List of usage examples for java.util Vector Vector
public Vector()
From source file:JpegImagesToMovie.java
public static void main(String args[]) { if (args.length == 0) prUsage();/* w w w . ja va 2 s . c o m*/ // Parse the arguments. int i = 0; int width = -1, height = -1, frameRate = 1; Vector inputFiles = new Vector(); String outputURL = null; while (i < args.length) { if (args[i].equals("-w")) { i++; if (i >= args.length) prUsage(); width = new Integer(args[i]).intValue(); } else if (args[i].equals("-h")) { i++; if (i >= args.length) prUsage(); height = new Integer(args[i]).intValue(); } else if (args[i].equals("-f")) { i++; if (i >= args.length) prUsage(); frameRate = new Integer(args[i]).intValue(); } else if (args[i].equals("-o")) { i++; if (i >= args.length) prUsage(); outputURL = args[i]; } else { for (int j = 0; j < 120; j++) { inputFiles.addElement(args[i]); } } i++; } if (outputURL == null || inputFiles.size() == 0) prUsage(); // Check for output file extension. if (!outputURL.endsWith(".mov") && !outputURL.endsWith(".MOV")) { System.err.println("The output file extension should end with a .mov extension"); prUsage(); } if (width < 0 || height < 0) { System.err.println("Please specify the correct image size."); prUsage(); } // Check the frame rate. if (frameRate < 1) frameRate = 1; // Generate the output media locators. MediaLocator oml; if ((oml = createMediaLocator(outputURL)) == null) { System.err.println("Cannot build media locator from: " + outputURL); System.exit(0); } JpegImagesToMovie imageToMovie = new JpegImagesToMovie(); imageToMovie.doIt(width, height, frameRate, inputFiles, oml); System.exit(0); }
From source file:com.app.server.Main.java
/** * This is the start of the all the services in web server * @param args/*from w w w. j a v a 2 s . co m*/ * @throws IOException * @throws SAXException */ public static void main(String[] args) throws IOException, SAXException { long startTime = System.currentTimeMillis(); Hashtable urlClassLoaderMap = new Hashtable(); Hashtable executorServicesMap = new Hashtable(); Hashtable ataMap = new Hashtable<String, ATAConfig>(); Hashtable messagingClassMap = new Hashtable(); ConcurrentHashMap servletMapping = new ConcurrentHashMap(); Vector deployerList = new Vector(), serviceList = new Vector(); DigesterLoader serverdigesterLoader = DigesterLoader.newLoader(new FromXmlRulesModule() { protected void loadRules() { // TODO Auto-generated method stub try { loadXMLRules(new InputSource(new FileInputStream("./config/serverconfig-rules.xml"))); } catch (FileNotFoundException e) { log.error("Error in loading the xml rules ./config/serverconfig-rules.xml", e); // TODO Auto-generated catch block //e.printStackTrace(); } } }); Digester serverdigester = serverdigesterLoader.newDigester(); final ServerConfig serverconfig = (ServerConfig) serverdigester .parse(new InputSource(new FileInputStream("./config/serverconfig.xml"))); //log.info(messagingconfig); ////log.info(serverconfig.getDeploydirectory()); PropertyConfigurator.configure("log4j.properties"); /*MemcachedClient cache=new MemcachedClient( new InetSocketAddress("localhost", 1000));*/ // Store a value (async) for one hour //c.set("someKey", 36, new String("arun")); // Retrieve a value. System.setProperty(Context.INITIAL_CONTEXT_FACTORY, "org.apache.naming.java.javaURLContextFactory"); System.setProperty(Context.URL_PKG_PREFIXES, "org.apache.naming"); ExecutorService executor = java.util.concurrent.Executors.newCachedThreadPool(); MBeanServer mbs = MBeanServerFactory.createMBeanServer("singham"); ObjectName name = null; try { mbs.registerMBean(serverconfig, new ObjectName("com.app.server:type=serverinfo")); } catch (Exception e1) { // TODO Auto-generated catch block e1.printStackTrace(); } /*try { name = new ObjectName("com.app.server:type=WarDeployer"); } catch (MalformedObjectNameException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } WarDeployer warDeployer=new WarDeployer(serverconfig.getDeploydirectory(),serverconfig.getFarmWarDir(),serverconfig.getClustergroup(),urlClassLoaderMap,executorServicesMap,messagingClassMap,servletMapping,messagingconfig,sessionObjects); warDeployer.setPriority(MIN_PRIORITY); try { mbs.registerMBean(warDeployer, name); } catch (InstanceAlreadyExistsException | MBeanRegistrationException | NotCompliantMBeanException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } //warDeployer.start(); executor.execute(warDeployer);*/ final byte[] shutdownBt = new byte[50]; /*WebServerRequestProcessor webserverRequestProcessor=new WebServer().new WebServerRequestProcessor(servletMapping,urlClassLoaderMap,serverSocketChannel,serverconfig.getDeploydirectory(),Integer.parseInt(serverconfig.getShutdownport()),1); webserverRequestProcessor.setPriority(MIN_PRIORITY); try { name = new ObjectName("com.app.server:type=WebServerRequestProcessor"); } catch (MalformedObjectNameException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } try { mbs.registerMBean(webserverRequestProcessor, name); } catch (InstanceAlreadyExistsException | MBeanRegistrationException | NotCompliantMBeanException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } //webserverRequestProcessor.start(); executor.execute(webserverRequestProcessor); for(int i=0;i<10;i++){ WebServerRequestProcessor webserverRequestProcessor1=new WebServer().new WebServerRequestProcessor(servletMapping,urlClassLoaderMap,serverSocketChannel,serverconfig.getDeploydirectory(),Integer.parseInt(serverconfig.getShutdownport()),2); webserverRequestProcessor1.setPriority(MIN_PRIORITY); try { name = new ObjectName("com.app.server:type=WebServerRequestProcessor"+(i+1)); } catch (MalformedObjectNameException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } try { mbs.registerMBean(webserverRequestProcessor1, name); } catch (InstanceAlreadyExistsException | MBeanRegistrationException | NotCompliantMBeanException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } executor.execute(webserverRequestProcessor1); }*/ /*ExecutorServiceThread executorService=new ExecutorServiceThread(serverSocketChannelServices,executorServicesMap,Integer.parseInt(serverconfig.getShutdownport()),ataMap,urlClassLoaderMap,serverconfig.getDeploydirectory(),serverconfig.getServicesdirectory(),serverconfig.getEarservicesdirectory(),serverconfig.getNodesport()); try { name = new