
import org.bridgedb.bio.DataSourceTxt; //导入方法依赖的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;
}
示例7: main
import org.bridgedb.bio.DataSourceTxt; //导入方法依赖的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!");
}
}
}
示例8: main
import org.bridgedb.bio.DataSourceTxt; //导入方法依赖的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());
}
示例9: main
import org.bridgedb.bio.DataSourceTxt; //导入方法依赖的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);
}
示例10: refreshUriPatterns
import org.bridgedb.bio.DataSourceTxt; //导入方法依赖的package包/类
public static void refreshUriPatterns() throws BridgeDBException{
if (initialized){
return;
}
DataSourceTxt.init();
DataSourceMetaDataProvidor.assumeUnknownsAreBio();
BridgeDBRdfHandler.init();
IdentifersOrgReader.init();
registerUriPatterns();
initialized = true;
}
示例11: testInit
import org.bridgedb.bio.DataSourceTxt; //导入方法依赖的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);
}
示例12: setUpIDMapper
import org.bridgedb.bio.DataSourceTxt; //导入方法依赖的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;
}
示例13: setUp
import org.bridgedb.bio.DataSourceTxt; //导入方法依赖的package包/类
@Before
public void setUp() throws Exception {
client = ConnectionSettings.createClient();
DataSourceTxt.init();
}
示例14: main
import org.bridgedb.bio.DataSourceTxt; //导入方法依赖的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);
}
示例15: setUp
import org.bridgedb.bio.DataSourceTxt; //导入方法依赖的package包/类
@Before public void setUp() throws ClassNotFoundException
{
DataSourceTxt.init();
Class.forName ("org.bridgedb.file.IDMapperText");
Class.forName ("org.bridgedb.rdb.IDMapperRdb");
}