List of usage examples for java.lang String trim
public String trim()
From source file:org.kuali.student.git.importer.ApplyManualBranchCleanup.java
/** * @param args/*from ww w.ja v a 2 s. co m*/ */ public static void main(String[] args) { if (args.length < 4 || args.length > 7) { usage(); } File inputFile = new File(args[0]); if (!inputFile.exists()) usage(); boolean bare = false; if (args[2].trim().equals("1")) { bare = true; } String remoteName = args[3].trim(); String refPrefix = Constants.R_HEADS; if (args.length == 5) refPrefix = args[4].trim(); String userName = null; String password = null; if (args.length == 6) userName = args[5].trim(); if (args.length == 7) password = args[6].trim(); try { Repository repo = GitRepositoryUtils.buildFileRepository(new File(args[1]).getAbsoluteFile(), false, bare); Git git = new Git(repo); RevWalk rw = new RevWalk(repo); ObjectInserter objectInserter = repo.newObjectInserter(); BufferedReader fileReader = new BufferedReader(new FileReader(inputFile)); String line = fileReader.readLine(); int lineNumber = 1; BatchRefUpdate batch = repo.getRefDatabase().newBatchUpdate(); List<RefSpec> branchesToDelete = new ArrayList<>(); while (line != null) { if (line.startsWith("#") || line.length() == 0) { // skip over comments and blank lines line = fileReader.readLine(); lineNumber++; continue; } String parts[] = line.trim().split(":"); String branchName = parts[0]; Ref branchRef = repo.getRef(refPrefix + "/" + branchName); if (branchRef == null) { log.warn("line: {}, No branch matching {} exists, skipping.", lineNumber, branchName); line = fileReader.readLine(); lineNumber++; continue; } String tagName = null; if (parts.length > 1) tagName = parts[1]; if (tagName != null) { if (tagName.equals("keep")) { log.info("keeping existing branch for {}", branchName); line = fileReader.readLine(); lineNumber++; continue; } if (tagName.equals("tag")) { /* * Shortcut to say make the tag start with the same name as the branch. */ tagName = branchName; } // create a tag RevCommit commit = rw.parseCommit(branchRef.getObjectId()); ObjectId tag = GitRefUtils.insertTag(tagName, commit, objectInserter); batch.addCommand(new ReceiveCommand(null, tag, Constants.R_TAGS + tagName, Type.CREATE)); log.info("converting branch {} into a tag {}", branchName, tagName); } if (remoteName.equals("local")) { batch.addCommand( new ReceiveCommand(branchRef.getObjectId(), null, branchRef.getName(), Type.DELETE)); } else { // if the branch is remote then remember its name so we can batch delete after we have the full list. branchesToDelete.add(new RefSpec(":" + Constants.R_HEADS + branchName)); } line = fileReader.readLine(); lineNumber++; } fileReader.close(); // run the batch update batch.execute(rw, new TextProgressMonitor()); if (!remoteName.equals("local")) { // push the tag to the remote right now log.info("pushing tags to {}", remoteName); PushCommand pushCommand = git.push().setRemote(remoteName).setPushTags() .setProgressMonitor(new TextProgressMonitor()); if (userName != null) pushCommand.setCredentialsProvider(new UsernamePasswordCredentialsProvider(userName, password)); Iterable<PushResult> results = pushCommand.call(); for (PushResult pushResult : results) { if (!pushResult.equals(Result.NEW)) { log.warn("failed to push tag " + pushResult.getMessages()); } } // delete the branches from the remote log.info("pushing branch deletes to remote: {}", remoteName); results = git.push().setRemote(remoteName).setRefSpecs(branchesToDelete) .setProgressMonitor(new TextProgressMonitor()).call(); } objectInserter.release(); rw.release(); } catch (Exception e) { log.error("unexpected Exception ", e); } }
From source file:friendsandfollowers.FilesThreaderFriendsIDsParser.java
public static void main(String[] args) throws ClassNotFoundException, SQLException, JSONException, FileNotFoundException, UnsupportedEncodingException { // Check how many arguments were passed in if ((args == null) || (args.length < 5)) { System.err.println("5 Parameters are required plus one optional " + "parameter to launch a Job."); System.err.println("First: String 'INPUT: DB or /input/path/'"); System.err.println("Second: String 'OUTPUT: /output/path/'"); System.err.println("Third: (int) Total Number Of Jobs"); System.err.println("Fourth: (int) This Job Number"); System.err.println("Fifth: (int) Number of seconds to pause"); System.err.println("Sixth: (int) Number of ids to fetch" + "Provide number which increment by 5000 " + "(5000, 10000, 15000 etc) " + "or -1 to fetch all ids."); System.err.println("Example: fileToRun /input/path/ " + "/output/path/ 10 1 3 75000"); System.exit(-1);//from www. j a v a 2 s .c om } // TODO documentation for command line AppOAuth AppOAuths = new AppOAuth(); Misc helpers = new Misc(); String endpoint = "/friends/ids"; String inputPath = null; try { inputPath = StringEscapeUtils.escapeJava(args[0]); } catch (Exception e) { System.err.println("Argument " + args[0] + " must be an String."); System.exit(-1); } String outputPath = null; try { outputPath = StringEscapeUtils.escapeJava(args[1]); } catch (Exception e) { System.err.println("Argument " + args[1] + " must be an String."); System.exit(-1); } int TOTAL_JOBS = 0; try { TOTAL_JOBS = Integer.parseInt(args[2]); } catch (NumberFormatException e) { System.err.println("Argument " + args[2] + " must be an integer."); System.exit(1); } int JOB_NO = 0; try { JOB_NO = Integer.parseInt(args[3]); } catch (NumberFormatException e) { System.err.println("Argument " + args[3] + " must be an integer."); System.exit(1); } int secondsToPause = 0; try { secondsToPause = Integer.parseInt(args[4]); } catch (NumberFormatException e) { System.err.println("Argument" + args[4] + " must be an integer."); System.exit(-1); } int IDS_TO_FETCH_INT = -1; if (args.length == 6) { try { IDS_TO_FETCH_INT = Integer.parseInt(args[5]); } catch (NumberFormatException e) { System.err.println("Argument" + args[5] + " must be an integer."); System.exit(-1); } } int IDS_TO_FETCH = 0; if (IDS_TO_FETCH_INT > 5000) { float IDS_TO_FETCH_F = (float) IDS_TO_FETCH_INT / 5000; IDS_TO_FETCH = (int) Math.ceil(IDS_TO_FETCH_F); } else if ((IDS_TO_FETCH_INT <= 5000) && (IDS_TO_FETCH_INT > 0)) { IDS_TO_FETCH = 1; } secondsToPause = (TOTAL_JOBS * secondsToPause) - (JOB_NO * secondsToPause); System.out.println("secondsToPause: " + secondsToPause); helpers.pause(secondsToPause); try { int TotalWorkLoad = 0; ArrayList<String> allFiles = null; try { final File folder = new File(inputPath); allFiles = helpers.listFilesForSingleFolder(folder); TotalWorkLoad = allFiles.size(); } catch (Exception e) { System.err.println("Input folder is not exists: " + e.getMessage()); System.exit(-1); } System.out.println("Total Workload is: " + TotalWorkLoad); if (TotalWorkLoad < 1) { System.err.println("No screen names file exists in: " + inputPath); System.exit(-1); } if (TOTAL_JOBS > TotalWorkLoad) { System.err.println("Number of jobs are more than total work" + " load. Please reduce 'Number of jobs' to launch."); System.exit(-1); } float TotalWorkLoadf = TotalWorkLoad; float TOTAL_JOBSf = TOTAL_JOBS; float res = (TotalWorkLoadf / TOTAL_JOBSf); int chunkSize = (int) Math.ceil(res); int offSet = JOB_NO * chunkSize; int chunkSizeToGet = (JOB_NO + 1) * chunkSize; System.out.println("My Share is " + chunkSize); System.out.println(); // Load OAuh User TwitterFactory tf = AppOAuths.loadOAuthUser(endpoint, TOTAL_JOBS, JOB_NO); Twitter twitter = tf.getInstance(); int RemainingCalls = AppOAuths.RemainingCalls; int RemainingCallsCounter = 0; System.out.println("First Time OAuth Remianing Calls: " + RemainingCalls); String Screen_name = AppOAuths.screen_name; System.out.println("First Time Loaded OAuth Screen_name: " + Screen_name); System.out.println(); IDs ids; System.out.println("Going to get friends ids."); // to write output in a file System.out.flush(); if (JOB_NO + 1 == TOTAL_JOBS) { chunkSizeToGet = TotalWorkLoad; } List<String> myFilesShare = allFiles.subList(offSet, chunkSizeToGet); for (String myFile : myFilesShare) { System.out.println("Going to parse file: " + myFile); try (BufferedReader br = new BufferedReader(new FileReader(inputPath + "/" + myFile))) { String line; OUTERMOST: while ((line = br.readLine()) != null) { // process the line. System.out.println("Going to get friends ids of Screen-name / user_id: " + line); System.out.println(); String targetedUser = line.trim(); // tmp long cursor = -1; int idsLoopCounter = 0; int totalIDs = 0; PrintWriter writer = new PrintWriter(outputPath + "/" + targetedUser, "UTF-8"); // call different functions for screen_name and id_str Boolean chckedNumaric = helpers.isNumeric(targetedUser); do { ids = null; try { if (chckedNumaric) { long LongValueTargetedUser = Long.valueOf(targetedUser).longValue(); ids = twitter.getFriendsIDs(LongValueTargetedUser, cursor); } else { ids = twitter.getFriendsIDs(targetedUser, cursor); } } catch (TwitterException te) { // do not throw if user has protected tweets, or // if they deleted their account if (te.getStatusCode() == HttpResponseCode.UNAUTHORIZED || te.getStatusCode() == HttpResponseCode.NOT_FOUND) { System.out.println(targetedUser + " is protected or account is deleted"); } else { System.out.println("Friends Get Exception: " + te.getMessage()); } // If rate limit reached then switch Auth user RemainingCallsCounter++; if (RemainingCallsCounter >= RemainingCalls) { // load auth user tf = AppOAuths.loadOAuthUser(endpoint, TOTAL_JOBS, JOB_NO); twitter = tf.getInstance(); System.out.println( "New Loaded OAuth User " + " Screen_name: " + AppOAuths.screen_name); RemainingCalls = AppOAuths.RemainingCalls; RemainingCallsCounter = 0; System.out.println("New OAuth Remianing Calls: " + RemainingCalls); } // Remove file if ids not found if (totalIDs == 0) { System.out.println("No ids fetched so removing " + "file " + targetedUser); File fileToDelete = new File(outputPath + "/" + targetedUser); fileToDelete.delete(); } System.out.println(); // If error then switch to next user continue OUTERMOST; } if (ids.getIDs().length > 0) { idsLoopCounter++; totalIDs += ids.getIDs().length; System.out.println(idsLoopCounter + ": IDS length: " + ids.getIDs().length); JSONObject responseDetailsJson = new JSONObject(); JSONArray jsonArray = new JSONArray(); for (long id : ids.getIDs()) { jsonArray.put(id); } Object idsJSON = responseDetailsJson.put("ids", jsonArray); writer.println(idsJSON); } // If rate limit reached then switch Auth user RemainingCallsCounter++; if (RemainingCallsCounter >= RemainingCalls) { // load auth user tf = AppOAuths.loadOAuthUser(endpoint, TOTAL_JOBS, JOB_NO); twitter = tf.getInstance(); System.out.println("New Loaded OAuth User Screen_name: " + AppOAuths.screen_name); RemainingCalls = AppOAuths.RemainingCalls; RemainingCallsCounter = 0; System.out.println("New OAuth Remianing Calls: " + RemainingCalls); } if (IDS_TO_FETCH_INT != -1) { if (idsLoopCounter == IDS_TO_FETCH) { break; } } } while ((cursor = ids.getNextCursor()) != 0); writer.close(); System.out.println("Total ids dumped of " + targetedUser + " are: " + totalIDs); // Remove file if ids not found if (totalIDs == 0) { System.out.println("No ids fetched so removing " + "file " + targetedUser); File fileToDelete = new File(outputPath + "/" + targetedUser); fileToDelete.delete(); } System.out.println(); } // while get records from single file } // read my single file catch (IOException e) { System.err.println("Failed to read lines from " + myFile); } // to write output in a file System.out.flush(); } // all my files share } catch (TwitterException te) { // te.printStackTrace(); System.err.println("Failed to get friends' ids: " + te.getMessage()); System.exit(-1); } System.out.println("!!!! DONE !!!!"); // Close System.out for this thread which will // flush and close this thread. System.out.close(); }
From source file:friendsandfollowers.FilesThreaderFollowersIDsParser.java
public static void main(String[] args) throws ClassNotFoundException, SQLException, JSONException, FileNotFoundException, UnsupportedEncodingException { // Check how many arguments were passed in if ((args == null) || (args.length < 5)) { System.err.println("5 Parameters are required plus one optional " + "parameter to launch a Job."); System.err.println("First: String 'INPUT: DB or /input/path/'"); System.err.println("Second: String 'OUTPUT: /output/path/'"); System.err.println("Third: (int) Total Number Of Jobs"); System.err.println("Fourth: (int) This Job Number"); System.err.println("Fifth: (int) Number of seconds to pause"); System.err.println("Sixth: (int) Number of ids to fetch" + "Provide number which increment by 5000 " + "(5000, 10000, 15000 etc) " + "or -1 to fetch all ids."); System.err.println("Example: fileToRun /input/path/ " + "/output/path/ 10 1 3 75000"); System.exit(-1);// w w w . j a v a2 s . c o m } // TODO documentation for command line AppOAuth AppOAuths = new AppOAuth(); Misc helpers = new Misc(); String endpoint = "/followers/ids"; String inputPath = null; try { inputPath = StringEscapeUtils.escapeJava(args[0]); } catch (Exception e) { System.err.println("Argument " + args[0] + " must be an String."); System.exit(-1); } String outputPath = null; try { outputPath = StringEscapeUtils.escapeJava(args[1]); } catch (Exception e) { System.err.println("Argument " + args[1] + " must be an String."); System.exit(-1); } int TOTAL_JOBS = 0; try { TOTAL_JOBS = Integer.parseInt(args[2]); } catch (NumberFormatException e) { System.err.println("Argument " + args[2] + " must be an integer."); System.exit(1); } int JOB_NO = 0; try { JOB_NO = Integer.parseInt(args[3]); } catch (NumberFormatException e) { System.err.println("Argument " + args[3] + " must be an integer."); System.exit(1); } int secondsToPause = 0; try { secondsToPause = Integer.parseInt(args[4]); } catch (NumberFormatException e) { System.err.println("Argument" + args[4] + " must be an integer."); System.exit(-1); } int IDS_TO_FETCH_INT = -1; if (args.length == 6) { try { IDS_TO_FETCH_INT = Integer.parseInt(args[5]); } catch (NumberFormatException e) { System.err.println("Argument" + args[5] + " must be an integer."); System.exit(-1); } } int IDS_TO_FETCH = 0; if (IDS_TO_FETCH_INT > 5000) { float IDS_TO_FETCH_F = (float) IDS_TO_FETCH_INT / 5000; IDS_TO_FETCH = (int) Math.ceil(IDS_TO_FETCH_F); } else if ((IDS_TO_FETCH_INT <= 5000) && (IDS_TO_FETCH_INT > 0)) { IDS_TO_FETCH = 1; } secondsToPause = (TOTAL_JOBS * secondsToPause) - (JOB_NO * secondsToPause); System.out.println("secondsToPause: " + secondsToPause); helpers.pause(secondsToPause); try { int TotalWorkLoad = 0; ArrayList<String> allFiles = null; try { final File folder = new File(inputPath); allFiles = helpers.listFilesForSingleFolder(folder); TotalWorkLoad = allFiles.size(); } catch (Exception e) { System.err.println("Input folder is not exists: " + e.getMessage()); System.exit(-1); } System.out.println("Total Workload is: " + TotalWorkLoad); if (TotalWorkLoad < 1) { System.err.println("No screen names file exists in: " + inputPath); System.exit(-1); } if (TOTAL_JOBS > TotalWorkLoad) { System.err.println("Number of jobs are more than total work" + " load. Please reduce 'Number of jobs' to launch."); System.exit(-1); } float TotalWorkLoadf = TotalWorkLoad; float TOTAL_JOBSf = TOTAL_JOBS; float res = (TotalWorkLoadf / TOTAL_JOBSf); int chunkSize = (int) Math.ceil(res); int offSet = JOB_NO * chunkSize; int chunkSizeToGet = (JOB_NO + 1) * chunkSize; System.out.println("My Share is " + chunkSize); System.out.println(); // Load OAuh User TwitterFactory tf = AppOAuths.loadOAuthUser(endpoint, TOTAL_JOBS, JOB_NO); Twitter twitter = tf.getInstance(); int RemainingCalls = AppOAuths.RemainingCalls; int RemainingCallsCounter = 0; System.out.println("First Time OAuth Remianing Calls: " + RemainingCalls); String Screen_name = AppOAuths.screen_name; System.out.println("First Time Loaded OAuth Screen_name: " + Screen_name); System.out.println(); IDs ids; System.out.println("Going to get followers ids."); // to write output in a file System.out.flush(); if (JOB_NO + 1 == TOTAL_JOBS) { chunkSizeToGet = TotalWorkLoad; } List<String> myFilesShare = allFiles.subList(offSet, chunkSizeToGet); for (String myFile : myFilesShare) { System.out.println("Going to parse file: " + myFile); try (BufferedReader br = new BufferedReader(new