ObjectName("com.app.services:type=ExecutorServiceThread"); } catch (MalformedObjectNameException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } try { mbs.registerMBean(executorService, name); } catch (InstanceAlreadyExistsException | MBeanRegistrationException | NotCompliantMBeanException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } //executorService.start(); executor.execute(executorService); for(int i=0;i<10;i++){ ExecutorServiceThread executorService1=new ExecutorServiceThread(serverSocketChannelServices,executorServicesMap,Integer.parseInt(serverconfig.getShutdownport()),ataMap,urlClassLoaderMap,serverconfig.getDeploydirectory(),serverconfig.getServicesdirectory(),serverconfig.getEarservicesdirectory(),serverconfig.getNodesport()); try { name = new ObjectName("com.app.services:type=ExecutorServiceThread"+(i+1)); } catch (MalformedObjectNameException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } try { mbs.registerMBean(executorService1, name); } catch (InstanceAlreadyExistsException | MBeanRegistrationException | NotCompliantMBeanException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } executor.execute(executorService1); }*/ /*WebServerHttpsRequestProcessor webserverHttpsRequestProcessor=new WebServer().new WebServerHttpsRequestProcessor(servletMapping,urlClassLoaderMap,Integer.parseInt(serverconfig.getHttpsport()),serverconfig.getDeploydirectory(),Integer.parseInt(serverconfig.getShutdownport()),serverconfig.getHttpscertificatepath(),serverconfig.getHttpscertificatepasscode(),1); try { name = new ObjectName("com.app.server:type=WebServerHttpsRequestProcessor"); } catch (MalformedObjectNameException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } try { mbs.registerMBean(webserverHttpsRequestProcessor, name); } catch (InstanceAlreadyExistsException | MBeanRegistrationException | NotCompliantMBeanException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } webserverHttpsRequestProcessor.setPriority(MAX_PRIORITY); //webserverRequestProcessor.start(); executor.execute(webserverHttpsRequestProcessor);*/ /* for(int i=0;i<2;i++){ webserverHttpsRequestProcessor=new WebServer().new WebServerHttpsRequestProcessor(urlClassLoaderMap,Integer.parseInt(serverconfig.getHttpsport())+(i+1),serverconfig.getDeploydirectory(),Integer.parseInt(serverconfig.getShutdownport()),serverconfig.getHttpscertificatepath(),serverconfig.getHttpscertificatepasscode(),1); try { name = new ObjectName("com.app.server:type=WebServerHttpsRequestProcessor"+(i+1)); } catch (MalformedObjectNameException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } try { mbs.registerMBean(webserverHttpsRequestProcessor, name); } catch (InstanceAlreadyExistsException | MBeanRegistrationException | NotCompliantMBeanException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } executor.execute(webserverHttpsRequestProcessor); }*/ /*ATAServer ataServer=new ATAServer(serverconfig.getAtaaddress(),serverconfig.getAtaport(),ataMap); try { name = new ObjectName("com.app.services:type=ATAServer"); } catch (MalformedObjectNameException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } try { mbs.registerMBean(ataServer, name); } catch (InstanceAlreadyExistsException | MBeanRegistrationException | NotCompliantMBeanException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } ataServer.start();*/ /*ATAConfigClient ataClient=new ATAConfigClient(serverconfig.getAtaaddress(),serverconfig.getAtaport(),serverconfig.getServicesport(),executorServicesMap); try { name = new ObjectName("com.app.services:type=ATAConfigClient"); } catch (MalformedObjectNameException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } try { mbs.registerMBean(ataClient, name); } catch (InstanceAlreadyExistsException | MBeanRegistrationException | NotCompliantMBeanException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } ataClient.start();*/ /*MessagingServer messageServer=new MessagingServer(serverconfig.getMessageport(),messagingClassMap); try { name = new ObjectName("com.app.messaging:type=MessagingServer"); } catch (MalformedObjectNameException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } try { mbs.registerMBean(messageServer, name); } catch (InstanceAlreadyExistsException | MBeanRegistrationException | NotCompliantMBeanException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } //messageServer.start(); executor.execute(messageServer);*/ /*RandomQueueMessagePicker randomqueuemessagepicker=new RandomQueueMessagePicker(messagingClassMap); try { name = new ObjectName("com.app.messaging:type=RandomQueueMessagePicker"); } catch (MalformedObjectNameException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } try { mbs.registerMBean(randomqueuemessagepicker, name); } catch (InstanceAlreadyExistsException | MBeanRegistrationException | NotCompliantMBeanException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } //randomqueuemessagepicker.start(); executor.execute(randomqueuemessagepicker);*/ /*RoundRobinQueueMessagePicker roundrobinqueuemessagepicker=new RoundRobinQueueMessagePicker(messagingClassMap); try { name = new ObjectName("com.app.messaging:type=RoundRobinQueueMessagePicker"); } catch (MalformedObjectNameException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } try { mbs.registerMBean(roundrobinqueuemessagepicker, name); } catch (InstanceAlreadyExistsException | MBeanRegistrationException | NotCompliantMBeanException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } //roundrobinqueuemessagepicker.start(); executor.execute(roundrobinqueuemessagepicker);*/ /*TopicMessagePicker topicpicker= new TopicMessagePicker(messagingClassMap); try { name = new ObjectName("com.app.messaging:type=TopicMessagePicker"); } catch (MalformedObjectNameException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } try { mbs.registerMBean(topicpicker, name); } catch (InstanceAlreadyExistsException | MBeanRegistrationException | NotCompliantMBeanException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } //topicpicker.start(); executor.execute(topicpicker);*/ try { name = new ObjectName(SARDeployer.OBJECT_NAME); } catch (Exception e) { log.error("Error in creating the object name " + SARDeployer.OBJECT_NAME, e); // TODO Auto-generated catch block //e1.printStackTrace(); } log.info(System.getProperty("user.dir")); try { mbs.createMBean("com.app.server.SARDeployer", name); mbs.invoke(name, "init", new Object[] { deployerList }, new String[] { Vector.class.getName() }); mbs.invoke(name, "init", new Object[] { serviceList, serverconfig, mbs }, new String[] { Vector.class.getName(), ServerConfig.class.getName(), MBeanServer.class.getName() }); mbs.invoke(name, "start", null, null); mbs.invoke(name, "deploy", new Object[] { new URL("file:///" + new File("").getAbsolutePath() + "/config/mbean-service.xml") }, new String[] { URL.class.getName() }); /*name=new ObjectName("com.app.server:type=deployer,service=WARDeployer"); mbs.invoke(name, "deploy", new Object[]{new URL("file:///"+serverconfig.getDeploydirectory()+"/TestDollar2.war")}, new String[]{URL.class.getName()}); mbs.invoke(name, "deploy", new Object[]{new URL("file:///"+serverconfig.getDeploydirectory()+"/StrutsProj.war")}, new String[]{URL.class.getName()});*/ //mbs.registerMBean("", name); } catch (Exception ex) { log.error("Error in SAR DEPLOYER ", ex); // TODO Auto-generated catch block //e1.printStackTrace(); } //scanner.deployPackages(new File[]{new File(serverconfig.getDeploydirectory()+"/AppServer.war")}); try { new NodeResourceReceiver(mbs).start(); } catch (Exception ex) { log.error("Node Receiver start", ex); //e2.printStackTrace(); } long endTime = System.currentTimeMillis(); log.info("Server started in " + ((endTime - startTime) / 1000) + " seconds"); /*try { mbs.invoke(name, "startDeployer", null, null); } catch (InstanceNotFoundException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } catch (ReflectionException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } catch (MBeanException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } */ /*JarDeployer jarDeployer=new JarDeployer(registry,serverconfig.getServicesdirectory(), serverconfig.getServiceslibdirectory(),serverconfig.getCachedir(),executorServicesMap, urlClassLoaderMap); try { name = new ObjectName("com.app.server:type=JarDeployer"); } catch (MalformedObjectNameException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } try { mbs.registerMBean(jarDeployer, name); } catch (InstanceAlreadyExistsException | MBeanRegistrationException | NotCompliantMBeanException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } //jarDeployer.start(); executor.execute(jarDeployer);*/ /*EARDeployer earDeployer=new EARDeployer(registry,serverconfig.getEarservicesdirectory(),serverconfig.getDeploydirectory(),executorServicesMap, urlClassLoaderMap,serverconfig.getCachedir(),warDeployer); try { name = new ObjectName("com.app.server:type=EARDeployer"); } catch (MalformedObjectNameException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } try { mbs.registerMBean(earDeployer, name); } catch (InstanceAlreadyExistsException | MBeanRegistrationException | NotCompliantMBeanException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } //earDeployer.start(); executor.execute(earDeployer);*/ /*JVMConsole jvmConsole=new JVMConsole(Integer.parseInt(serverconfig.getJvmConsolePort())); try { name = new ObjectName("com.app.server:type=JVMConsole"); } catch (MalformedObjectNameException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } try { mbs.registerMBean(jvmConsole, name); } catch (InstanceAlreadyExistsException | MBeanRegistrationException | NotCompliantMBeanException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } executor.execute(jvmConsole);*/ /*ScheduledExecutorService exec = Executors.newSingleThreadScheduledExecutor(); XMLDeploymentScanner xmlDeploymentScanner =new XMLDeploymentScanner(serverconfig.getDeploydirectory(),serverconfig.getServiceslibdirectory()); exec.scheduleAtFixedRate(xmlDeploymentScanner, 0, 1000, TimeUnit.MILLISECONDS);*/ /*EmbeddedJMS embeddedJMS=null; try { embeddedJMS=new EmbeddedJMS(); embeddedJMS.start(); } catch (Exception ex) { // TODO Auto-generated catch block ex.printStackTrace(); } EJBDeployer ejbDeployer=new EJBDeployer(serverconfig.getServicesdirectory(),registry,Integer.parseInt(serverconfig.getServicesregistryport()),embeddedJMS); try { name = new ObjectName("com.app.server:type=EJBDeployer"); } catch (MalformedObjectNameException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } try { mbs.registerMBean(ejbDeployer, name); } catch (InstanceAlreadyExistsException | MBeanRegistrationException | NotCompliantMBeanException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } //jarDeployer.start(); executor.execute(ejbDeployer);*/ new Thread() { public void run() { try { ServerSocket serverSocket = new ServerSocket(Integer.parseInt(serverconfig.getShutdownport())); while (true) { Socket sock = serverSocket.accept(); InputStream istream = sock.getInputStream(); istream.read(shutdownBt); String shutdownStr = new String(shutdownBt); String[] shutdownToken = shutdownStr.split("\r\n\r\n"); //log.info(shutdownStr); if (shutdownToken[0].startsWith("shutdown WebServer")) { synchronized (shutDownObject) { shutDownObject.notifyAll(); } } } } catch (Exception e) { log.error("Shutdown error", e); // TODO Auto-generated catch block //e.printStackTrace(); } } }.start(); Runtime.getRuntime().addShutdownHook(new Thread(new Runnable() { public void run() { log.info("IN shutdown Hook"); synchronized (shutDownObject) { shutDownObject.notifyAll(); } } })); try { synchronized (shutDownObject) { shutDownObject.wait(); } //executor.shutdownNow(); //serverSocketChannelServices.close(); //embeddedJMS.stop(); } catch (Exception e) { log.error("Error in object wait ", e); // TODO Auto-generated catch block //e1.printStackTrace(); } try { mbs.invoke(name, "stop", null, null); mbs.invoke(name, "destroy", null, null); } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } log.info("Halting JVM"); log.info("Exiting JVM"); /*try{ Thread.sleep(10000); } catch(Exception ex){ }*/ //webserverRequestProcessor.stop(); //webserverRequestProcessor1.stop(); /*warDeployer.stop(); executorService.stop(); //ataServer.stop(); //ataClient.stop(); messageServer.stop(); randomqueuemessagepicker.stop(); roundrobinqueuemessagepicker.stop(); topicpicker.stop();*/ /*try { mbs.invoke(new ObjectName("com.app.server:type=SARDeployer"), "destroyDeployer", null, null); } catch (InstanceNotFoundException | MalformedObjectNameException | ReflectionException | MBeanException e) { // TODO Auto-generated catch block e.printStackTrace(); }*/ //earDeployer.stop(); System.exit(0); }
