List of usage examples for java.lang String split
public String[] split(String regex)
From source file:com.esri.geoevent.test.tools.RunTcpInBdsOutTest.java
public static void main(String args[]) { // Example Command line args //-n 10000 -g w12ags104a.jennings.home -i 5565 -m https://w12ags104a.jennings.home/arcgis/rest/services/Hosted/FAA-Stream/MapServer/0 -f D:\github\performance-test-harness-for-geoevent\app\simulations\faa-stream.csv -r 1000,3000,1000 int numberEvents = 10000; // Number of Events String gisServer = "w12ags104a.jennings.home"; // GIS Server int inputTcpPort = 5565; // TCP Input Port String msLayerUrl = "http://w12ags104a.jennings.home/arcgis/rest/services/Hosted/FAA-Stream/MapServer/0"; String EventsInputFile = "D:\\github\\performance-test-harness-for-geoevent\\app\\simulations\\faa-stream.csv"; // Events input File int start_rate = 5000; int end_rate = 5005; int rate_step = 1; Options opts = new Options(); opts.addOption("n", true, "Number of Events"); opts.addOption("g", true, "GIS Server"); opts.addOption("i", true, "Input TCP Port"); opts.addOption("m", true, "Map Service Layer URL"); opts.addOption("f", true, "File with GeoEvents to Send"); opts.addOption("r", true, "Rates to test Start,End,Step"); opts.addOption("h", false, "Help"); try {//from www . jav a2s. co m CommandLineParser parser = new BasicParser(); CommandLine cmd = null; try { cmd = parser.parse(opts, args, false); } catch (org.apache.commons.cli.ParseException ignore) { System.err.println(ignore.getMessage()); } String cmdInputErrorMsg = ""; if (cmd.getOptions().length == 0 || cmd.hasOption("h")) { throw new org.apache.commons.cli.ParseException("Show Help"); } if (cmd.hasOption("n")) { String val = cmd.getOptionValue("n"); try { numberEvents = Integer.valueOf(val); } catch (NumberFormatException e) { cmdInputErrorMsg += "Invalid value for n. Must be integer.\n"; } } if (cmd.hasOption("g")) { gisServer = cmd.getOptionValue("g"); } if (cmd.hasOption("i")) { String val = cmd.getOptionValue("i"); try { inputTcpPort = Integer.valueOf(val); } catch (NumberFormatException e) { cmdInputErrorMsg += "Invalid value for i. Must be integer.\n"; } } if (cmd.hasOption("m")) { msLayerUrl = cmd.getOptionValue("m"); } if (cmd.hasOption("f")) { EventsInputFile = cmd.getOptionValue("f"); } if (cmd.hasOption("r")) { String val = cmd.getOptionValue("r"); try { String parts[] = val.split(","); if (parts.length == 3) { start_rate = Integer.parseInt(parts[0]); end_rate = Integer.parseInt(parts[1]); rate_step = Integer.parseInt(parts[2]); } else if (parts.length == 1) { // Run single rate start_rate = Integer.parseInt(parts[0]); end_rate = start_rate; rate_step = start_rate; } else { throw new org.apache.commons.cli.ParseException( "Rate must be three comma seperated values or a single value"); } } catch (org.apache.commons.cli.ParseException e) { cmdInputErrorMsg += e.getMessage(); } catch (NumberFormatException e) { cmdInputErrorMsg += "Invalid value for r. Must be integers.\n"; } } if (!cmdInputErrorMsg.equalsIgnoreCase("")) { throw new org.apache.commons.cli.ParseException(cmdInputErrorMsg); } // Assuming the ES port is 9220 RunTcpInBdsOutTest t = new RunTcpInBdsOutTest(); DecimalFormat df = new DecimalFormat("##0"); if (start_rate == end_rate) { // Single Rate Test System.out.println("*********************************"); System.out.println("Incremental testing at requested rate: " + start_rate); System.out.println("Count,Incremental Rate"); t.runTest(numberEvents, start_rate, gisServer, inputTcpPort, EventsInputFile, msLayerUrl, true); if (t.send_rate < 0 || t.rcv_rate < 0) { throw new Exception("Test Run Failed!"); } System.out.println("Overall Average Send Rate, Received Rate"); System.out.println(df.format(t.send_rate) + "," + df.format(t.rcv_rate)); } else { System.out.println("*********************************"); System.out.println("rateRqstd,avgSendRate,avgRcvdRate"); for (int rate = start_rate; rate <= end_rate; rate += rate_step) { t.runTest(numberEvents, rate, gisServer, inputTcpPort, EventsInputFile, msLayerUrl, false); if (t.send_rate < 0 || t.rcv_rate < 0) { throw new Exception("Test Run Failed!"); } System.out.println( Integer.toString(rate) + "," + df.format(t.send_rate) + "," + df.format(t.rcv_rate)); Thread.sleep(3 * 1000); } } } catch (ParseException e) { System.out.println("Invalid Command Options: "); System.out.println(e.getMessage()); System.out.println( "Command line options: -n NumberOfEvents -g GISServer -i InputTCPPort -m MapServerLayerURL -f FileWithEvents -r StartRate,EndRate,Step"); } catch (Exception e) { System.out.println(e.getMessage()); } }
From source file:com.aguin.stock.recommender.UserOptions.java
public static void main(String[] args) { options = new Options(); Option optU = OptionBuilder.hasArg().withArgName("uid").isRequired(true).withType(String.class) .withDescription(// w w w . j av a2 s .com "User ID : must be a valid email address which serves as the unique identity of the portfolio") .create("u"); Option optI = OptionBuilder.hasOptionalArgs().withArgName("item").withType(String.class).isRequired(false) .withDescription( "Stock(s) in your portfolio: Print all stocks selected by this option and preferences against them") .create("i"); Option optP = OptionBuilder.hasOptionalArgs().withArgName("pref").isRequired(false).withType(Long.class) .withDescription( "Preference(s) against stocks in portfolio : Print all preferences specified in option and all stocks listed against that preference. Multiple preferences may be specified to draw on the many-many relationship between stocks and preferences matrices") .create("p"); Option optIP = OptionBuilder.hasArg().withArgName("itempref").withValueSeparator(':').isRequired(false) .withDescription( "Enter stock and preferences over command line. Any new stock will be registered as a new entry along with preference. Each new preference for an already existing stock will overwrite the existing preference(so be careful!)") .create("ip"); Option optF = OptionBuilder.hasArg().withArgName("itempreffile").withType(String.class) .withDescription("File to read stock preference data from").isRequired(false).create("f"); Option optH = OptionBuilder.hasArg(false).withArgName("help").withType(String.class) .withDescription("Display usage").isRequired(false).create("h"); options.addOption(optU); options.addOption(optI); options.addOption(optP); options.addOption(optIP); options.addOption(optF); options.addOption(optH); parser = new BasicParser(); CommandLine line = null; try { line = parser.parse(options, args); } catch (MissingOptionException e) { System.out.println("Missing options"); printUsage(); } catch (ParseException e) { e.printStackTrace(); } catch (Exception e) { e.printStackTrace(); } if (line.hasOption("help")) { printUsage(); } UserArgumentEmailType uEmailId = new UserArgumentEmailType(line.getOptionValue("u")); String uEmailIdStr = uEmailId.toString(); if (MongoDBUserModel.registered(uEmailIdStr)) { System.out.format("Already registered user %s\n", uEmailIdStr); } else { System.out.format("+--Starting transaction for user %s --+\n", uEmailIdStr); } if (line.hasOption("f")) { System.out.println("Query::UpdateDB: itempreffile(s)\n"); String[] uItemPrefFiles = line.getOptionValues("f"); for (String it : uItemPrefFiles) { System.out.format("Updating db with user file %s\n", it); UserItemPrefFile uItemPrefFile = new UserItemPrefFile(uEmailIdStr, it); uItemPrefFile.writeToDB(); } } if (line.hasOption("i")) { System.out.println("Query::ReadDB: item(s)\n"); String[] uItems = line.getOptionValues("i"); for (String it : uItems) { System.out.format("Searching for item %s in db\n", it); UserItem uItem = new UserItem(uEmailIdStr, it); uItem.readFromDB(); } } if (line.hasOption("p")) { System.out.println("Query::ReadDB: preference(s)"); String[] uPrefs = line.getOptionValues("p"); for (String it : uPrefs) { System.out.format("Searching for preference %s in db\n", it); UserPreference uPref = new UserPreference(uEmailIdStr, it); uPref.readFromDB(); } } if (line.hasOption("ip")) { System.out.println("Query::UpdateDB: itempref(s)\n"); String[] uItemPrefs = line.getOptionValues("ip"); for (String it : uItemPrefs) { System.out.format("Updating item:preference pair %s\n", it); String[] pair = it.split(":"); System.out.format("%s:%s:%s", uEmailIdStr, pair[0], pair[1]); UserItemPreference uItemPref = new UserItemPreference(uEmailIdStr, pair[0], pair[1]); uItemPref.writeToDB(); } } System.out.format("+-- Ending transaction for user %s --+\n", uEmailIdStr); }