FileReader(inputPath + "/" + myFile))) { String line; OUTERMOST: while ((line = br.readLine()) != null) { // process the line. System.out.println("Going to get followers ids of Screen-name / user_id: " + line); System.out.println(); String targetedUser = line.trim(); // tmp long cursor = -1; int idsLoopCounter = 0; int totalIDs = 0; PrintWriter writer = new PrintWriter(outputPath + "/" + targetedUser, "UTF-8"); // call different functions for screen_name and id_str Boolean chckedNumaric = helpers.isNumeric(targetedUser); do { ids = null; try { if (chckedNumaric) { long LongValueTargetedUser = Long.valueOf(targetedUser).longValue(); ids = twitter.getFollowersIDs(LongValueTargetedUser, cursor); } else { ids = twitter.getFollowersIDs(targetedUser, cursor); } } catch (TwitterException te) { // do not throw if user has protected tweets, or // if they deleted their account if (te.getStatusCode() == HttpResponseCode.UNAUTHORIZED || te.getStatusCode() == HttpResponseCode.NOT_FOUND) { System.out.println(targetedUser + " is protected or account is deleted"); } else { System.out.println("Followers Get Exception: " + te.getMessage()); } // If rate limit reached then switch Auth user RemainingCallsCounter++; if (RemainingCallsCounter >= RemainingCalls) { // load auth user tf = AppOAuths.loadOAuthUser(endpoint, TOTAL_JOBS, JOB_NO); twitter = tf.getInstance(); System.out.println( "New Loaded OAuth User " + " Screen_name: " + AppOAuths.screen_name); RemainingCalls = AppOAuths.RemainingCalls; RemainingCallsCounter = 0; System.out.println("New OAuth Remianing Calls: " + RemainingCalls); } // Remove file if ids not found if (totalIDs == 0) { System.out.println("No ids fetched so removing " + "file " + targetedUser); File fileToDelete = new File(outputPath + "/" + targetedUser); fileToDelete.delete(); } System.out.println(); // If error then switch to next user continue OUTERMOST; } if (ids.getIDs().length > 0) { idsLoopCounter++; totalIDs += ids.getIDs().length; System.out.println(idsLoopCounter + ": IDS length: " + ids.getIDs().length); JSONObject responseDetailsJson = new JSONObject(); JSONArray jsonArray = new JSONArray(); for (long id : ids.getIDs()) { jsonArray.put(id); } Object idsJSON = responseDetailsJson.put("ids", jsonArray); writer.println(idsJSON); } // If rate limit reached then switch Auth user RemainingCallsCounter++; if (RemainingCallsCounter >= RemainingCalls) { // load auth user tf = AppOAuths.loadOAuthUser(endpoint, TOTAL_JOBS, JOB_NO); twitter = tf.getInstance(); System.out.println("New Loaded OAuth User Screen_name: " + AppOAuths.screen_name); RemainingCalls = AppOAuths.RemainingCalls; RemainingCallsCounter = 0; System.out.println("New OAuth Remianing Calls: " + RemainingCalls); } if (IDS_TO_FETCH_INT != -1) { if (idsLoopCounter == IDS_TO_FETCH) { break; } } } while ((cursor = ids.getNextCursor()) != 0); writer.close(); System.out.println("Total ids dumped of " + targetedUser + " are: " + totalIDs); // Remove file if ids not found if (totalIDs == 0) { System.out.println("No ids fetched so removing " + "file " + targetedUser); File fileToDelete = new File(outputPath + "/" + targetedUser); fileToDelete.delete(); } System.out.println(); } // while get records from single file } // read my single file catch (IOException e) { System.err.println("Failed to read lines from " + myFile); } // to write output in a file System.out.flush(); } // all my files share } catch (TwitterException te) { // te.printStackTrace(); System.err.println("Failed to get followers' ids: " + te.getMessage()); System.exit(-1); } System.out.println("!!!! DONE !!!!"); // Close System.out for this thread which will // flush and close this thread. System.out.close(); }
From source file:edu.cmu.lti.oaqa.knn4qa.apps.CollectionSplitter.java
public static void main(String[] args) { Options options = new Options(); options.addOption("i", null, true, "Input file"); options.addOption("o", null, true, "Output file prefix"); options.addOption("p", null, true, "Comma separated probabilities e.g., 0.1,0.2,0.7."); options.addOption("n", null, true, "Comma separated part names, e.g., dev,test,train"); CommandLineParser parser = new org.apache.commons.cli.GnuParser(); try {//from w w w . j a va 2 s . co m CommandLine cmd = parser.parse(options, args); InputStream input = null; if (cmd.hasOption("i")) { input = CompressUtils.createInputStream(cmd.getOptionValue("i")); } else { Usage("Specify Input file"); } ArrayList<Double> probs = new ArrayList<Double>(); String[] partNames = null; if (cmd.hasOption("p")) { String parts[] = cmd.getOptionValue("p").split(","); try { double sum = 0; for (String s : parts) { double p = Double.parseDouble(s); if (p <= 0 || p > 1) Usage("All probabilities must be in the range (0,1)"); sum += p; probs.add(p); } if (Math.abs(sum - 1.0) > Float.MIN_NORMAL) { Usage("The sum of probabilities should be equal to 1, but it's: " + sum); } } catch (NumberFormatException e) { Usage("Can't convert some of the probabilities to a floating-point number."); } } else { Usage("Specify part probabilities."); } if (cmd.hasOption("n")) { partNames = cmd.getOptionValue("n").split(","); if (partNames.length != probs.size()) Usage("The number of probabilities is not equal to the number of parts!"); } else { Usage("Specify part names"); } BufferedWriter[] outFiles = new BufferedWriter[partNames.length]; if (cmd.hasOption("o")) { String outPrefix = cmd.getOptionValue("o"); for (int partId = 0; partId < partNames.length; ++partId) { outFiles[partId] = new BufferedWriter(new OutputStreamWriter( CompressUtils.createOutputStream(outPrefix + "_" + partNames[partId] + ".gz"))); } } else { Usage("Specify Output file prefix"); } System.out.println("Using probabilities:"); for (int partId = 0; partId < partNames.length; ++partId) System.out.println(partNames[partId] + " : " + probs.get(partId)); System.out.println("================================================="); XmlIterator inpIter = new XmlIterator(input, YahooAnswersReader.DOCUMENT_TAG); String oneRec = inpIter.readNext(); int docNum = 1; for (; !oneRec.isEmpty(); ++docNum, oneRec = inpIter.readNext()) { double p = Math.random(); if (docNum % 1000 == 0) { System.out.println(String.format("Processed %d documents", docNum)); } BufferedWriter out = null; for (int partId = 0; partId < partNames.length; ++partId) { double pp = probs.get(partId); if (p <= pp || partId + 1 == partNames.length) { out = outFiles[partId]; break; } p -= pp; } oneRec = oneRec.trim() + System.getProperty("line.separator"); out.write(oneRec); } System.out.println(String.format("Processed %d documents", docNum - 1)); // It's important to close all the streams here! for (BufferedWriter f : outFiles) f.close(); } catch (ParseException e) { Usage("Cannot parse arguments"); } catch (Exception e) { System.err.println("Terminating due to an exception: " + e); System.exit(1); } }
From source file:AverageCost.java
public static void main(String[] args) throws FileNotFoundException, IOException { //Directory of the n files String directory_path = "/home/gauss/rgrunitzki/Dropbox/Profissional/UFRGS/Doutorado/Artigo TRI15/SF Experiments/IQ-Learning/"; BufferedReader reader = null; //Line to analyse String line = ""; String csvDivisor = ";"; int totalLines = 1002; int totalRows = 532; String filesToRead[] = new File(directory_path).list(); Arrays.sort(filesToRead);// ww w.ja va 2 s. c om System.out.println(filesToRead.length); List<List<DescriptiveStatistics>> summary = new ArrayList<>(); for (int i = 0; i <= totalLines; i++) { summary.add(new ArrayList<DescriptiveStatistics>()); for (int j = 0; j <= totalRows; j++) { summary.get(i).add(new DescriptiveStatistics()); } } //reads all files for (String file : filesToRead) { reader = new BufferedReader(new FileReader(directory_path + file)); int lineCounter = 0; //reads all file's line while ((line = reader.readLine()) != null) { if (lineCounter > 0) { String[] rows = line.trim().split(csvDivisor); //reads all line's row for (int r = 0; r < rows.length; r++) { summary.get(lineCounter).get(r).addValue(Double.parseDouble(rows[r])); } } lineCounter++; } //System.out.println(file.split("/")[file.split("/").length - 1] + csvDivisor + arithmeticMean(avgCost) + csvDivisor + standardDeviation(avgCost)); } //generate mean and standard deviation; for (List<DescriptiveStatistics> summaryLines : summary) { System.out.println(); for (DescriptiveStatistics summaryLineRow : summaryLines) { System.out.print(summaryLineRow.getMean() + ";" + summaryLineRow.getStandardDeviation() + ";"); } } }
From source file:TerminalMonitor.java
static public void main(String args[]) { DriverPropertyInfo[] required; StringBuffer buffer = new StringBuffer(); Properties props = new Properties(); boolean connected = false; Driver driver;//from w w w. ja va 2 s .c o m String url; int line = 1; // Mark current input line if (args.length < 1) { System.out.println("Syntax: <java -Djdbc.drivers=DRIVER_NAME " + "TerminalMonitor JDBC_URL>"); return; } url = args[0]; // We have to get a reference to the driver so we can // find out what values to prompt the user for in order // to make a connection. try { driver = DriverManager.getDriver(url); } catch (SQLException e) { e.printStackTrace(); System.err.println("Unable to find a driver for the specified " + "URL."); System.err.println("Make sure you passed the jdbc.drivers " + "property on the command line to specify " + "the driver to be used."); return; } try { required = driver.getPropertyInfo(url, props); } catch (SQLException e) { e.printStackTrace(); System.err.println("Unable to get driver property information."); return; } input = new BufferedReader(new InputStreamReader(System.in)); // some drivers do not implement this properly // if that is the case, prompt for user name and password try { if (required.length < 1) { props.put("user", prompt("user: ")); props.put("password", prompt("password: ")); } else { // for each required attribute in the driver property info // prompt the user for the value for (int i = 0; i < required.length; i++) { if (!required[i].required) { continue; } props.put(required[i].name, prompt(required[i].name + ": ")); } } } catch (IOException e) { e.printStackTrace(); System.err.println("Unable to read property info."); return; } // Make the connection. try { connection = DriverManager.getConnection(url, props); } catch (SQLException e) { e.printStackTrace(); System.err.println("Unable to connect to the database."); } connected = true; System.out.println("Connected to " + url); // Enter into a user input loop while (connected) { String tmp, cmd; // Print a prompt if (line == 1) { System.out.print("TM > "); } else { System.out.print(line + " -> "); } System.out.flush(); // Get the next line of input try { tmp = input.readLine(); } catch (java.io.IOException e) { e.printStackTrace(); return; } // Get rid of extra space in