From source file:mzmatch.ipeak.normalisation.VanDeSompele.java
public static void main(String args[]) { try {//from w ww . ja v a 2 s . co m Tool.init(); // parse the commandline options Options options = new Options(); CmdLineParser cmdline = new CmdLineParser(options); // check whether we need to show the help cmdline.parse(args); if (options.help) { Tool.printHeader(System.out, application, version); cmdline.printUsage(System.out, ""); return; } if (options.verbose) { Tool.printHeader(System.out, application, version); cmdline.printOptions(); } // check the command-line parameters { // if the output directories do not exist, create them if (options.output != null) Tool.createFilePath(options.output, true); } // load the data if (options.verbose) System.out.println("Loading data"); ParseResult result = PeakMLParser.parse(new FileInputStream(options.input), true); Header header = result.header; IPeakSet<IPeakSet<? extends IPeak>> peaksets = (IPeakSet<IPeakSet<? extends IPeak>>) result.measurement; int nrmeasurements = header.getNrMeasurementInfos(); // remove the stability factor annotation for (IPeak peak : peaksets) peak.removeAnnotation("stability factor"); // load the database if (options.verbose) System.out.println("Loading the molecule database"); HashMap<String, Molecule> database = MoleculeIO.parseXml(new FileInputStream(options.database)); // filter the set to include only identifiable metabolites if (options.verbose) System.out.println("Creating selection"); Vector<IPeakSet<? extends IPeak>> selection = new Vector<IPeakSet<? extends IPeak>>(); for (Molecule molecule : database.values()) { double mass = molecule.getMass(Mass.MONOISOTOPIC); double delta = PeriodicTable.PPM(mass, options.ppm); // get the most intense peak containing all the measurements Vector<IPeakSet<? extends IPeak>> neighbourhoud = peaksets.getPeaksInMassRange(mass - delta, mass + delta); Collections.sort(neighbourhoud, IPeak.sort_intensity_descending); for (IPeakSet<? extends IPeak> neighbour : neighbourhoud) if (count(neighbour) == nrmeasurements) { selection.add(neighbour); break; } } // calculate the stability factor for each peak in the selection if (options.verbose) System.out.println("Calculating stability factors"); for (int peakid1 = 0; peakid1 < selection.size(); ++peakid1) { double stddeviations[] = new double[selection.size()]; IPeakSet<? extends IPeak> peakset1 = selection.get(peakid1); for (int peakid2 = 0; peakid2 < selection.size(); ++peakid2) { IPeakSet<? extends IPeak> peakset2 = selection.get(peakid2); double values[] = new double[nrmeasurements]; for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) { int measurementid1 = peakset1.get(measurementid).getMeasurementID(); int setid1 = header.indexOfSetInfo(header.getSetInfoForMeasurementID(measurementid1)); int measurementid2 = peakset2.get(measurementid).getMeasurementID(); int setid2 = header.indexOfSetInfo(header.getSetInfoForMeasurementID(measurementid2)); if (setid1 != setid2 || measurementid1 != measurementid2) System.err.println("[WARNING]: differing setid or spectrumid for comparison"); values[measurementid] = Math.log(peakset1.get(measurementid).getIntensity() / peakset2.get(measurementid).getIntensity()) / Math.log(2); } stddeviations[peakid2] = Statistical.stddev(values); } peakset1.addAnnotation("stability factor", Statistical.mean(stddeviations)); } // sort on the stability factor Collections.sort(selection, new IPeak.AnnotationAscending("stability factor")); // take the top 10% and calculate the geometric mean if (options.verbose) System.out.println("Calculating normalisation factors"); int nrselected = (int) (0.1 * selection.size()); if (nrselected < 10) nrselected = (10 < selection.size() ? 10 : selection.size()); double normalization_factors[] = new double[nrmeasurements]; for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) { double values[] = new double[nrselected]; for (int i = 0; i < nrselected; ++i) { IPeak peak = selection.get(i).get(measurementid); values[i] = peak.getIntensity(); } normalization_factors[measurementid] = Statistical.geomean(values); } // scale the found normalization factors double maxnf = Statistical.max(normalization_factors); for (int sampleid = 0; sampleid < nrmeasurements; ++sampleid) normalization_factors[sampleid] /= maxnf; // write the selection if needed if (options.selection != null) { if (options.verbose) System.out.println("Writing original selection data"); PeakMLWriter.write(result.header, selection, null, new GZIPOutputStream(new FileOutputStream(options.selection)), null); } // normalize all the peaks if (options.verbose) System.out.println("Normalizing all the entries"); for (IPeakSet<? extends IPeak> peakset : peaksets) { for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) { // TODO why did I do this again ? int id = 0; int setid = 0; int spectrumid = 0; for (int i = 0; i < header.getNrSetInfos(); ++i) { SetInfo set = header.getSetInfos().get(i); if (id + set.getNrMeasurementIDs() > measurementid) { setid = i; spectrumid = measurementid - id; break; } else id += set.getNrMeasurementIDs(); } MassChromatogram<Peak> masschromatogram = null; for (IPeak p : peakset) { int mymeasurementid = p.getMeasurementID(); int mysetid = header.indexOfSetInfo(header.getSetInfoForMeasurementID(mymeasurementid)); if (mysetid == setid && mymeasurementid == spectrumid) { masschromatogram = (MassChromatogram<Peak>) p; break; } } if (masschromatogram == null) continue; for (IPeak peak : masschromatogram.getPeaks()) peak.setIntensity(peak.getIntensity() / normalization_factors[measurementid]); } } // write the selection if needed if (options.selection_normalized != null) { if (options.verbose) System.out.println("Writing the normalized selection data"); PeakMLWriter.write(result.header, selection, null, new GZIPOutputStream(new FileOutputStream(options.selection_normalized)), null); } // write the factors if needed if (options.factors != null) { if (options.verbose) System.out.println("Writing the normalization factors"); PrintStream out = new PrintStream(options.factors); for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) out.println(header.getMeasurementInfo(measurementid).getLabel() + "\t" + normalization_factors[measurementid]); } // write the plot if needed if (options.img != null) { if (options.verbose) System.out.println("Writing the graph"); DefaultCategoryDataset dataset = new DefaultCategoryDataset(); JFreeChart linechart = ChartFactory.createLineChart(null, "measurement", "normalization factor", dataset, PlotOrientation.VERTICAL, false, // legend false, // tooltips false // urls ); CategoryPlot plot = (CategoryPlot) linechart.getPlot(); CategoryAxis axis = (CategoryAxis) plot.getDomainAxis(); axis.setCategoryLabelPositions(CategoryLabelPositions.UP_45); LineAndShapeRenderer renderer = (LineAndShapeRenderer) plot.getRenderer(); renderer.setSeriesShapesFilled(0, true); renderer.setSeriesShapesVisible(0, true); linechart.setBackgroundPaint(Color.WHITE); linechart.setBorderVisible(false); linechart.setAntiAlias(true); plot.setBackgroundPaint(Color.WHITE); plot.setDomainGridlinesVisible(true); plot.setRangeGridlinesVisible(true); // create the datasets for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) dataset.addValue(normalization_factors[measurementid], "", header.getMeasurementInfo(measurementid).getLabel()); JFreeChartTools.writeAsPDF(new FileOutputStream(options.img), linechart, 800, 500); } // write the normalized values if (options.verbose) System.out.println("Writing the normalized data"); PeakMLWriter.write(result.header, peaksets.getPeaks(), null, new GZIPOutputStream(new FileOutputStream(options.output)), null); } catch (Exception e) { Tool.unexpectedError(e, application); } }
From source file:it.acubelab.smaph.learn.TuneModel.java
public static void main(String[] args) throws Exception { Locale.setDefault(Locale.US); String freebKey = "<FREEBASE_KEY>"; String bingKey = "<BING_KEY>"; WikipediaApiInterface wikiApi = new WikipediaApiInterface("benchmark/cache/wid.cache", "benchmark/cache/redirect.cache"); FreebaseApi freebApi = new FreebaseApi(freebKey, "freeb.cache"); Vector<ModelConfigurationResult> bestEQFModels = new Vector<>(); Vector<ModelConfigurationResult> bestEFModels = new Vector<>(); int wikiSearchTopK = 5; // <======== mind this double gamma = 1.0; double C = 1.0; for (double editDistanceThr = 0.7; editDistanceThr <= 0.7; editDistanceThr += 0.1) { WikipediaToFreebase wikiToFreebase = new WikipediaToFreebase("mapdb"); SmaphAnnotator bingAnnotator = GenerateTrainingAndTest.getDefaultBingAnnotator(wikiApi, wikiToFreebase, editDistanceThr, wikiSearchTopK, bingKey); SmaphAnnotator.setCache("bing.cache.full"); BinaryExampleGatherer trainEntityFilterGatherer = new BinaryExampleGatherer(); BinaryExampleGatherer develEntityFilterGatherer = new BinaryExampleGatherer(); GenerateTrainingAndTest.gatherExamplesTrainingAndDevel(bingAnnotator, trainEntityFilterGatherer, develEntityFilterGatherer, wikiApi, wikiToFreebase, freebApi); SmaphAnnotator.unSetCache();/*from ww w. ja v a2 s .c o m*/ Pair<Vector<ModelConfigurationResult>, ModelConfigurationResult> modelAndStatsEF = trainIterative( trainEntityFilterGatherer, develEntityFilterGatherer, editDistanceThr, OptimizaionProfiles.MAXIMIZE_MACRO_F1, -1.0, gamma, C); /* * Pair<Vector<ModelConfigurationResult>, ModelConfigurationResult> * modelAndStatsEF = trainIterative( trainEmptyQueryGatherer, * develEmptyQueryGatherer, editDistanceThr, * OptimizaionProfiles.MAXIMIZE_TN, 0.02); */ /* * for (ModelConfigurationResult res : modelAndStatsEQF.first) * System.out.println(res.getReadable()); */ for (ModelConfigurationResult res : modelAndStatsEF.first) System.out.println(res.getReadable()); /* bestEQFModels.add(modelAndStatsEQF.second); */ bestEFModels.add(modelAndStatsEF.second); System.gc(); } for (ModelConfigurationResult modelAndStatsEQF : bestEQFModels) System.out.println("Best EQF:" + modelAndStatsEQF.getReadable()); for (ModelConfigurationResult modelAndStatsEF : bestEFModels) System.out.println("Best EF:" + modelAndStatsEF.getReadable()); System.out.println("Flushing Bing API..."); SmaphAnnotator.flush(); wikiApi.flush(); }
From source file:Gen.java
public static void main(String[] args) throws Exception { try {//w ww. j a v a 2 s . c om File[] files = null; if (System.getProperty("dir") != null && !System.getProperty("dir").equals("")) { files = new File(System.getProperty("dir")).listFiles(new FilenameFilter() { public boolean accept(File dir, String name) { return name.toUpperCase().endsWith(".XML"); }; }); } else { String fileName = System.getProperty("file") != null && !System.getProperty("file").equals("") ? System.getProperty("file") : "rjmap.xml"; files = new File[] { new File(fileName) }; } log.info("files : " + Arrays.toString(files)); if (files == null || files.length == 0) { log.info("no files to parse"); System.exit(0); } boolean formatsource = true; if (System.getProperty("formatsource") != null && !System.getProperty("formatsource").equals("") && System.getProperty("formatsource").equalsIgnoreCase("false")) { formatsource = false; } GEN_ROOT = System.getProperty("outputdir"); if (GEN_ROOT == null || GEN_ROOT.equals("")) { GEN_ROOT = new File(files[0].getAbsolutePath()).getParent() + FILE_SEPARATOR + "distrib"; } GEN_ROOT = new File(GEN_ROOT).getAbsolutePath().replace('\\', '/'); if (GEN_ROOT.endsWith("/")) GEN_ROOT = GEN_ROOT.substring(0, GEN_ROOT.length() - 1); System.out.println("GEN ROOT:" + GEN_ROOT); MAPPING_JAR_NAME = System.getProperty("mappingjar") != null && !System.getProperty("mappingjar").equals("") ? System.getProperty("mappingjar") : "mapping.jar"; if (!MAPPING_JAR_NAME.endsWith(".jar")) MAPPING_JAR_NAME += ".jar"; GEN_ROOT_SRC = GEN_ROOT + FILE_SEPARATOR + "src"; GEN_ROOT_LIB = GEN_ROOT + FILE_SEPARATOR + ""; DocumentBuilderFactory domFactory = DocumentBuilderFactory.newInstance(); domFactory.setNamespaceAware(true); domFactory.setValidating(false); DocumentBuilder documentBuilder = domFactory.newDocumentBuilder(); for (int f = 0; f < files.length; ++f) { log.info("parsing file : " + files[f]); Document document = documentBuilder.parse(files[f]); Vector<Node> initNodes = new Vector<Node>(); Utils.catchNodes(Utils.catchNode(document.getDocumentElement(), "scripts"), "initScript", initNodes); for (int i = 0; i < initNodes.size(); ++i) { NamedNodeMap attrs = initNodes.elementAt(i).getAttributes(); boolean embed = attrs.getNamedItem("embed") != null && attrs.getNamedItem("embed").getNodeValue().equalsIgnoreCase("true"); StringBuffer vbuffer = new StringBuffer(); if (attrs.getNamedItem("inline") != null) { vbuffer.append(attrs.getNamedItem("inline").getNodeValue()); vbuffer.append('\n'); } else { String fname = attrs.getNamedItem("name").getNodeValue(); if (!fname.startsWith("\\") && !fname.startsWith("/") && fname.toCharArray()[1] != ':') { String path = files[f].getAbsolutePath(); path = path.substring(0, path.lastIndexOf(FILE_SEPARATOR)); fname = new File(path + FILE_SEPARATOR + fname).getCanonicalPath(); } vbuffer.append(Utils.getFileAsStringBuffer(fname)); } initScriptBuffer.append(vbuffer); if (embed) embedScriptBuffer.append(vbuffer); } Vector<Node> packageInitNodes = new Vector<Node>(); Utils.catchNodes(Utils.catchNode(document.getDocumentElement(), "scripts"), "packageScript", packageInitNodes); for (int i = 0; i < packageInitNodes.size(); ++i) { NamedNodeMap attrs = packageInitNodes.elementAt(i).getAttributes(); String packageName = attrs.getNamedItem("package").getNodeValue(); if (packageName.equals("")) packageName = "rGlobalEnv"; if (!packageName.endsWith("Function")) packageName += "Function"; if (packageEmbedScriptHashMap.get(packageName) == null) { packageEmbedScriptHashMap.put(packageName, new StringBuffer()); } StringBuffer vbuffer = packageEmbedScriptHashMap.get(packageName); // if (!packageName.equals("rGlobalEnvFunction")) { // vbuffer.append("library("+packageName.substring(0,packageName.lastIndexOf("Function"))+")\n"); // } if (attrs.getNamedItem("inline") != null) { vbuffer.append(attrs.getNamedItem("inline").getNodeValue() + "\n"); initScriptBuffer.append(attrs.getNamedItem("inline").getNodeValue() + "\n"); } else { String fname = attrs.getNamedItem("name").getNodeValue(); if (!fname.startsWith("\\") && !fname.startsWith("/") && fname.toCharArray()[1] != ':') { String path = files[f].getAbsolutePath(); path = path.substring(0, path.lastIndexOf(FILE_SEPARATOR)); fname = new File(path + FILE_SEPARATOR + fname).getCanonicalPath(); } StringBuffer fileBuffer = Utils.getFileAsStringBuffer(fname); vbuffer.append(fileBuffer); initScriptBuffer.append(fileBuffer); } } Vector<Node> functionsNodes = new Vector<Node>(); Utils.catchNodes(Utils.catchNode(document.getDocumentElement(), "functions"), "function", functionsNodes); for (int i = 0; i < functionsNodes.size(); ++i) { NamedNodeMap attrs = functionsNodes.elementAt(i).getAttributes(); String functionName = attrs.getNamedItem("name").getNodeValue(); boolean forWeb = attrs.getNamedItem("forWeb") != null && attrs.getNamedItem("forWeb").getNodeValue().equalsIgnoreCase("true"); String signature = (attrs.getNamedItem("signature") == null ? "" : attrs.getNamedItem("signature").getNodeValue() + ","); String renameTo = (attrs.getNamedItem("renameTo") == null ? null : attrs.getNamedItem("renameTo").getNodeValue()); HashMap<String, FAttributes> sigMap = Globals._functionsToPublish.get(functionName); if (sigMap == null) { sigMap = new HashMap<String, FAttributes>(); Globals._functionsToPublish.put(functionName, sigMap); if (attrs.getNamedItem("returnType") == null) { _functionsVector.add(new String[] { functionName }); } else { _functionsVector.add( new String[] { functionName, attrs.getNamedItem("returnType").getNodeValue() }); } } sigMap.put(signature, new FAttributes(renameTo, forWeb)); if (forWeb) _webPublishingEnabled = true; } if (System.getProperty("targetjdk") != null && !System.getProperty("targetjdk").equals("") && System.getProperty("targetjdk").compareTo("1.5") < 0) { if (_webPublishingEnabled || (System.getProperty("ws.r.api") != null && System.getProperty("ws.r.api").equalsIgnoreCase("true"))) { log.info("be careful, web publishing disabled beacuse target JDK<1.5"); } _webPublishingEnabled = false; } else { if (System.getProperty("ws.r.api") == null || System.getProperty("ws.r.api").equals("") || !System.getProperty("ws.r.api").equalsIgnoreCase("false")) { _webPublishingEnabled = true; } if (_webPublishingEnabled && System.getProperty("java.version").compareTo("1.5") < 0) { log.info("be careful, web publishing disabled beacuse a JDK<1.5 is in use"); _webPublishingEnabled = false; } } Vector<Node> s4Nodes = new Vector<Node>(); Utils.catchNodes(Utils.catchNode(document.getDocumentElement(), "s4classes"), "class", s4Nodes); if (s4Nodes.size() > 0) { String formalArgs = ""; String signature = ""; for (int i = 0; i < s4Nodes.size(); ++i) { NamedNodeMap attrs = s4Nodes.elementAt(i).getAttributes(); String s4Name = attrs.getNamedItem("name").getNodeValue(); formalArgs += "p" + i + (i == s4Nodes.size() - 1 ? "" : ","); signature += "'" + s4Name + "'" + (i == s4Nodes.size() - 1 ? "" : ","); } String genBeansScriptlet = "setGeneric('" + PUBLISH_S4_HEADER + "', function(" + formalArgs + ") standardGeneric('" + PUBLISH_S4_HEADER + "'));" + "setMethod('" + PUBLISH_S4_HEADER + "', signature(" + signature + ") , function(" + formalArgs + ") { })"; initScriptBuffer.append(genBeansScriptlet); _functionsVector.add(new String[] { PUBLISH_S4_HEADER, "numeric" }); } } if (!new File(GEN_ROOT_LIB).exists()) regenerateDir(GEN_ROOT_LIB); else { clean(GEN_ROOT_LIB, true); } for (int i = 0; i < rwebservicesScripts.length; ++i) DirectJNI.getInstance().getRServices().sourceFromResource(rwebservicesScripts[i]); String lastStatus = DirectJNI.getInstance().runR(new ExecutionUnit() { public void run(Rengine e) { DirectJNI.getInstance().toggleMarker(); DirectJNI.getInstance().sourceFromBuffer(initScriptBuffer.toString()); log.info(" init script status : " + DirectJNI.getInstance().cutStatusSinceMarker()); for (int i = 0; i < _functionsVector.size(); ++i) { String[] functionPair = _functionsVector.elementAt(i); log.info("dealing with : " + functionPair[0]); regenerateDir(GEN_ROOT_SRC); String createMapStr = "createMap("; boolean isGeneric = e.rniGetBoolArrayI( e.rniEval(e.rniParse("isGeneric(\"" + functionPair[0] + "\")", 1), 0))[0] == 1; log.info("is Generic : " + isGeneric); if (isGeneric) { createMapStr += functionPair[0]; } else { createMapStr += "\"" + functionPair[0] + "\""; } createMapStr += ", outputDirectory=\"" + GEN_ROOT_SRC .substring(0, GEN_ROOT_SRC.length() - "/src".length()).replace('\\', '/') + "\""; createMapStr += ", typeMode=\"robject\""; createMapStr += (functionPair.length == 1 || functionPair[1] == null || functionPair[1].trim().equals("") ? "" : ", S4DefaultTypedSig=TypedSignature(returnType=\"" + functionPair[1] + "\")"); createMapStr += ")"; log.info("------------------------------------------"); log.info("-- createMapStr=" + createMapStr); DirectJNI.getInstance().toggleMarker(); e.rniEval(e.rniParse(createMapStr, 1), 0); String createMapStatus = DirectJNI.getInstance().cutStatusSinceMarker(); log.info(" createMap status : " + createMapStatus); log.info("------------------------------------------"); deleteDir(GEN_ROOT_SRC + "/org/kchine/r/rserviceJms"); compile(GEN_ROOT_SRC); jar(GEN_ROOT_SRC, GEN_ROOT_LIB + FILE_SEPARATOR + TEMP_JARS_PREFIX + i + ".jar", null); URL url = null; try { url = new URL( "jar:file:" + (GEN_ROOT_LIB + FILE_SEPARATOR + TEMP_JARS_PREFIX + i + ".jar") .replace('\\', '/') + "!