From source file:frankhassanabad.com.github.Jasperize.java
/** * Main method to call through Java in order to take a LinkedInProfile on disk and load it. * * @param args command line arguments where the options are stored * @throws FileNotFoundException Thrown if any file its expecting cannot be found. * @throws JRException If there's generic overall Jasper issues. * @throws ParseException If there's command line parsing issues. */// w w w.java2s.co m public static void main(String[] args) throws IOException, JRException, ParseException { Options options = new Options(); options.addOption("h", "help", false, "Shows the help documentation"); options.addOption("v", "version", false, "Shows the help documentation"); options.addOption("cl", "coverLetter", false, "Utilizes a cover letter defined in coverletter.xml"); options.addOption("sig", true, "Picture of your signature to add to the cover letter."); CommandLineParser parser = new GnuParser(); CommandLine cmd = parser.parse(options, args); if (cmd.hasOption("h")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("Jasperize [OPTIONS] [InputJrxmlFile] [OutputExportFile]", options); System.exit(0); } if (cmd.hasOption("v")) { System.out.println("Version:" + version); System.exit(0); } boolean useCoverLetter = cmd.hasOption("cl"); String signatureLocation = cmd.getOptionValue("sig"); BufferedImage signatureImage = null; if (signatureLocation != null) { signatureImage = ImageIO.read(new File(signatureLocation)); ; } @SuppressWarnings("unchecked") List<String> arguments = cmd.getArgList(); final String jrxmlFile; final String jasperOutput; if (arguments.size() == 2) { jrxmlFile = arguments.get(0); jasperOutput = arguments.get(1); System.out.println("*Detected* the command line arguments of:"); System.out.println(" [InputjrxmlFile] " + jrxmlFile); System.out.println(" [OutputExportFile] " + jasperOutput); } else if (arguments.size() == 3) { jrxmlFile = arguments.get(1); jasperOutput = arguments.get(2); System.out.println("*Detected* the command line arguments of:"); System.out.println(" [InputjrxmlFile] " + jrxmlFile); System.out.println(" [OutputExportFile] " + jasperOutput); } else { System.out.println("Using the default arguments of:"); jrxmlFile = "data/jasperTemplates/resume1.jrxml"; jasperOutput = "data/jasperOutput/linkedInResume.pdf"; System.out.println(" [InputjrxmlFile] " + jrxmlFile); System.out.println(" [OutputExportFile] " + jasperOutput); } final String compiledMasterFile; final String outputType; final String jrPrintFile; //Split the inputFile final String[] inputSplit = jrxmlFile.split("\\."); if (inputSplit.length != 2 || !(inputSplit[1].equalsIgnoreCase("jrxml"))) { //Error System.out.println("Your [InputjrxmlFile] (1st argument) should have a jrxml extension like such:"); System.out.println(" data/jasperTemplates/resume1.jrxml"); System.exit(1); } //Split the outputFile final String[] outputSplit = jasperOutput.split("\\."); if (outputSplit.length != 2) { //Error System.out.println("Your [OutputExportFile] (2nd argument) should have a file extension like such:"); System.out.println(" data/jasperOutput/linkedInResume.pdf"); System.exit(1); } File inputFile = new File(inputSplit[0]); String inputFileName = inputFile.getName(); String inputFileParentPath = inputFile.getParent(); File outputFile = new File(outputSplit[0]); String outputFileParentPath = outputFile.getParent(); System.out.println("Compiling report(s)"); compileAllJrxmlTemplateFiles(inputFileParentPath, outputFileParentPath); System.out.println("Done compiling report(s)"); compiledMasterFile = outputFileParentPath + File.separator + inputFileName + ".jasper"; jrPrintFile = outputFileParentPath + File.separator + inputFileName + ".jrprint"; System.out.println("Filling report: " + compiledMasterFile); Reporting.fill(compiledMasterFile, useCoverLetter, signatureImage); System.out.println("Done filling reports"); outputType = outputSplit[1]; System.out.println("Creating output export file of: " + jasperOutput); if (outputType.equalsIgnoreCase("pdf")) { Reporting.pdf(jrPrintFile, jasperOutput); } if (outputType.equalsIgnoreCase("pptx")) { Reporting.pptx(jrPrintFile, jasperOutput); } if (outputType.equalsIgnoreCase("docx")) { Reporting.docx(jrPrintFile, jasperOutput); } if (outputType.equalsIgnoreCase("odt")) { Reporting.odt(jrPrintFile, jasperOutput); } if (outputType.equalsIgnoreCase("xhtml")) { Reporting.xhtml(jrPrintFile, jasperOutput); } System.out.println("Done creating output export file of: " + jasperOutput); }
From source file:com.github.vatbub.awsvpnlauncher.Main.java
public static void main(String[] args) { Common.getInstance().setAppName("awsVpnLauncher"); FOKLogger.enableLoggingOfUncaughtExceptions(); prefs = new Preferences(Main.class.getName()); // enable the shutdown hook Runtime.getRuntime().addShutdownHook(new Thread(() -> { if (session != null) { if (session.isConnected()) { session.disconnect();//from w w w . j av a 2 s . c o m } } })); UpdateChecker.completeUpdate(args, (oldVersion, oldFile) -> { if (oldVersion != null) { FOKLogger.info(Main.class.getName(), "Successfully upgraded " + Common.getInstance().getAppName() + " from v" + oldVersion.toString() + " to v" + Common.getInstance().getAppVersion()); } }); List<String> argsAsList = new ArrayList<>(Arrays.asList(args)); for (String arg : args) { if (arg.toLowerCase().matches("mockappversion=.*")) { // Set the mock version String version = arg.substring(arg.toLowerCase().indexOf('=') + 1); Common.getInstance().setMockAppVersion(version); argsAsList.remove(arg); } else if (arg.toLowerCase().matches("mockbuildnumber=.*")) { // Set the mock build number String buildnumber = arg.substring(arg.toLowerCase().indexOf('=') + 1); Common.getInstance().setMockBuildNumber(buildnumber); argsAsList.remove(arg); } else if (arg.toLowerCase().matches("mockpackaging=.