the command cmd = tmp.trim(); // The user wants to commit pending transactions if (cmd.equals("commit")) { try { connection.commit(); System.out.println("Commit successful."); } catch (SQLException e) { System.out.println("Error in commit: " + e.getMessage()); } buffer = new StringBuffer(); line = 1; } // The user wants to execute the current buffer else if (cmd.equals("go")) { if (!buffer.equals("")) { try { executeStatement(buffer); } catch (SQLException e) { System.out.println(e.getMessage()); } } buffer = new StringBuffer(); line = 1; continue; } // The user wants to quit else if (cmd.equals("quit")) { connected = false; continue; } // The user wants to clear the current buffer else if (cmd.equals("reset")) { buffer = new StringBuffer(); line = 1; continue; } // The user wants to abort a pending transaction else if (cmd.equals("rollback")) { try { connection.rollback(); System.out.println("Rollback successful."); } catch (SQLException e) { System.out.println("An error occurred during rollback: " + e.getMessage()); } buffer = new StringBuffer(); line = 1; } // The user wants version info else if (cmd.startsWith("show")) { DatabaseMetaData meta; try { meta = connection.getMetaData(); cmd = cmd.substring(5, cmd.length()).trim(); if (cmd.equals("version")) { showVersion(meta); } else { System.out.println("show version"); // Bad arg } } catch (SQLException e) { System.out.println("Failed to load meta data: " + e.getMessage()); } buffer = new StringBuffer(); line = 1; } // The input that is not a keyword should appended be to the buffer else { buffer.append(" " + tmp); line++; continue; } } try { connection.close(); } catch (SQLException e) { System.out.println("Error closing connection: " + e.getMessage()); } System.out.println("Connection closed."); }
From source file:DIA_Umpire_Quant.DIA_Umpire_ExtLibSearch.java
/** * @param args the command line arguments *//*from w w w.j ava2s . c o m*/ public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println("DIA-Umpire targeted re-extraction analysis using external library (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_ExtLibSearch.jar diaumpire_module.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_extlibsearch.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; String ExternalLibPath = ""; String ExternalLibDecoyTag = "DECOY"; float ExtProbThreshold = 0.99f; float RTWindow_Ext = -1f; 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 "Fasta": { tandemPara.FastaPath = value; break; } case "DecoyPrefix": { if (!"".equals(value)) { tandemPara.DecoyPrefix = value; } break; } case "ExternalLibPath": { ExternalLibPath = value; break; } case "ExtProbThreshold": { ExtProbThreshold = Float.parseFloat(value); break; } case "RTWindow_Ext": { RTWindow_Ext = Float.parseFloat(value); break; } case "ExternalLibDecoyTag": { ExternalLibDecoyTag = value; if (ExternalLibDecoyTag.endsWith("_")) { ExternalLibDecoyTag = ExternalLibDecoyTag.substring(0, ExternalLibDecoyTag.length() - 1); } break; } } } } //</editor-fold> //Initialize PTM manager using compomics library PTMManager.GetInstance(); //Check if the fasta file can be found if (!new File(tandemPara.FastaPath).exists()) { Logger.getRootLogger().info("Fasta file :" + tandemPara.FastaPath + " cannot be found, the process will be terminated, please check."); System.exit(1); } //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()); } for (File fileEntry : AssignFiles.values()) { String mzXMLFile = fileEntry.getAbsolutePath(); if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) { DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs); 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 + "...."); //If the serialization file for ID file existed if (DiaFile.ReadSerializedLCMSID()) { DiaFile.IDsummary.ReduceMemoryUsage(); DiaFile.IDsummary.FastaPath = tandemPara.FastaPath; FileList.add(DiaFile); } } } //<editor-fold defaultstate="collapsed" desc="Targeted re-extraction using external library"> //External library search Logger.getRootLogger().info("Targeted extraction using external library"); //Read exteranl library FragmentLibManager ExlibManager = FragmentLibManager.ReadFragmentLibSerialization(WorkFolder, FilenameUtils.getBaseName(ExternalLibPath)); if (ExlibManager == null) { ExlibManager = new FragmentLibManager(FilenameUtils.getBaseName(ExternalLibPath)); //Import traML file ExlibManager.ImportFragLibByTraML(ExternalLibPath, ExternalLibDecoyTag); //Check if there are decoy spectra ExlibManager.CheckDecoys(); //ExlibManager.ImportFragLibBySPTXT(ExternalLibPath); ExlibManager.WriteFragmentLibSerialization(WorkFolder); } Logger.getRootLogger() .info("No. of peptide ions in external lib:" + ExlibManager.PeptideFragmentLib.size()); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); } //Generate RT mapping RTMappingExtLib RTmap = new RTMappingExtLib(diafile.IDsummary, ExlibManager, diafile.GetParameter()); RTmap.GenerateModel(); RTmap.GenerateMappedPepIon(); diafile.BuildStructure(); diafile.MS1FeatureMap.ReadPeakCluster(); diafile.GenerateMassCalibrationRTMap(); //Perform targeted re-extraction diafile.TargetedExtractionQuant(false, ExlibManager, ExtProbThreshold, RTWindow_Ext); diafile.MS1FeatureMap.ClearAllPeaks(); diafile.IDsummary.ReduceMemoryUsage(); //Remove target IDs below the defined probability threshold diafile.IDsummary.RemoveLowProbMappedIon(ExtProbThreshold); diafile.ExportID(); diafile.ClearStructure(); Logger.getRootLogger().info("Peptide ions: " + diafile.IDsummary.GetPepIonList().size() + " Mapped ions: " + diafile.IDsummary.GetMappedPepIonList().size()); } //</editor-fold> Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); }