/"); } catch (Exception ex) { ex.printStackTrace(); } DirectJNI.generateMaps(url, true); } } }); log.info(lastStatus); log.info(DirectJNI._rPackageInterfacesHash); regenerateDir(GEN_ROOT_SRC); for (int i = 0; i < _functionsVector.size(); ++i) { unjar(GEN_ROOT_LIB + FILE_SEPARATOR + TEMP_JARS_PREFIX + i + ".jar", GEN_ROOT_SRC); } regenerateRPackageClass(true); generateS4BeanRef(); if (formatsource) applyJalopy(GEN_ROOT_SRC); compile(GEN_ROOT_SRC); for (String k : DirectJNI._rPackageInterfacesHash.keySet()) { Rmic rmicTask = new Rmic(); rmicTask.setProject(_project); rmicTask.setTaskName("rmic_packages"); rmicTask.setClasspath(new Path(_project, GEN_ROOT_SRC)); rmicTask.setBase(new File(GEN_ROOT_SRC)); rmicTask.setClassname(k + "ImplRemote"); rmicTask.init(); rmicTask.execute(); } // DirectJNI._rPackageInterfacesHash=new HashMap<String, // Vector<Class<?>>>(); // DirectJNI._rPackageInterfacesHash.put("org.bioconductor.packages.rGlobalEnv.rGlobalEnvFunction",new // Vector<Class<?>>()); if (_webPublishingEnabled) { jar(GEN_ROOT_SRC, GEN_ROOT_LIB + FILE_SEPARATOR + "__temp.jar", null); URL url = new URL( "jar:file:" + (GEN_ROOT_LIB + FILE_SEPARATOR + "__temp.jar").replace('\\', '/') + "!/"); ClassLoader cl = new URLClassLoader(new URL[] { url }, Globals.class.getClassLoader()); for (String className : DirectJNI._rPackageInterfacesHash.keySet()) { if (cl.loadClass(className + "Web").getDeclaredMethods().length == 0) continue; log.info("######## " + className); WsGen wsgenTask = new WsGen(); wsgenTask.setProject(_project); wsgenTask.setTaskName("wsgen"); FileSet rjb_fileSet = new FileSet(); rjb_fileSet.setProject(_project); rjb_fileSet.setDir(new File(".")); rjb_fileSet.setIncludes("RJB.jar"); DirSet src_dirSet = new DirSet(); src_dirSet.setDir(new File(GEN_ROOT_LIB + FILE_SEPARATOR + "src/")); Path classPath = new Path(_project); classPath.addFileset(rjb_fileSet); classPath.addDirset(src_dirSet); wsgenTask.setClasspath(classPath); wsgenTask.setKeep(true); wsgenTask.setDestdir(new File(GEN_ROOT_LIB + FILE_SEPARATOR + "src/")); wsgenTask.setResourcedestdir(new File(GEN_ROOT_LIB + FILE_SEPARATOR + "src/")); wsgenTask.setSei(className + "Web"); wsgenTask.init(); wsgenTask.execute(); } new File(GEN_ROOT_LIB + FILE_SEPARATOR + "__temp.jar").delete(); } embedRScripts(); HashMap<String, String> marker = new HashMap<String, String>(); marker.put("RJBMAPPINGJAR", "TRUE"); Properties props = new Properties(); props.put("PACKAGE_NAMES", PoolUtils.objectToHex(DirectJNI._packageNames)); props.put("S4BEANS_MAP", PoolUtils.objectToHex(DirectJNI._s4BeansMapping)); props.put("S4BEANS_REVERT_MAP", PoolUtils.objectToHex(DirectJNI._s4BeansMappingRevert)); props.put("FACTORIES_MAPPING", PoolUtils.objectToHex(DirectJNI._factoriesMapping)); props.put("S4BEANS_HASH", PoolUtils.objectToHex(DirectJNI._s4BeansHash)); props.put("R_PACKAGE_INTERFACES_HASH", PoolUtils.objectToHex(DirectJNI._rPackageInterfacesHash)); props.put("ABSTRACT_FACTORIES", PoolUtils.objectToHex(DirectJNI._abstractFactories)); new File(GEN_ROOT_SRC + "/" + "maps").mkdirs(); FileOutputStream fos = new FileOutputStream(GEN_ROOT_SRC + "/" + "maps/rjbmaps.xml"); props.storeToXML(fos, null); fos.close(); jar(GEN_ROOT_SRC, GEN_ROOT_LIB + FILE_SEPARATOR + MAPPING_JAR_NAME, marker); if (_webPublishingEnabled) genWeb(); DirectJNI._mappingClassLoader = null; } finally { System.exit(0); } }
From source file:edu.umn.cs.spatialHadoop.operations.RangeQuery.java
public static void main(String[] args) throws IOException, ClassNotFoundException, InterruptedException { final OperationsParams params = new OperationsParams(new GenericOptionsParser(args)); final Path[] paths = params.getPaths(); if (paths.length <= 1 && !params.checkInput()) { printUsage();//from w w w .ja v a2s . c om System.exit(1); } if (paths.length >= 2 && !params.checkInputOutput()) { printUsage(); System.exit(1); } if (params.get("rect") == null) { System.err.println("You must provide a query range"); printUsage(); System.exit(1); } final Path inPath = params.getInputPath(); final Path outPath = params.getOutputPath(); final Rectangle[] queryRanges = params.getShapes("rect", new Rectangle()); // All running jobs final Vector<Long> resultsCounts = new Vector<Long>(); Vector<Job> jobs = new Vector<Job>(); Vector<Thread> threads = new Vector<Thread>(); long t1 = System.currentTimeMillis(); for (int i = 0; i < queryRanges.length; i++) { final OperationsParams queryParams = new OperationsParams(params); OperationsParams.setShape(queryParams, "rect", queryRanges[i]); if (OperationsParams.isLocal(new JobConf(queryParams), inPath)) { // Run in local mode final Rectangle queryRange = queryRanges[i]; final Shape shape = queryParams.getShape("shape"); final Path output = outPath == null ? null : (queryRanges.length == 1 ? outPath : new Path(outPath, String.format("%05d", i))); Thread thread = new Thread() { @Override public void run() { FSDataOutputStream outFile = null; final byte[] newLine = System.getProperty("line.separator", "\n").getBytes(); try { ResultCollector<Shape> collector = null; if (output != null) { FileSystem outFS = output.getFileSystem(queryParams); final FSDataOutputStream foutFile = outFile = outFS.create(output); collector = new ResultCollector<Shape>() { final Text tempText = new Text2(); @Override public synchronized void collect(Shape r) { try { tempText.clear(); r.toText(tempText); foutFile.write(tempText.getBytes(), 0, tempText.getLength()); foutFile.write(newLine); } catch (IOException e) { e.printStackTrace(); } } }; } else { outFile = null; } long resultCount = rangeQueryLocal(inPath, queryRange, shape, queryParams, collector); resultsCounts.add(resultCount); } catch (IOException e) { e.printStackTrace(); } catch (InterruptedException e) { e.printStackTrace(); } finally { try { if (outFile != null) outFile.close(); } catch (IOException e) { e.printStackTrace(); } } } }; thread.start(); threads.add(thread); } else { // Run in MapReduce mode queryParams.setBoolean("background", true); Job job = rangeQueryMapReduce(inPath, outPath, queryParams); jobs.add(job); } } while (!jobs.isEmpty()) { Job firstJob = jobs.firstElement(); firstJob.waitForCompletion(false); if (!firstJob.isSuccessful()) { System.err.println("Error running job " + firstJob); System.err.println("Killing all remaining jobs"); for (int j = 1; j < jobs.size(); j++) jobs.get(j).killJob(); System.exit(1); } Counters counters = firstJob.getCounters(); Counter outputRecordCounter = counters.findCounter(Task.Counter.MAP_OUTPUT_RECORDS); resultsCounts.add(outputRecordCounter.getValue()); jobs.remove(0); } while (!threads.isEmpty()) { try { Thread thread = threads.firstElement(); thread.join(); threads.remove(0); } catch (InterruptedException e) { e.printStackTrace(); } } long t2 = System.currentTimeMillis(); System.out.println("Time for " + queryRanges.length + " jobs is " + (t2 - t1) + " millis"); System.out.println("Results counts: " + resultsCounts); }
From source file:net.iiit.siel.analysis.lang.LanguageIdentifier.java
/** * The main method.//from www. j a v a 2s . co m * * @param args the arguments */ public static void main(String args[]) { String usage = "Usage: LanguageIdentifier " + "[-identifyrows filename maxlines] " + "[-identifyfile charset filename] " + "[-identifyfileset charset files] " + "[-identifytext text] " + "[-identifyurl url]"; int command = 0; final int IDFILE = 1; final int IDTEXT = 2; final int IDURL = 3; final int IDFILESET = 4; final int IDROWS = 5; Vector fileset = new Vector(); String filename = ""; String charset = ""; String url = ""; String text = ""; int max = 0; // TODO niket writing test args here.. /* args = new String[2]; args[0] = "-identifyurl"; args[1] = "file:/home1/niket/TamilSamplePage.html"; //args[2] = "/home1/niket/nutch-clia/input.txt"; */ // TODO niket end here if (args.length == 0) { System.err.println(usage); System.exit(-1); } for (int i = 0; i < args.length; i++) { // parse command line if (args[i].equals("-identifyfile")) { command = IDFILE; charset = args[++i]; filename = args[++i]; } if (args[i].equals("-identifyurl")) { command = IDURL; filename = args[++i]; } if (args[i].equals("-identifyrows")) { command = IDROWS; filename = args[++i]; max = Integer.parseInt(args[++i]); } if (args[i].equals("-identifytext")) { command = IDTEXT; for (i++; i < args.length - 1; i++) text += args[i] + " "; } if (args[i].equals("-identifyfileset")) { command = IDFILESET; charset = args[++i]; for (i++; i < args.length; i++) { File[] files = null; File f = new File(args[i]); if (f.isDirectory()) { files = f.listFiles(); } else { files = new File[] { f }; } for (int j = 0; j < files.length; j++) { fileset.add(files[j].getAbsolutePath()); } } } } Configuration conf = NutchConfiguration.create(); String lang = null; LanguageIdentifier idfr = new LanguageIdentifier(conf); File f; FileInputStream fis; try { switch (command) { case IDTEXT: lang = idfr.identify(text); System.out.println("Lang :" + lang); break; case IDFILE: f = new File(filename); fis = new FileInputStream(f); lang = idfr.identify(fis, charset); fis.close(); break; case IDURL: lang = LangIdentifierUtility.IdentifyLangFromURLDirectly(filename); /* * our url identifier is confused or couldn't identify lang from * URL */ if (lang == null || lang.equalsIgnoreCase("en")) { System.out.println("Ambuguity in identifying language from URL"); } else { System.out.println("Lang was identified(using URL) as: " + lang); } break; case IDROWS: f = new File(filename); BufferedReader br = new BufferedReader(new InputStreamReader(new FileInputStream(f))); String line; while (max > 0 && (line = br.readLine()) != null) { line = line.trim(); if (line.length() > 2) { max--; lang = idfr.identify(line); System.out.println("R=" + lang + ":" + line); } } br.close(); System.exit(0); break; case IDFILESET: /* * used for benchs for (int j=128; j<=524288; j*=2) { long start * = System.currentTimeMillis(); idfr.analyzeLength = j; */ System.out.println("FILESET"); Iterator i = fileset.iterator(); while (i.hasNext()) { try { filename = (String) i.next(); f = new File(filename); fis = new FileInputStream(f); lang = idfr.identify(fis, charset); fis.close(); } catch (Exception e) { System.out.println(e); } System.out.println(filename + " was identified as " + lang); } /* * used for benchs System.out.println(j + "/" + * (System.currentTimeMillis()-start)); } */ System.exit(0); break; } } catch (Exception e) { System.out.println(e); System.out.println("lang could not be identified properly"); e.printStackTrace(); } System.out.println("text was identified as " + lang); /* * DONOT delete the next few lines, they should be enabled, when a lang. * mapping map needs to be generated. TODO this is for printing * the hashMapRangeLangIDTable only * * idfr.langMarkerObject.printHashmapTableWithFormatting(); * * System.out * .println("\n\n\n Printing english text contents in this file:\n"); * System.out.println(idfr.langMarkerObject.getLangCharacters( * LanguageIdentifierConstants.LangShortNames.ENGLISH * .langShortName()).toString()); * * System.out * .println("\n\n\n Printing telugu text contents in this file:\n"); * System.out.println(idfr.langMarkerObject.getLangCharacters( * LanguageIdentifierConstants.LangShortNames.TELUGU * .langShortName()).toString()); * * System.out * .println("\n\n\n Printing unknown text contents in this file:\n"); * System.out.println(idfr.langMarkerObject.getLangCharacters( * LanguageIdentifierConstants.LangShortNames.UNKNOWN_LANG * .langShortName()).toString()); */ }
From source file:RemoveVector.java
static boolean removeAll(Vector v, Object e) { Vector v1 = new Vector(); v1.add(e); return v.removeAll(v1); }
From source file:Main.java
public static <K> Vector<K> newVector() { return new Vector<K>(); }
From source file:Main.java
public static Vector tail(Vector v) { Vector result = new Vector(); Enumeration e = v.elements(); e.nextElement();// www .jav a 2 s .c o m while (e.hasMoreElements()) result.addElement(e.nextElement()); return result; }