*")) { // Set the mock packaging String packaging = arg.substring(arg.toLowerCase().indexOf('=') + 1); Common.getInstance().setMockPackaging(packaging); argsAsList.remove(arg); } } args = argsAsList.toArray(new String[0]); try { mvnRepoConfig = new Config( new URL("https://www.dropbox.com/s/vnhs4nax2lczccf/mavenRepoConfig.properties?dl=1"), Main.class.getResource("mvnRepoFallbackConfig.properties"), true, "mvnRepoCachedConfig", true); projectConfig = new Config( new URL("https://www.dropbox.com/s/d36hwrrufoxfmm7/projectConfig.properties?dl=1"), Main.class.getResource("projectFallbackConfig.properties"), true, "projectCachedConfig", true); } catch (IOException e) { FOKLogger.log(Main.class.getName(), Level.SEVERE, "Could not load the remote config", e); } try { installUpdates(args); } catch (Exception e) { FOKLogger.log(Main.class.getName(), Level.SEVERE, "Could not install updates", e); } if (args.length == 0) { // not enough arguments printHelpMessage(); throw new NotEnoughArgumentsException(); } switch (args[0].toLowerCase()) { case "setup": setup(); break; case "launch": initAWSConnection(); launch(); break; case "terminate": initAWSConnection(); terminate(); break; case "config": // require a second arg if (args.length == 2) { // not enough arguments printHelpMessage(); throw new NotEnoughArgumentsException(); } config(Property.valueOf(args[1]), args[2]); break; case "getconfig": // require a second arg if (args.length == 1) { // not enough arguments printHelpMessage(); throw new NotEnoughArgumentsException(); } getConfig(Property.valueOf(args[1])); break; case "printconfig": printConfig(); break; case "deleteconfig": // require a second arg if (args.length == 1) { // not enough arguments printHelpMessage(); throw new NotEnoughArgumentsException(); } deleteConfig(Property.valueOf(args[1])); break; case "ssh": String sshInstanceId; if (args.length == 2) { // a instanceID is specified sshInstanceId = args[1]; } else { String instanceIdsPrefValue = prefs.getPreference("instanceIDs", ""); if (instanceIdsPrefValue.equals("")) { throw new NotEnoughArgumentsException( "No instanceId was specified to connect to and no instanceId was saved in the preference file. Please either start another instance using the launch command or specify the instance id of the instance to connect to as a additional parameter."); } List<String> instanceIds = Arrays.asList(instanceIdsPrefValue.split(";")); if (instanceIds.size() == 1) { // exactly one instance found sshInstanceId = instanceIds.get(0); } else { FOKLogger.severe(Main.class.getName(), "Multiple instance ids found:"); for (String instanceId : instanceIds) { FOKLogger.severe(Main.class.getName(), instanceId); } throw new NotEnoughArgumentsException( "Multiple instance ids were found in the preference file. Please specify the instance id of the instance to connect to as a additional parameter."); } } initAWSConnection(); ssh(sshInstanceId); break; default: printHelpMessage(); } }
From source file:com.esri.geoevent.test.tools.RunTcpInTcpOutTest.java
public static void main(String args[]) { int numberEvents = 10000; //int brake = 1000; String server = "ags104"; int in_port = 5565; int out_port = 5575; int start_rate = 5000; int end_rate = 5005; int rate_step = 1; Options opts = new Options(); opts.addOption("n", true, "Number of Events"); opts.addOption("s", true, "Server"); opts.addOption("i", true, "Input TCP Port"); opts.addOption("o", true, "Output TCP Port"); opts.addOption("r", true, "Range"); opts.addOption("h", false, "Help"); try {/* ww w. ja v a2 s .c o m*/ CommandLineParser parser = new BasicParser(); CommandLine cmd = null; try { cmd = parser.parse(opts, args, false); } catch (ParseException ignore) { System.err.println(ignore.getMessage()); } String cmdInputErrorMsg = ""; if (cmd.getOptions().length == 0 || cmd.hasOption("h")) { throw new ParseException("Show Help"); } if (cmd.hasOption("n")) { String val = cmd.getOptionValue("n"); try { numberEvents = Integer.valueOf(val); } catch (NumberFormatException e) { cmdInputErrorMsg += "Invalid value for n. Must be integer.\n"; } } if (cmd.hasOption("s")) { server = cmd.getOptionValue("s"); } if (cmd.hasOption("i")) { String val = cmd.getOptionValue("i"); try { in_port = Integer.valueOf(val); } catch (NumberFormatException e) { cmdInputErrorMsg += "Invalid value for i. Must be integer.\n"; } } if (cmd.hasOption("o")) { String val = cmd.getOptionValue("o"); try { out_port = Integer.valueOf(val); } catch (NumberFormatException e) { cmdInputErrorMsg += "Invalid value for o. Must be integer.\n"; } } if (cmd.hasOption("r")) { String val = cmd.getOptionValue("r"); try { String parts[] = val.split(","); if (parts.length == 3) { start_rate = Integer.parseInt(parts[0]); end_rate = Integer.parseInt(parts[1]); rate_step = Integer.parseInt(parts[2]); } else if (parts.length == 1) { // Run single rate start_rate = Integer.parseInt(parts[0]); end_rate = start_rate; rate_step = start_rate; } else { throw new ParseException("Rate must be three comma seperated values or a single value"); } } catch (ParseException e) { cmdInputErrorMsg += e.getMessage(); } catch (NumberFormatException e) { cmdInputErrorMsg += "Invalid value for r. Must be integers.\n"; } } if (!cmdInputErrorMsg.equalsIgnoreCase("")) { throw new ParseException(cmdInputErrorMsg); } DecimalFormat df = new DecimalFormat("##0"); RunTcpInTcpOutTest t = new RunTcpInTcpOutTest(); if (start_rate == end_rate) { // Single Rate Test System.out.println("*********************************"); System.out.println("Incremental testing at requested rate: " + start_rate); System.out.println("Count,Incremental Rate"); t.runTest(numberEvents, start_rate, server, in_port, out_port, true); if (t.send_rate < 0 || t.rcv_rate < 0) { throw new Exception("Test Run Failed!"); } System.out.println("Overall Average Send Rate, Received Rate"); System.out.println(df.format(t.send_rate) + "," + df.format(t.rcv_rate)); } else { System.out.println("*********************************"); System.out.println("rateRqstd,avgSendRate,avgRcvdRate"); //for (int rate: rates) { for (int rate = start_rate; rate <= end_rate; rate += rate_step) { t.runTest(numberEvents, rate, server, in_port, out_port, false); if (t.send_rate < 0 || t.rcv_rate < 0) { throw new Exception("Test Run Failed!"); } System.out.println( Integer.toString(rate) + "," + df.format(t.send_rate) + "," + df.format(t.rcv_rate)); } } } catch (ParseException e) { System.out.println("Invalid Command Options: "); System.out.println(e.getMessage()); System.out.println( "Command line options: -n NumEvents -s Server -i InputPort -o OutputPort -r StartRate,EndRate,Step"); } catch (Exception e) { System.out.println(e.getMessage()); } }
From source file:CourserankConnector.java
public static void main(String[] args) throws Exception { /////////////////////////////////////// //Tagger init //MaxentTagger tagger = new MaxentTagger("models/english-left3words-distsim.tagger"); ///// w w w. j a va2s.c o m //CLIENT INITIALIZATION ImportData importCourse = new ImportData(); HttpClient httpclient = new DefaultHttpClient(); httpclient = WebClientDevWrapper.wrapClient(httpclient); try { /* httpclient.getCredentialsProvider().setCredentials( new AuthScope(null, -1), new UsernamePasswordCredentials("eadrian", "eactresp1")); */ ////////////////////////////////////////////////// //Get Course Bulletin Departments page List<Course> courses = new ArrayList<Course>(); HttpGet httpget = new HttpGet("http://explorecourses.stanford.edu"); System.out.println("executing request" + httpget.getRequestLine()); HttpResponse response = httpclient.execute(httpget); HttpEntity entity = response.getEntity(); System.out.println("----------------------------------------"); System.out.println(response.getStatusLine()); String bulletinpage = ""; //STORE RETURNED HTML TO BULLETINPAGE if (entity != null) { //System.out.println("Response content length: " + entity.getContentLength()); InputStream i = entity.getContent(); BufferedReader br = new BufferedReader(new InputStreamReader(i)); String line; while ((line = br.readLine()) != null) { bulletinpage += line; //System.out.println(line); } br.close(); i.close(); } EntityUtils.consume(entity); /////////////////////////////////////////////////////////////////////////////// //Login to Courserank httpget = new HttpGet("https://courserank.com/stanford/main"); System.out.println("executing request" + httpget.getRequestLine()); response = httpclient.execute(httpget); entity = response.getEntity(); System.out.println("----------------------------------------"); System.out.println(response.getStatusLine()); String page = ""; if (entity != null) { System.out.println("Response content length: " + entity.getContentLength()); InputStream i = entity.getContent(); BufferedReader br = new BufferedReader(new InputStreamReader(i)); String line; while ((line = br.readLine()) != null) { page += line; //System.out.println(line); } br.close(); i.close(); } EntityUtils.consume(entity); //////////////////////////////////////////////////// //POST REQUEST LOGIN HttpPost post = new HttpPost("https://www.courserank.com/stanford/main"); List<NameValuePair> pairs = new ArrayList<NameValuePair>(2); pairs.add(new BasicNameValuePair("RT", "")); pairs.add(new BasicNameValuePair("action", "login")); pairs.add(new BasicNameValuePair("password", "trespass")); pairs.add(new BasicNameValuePair("username", "eaconte@stanford.edu")); post.setEntity(new UrlEncodedFormEntity(pairs)); System.out.println("executing request" + post.getRequestLine()); HttpResponse resp = httpclient.execute(post); HttpEntity ent = resp.getEntity(); System.out.println("----------------------------------------"); if (ent != null) { System.out.println("Response content length: " + ent.getContentLength()); InputStream i = ent.getContent(); BufferedReader br = new BufferedReader(new InputStreamReader(i)); String line; while ((line = br.readLine()) != null) { //System.out.println(line); } br.close(); i.close(); } EntityUtils.consume(ent); /////////////////////////////////////////////////// //THIS STEP MAY NOT BE NEEDED BUT GETS MAIN PROFILE PAGE HttpGet gethome = new HttpGet("https://www.courserank.com/stanford/home"); System.out.println("executing request" + gethome.getRequestLine()); HttpResponse gresp = httpclient.execute(gethome); HttpEntity gent = gresp.getEntity(); System.out.println("----------------------------------------"); if (ent != null) { System.out.println("Response content length: " + gent.getContentLength()); InputStream i = gent.getContent(); BufferedReader br = new BufferedReader(new InputStreamReader(i)); String line; while ((line = br.readLine()) != null) { //System.out.println(line); } br.close(); i.close(); } ///////////////////////////////////////////////////////////////////////////////// //Parse Bulletin String results = getToken(bulletinpage, "RESULTS HEADER", "Additional Searches"); String[] depts = results.split("href"); //SPLIT FOR EACH DEPARTMENT LINK, ITERATE boolean ready = false; for (int i = 1; i < depts.length; i++) { //EXTRACT LINK, DEPARTMENT NAME AND ABBREVIATION String dept = new String(depts[i]); String abbr = getToken(dept, "(", ")"); String name = getToken(dept, ">", "("); name.trim(); //System.out.println(tagger.tagString(name)); String link = getToken(dept, "=\"", "\">"); System.out.println(name + " : " + abbr + " : " + link); System.out.println("======================================================================"); if (i <= 10 || i >= 127) //values to keep it to undergraduate courses. Excludes law, med, business, overseas continue; /*if (i<=46) continue; */ //Start at BIOHOP /*if (abbr.equals("INTNLREL")) ready = true; if (!ready) continue;*/ //Construct department course search URL //Then request page String URL = "http://explorecourses.stanford.edu/" + link + "&filter-term-Autumn=on&filter-term-Winter=on&filter-term-Spring=on"; httpget = new HttpGet(URL); //System.out.println("executing request" + httpget.getRequestLine()); response = httpclient.execute(httpget); entity = response.getEntity(); //ystem.out.println("----------------------------------------"); //System.out.println(response.getStatusLine()); String rpage = ""; if (entity != null) { //System.out.println("Response content length: " + entity.getContentLength()); InputStream in = entity.getContent(); BufferedReader br = new BufferedReader(new InputStreamReader(in)); String line; while ((line = br.readLine()) != null) { rpage += line; //System.out.println(line); } br.close(); in.close(); } EntityUtils.consume(entity); //Process results page List<Course> deptCourses = new ArrayList<Course>(); List<Course> result = processResultPage(rpage); deptCourses.addAll(result); //While there are more result pages, keep going boolean more = (!(result.size() == 0) && (result.get((result.size() - 1)).courseNumber < 299)); boolean morepages = anotherPage(rpage); while (morepages && more) { URL = nextURL(URL); httpget = new HttpGet(URL); //System.out.println("executing request" + httpget.getRequestLine()); response = httpclient.execute(httpget); entity = response.getEntity(); //System.out.println("----------------------------------------"); //System.out.println(response.getStatusLine()); rpage = ""; if (entity != null) { //System.out.println("Response content length: " + entity.getContentLength()); InputStream in = entity.getContent(); BufferedReader br = new BufferedReader(new InputStreamReader(in)); String line; while ((line = br.readLine()) != null) { rpage += line; //System.out.println(line); } br.close(); in.close(); } EntityUtils.consume(entity); morepages = anotherPage(rpage); result = processResultPage(rpage); deptCourses.addAll(result); more = (!(result.size() == 0) && (result.get((result.size() - 1)).courseNumber < 299)); /*String mores = more? "yes": "no"; String pagess = morepages?"yes":"no"; System.out.println("more: "+mores+" morepages: "+pagess); System.out.println("more");*/ } //Get course ratings for all department courses via courserank deptCourses = getRatings(httpclient, abbr, deptCourses); for (int j = 0; j < deptCourses.size(); j++) { Course c = deptCourses.get(j); System.out.println("" + c.title + " : " + c.rating); c.tags = name; c.code = c.code.trim(); c.department = name; c.deptAB = abbr; c.writeToDatabase(); //System.out.println(tagger.tagString(c.title)); } } if (!page.equals("")) return; /////////////////////////////////////////////////// //Get Course Bulletin Department courses /* httpget = new HttpGet("https://courserank.com/stanford/main"); System.out.println("executing request" + httpget.getRequestLine()); response = httpclient.execute(httpget); entity = response.getEntity(); System.out.println("----------------------------------------"); System.out.println(response.getStatusLine()); page = ""; if (entity != null) { System.out.println("Response content length: " + entity.getContentLength()); InputStream i = entity.getContent(); BufferedReader br = new BufferedReader(new InputStreamReader(i)); String line; while ((line = br.readLine()) != null) { page +=line; //System.out.println(line); } br.close(); i.close(); } EntityUtils.consume(entity); //////////////////////////////////////////////////// //POST REQUEST LOGIN HttpPost post = new HttpPost("https://www.courserank.com/stanford/main"); List<NameValuePair> pairs = new ArrayList<NameValuePair>(2); pairs.add(new BasicNameValuePair("RT", "")); pairs.add(new BasicNameValuePair("action", "login")); pairs.add(new BasicNameValuePair("password", "trespass")); pairs.add(new BasicNameValuePair("username", "eaconte@stanford.edu")); post.setEntity(new UrlEncodedFormEntity(pairs)); System.out.println("executing request" + post.getRequestLine()); HttpResponse resp = httpclient.execute(post); HttpEntity ent = resp.getEntity(); System.out.println("----------------------------------------"); if (ent != null) { System.out.println("Response content length: " + ent.getContentLength()); InputStream i = ent.getContent(); BufferedReader br = new BufferedReader(new InputStreamReader(i)); String line; while ((line = br.readLine()) != null) { //System.out.println(line); } br.close(); i.close(); } EntityUtils.consume(ent); /////////////////////////////////////////////////// //THIS