From source file:de.tudarmstadt.ukp.csniper.resbuild.EvaluationItemFixer.java
public static void main(String[] args) { connect(HOST, DATABASE, USER, PASSWORD); Map<Integer, String> items = new HashMap<Integer, String>(); Map<Integer, String> failed = new HashMap<Integer, String>(); // fetch coveredTexts of dubious items and clean it PreparedStatement select = null; try {//from w w w . java 2 s. c o m StringBuilder selectQuery = new StringBuilder(); selectQuery.append("SELECT * FROM EvaluationItem "); selectQuery.append("WHERE LOCATE(coveredText, ' ') > 0 "); selectQuery.append("OR LOCATE('" + LRB + "', coveredText) > 0 "); selectQuery.append("OR LOCATE('" + RRB + "', coveredText) > 0 "); selectQuery.append("OR LEFT(coveredText, 1) = ' ' "); selectQuery.append("OR RIGHT(coveredText, 1) = ' ' "); select = connection.prepareStatement(selectQuery.toString()); log.info("Running query [" + selectQuery.toString() + "]."); ResultSet rs = select.executeQuery(); while (rs.next()) { int id = rs.getInt("id"); String coveredText = rs.getString("coveredText"); try { // special handling of double whitespace: in this case, re-fetch the text if (coveredText.contains(" ")) { coveredText = retrieveCoveredText(rs.getString("collectionId"), rs.getString("documentId"), rs.getInt("beginOffset"), rs.getInt("endOffset")); } // replace bracket placeholders and trim the text coveredText = StringUtils.replace(coveredText, LRB, "("); coveredText = StringUtils.replace(coveredText, RRB, ")"); coveredText = coveredText.trim(); items.put(id, coveredText); } catch (IllegalArgumentException e) { failed.put(id, e.getMessage()); } } } catch (SQLException e) { log.error("Exception while selecting: " + e.getMessage()); } finally { closeQuietly(select); } // write logs BufferedWriter bwf = null; BufferedWriter bws = null; try { bwf = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(new File(LOG_FAILED)), "UTF-8")); for (Entry<Integer, String> e : failed.entrySet()) { bwf.write(e.getKey() + " - " + e.getValue() + "\n"); } bws = new BufferedWriter( new OutputStreamWriter(new FileOutputStream(new File(LOG_SUCCESSFUL)), "UTF-8")); for (Entry<Integer, String> e : items.entrySet()) { bws.write(e.getKey() + " - " + e.getValue() + "\n"); } } catch (IOException e) { log.error("Got an IOException while writing the log files."); } finally { IOUtils.closeQuietly(bwf); IOUtils.closeQuietly(bws); } log.info("Texts for [" + items.size() + "] items need to be cleaned up."); // update the dubious items with the cleaned coveredText PreparedStatement update = null; try { String updateQuery = "UPDATE EvaluationItem SET coveredText = ? WHERE id = ?"; update = connection.prepareStatement(updateQuery); int i = 0; for (Entry<Integer, String> e : items.entrySet()) { int id = e.getKey(); String coveredText = e.getValue(); // update item in database update.setString(1, coveredText); update.setInt(2, id); update.executeUpdate(); log.debug("Updating " + id + " with [" + coveredText + "]"); // show percentage of updated items i++; int part = (int) Math.ceil((double) items.size() / 100); if (i % part == 0) { log.info(i / part + "% finished (" + i + "/" + items.size() + ")."); } } } catch (SQLException e) { log.error("Exception while updating: " + e.getMessage()); } finally { closeQuietly(update); } closeQuietly(connection); }
From source file:edu.harvard.liblab.ecru.LoadCsvData.java
/** * @param args/*from w ww . j ava 2 s . co m*/ */ public static void main(String[] args) { if (args.length > 7 | args.length == 0 || !args[0].equals("-f") || !args[2].equals("-u") || !args[4].equals("-i")) { System.err.println(USAGE); System.exit(1); } String filename = args[1].trim(); url = args[3].trim(); needsPrefix = !args[5].equals("unique"); isVerbose = (args.length == 7 && args[6].equals("-v")); System.out.println("Loading data from " + filename + " " + (needsPrefix ? "IDs will be prefixed " : " ")); long start = System.currentTimeMillis(); boolean isReading = false; CSVPrinter printer = null; CSVFormat format = CSVFormat.EXCEL.withHeader().withDelimiter(',').withAllowMissingColumnNames(true); CSVParser parser; try { if (isVerbose) { printer = new CSVPrinter(System.err, format.withDelimiter('|')); } parser = CSVParser.parse(new File(filename), Charset.forName("UTF-8"), format); solrSrvr = SingletonSolrServer.getSolrServer(url); for (CSVRecord record : parser) { numRecs++; HashMap<String, String> recMap = new HashMap<String, String>(); for (String field : FIELDS) { String value = null; try { value = record.get(field); } catch (IllegalArgumentException e) { if (e.getMessage().indexOf("expected one of") == -1) { e.printStackTrace(); System.exit(1); } } value = value == null ? "" : value.trim(); recMap.put(field, value); } String id = recMap.get("ID"); if (id.isEmpty()) { if (isVerbose) { System.err.println("Record missing ID: "); printer.printRecord(record); } } else { String type = recMap.get("Type"); SolrDocument sdoc = getDocFromSolr(recMap.get("ID")); try { if (type.toLowerCase().equals("course")) { processCourse(recMap, sdoc); isReading = false; } else { if (!isReading) { addUpdateCommit(); // just in case the preceeding course(s) are related } processReading(recMap, sdoc); isReading = true; } } catch (Exception e) { if (isVerbose) { System.err.println("Record # " + numRecs + " not used:\n\t" + e.getMessage()); } errRecs++; } } if (beans.size() > 20) { addUpdateCommit(); } } parser.close(); if (beans.size() > 0 || docUpdates.size() > 0) { addUpdateCommit(); } } catch (FileNotFoundException e) { System.err.println(filename + " not found"); System.exit(1); } catch (Exception e) { e.printStackTrace(); System.exit(1); } long end = System.currentTimeMillis(); long courseTime = (end - start) / (long) 1000; try { solrSrvr.optimize(); } catch (SolrServerException e) { e.printStackTrace(); System.exit(1); } catch (IOException e) { e.printStackTrace(); System.exit(1); } System.out.println(numRecs + " records found, of which " + errRecs + " had a problem; time: " + courseTime + " seconds " + ((courseTime > 60) ? ("(" + (courseTime / (long) 60) + " minutes)") : "")); System.exit(0); }
From source file:DIA_Umpire_Quant.DIA_Umpire_IntLibSearch.java
/** * @param args the command line arguments *///w ww . ja v a2 s .c o m public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println("DIA-Umpire targeted re-extraction analysis using internal library (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, the correct format should be : java -jar -Xmx10G DIA_Umpire_IntLibSearch.jar diaumpire_module.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_intlibsearch.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; String InternalLibID = ""; float ProbThreshold = 0.99f; float RTWindow_Int = -1f; float Freq = 0f; int TopNFrag = 6; 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 "InternalLibID": { InternalLibID = value; break; } case "RTWindow_Int": { RTWindow_Int = Float.parseFloat(value); break; } case "ProbThreshold": { ProbThreshold = Float.parseFloat(value); break; } case "TopNFrag": { TopNFrag = Integer.parseInt(value); break; } case "Freq": { Freq = Float.parseFloat(value); break; } case "Fasta": { tandemPara.FastaPath = value; break; } } } } //</editor-fold> //Initialize PTM manager using compomics library PTMManager.GetInstance(); //Check if the fasta file can be found if (!new File(tandemPara.FastaPath).exists()) { Logger.getRootLogger().info("Fasta file :" + tandemPara.FastaPath + " cannot be found, the process will be terminated, please check."); System.exit(1); } //Generate DIA file list ArrayList<DIAPack> FileList = new ArrayList<>(); try { 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()); } for (File fileEntry : AssignFiles.values()) { String mzXMLFile = fileEntry.getAbsolutePath(); if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) { DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs); 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 + "...."); //If the serialization file for ID file existed if (DiaFile.ReadSerializedLCMSID()) { DiaFile.IDsummary.ReduceMemoryUsage(); DiaFile.IDsummary.FastaPath = tandemPara.FastaPath; FileList.add(DiaFile); } } } //<editor-fold defaultstate="collapsed" desc="Targete re-extraction using internal library"> Logger.getRootLogger().info( "================================================================================================="); if (FileList.size() > 1) { Logger.getRootLogger().info("Targeted re-extraction using internal library"); FragmentLibManager libManager = FragmentLibManager.ReadFragmentLibSerialization(WorkFolder, InternalLibID); if (libManager == null) { Logger.getRootLogger().info("Building internal spectral library"); libManager = new FragmentLibManager(InternalLibID); ArrayList<LCMSID> LCMSIDList = new ArrayList<>(); for (DIAPack dia : FileList) { LCMSIDList.add(dia.IDsummary); } libManager.ImportFragLibTopFrag(LCMSIDList, Freq, TopNFrag); libManager.WriteFragmentLibSerialization(WorkFolder); } libManager.ReduceMemoryUsage(); Logger.getRootLogger() .info("Building retention time prediction model and generate candidate peptide list"); for (int i = 0; i < FileList.size(); i++) { FileList.get(i).IDsummary.ClearMappedPep(); } for (int i = 0; i < FileList.size(); i++) { for (int j = i + 1; j < FileList.size(); j++) { RTAlignedPepIonMapping alignment = new RTAlignedPepIonMapping(WorkFolder, FileList.get(i).GetParameter(), FileList.get(i).IDsummary, FileList.get(j).IDsummary); alignment.GenerateModel(); alignment.GenerateMappedPepIon(); } FileList.get(i).ExportID(); FileList.get(i).IDsummary = null; } Logger.getRootLogger().info("Targeted matching........"); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); } if (!diafile.IDsummary.GetMappedPepIonList().isEmpty()) { diafile.UseMappedIon = true; diafile.FilterMappedIonByProb = false; diafile.BuildStructure(); diafile.MS1FeatureMap.ReadPeakCluster(); diafile.MS1FeatureMap.ClearMonoisotopicPeakOfCluster(); diafile.GenerateMassCalibrationRTMap(); diafile.TargetedExtractionQuant(false, libManager, ProbThreshold, RTWindow_Int); diafile.MS1FeatureMap.ClearAllPeaks(); diafile.IDsummary.ReduceMemoryUsage(); diafile.IDsummary.RemoveLowProbMappedIon(ProbThreshold); diafile.ExportID(); Logger.getRootLogger().info("Peptide ions: " + diafile.IDsummary.GetPepIonList().size() + " Mapped ions: " + diafile.IDsummary.GetMappedPepIonList().size()); diafile.ClearStructure(); } diafile.IDsummary = null; System.gc(); } Logger.getRootLogger().info( "================================================================================================="); } //</editor-fold> Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }