List of usage examples for java.io FileWriter write
public void write(int c) throws IOException
From source file:eu.smartfp7.foursquare.AttendanceCrawler.java
/** * The main takes an undefined number of cities as arguments, then initializes * the specific crawling of all the trending venues of these cities. * The trending venues must have been previously identified using the `DownloadPages` * program./*from ww w .j a v a 2 s . c o m*/ * * Current valid cities are: london, amsterdam, goldcoast, sanfrancisco. * */ public static void main(String[] args) throws Exception { Settings settings = Settings.getInstance(); String folder = settings.getFolder(); // We keep info and error logs, so that we know what happened in case // of incoherence in the time series. Map<String, FileWriter> info_logs = new HashMap<String, FileWriter>(); Map<String, FileWriter> error_logs = new HashMap<String, FileWriter>(); // For each city we monitor, we store the venue IDs that we got from // a previous crawl. Map<String, Collection<String>> city_venues = new HashMap<String, Collection<String>>(); // Contains the epoch time when the last API call has been made for each // venue. Ensures that we get data only once each hour. Map<String, Long> venue_last_call = new HashMap<String, Long>(); // Contains the epoch time when we last checked if time series were broken // for each city. // We do these checks once every day before the batch forecasting begins. Map<String, Long> sanity_checks = new HashMap<String, Long>(); // We also keep in memory the number of checkins for the last hour for // each venue. Map<String, Integer> venue_last_checkin = new HashMap<String, Integer>(); Map<Long, Integer> APICallsCount = new HashMap<Long, Integer>(); DateFormat df = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss"); int total_venues = 0; long total_calls = 0; long time_spent_on_API = 0; for (String c : args) { settings.checkFileHierarchy(c); city_venues.put(c, loadVenues(c)); total_venues += city_venues.get(c).size(); info_logs.put(c, new FileWriter(folder + c + File.separator + "log" + File.separator + "info.log", true)); error_logs.put(c, new FileWriter(folder + c + File.separator + "log" + File.separator + "error.log", true)); Calendar cal = Calendar.getInstance(); info_logs.get(c).write("[" + df.format(cal.getTime()) + "] Crawler initialization for " + c + ". " + city_venues.get(c).size() + " venues loaded.\n"); info_logs.get(c).flush(); // If we interrupted the program for some reason, we can get back // the in-memory data. // Important: the program must not be interrupted for more than one // hour, or we will lose time series data. for (String venue_id : city_venues.get(c)) { String ts_file = folder + c + File.separator + "attendances_crawl" + File.separator + venue_id + ".ts"; if (new File(ts_file).exists()) { BufferedReader buffer = new BufferedReader(new FileReader(ts_file)); String mem = null, line = null; for (; (line = buffer.readLine()) != null; mem = line) ; buffer.close(); if (mem == null) continue; String[] tmp = mem.split(","); venue_last_call.put(venue_id, df.parse(tmp[0]).getTime()); venue_last_checkin.put(venue_id, Integer.parseInt(tmp[3])); VenueUtil.fixBrokenTimeSeriesVenue(new File(ts_file)); } // if } // for sanity_checks.put(c, cal.getTimeInMillis()); } // for if (total_venues > 5000) { System.out.println( "Too much venues for a single API account (max 5000).\nPlease create a new Foursquare API account and use these credentials.