STEP MAY NOT BE NEEDED BUT GETS MAIN PROFILE PAGE HttpGet gethome = new HttpGet("https://www.courserank.com/stanford/home"); System.out.println("executing request" + gethome.getRequestLine()); HttpResponse gresp = httpclient.execute(gethome); HttpEntity gent = gresp.getEntity(); System.out.println("----------------------------------------"); if (ent != null) { System.out.println("Response content length: " + gent.getContentLength()); InputStream i = gent.getContent(); BufferedReader br = new BufferedReader(new InputStreamReader(i)); String line; while ((line = br.readLine()) != null) { //System.out.println(line); } br.close(); i.close(); } //////////////////////////////////////// //GETS FIRST PAGE OF RESULTS EntityUtils.consume(gent); post = new HttpPost("https://www.courserank.com/stanford/search_results"); pairs = new ArrayList<NameValuePair>(2); pairs.add(new BasicNameValuePair("filter_term_currentYear", "on")); pairs.add(new BasicNameValuePair("query", "")); post.setEntity(new UrlEncodedFormEntity(pairs)); System.out.println("executing request" + post.getRequestLine()); resp = httpclient.execute(post); ent = resp.getEntity(); System.out.println("----------------------------------------"); String rpage = ""; if (ent != null) { System.out.println("Response content length: " + ent.getContentLength()); InputStream i = ent.getContent(); BufferedReader br = new BufferedReader(new InputStreamReader(i)); String line; while ((line = br.readLine()) != null) { rpage += line; System.out.println(line); } br.close(); i.close(); } EntityUtils.consume(ent); //////////////////////////////////////////////////// //PARSE FIRST PAGE OF RESULTS //int index = rpage.indexOf("div class=\"searchItem"); String []classSplit = rpage.split("div class=\"searchItem"); for (int i=1; i<classSplit.length; i++) { String str = classSplit[i]; //ID String CID = getToken(str, "course?id=","\">"); // CODE String CODE = getToken(str,"class=\"code\">" ,":</"); //TITLE String NAME = getToken(str, "class=\"title\">","</"); //DESCRIP String DES = getToken(str, "class=\"description\">","</"); //TERM String TERM = getToken(str, "Terms:", "|"); //UNITS String UNITS = getToken(str, "Units:", "<br/>"); //WORKLOAD String WLOAD = getToken(str, "Workload:", "|"); //GER String GER = getToken(str, "GERs:", "</d"); //RATING int searchIndex = 0; float rating = 0; while (true) { int ratingIndex = str.indexOf("large_Full", searchIndex); if (ratingIndex ==-1) { int halfratingIndex = str.indexOf("large_Half", searchIndex); if (halfratingIndex == -1) break; else rating += .5; break; } searchIndex = ratingIndex+1; rating++; } String RATING = ""+rating; //GRADE String GRADE = getToken(str, "div class=\"unofficialGrade\">", "</"); if (GRADE.equals("NOT FOUND")) { GRADE = getToken(str, "div class=\"officialGrade\">", "</"); } //REVIEWS String REVIEWS = getToken(str, "class=\"ratings\">", " ratings"); System.out.println(""+CODE+" : "+NAME + " : "+CID); System.out.println("----------------------------------------"); System.out.println("Term: "+TERM+" Units: "+UNITS+ " Workload: "+WLOAD + " Grade: "+ GRADE); System.out.println("Rating: "+RATING+ " Reviews: "+REVIEWS); System.out.println("=========================================="); System.out.println(DES); System.out.println("=========================================="); } /////////////////////////////////////////////////// //GETS SECOND PAGE OF RESULTS post = new HttpPost("https://www.courserank.com/stanford/search_results"); pairs = new ArrayList<NameValuePair>(2); pairs.add(new BasicNameValuePair("filter_term_currentYear", "on")); pairs.add(new BasicNameValuePair("page", "2")); pairs.add(new BasicNameValuePair("query", "")); post.setEntity(new UrlEncodedFormEntity(pairs)); System.out.println("executing request" + post.getRequestLine()); resp = httpclient.execute(post); ent = resp.getEntity(); System.out.println("----------------------------------------"); if (ent != null) { System.out.println("Response content length: " + ent.getContentLength()); InputStream i = ent.getContent(); BufferedReader br = new BufferedReader(new InputStreamReader(i)); String line; while ((line = br.readLine()) != null) { //System.out.println(line); } br.close(); i.close(); } EntityUtils.consume(ent); /* httpget = new HttpGet("https://github.com/"); System.out.println("executing request" + httpget.getRequestLine()); response = httpclient.execute(httpget); entity = response.getEntity(); System.out.println("----------------------------------------"); System.out.println(response.getStatusLine()); page = ""; if (entity != null) { System.out.println("Response content length: " + entity.getContentLength()); InputStream i = entity.getContent(); BufferedReader br = new BufferedReader(new InputStreamReader(i)); String line; while ((line = br.readLine()) != null) { page +=line; System.out.println(line); } br.close(); i.close(); }*/ EntityUtils.consume(entity); } finally { // When HttpClient instance is no longer needed, // shut down the connection manager to ensure // immediate deallocation of all system resources httpclient.getConnectionManager().shutdown(); } }
From source file:jhc.redsniff.generation.PackageScanningGenerator.java
public static void main(String[] args) throws Exception { if (args.length != 5) { System.err.println("Args: source-dir package-class-filter parent-class generated-class output-dir"); System.err.println(""); System.err.println(" source-dir : Path to Java source containing matchers to generate sugar for."); System.err.println(" May contain multiple paths, separated by commas."); System.err.println(" e.g. src/java,src/more-java"); System.err.println(/* w ww .j a v a 2s. c om*/ " package-class-filter : base of package to look for classes with methods, eg jhc.selenium.matchers"); System.err.println(""); System.err.println( "parent-class : Full name of parent class type to examine - eg org.hamcrest.Matcher, jhc.selenium.seeker.Seeker"); System.err.println(" e.g. org.myproject.MyMatchers"); System.err.println("generated-class : Full name of class to generate."); System.err.println(" e.g. org.myproject.MyMatchers"); System.err.println(""); System.err.println(" output-dir : Where to output generated code (package subdirs will be"); System.err.println(" automatically created)."); System.err.println(" e.g. build/generated-code"); System.exit(-1); } String srcDirs = args[0]; String package_name_prefix = args[1]; String parentClassName = args[2]; String fullClassName = args[3]; File outputDir = new File(args[4]); String fileName = fullClassName.replace('.', File.separatorChar) + ".java"; int dotIndex = fullClassName.lastIndexOf("."); String packageName = dotIndex == -1 ? "" : fullClassName.substring(0, dotIndex); String shortClassName = fullClassName.substring(dotIndex + 1); if (!outputDir.isDirectory()) { System.err.println("Output directory not found : " + outputDir.getAbsolutePath()); System.exit(-1); } Class<?> parentClass = Class.forName(parentClassName); File outputFile = new File(outputDir, fileName); outputFile.getParentFile().mkdirs(); File tmpFile = new File(outputDir, fileName + ".tmp"); SugarGenerator sugarGenerator = new SugarGenerator(); try { sugarGenerator .addWriter(new SeleniumFactoryWriter(packageName, shortClassName, new FileWriter(tmpFile))); sugarGenerator.addWriter(new QuickReferenceWriter(System.out)); PackageScanningGenerator pkgScanningGenerator = new PackageScanningGenerator(sugarGenerator, PackageScanningGenerator.class.getClassLoader(), parentClass); if (srcDirs.trim().length() > 0) { for (String srcDir : srcDirs.split(",")) { pkgScanningGenerator.addSourceDir(new File(srcDir)); } } // could add use of xml just to list filter expressions // pkgScanningGenerator.load(new InputSource(configFile)); pkgScanningGenerator.addClasses(package_name_prefix); System.out.println("Generating " + fullClassName); sugarGenerator.generate(); sugarGenerator.close(); outputFile.delete(); FileUtils.moveFile(tmpFile, outputFile); } finally { tmpFile.delete(); sugarGenerator.close(); } }
From source file:DIA_Umpire_Quant.DIA_Umpire_LCMSIDGen.java
/** * @param args the command line arguments *///from w w w .ja va2s . c om public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println("DIA-Umpire LCMSID geneartor (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_LCMSIDGen.jar diaumpire_module.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_lcmsidgen.log"); } catch (Exception e) { } Logger.getRootLogger().info("Version: " + UmpireInfo.GetInstance().Version); Logger.getRootLogger().info("Parameter file:" + args[0]); BufferedReader reader = new BufferedReader(new FileReader(args[0])); String line = ""; String WorkFolder = ""; int NoCPUs = 2; TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); HashMap<String, File> AssignFiles = new HashMap<>(); //<editor-fold defaultstate="collapsed" desc="Reading parameter file"> while ((line = reader.readLine()) != null) { line = line.trim(); Logger.getRootLogger().info(line); if (!"".equals(line) && !line.startsWith("#")) { //System.out.println(line); if (line.equals("==File list begin")) { do { line = reader.readLine(); line = line.trim(); if (line.equals("==File list end")) { continue; } else if (!"".equals(line)) { File newfile = new File(line); if (newfile.exists()) { AssignFiles.put(newfile.getAbsolutePath(), newfile); } else { Logger.getRootLogger().info("File: " + newfile + " does not exist."); } } } while (!line.equals("==File list end")); } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); String value = line.split("=")[1].trim(); switch (type) { case "Path": { WorkFolder = value; break; } case "path": { WorkFolder = value; break; } case "Thread": { NoCPUs = Integer.parseInt(value); break; } case "DecoyPrefix": { if (!"".equals(value)) { tandemPara.DecoyPrefix = value; } break; } case "PeptideFDR": { tandemPara.PepFDR = Float.parseFloat(value); break; } } } } //</editor-fold> //Initialize PTM manager using compomics library PTMManager.GetInstance(); //Generate DIA file list ArrayList<DIAPack> FileList = new ArrayList<>(); File folder = new File(WorkFolder); if (!folder.exists()) { Logger.getRootLogger().info("The path : " + WorkFolder + " cannot be found."); System.exit(1); } for (final File fileEntry : folder.listFiles()) { if (fileEntry.isFile() && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry.getAbsolutePath(), fileEntry); } if (fileEntry.isDirectory()) { for (final File fileEntry2 : fileEntry.listFiles()) { if (fileEntry2.isFile() && (fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry2.getAbsolutePath(), fileEntry2); } } } } Logger.getRootLogger().info("No. of files assigned :" + AssignFiles.size()); for (File fileEntry : AssignFiles.values()) { Logger.getRootLogger().info(fileEntry.getAbsolutePath()); } //process each DIA file to genearate untargeted identifications for (File fileEntry : AssignFiles.values()) { String mzXMLFile = fileEntry.getAbsolutePath(); if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) { long time = System.currentTimeMillis(); DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs); FileList.add(DiaFile); Logger.getRootLogger().info( "================================================================================================="); Logger.getRootLogger().info("Processing " + mzXMLFile); if (!DiaFile.LoadDIASetting()) { Logger.getRootLogger().info("Loading DIA setting failed, job is incomplete"); System.exit(1); } if (!DiaFile.LoadParams()) { Logger.getRootLogger().info("Loading parameters failed, job is incomplete"); System.exit(1); } Logger.getRootLogger().info("Loading identification results " + mzXMLFile + "...."); DiaFile.ParsePepXML(tandemPara, null); DiaFile.BuildStructure(); if (!DiaFile.MS1FeatureMap.ReadPeakCluster()) { Logger.getRootLogger().info("Loading peak and structure failed, job is incomplete"); System.exit(1); } DiaFile.MS1FeatureMap.ClearMonoisotopicPeakOfCluster(); //Generate mapping between index of precursor feature and pseudo MS/MS scan index DiaFile.GenerateClusterScanNomapping(); //Doing quantification DiaFile.AssignQuant(); DiaFile.ClearStructure(); DiaFile.IDsummary.ReduceMemoryUsage(); time = System.currentTimeMillis() - time; Logger.getRootLogger().info(mzXMLFile + " processed time:" + String.format("%d hour, %d min, %d sec", TimeUnit.MILLISECONDS.toHours(time), TimeUnit.MILLISECONDS.toMinutes(time) - TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(time)), TimeUnit.MILLISECONDS.toSeconds(time) - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(time)))); } Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); } }
From source file:DIA_Umpire_SE.DIA_Umpire_SE.java
/** * @param args the command line arguments DIA_Umpire parameterfile *///from www. j a va 2 s .c o m public static void main(String[] args) throws InterruptedException, FileNotFoundException, ExecutionException, IOException, ParserConfigurationException, DataFormatException, SAXException, Exception { System.out.println( "================================================================================================="); System.out.println( "DIA-Umpire singal extraction analysis (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length < 2 || args.length > 3) { System.out.println( "command format error, the correct format is: java -jar -Xmx8G DIA_Umpire_SE.jar mzMXL_file diaumpire_se.params"); System.out.println( "To fix DIA setting, use : java -jar -Xmx8G DIA_Umpire_SE.jar mzMXL_file diaumpire_se.params -f"); return; } try { //Define logger level for console ConsoleLogger.SetConsoleLogger(Level.INFO); //Define logger level and file path for text log file ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_se.log"); } catch (Exception e) { } boolean Fix = false; boolean Resume = false; if (args.length == 3 && args[2].equals("-f")) { Fix = true; } String parameterfile = args[1]; String MSFilePath = args[0]; Logger.getRootLogger().info("Version: " + UmpireInfo.GetInstance().Version); Logger.getRootLogger().info("Parameter file:" + parameterfile); Logger.getRootLogger().info("Spectra file:" + MSFilePath); BufferedReader reader = new BufferedReader(new FileReader(parameterfile)); String line = ""; InstrumentParameter param = new InstrumentParameter(InstrumentParameter.InstrumentType.TOF5600); param.DetermineBGByID = false; param.EstimateBG = true; int NoCPUs = 2; SpectralDataType.DataType dataType = SpectralDataType.DataType.DIA_F_Window; String WindowType = ""; int WindowSize = 25; ArrayList<XYData> WindowList = new ArrayList<>(); boolean ExportPrecursorPeak = false; boolean ExportFragmentPeak = false; //<editor-fold defaultstate="collapsed" desc="Read parameter file"> while ((line = reader.readLine()) != null) { Logger.getRootLogger().info(line); if (!"".equals(line) && !line.startsWith("#")) { //System.out.println(line); if (line.equals("==window setting begin")) { while (!(line = reader.readLine()).equals("==window setting end")) { if (!"".equals(line)) { WindowList.add(new XYData(Float.parseFloat(line.split("\t")[0]), Float.parseFloat(line.split("\t")[1]))); } } continue; } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); if (type.startsWith("para.")) { type = type.replace("para.", "SE."); } String value = line.split("=")[1].trim(); switch (type) { case "Thread": { NoCPUs = Integer.parseInt(value); break; } case "ExportPrecursorPeak": { ExportPrecursorPeak = Boolean.parseBoolean(value); break; } case "ExportFragmentPeak": { ExportFragmentPeak = Boolean.parseBoolean(value); break; } //<editor-fold defaultstate="collapsed" desc="instrument parameters"> case "RPmax": { param.PrecursorRank = Integer.parseInt(value); break; } case "RFmax": { param.FragmentRank = Integer.parseInt(value); break; } case "CorrThreshold": { param.CorrThreshold = Float.parseFloat(value); break; } case "DeltaApex": { param.ApexDelta = Float.parseFloat(value); break; } case "RTOverlap": { param.RTOverlapThreshold = Float.parseFloat(value); break; } case "BoostComplementaryIon": { param.BoostComplementaryIon = Boolean.parseBoolean(value); break; } case "AdjustFragIntensity": { param.AdjustFragIntensity = Boolean.parseBoolean(value); break; } case "SE.MS1PPM": { param.MS1PPM = Float.parseFloat(value); break; } case "SE.MS2PPM": { param.MS2PPM = Float.parseFloat(value); break; } case "SE.SN": { param.SNThreshold = Float.parseFloat(value); break; } case "SE.MS2SN": { param.MS2SNThreshold = Float.parseFloat(value); break; } case "SE.MinMSIntensity": { param.MinMSIntensity = Float.parseFloat(value); break; } case "SE.MinMSMSIntensity": { param.MinMSMSIntensity = Float.parseFloat(value); break; } case "SE.MinRTRange": { param.MinRTRange = Float.parseFloat(value); break; } case "SE.MaxNoPeakCluster": { param.MaxNoPeakCluster = Integer.parseInt(value); param.MaxMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MinNoPeakCluster": { param.MinNoPeakCluster = Integer.parseInt(value); param.MinMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MinMS2NoPeakCluster": { param.MinMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MaxCurveRTRange": { param.MaxCurveRTRange = Float.parseFloat(value); break; } case "SE.Resolution": { param.Resolution = Integer.parseInt(value); break; } case "SE.RTtol": { param.RTtol = Float.parseFloat(value); break; } case "SE.NoPeakPerMin": { param.NoPeakPerMin = Integer.parseInt(value); break; } case "SE.StartCharge": { param.StartCharge = Integer.parseInt(value); break; } case "SE.EndCharge": { param.EndCharge = Integer.parseInt(value); break; } case "SE.MS2StartCharge": { param.MS2StartCharge = Integer.parseInt(value); break; } case "SE.MS2EndCharge": { param.MS2EndCharge = Integer.parseInt(value); break; } case "SE.NoMissedScan": { param.NoMissedScan = Integer.parseInt(value); break; } case "SE.Denoise": { param.Denoise = Boolean.valueOf(value); break; } case "SE.EstimateBG": { param.EstimateBG = Boolean.valueOf(value); break; } case "SE.RemoveGroupedPeaks": { param.RemoveGroupedPeaks = Boolean.valueOf(value); break; } case "SE.MinFrag": { param.MinFrag = Integer.parseInt(value); break; } case "SE.IsoPattern": { param.IsoPattern = Float.valueOf(value); break; } case "SE.StartRT": { param.startRT = Float.valueOf(value); break; } case "SE.EndRT": { param.endRT = Float.valueOf(value); break; } case "SE.RemoveGroupedPeaksRTOverlap": { param.RemoveGroupedPeaksRTOverlap = Float.valueOf(value); break; } case "SE.RemoveGroupedPeaksCorr": { param.RemoveGroupedPeaksCorr = Float.valueOf(value); break; } case "SE.MinMZ": { param.MinMZ = Float.valueOf(value); break; } case "SE.MinPrecursorMass": { param.MinPrecursorMass = Float.valueOf(value); break; } case "SE.MaxPrecursorMass": { param.MaxPrecursorMass = Float.valueOf(value); break; } case "SE.IsoCorrThreshold": { param.IsoCorrThreshold = Float.valueOf(value); break; } case "SE.MassDefectFilter": { param.MassDefectFilter = Boolean.parseBoolean(value); break; } case "SE.MassDefectOffset": { param.MassDefectOffset = Float.valueOf(value); break; } //</editor-fold>//</editor-fold> case "WindowType": { WindowType = value; switch (WindowType) { case "SWATH": { dataType = SpectralDataType.DataType.DIA_F_Window; break; } case "V_SWATH": { dataType = SpectralDataType.DataType.DIA_V_Window; break; } case "MSX": { dataType = SpectralDataType.DataType.MSX; break; } case "MSE": { dataType = SpectralDataType.DataType.MSe; break; } } break; } case "WindowSize": { WindowSize = Integer.parseInt(value); break; } } } } //</editor-fold> try { File MSFile = new File(MSFilePath); if (MSFile.exists()) { long time = System.currentTimeMillis(); Logger.getRootLogger().info( "================================================================================================="); Logger.getRootLogger().info("Processing " + MSFilePath + "...."); //Initialize a DIA file data structure DIAPack DiaFile = new DIAPack(MSFile.getAbsolutePath(), NoCPUs); DiaFile.Resume = Resume; DiaFile.SetDataType(dataType); DiaFile.SetParameter(param); //Set DIA isolation window setting if (dataType == SpectralDataType.DataType.DIA_F_Window) { DiaFile.SetWindowSize(WindowSize); } else if (dataType == SpectralDataType.DataType.DIA_V_Window) { for (XYData window : WindowList) { DiaFile.AddVariableWindow(window); } } DiaFile.SaveDIASetting(); DiaFile.SaveParams(); if (Fix) { DiaFile.FixScanidx(); return; } DiaFile.ExportPrecursorPeak = ExportPrecursorPeak; DiaFile.ExportFragmentPeak = ExportFragmentPeak; Logger.getRootLogger().info("Module A: Signal extraction"); //Start DIA signal extraction process to generate pseudo MS/MS files DiaFile.process(); time = System.currentTimeMillis() - time; Logger.getRootLogger().info(MSFilePath + " processed time:" + String.format("%d hour, %d min, %d sec", TimeUnit.MILLISECONDS.toHours(time), TimeUnit.MILLISECONDS.toMinutes(time) - TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(time)), TimeUnit.MILLISECONDS.toSeconds(time) - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(time)))); } else { throw new RuntimeException("file: " + MSFile + "? does not exist!"); } Logger.getRootLogger().info("Job complete"); Logger.getRootLogger().info( "================================================================================================="); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:it.units.malelab.ege.MappingPropertiesExperimenter.java
public static void main(String[] args) throws IOException, InterruptedException, ExecutionException { final int n = 10000; final int nDist = 10000; //prepare problems and methods List<String> problems = Lists.newArrayList("bool-parity5", "bool-mopm3", "sr-keijzer6", "sr-nguyen7", "sr-pagie1", "sr-vladislavleva4", "other-klandscapes3", "other-klandscapes7", "other-text"); List<String> mappers = new ArrayList<>(); for (int gs : new int[] { 64, 128, 256, 512, 1024 }) { mappers.add("ge-" + gs + "-2"); mappers.add("ge-" + gs + "-4"); mappers.add("ge-" + gs + "-8"); mappers.add("ge-" + gs + "-12"); mappers.add("pige-" + gs + "-4"); mappers.add("pige-" + gs + "-8"); mappers.add("pige-" + gs + "-16"); mappers.add("pige-" + gs + "-24"); mappers.add("hge-" + gs + "-0"); mappers.add("whge-" + gs + "-2"); mappers.add("whge-" + gs + "-3"); mappers.add("whge-" + gs + "-5"); }/*from w w w . j av a 2 s .c om*/ mappers.add("sge-0-5"); mappers.add("sge-0-6"); mappers.add("sge-0-7"); mappers.add("sge-0-8"); mappers.clear(); mappers.addAll(Lists.newArrayList("ge-1024-8", "pige-1024-16", "hge-1024-0", "whge-1024-3", "sge-0-6")); PrintStream filePrintStream = null; if (args.length > 0) { filePrintStream = new PrintStream(args[0]); } else { filePrintStream = System.out; } filePrintStream.printf("problem;mapper;genotypeSize;param;property;value%n"); //prepare distances Distance<Node<String>> phenotypeDistance = new CachedDistance<>(new LeavesEdit<String>()); Distance<Sequence> genotypeDistance = new CachedDistance<>(new Hamming()); //iterate for (String problemName : problems) { for (String mapperName : mappers) { System.out.printf("%20.20s, %20.20s", problemName, mapperName); //build problem Problem<String, NumericFitness> problem = null; if (problemName.equals("bool-parity5")) { problem = new Parity(5); } else if (problemName.equals("bool-mopm3")) { problem = new MultipleOutputParallelMultiplier(3); } else if (problemName.equals("sr-keijzer6")) { problem = new HarmonicCurve(); } else if (problemName.equals("sr-nguyen7")) { problem = new Nguyen7(1); } else if (problemName.equals("sr-pagie1")) { problem = new Pagie1(); } else if (problemName.equals("sr-vladislavleva4")) { problem = new Vladislavleva4(1); } else if (problemName.equals("other-klandscapes3")) { problem = new KLandscapes(3); } else if (problemName.equals("other-klandscapes7")) { problem = new KLandscapes(7); } else if (problemName.equals("other-text")) { problem = new Text(); } //build configuration and evolver Mapper mapper = null; int genotypeSize = Integer.parseInt(mapperName.split("-")[1]); int mapperMainParam = Integer.parseInt(mapperName.split("-")[2]); if (mapperName.split("-")[0].equals("ge")) { mapper = new StandardGEMapper<>(mapperMainParam, 1, problem.getGrammar()); } else if (mapperName.split("-")[0].equals("pige")) { mapper = new PiGEMapper<>(mapperMainParam, 1, problem.getGrammar()); } else if (mapperName.split("-")[0].equals("sge")) { mapper = new SGEMapper<>(mapperMainParam, problem.getGrammar()); } else if (mapperName.split("-")[0].equals("hge")) { mapper = new HierarchicalMapper<>(problem.getGrammar()); } else if (mapperName.split("-")[0].equals("whge")) { mapper = new WeightedHierarchicalMapper<>(mapperMainParam, false, true, problem.getGrammar()); } //prepare things Random random = new Random(1); Set<Sequence> genotypes = new LinkedHashSet<>(n); //build genotypes if (mapperName.split("-")[0].equals("sge")) { SGEGenotypeFactory<String> factory = new SGEGenotypeFactory<>((SGEMapper) mapper); while (genotypes.size() < n) { genotypes.add(factory.build(random)); } genotypeSize = factory.getBitSize(); } else { BitsGenotypeFactory factory = new BitsGenotypeFactory(genotypeSize); while (genotypes.size() < n) { genotypes.add(factory.build(random)); } } //build and fill map Multimap<Node<String>, Sequence> multimap = HashMultimap.create(); int progress = 0; for (Sequence genotype : genotypes) { Node<String> phenotype; try { if (mapperName.split("-")[0].equals("sge")) { phenotype = mapper.map((SGEGenotype<String>) genotype, new HashMap<>()); } else { phenotype = mapper.map((BitsGenotype) genotype, new HashMap<>()); } } catch (MappingException e) { phenotype = Node.EMPTY_TREE; } multimap.put(phenotype, genotype); progress = progress + 1; if (progress % Math.round(n / 10) == 0) { System.out.print("."); } } System.out.println(); //compute distances List<Pair<Double, Double>> allDistances = new ArrayList<>(); List<Pair<Double, Double>> allValidDistances = new ArrayList<>(); Multimap<Node<String>, Double> genotypeDistances = ArrayListMultimap.create(); for (Node<String> phenotype : multimap.keySet()) { for (Sequence genotype1 : multimap.get(phenotype)) { for (Sequence genotype2 : multimap.get(phenotype)) { double gDistance = genotypeDistance.d(genotype1, genotype2); genotypeDistances.put(phenotype, gDistance); if (genotypeDistances.get(phenotype).size() > nDist) { break; } } if (genotypeDistances.get(phenotype).size() > nDist) { break; } } } List<Map.Entry<Node<String>, Sequence>> entries = new ArrayList<>(multimap.entries()); Collections.shuffle(entries, random); for (Map.Entry<Node<String>, Sequence> entry1 : entries) { for (Map.Entry<Node<String>, Sequence> entry2 : entries) { double gDistance = genotypeDistance.d(entry1.getValue(), entry2.getValue()); double pDistance = phenotypeDistance.d(entry1.getKey(), entry2.getKey()); allDistances.add(new Pair<>(gDistance, pDistance)); if (!Node.EMPTY_TREE.equals(entry1.getKey()) && !Node.EMPTY_TREE.equals(entry2.getKey())) { allValidDistances.add(new Pair<>(gDistance, pDistance)); } if (allDistances.size() > nDist) { break; } } if (allDistances.size() > nDist) { break; } } //compute properties double invalidity = (double) multimap.get(Node.EMPTY_TREE).size() / (double) genotypes.size(); double redundancy = 1 - (double) multimap.keySet().size() / (double) genotypes.size(); double validRedundancy = redundancy; if (multimap.keySet().contains(Node.EMPTY_TREE)) { validRedundancy = 1 - ((double) multimap.keySet().size() - 1d) / (double) (genotypes.size() - multimap.get(Node.EMPTY_TREE).size()); } double locality = Utils.pearsonCorrelation(allDistances); double validLocality = Utils.pearsonCorrelation(allValidDistances); double[] sizes = new double[multimap.keySet().size()]; double[] meanGenotypeDistances = new double[multimap.keySet().size()]; int invalidIndex = -1; int c = 0; for (Node<String> phenotype : multimap.keySet()) { if (Node.EMPTY_TREE.equals(phenotype)) { invalidIndex = c; } sizes[c] = multimap.get(phenotype).size(); double[] distances = new double[genotypeDistances.get(phenotype).size()]; int k = 0; for (Double distance : genotypeDistances.get(phenotype)) { distances[k] = distance; k = k + 1; } meanGenotypeDistances[c] = StatUtils.mean(distances); c = c + 1; } double nonUniformity = Math.sqrt(StatUtils.variance(sizes)) / StatUtils.mean(sizes); double nonSynonymousity = StatUtils.mean(meanGenotypeDistances) / StatUtils.mean(firsts(allDistances)); double validNonUniformity = nonUniformity; double validNonSynonymousity = nonSynonymousity; if (invalidIndex != -1) { double[] validSizes = new double[multimap.keySet().size() - 1]; double[] validMeanGenotypeDistances = new double[multimap.keySet().size() - 1]; if (invalidIndex > 0) { System.arraycopy(sizes, 0, validSizes, 0, invalidIndex); System.arraycopy(meanGenotypeDistances, 0, validMeanGenotypeDistances, 0, invalidIndex); } System.arraycopy(sizes, invalidIndex + 1, validSizes, invalidIndex, sizes.length - invalidIndex - 1); System.arraycopy(meanGenotypeDistances, invalidIndex + 1, validMeanGenotypeDistances, invalidIndex, meanGenotypeDistances.length - invalidIndex - 1); validNonUniformity = Math.sqrt(StatUtils.variance(validSizes)) / StatUtils.mean(validSizes); validNonSynonymousity = StatUtils.mean(validMeanGenotypeDistances) / StatUtils.mean(firsts(allValidDistances)); } //compute locality filePrintStream.printf("%s;%s;%d;%d;invalidity;%f %n", problemName, mapperName.split("-")[0], genotypeSize, mapperMainParam, invalidity); filePrintStream.printf("%s;%s;%d;%d;redundancy;%f %n", problemName, mapperName.split("-")[0], genotypeSize, mapperMainParam, redundancy); filePrintStream.printf("%s;%s;%d;%d;validRedundancy;%f %n", problemName, mapperName.split("-")[0], genotypeSize, mapperMainParam, validRedundancy); filePrintStream.printf("%s;%s;%d;%d;locality;%f %n", problemName, mapperName.split("-")[0], genotypeSize, mapperMainParam, locality); filePrintStream.printf("%s;%s;%d;%d;validLLocality;%f %n", problemName, mapperName.split("-")[0], genotypeSize, mapperMainParam, validLocality); filePrintStream.printf("%s;%s;%d;%d;nonUniformity;%f %n", problemName, mapperName.split("-")[0], genotypeSize, mapperMainParam, nonUniformity); filePrintStream.printf("%s;%s;%d;%d;validNonUniformity;%f %n", problemName, mapperName.split("-")[0], genotypeSize, mapperMainParam, validNonUniformity); filePrintStream.printf("%s;%s;%d;%d;nonSynonymousity;%f %n", problemName, mapperName.split("-")[0], genotypeSize, mapperMainParam, nonSynonymousity); filePrintStream.printf("%s;%s;%d;%d;validNonSynonymousity;%f %n", problemName, mapperName.split("-")[0], genotypeSize, mapperMainParam, validNonSynonymousity); } } if (filePrintStream != null) { filePrintStream.close(); } }