\nExiting now."); return; } while (true) { for (String c : args) { // We create a FIFO queue and pop venue IDs one at a time. LinkedList<String> city_venues_buffer = new LinkedList<String>(city_venues.get(c)); String venue_id = null; // Artificial wait to avoid processors looping at 100% of their capacity // when there is no more venues to crawl for the current hour. Thread.sleep(3000); while ((venue_id = city_venues_buffer.pollFirst()) != null) { // We get the current time according to the city's time zone Calendar cal = Calendar.getInstance(); cal.add(Calendar.MILLISECOND, TimeZone.getTimeZone(settings.getCityTimezone(c)).getOffset(cal.getTime().getTime()) - Calendar.getInstance().getTimeZone().getOffset(cal.getTime().getTime())); //TimeZone.getTimeZone("Europe/London").getOffset(cal.getTime().getTime())); long current_time = DateUtils.truncate(cal.getTime(), Calendar.HOUR).getTime(); // We query Foursquare only once per hour per venue. if (venue_last_call.get(venue_id) != null && current_time < venue_last_call.get(venue_id) + 3600000) continue; intelligentWait(total_venues, cal.getTime().getTime(), (total_calls == 0 ? 0 : Math.round(time_spent_on_API / total_calls))); Venue venue = null; try { long beforeCall = System.currentTimeMillis(); venue = new Venue(getFoursquareVenueById(venue_id, c)); // If there is no last call, this is the beginning of the time series // for this venue. We get the number of people "here now" to initialize // the series. if (venue_last_call.get(venue_id) == null) { /** TODO: by doing this, we keep a representation of the venue dating from the beginning * of the specific crawl. we might want to change this and update this file once * in a while. */ FileWriter info = new FileWriter(folder + c + File.separator + "foursquare_venues" + File.separator + venue_id + ".info"); info.write(venue.getFoursquareJson()); info.close(); FileWriter out = new FileWriter(folder + c + File.separator + "attendances_crawl" + File.separator + venue_id + ".ts"); out.write("Date,here_now,hour_checkins,total_checkins\n"); out.write(df.format(current_time) + "," + venue.getHereNow() + "," + venue.getHereNow() + "," + venue.getCheckincount() + "\n"); out.close(); } else { FileWriter out = new FileWriter(folder + c + File.separator + "attendances_crawl" + File.separator + venue_id + ".ts", true); int checks = venue.getCheckincount() - venue_last_checkin.get(venue_id); out.write(df.format(current_time) + "," + venue.getHereNow() + "," + Integer.toString(checks) + "," + venue.getCheckincount() + "\n"); out.close(); } if (APICallsCount.get(current_time) == null) APICallsCount.put(current_time, 1); else APICallsCount.put(current_time, APICallsCount.get(current_time) + 1); total_calls++; venue_last_call.put(venue_id, current_time); venue_last_checkin.put(venue_id, venue.getCheckincount()); time_spent_on_API += System.currentTimeMillis() - beforeCall; } catch (Exception e) { // If something bad happens (crawler not available, IO error, ...), we put the // venue_id in the FIFO queue so that it gets reevaluated later. //e.printStackTrace(); error_logs.get(c) .write("[" + df.format(cal.getTime().getTime()) + "] Error with venue " + venue_id + " (" + e.getMessage() + "). " + APICallsCount.get(current_time) + " API calls so far this hour, " + city_venues_buffer.size() + " venues remaining in the buffer.\n"); error_logs.get(c).flush(); System.out.println("[" + df.format(cal.getTime().getTime()) + "] " + c + " -- " + APICallsCount.get(current_time) + " API calls // " + city_venues_buffer.size() + " venues remaining " + " (" + e.getMessage() + ")"); if (e instanceof FoursquareAPIException) if (((FoursquareAPIException) e).getHttp_code().equals("400") && ((FoursquareAPIException) e).getError_detail() .equals("Venue " + venue_id + " has been deleted")) { city_venues.get(c).remove(venue_id); removeVenue(venue_id, c); } else city_venues_buffer.add(venue_id); continue; } } // while // Every day between 0am and 2am, we repair all the broken time series (if there // is something to repair). Calendar cal = Calendar.getInstance(); if (city_venues_buffer.peekFirst() == null && (cal.getTimeInMillis() - sanity_checks.get(c)) >= 86400000 && cal.get(Calendar.HOUR_OF_DAY) < 2) { VenueUtil.fixBrokenTimeSeriesCity(c, folder); sanity_checks.put(c, cal.getTimeInMillis()); info_logs.get(c).write("[" + df.format(cal.getTime()) + "] Sanity check OK.\n"); info_logs.get(c).flush(); } } // for } // while }
From source file:com.joliciel.frenchTreebank.FrenchTreebank.java
/** * @param args/*from ww w . j a v a2 s .c o m*/ */ public static void main(String[] args) throws Exception { String command = args[0]; String outFilePath = ""; String outDirPath = ""; String treebankPath = ""; String ftbFileName = ""; String rawTextDir = ""; String queryPath = ""; String sentenceNumber = null; boolean firstArg = true; for (String arg : args) { if (firstArg) { firstArg = false; continue; } int equalsPos = arg.indexOf('='); String argName = arg.substring(0, equalsPos); String argValue = arg.substring(equalsPos + 1); if (argName.equals("outfile")) outFilePath = argValue; else if (argName.equals("outdir")) outDirPath = argValue; else if (argName.equals("ftbFileName")) ftbFileName = argValue; else if (argName.equals("treebank")) treebankPath = argValue; else if (argName.equals("sentence")) sentenceNumber = argValue; else if (argName.equals("query")) queryPath = argValue; else if (argName.equals("rawTextDir")) rawTextDir = argValue; else throw new RuntimeException("Unknown argument: " + argName); } TalismaneServiceLocator talismaneServiceLocator = TalismaneServiceLocator.getInstance(); TreebankServiceLocator locator = TreebankServiceLocator.getInstance(talismaneServiceLocator); if (treebankPath.length() == 0) locator.setDataSourcePropertiesFile("jdbc-live.properties"); if (command.equals("search")) { final SearchService searchService = locator.getSearchService(); final XmlPatternSearch search = searchService.newXmlPatternSearch(); search.setXmlPatternFile(queryPath); List<SearchResult> searchResults = search.perform(); FileWriter fileWriter = new FileWriter(outFilePath); for (SearchResult searchResult : searchResults) { String lineToWrite = ""; Sentence sentence = searchResult.getSentence(); Phrase phrase = searchResult.getPhrase(); lineToWrite += sentence.getFile().getFileName() + "|"; lineToWrite += sentence.getSentenceNumber() + "|"; List<PhraseUnit> phraseUnits = searchResult.getPhraseUnits(); LOG.debug("Phrase: " + phrase.getId()); for (PhraseUnit phraseUnit : phraseUnits) lineToWrite += phraseUnit.getLemma().getText() + "|"; lineToWrite += phrase.getText(); fileWriter.write(lineToWrite + "\n"); } fileWriter.flush(); fileWriter.close(); } else if (command.equals("load")) { final TreebankService treebankService = locator.getTreebankService(); final TreebankSAXParser parser = new TreebankSAXParser(); parser.setTreebankService(treebankService); parser.parseDocument(treebankPath); } else if (command.equals("loadAll")) { final TreebankService treebankService = locator.getTreebankService(); File dir = new File(treebankPath); String firstFile = null; if (args.length > 2) firstFile = args[2]; String[] files = dir.list(); if (files == null) { throw new RuntimeException("Not a directory or no children: " + treebankPath); } else { boolean startProcessing = true; if (firstFile != null) startProcessing = false; for (int i = 0; i < files.length; i++) { if (!startProcessing && files[i].equals(firstFile)) startProcessing = true; if (startProcessing) { String filePath = args[1] + "/" + files[i]; LOG.debug(filePath); final TreebankSAXParser parser = new TreebankSAXParser(); parser.setTreebankService(treebankService); parser.parseDocument(filePath); } } } } else if (command.equals("loadRawText")) { final TreebankService treebankService = locator.getTreebankService(); final TreebankRawTextAssigner assigner = new TreebankRawTextAssigner(); assigner.setTreebankService(treebankService); assigner.setRawTextDirectory(rawTextDir); assigner.loadRawText(); } else if (command.equals("tokenize")) { Writer csvFileWriter = null; if (outFilePath != null && outFilePath.length() > 0) { if (outFilePath.lastIndexOf("/") > 0) { String outputDirPath = outFilePath.substring(0, outFilePath.lastIndexOf("/")); File outputDir = new File(outputDirPath); outputDir.mkdirs(); } File csvFile = new File(outFilePath); csvFile.delete(); csvFile.createNewFile(); csvFileWriter = new BufferedWriter( new OutputStreamWriter(new FileOutputStream(csvFile, false), "UTF8")); } try { final TreebankService treebankService = locator.getTreebankService(); TreebankExportService treebankExportService = locator.getTreebankExportServiceLocator() .getTreebankExportService(); TreebankUploadService treebankUploadService = locator.getTreebankUploadServiceLocator() .getTreebankUploadService(); TreebankReader treebankReader = null; if (treebankPath.length() > 0) { File treebankFile = new File(treebankPath); if (sentenceNumber != null) treebankReader = treebankUploadService.getXmlReader(treebankFile, sentenceNumber); else treebankReader = treebankUploadService.getXmlReader(treebankFile); } else { treebankReader = treebankService.getDatabaseReader(TreebankSubSet.ALL, 0); } TokeniserAnnotatedCorpusReader reader = treebankExportService .getTokeniserAnnotatedCorpusReader(treebankReader, csvFileWriter); while (reader.hasNextTokenSequence()) { TokenSequence tokenSequence = reader.nextTokenSequence(); List<Integer> tokenSplits = tokenSequence.getTokenSplits(); String sentence = tokenSequence.getText(); LOG.debug(sentence); int currentPos = 0; StringBuilder sb = new StringBuilder(); for (int split : tokenSplits) { if (split == 0) continue; String token = sentence.substring(currentPos, split); sb.append('|'); sb.append(token); currentPos = split; } LOG.debug(sb.toString()); } } finally { csvFileWriter.flush(); csvFileWriter.close(); } } else if (command.equals("export")) { if (outDirPath.length() == 0) throw new RuntimeException("Parameter required: outdir"); File outDir = new File(outDirPath); outDir.mkdirs(); final TreebankService treebankService = locator.getTreebankService(); FrenchTreebankXmlWriter xmlWriter = new FrenchTreebankXmlWriter(); xmlWriter.setTreebankService(treebankService); if (ftbFileName.length() == 0) { xmlWriter.write(outDir); } else { TreebankFile ftbFile = treebankService.loadTreebankFile(ftbFileName); String fileName = ftbFileName.substring(ftbFileName.lastIndexOf('/') + 1); File xmlFile = new File(outDir, fileName); xmlFile.delete(); xmlFile.createNewFile(); Writer xmlFileWriter = new BufferedWriter( new OutputStreamWriter(new FileOutputStream(xmlFile, false), "UTF8")); xmlWriter.write(xmlFileWriter, ftbFile); xmlFileWriter.flush(); xmlFileWriter.close(); } } else { throw new RuntimeException("Unknown command: " + command); } LOG.debug("========== END ============"); }
From source file:com.icesoft.faces.webapp.parser.TagToComponentMap.java
/** * Main method for when this class is run to build the serialized data from * a set of TLDS./*from w w w . j a v a 2 s . c om*/ * * @param args The runtime arguements. */ public static void main(String args[]) { /* arg[0] is "new" to create serialzed data or 'old' to read serialized data arg[1] is filename for serialized data; arg[2...] are tld's to process */ FileInputStream tldFile = null; TagToComponentMap map = new TagToComponentMap(); if (args[0].equals("new")) { // Build new component map from tlds and serialize it; for (int i = 2; i < args.length; i++) { try { tldFile = new FileInputStream(args[i]); map.addTagAttrib((InputStream) tldFile); } catch (IOException e) { e.printStackTrace(); return; } } try { FileOutputStream fos = new FileOutputStream(args[1]); ObjectOutputStream oos = new ObjectOutputStream(fos); oos.writeObject(map); oos.flush(); oos.close(); } catch (Exception e) { e.printStackTrace(); } } else if (args[0].equals("old")) { // Build component from serialized data; try { FileInputStream fis = new FileInputStream(args[1]); ObjectInputStream ois = new ObjectInputStream(fis); map = (TagToComponentMap) ois.readObject(); } catch (Exception e) { e.printStackTrace(); } } else if (args[0].equals("facelets")) { // Build new component map from tld, and use that to // generate a Facelets taglib.xml // args[0] is command // args[1] is output taglib.xml // args[2] is input tld try { FileWriter faceletsTaglibXmlWriter = new FileWriter(args[1]); String preamble = "<?xml version=\"1.0\"?>\n" + "<facelet-taglib xmlns=\"http://java.sun.com/xml/ns/javaee\"\n" + "xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n" + "xsi:schemaLocation=\"http://java.sun.com/xml/ns/javaee " + "http://java.sun.com/xml/ns/javaee/web-facelettaglibrary_2_0.xsd\"\n" + "version=\"2.0\">\n"; String trailer = "</facelet-taglib>\n"; faceletsTaglibXmlWriter.write(preamble); map.setFaceletsTaglibXmlWriter(faceletsTaglibXmlWriter); tldFile = new FileInputStream(args[2]); map.addTagAttrib((InputStream) tldFile); faceletsTaglibXmlWriter.write(trailer); faceletsTaglibXmlWriter.flush(); faceletsTaglibXmlWriter.close(); } catch (IOException e) { e.printStackTrace(); return; } } }
From source file:ms1quant.MS1Quant.java
/** * @param args the command line arguments MS1Quant parameterfile *//*ww w. j av a2 s . co m*/ public static void main(String[] args) throws Exception { BufferedReader reader = null; try { System.out.println( "================================================================================================="); System.out.println("Umpire MS1 quantification and feature detection analysis (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length < 3 || !args[1].startsWith("-mode")) { System.out .println("command : java -jar -Xmx10G MS1Quant.jar ms1quant.params -mode[1 or 2] [Option]"); System.out.println("\n-mode"); System.out.println("\t1:Single file mode--> mzXML_file PepXML_file"); System.out.println("\t\tEx: -mode1 file1.mzXML file1.pep.xml"); System.out.println( "\t2:Folder mode--> mzXML_Folder PepXML_Folder, all generated csv tables will be merged into a single csv file"); System.out.println("\t\tEx: -mode2 /data/mzxml/ /data/pepxml/"); System.out.println("\nOptions"); System.out.println( "\t-C\tNo of concurrent files to be processed (only for folder mode), Ex. -C5, default:1"); System.out.println("\t-p\tMinimum probability, Ex. -p0.9, default:0.9"); System.out.println("\t-ID\tDetect identified feature only"); System.out.println("\t-O\toutput folder, Ex. -O/data/"); return; } ConsoleLogger consoleLogger = new ConsoleLogger(); consoleLogger.SetConsoleLogger(Level.DEBUG); consoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "ms1quant_debug.log"); Logger logger = Logger.getRootLogger(); logger.debug("Command: " + Arrays.toString(args)); logger.info("MS1Quant version: " + UmpireInfo.GetInstance().Version); String parameterfile = args[0]; logger.info("Parameter file: " + parameterfile); File paramfile = new File(parameterfile); if (!paramfile.exists()) { logger.error("Parameter file " + paramfile.getAbsolutePath() + " cannot be found. The program will exit."); } reader = new BufferedReader(new FileReader(paramfile.getAbsolutePath())); String line = ""; InstrumentParameter param = new InstrumentParameter(InstrumentParameter.InstrumentType.TOF5600); int NoCPUs = 2; int NoFile = 1; param.DetermineBGByID = false; param.EstimateBG = true; //<editor-fold defaultstate="collapsed" desc="Read parameter file"> while ((line = reader.readLine()) != null) { if (!"".equals(line) && !line.startsWith("#")) { logger.info(line); //System.out.println(line); if (line.split("=").length < 2) { 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; } //<editor-fold defaultstate="collapsed" desc="instrument parameters"> 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); } case "SE.EndRT": { param.endRT = Float.valueOf(value); } //</editor-fold> } } } //</editor-fold> int mode = 1; if (args[1].equals("-mode2")) { mode = 2; } else if (args[1].equals("-mode1")) { mode = 1; } else { logger.error("-mode number not recongized. The program will exit."); } String mzXML = ""; String pepXML = ""; String mzXMLPath = ""; String pepXMLPath = ""; File mzXMLfile = null; File pepXMLfile = null; File mzXMLfolder = null; File pepXMLfolder = null; int idx = 0; if (mode == 1) { mzXML = args[2]; logger.info("Mode1 mzXML file: " + mzXML); mzXMLfile = new File(mzXML); if (!mzXMLfile.exists()) { logger.error("Mode1 mzXML file " + mzXMLfile.getAbsolutePath() + " cannot be found. The program will exit."); return; } pepXML = args[3]; logger.info("Mode1 pepXML file: " + pepXML); pepXMLfile = new File(pepXML); if (!pepXMLfile.exists()) { logger.error("Mode1 pepXML file " + pepXMLfile.getAbsolutePath() + " cannot be found. The program will exit."); return; } idx = 4; } else if (mode == 2) { mzXMLPath = args[2]; logger.info("Mode2 mzXML folder: " + mzXMLPath); mzXMLfolder = new File(mzXMLPath); if (!mzXMLfolder.exists()) { logger.error("Mode2 mzXML folder " + mzXMLfolder.getAbsolutePath() + " does not exist. The program will exit."); return; } pepXMLPath = args[3]; logger.info("Mode2 pepXML folder: " + pepXMLPath); pepXMLfolder = new File(pepXMLPath); if (!pepXMLfolder.exists()) { logger.error("Mode2 pepXML folder " + pepXMLfolder.getAbsolutePath() + " does not exist. The program will exit."); return; } idx = 4; } String outputfolder = ""; float MinProb = 0f; for (int i = idx; i < args.length; i++) { if (args[i].startsWith("-")) { if (args[i].equals("-ID")) { param.TargetIDOnly = true; logger.info("Detect ID feature only: true"); } if (args[i].startsWith("-O")) { outputfolder = args[i].substring(2); logger.info("Output folder: " + outputfolder); File outputfile = new File(outputfolder); if (!outputfolder.endsWith("\\") | outputfolder.endsWith("/")) { outputfolder += "/"; } if (!outputfile.exists()) { outputfile.mkdir(); } } if (args[i].startsWith("-C")) { try { NoFile = Integer.parseInt(args[i].substring(2)); logger.info("No of concurrent files: " + NoFile); } catch (Exception ex) { logger.error(args[i] + " is not a correct integer format, will process only one file at a time."); } } if (args[i].startsWith("-p")) { try { MinProb = Float.parseFloat(args[i].substring(2)); logger.info("probability threshold: " + MinProb); } catch (Exception ex) { logger.error(args[i] + " is not a correct format, will use 0 as threshold instead."); } } } } reader.close(); TandemParam tandemparam = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); PTMManager.GetInstance(); if (param.TargetIDOnly) { param.EstimateBG = false; param.ApexDelta = 1.5f; param.NoMissedScan = 10; param.MiniOverlapP = 0.2f; param.RemoveGroupedPeaks = false; param.CheckMonoIsotopicApex = false; param.DetectByCWT = false; param.FillGapByBK = false; param.IsoCorrThreshold = -1f; param.SmoothFactor = 3; } if (mode == 1) { logger.info("Processing " + mzXMLfile.getAbsolutePath() + "...."); long time = System.currentTimeMillis(); LCMSPeakMS1 LCMS1 = new LCMSPeakMS1(mzXMLfile.getAbsolutePath(), NoCPUs); LCMS1.SetParameter(param); LCMS1.Resume = false; if (!param.TargetIDOnly) { LCMS1.CreatePeakFolder(); } LCMS1.ExportPeakClusterTable = true; if (pepXMLfile.exists()) { tandemparam.InteractPepXMLPath = pepXMLfile.getAbsolutePath(); LCMS1.ParsePepXML(tandemparam, MinProb); logger.info("No. of PSMs included: " + LCMS1.IDsummary.PSMList.size()); logger.info("No. of Peptide ions included: " + LCMS1.IDsummary.GetPepIonList().size()); } if (param.TargetIDOnly) { LCMS1.SaveSerializationFile = false; } if (param.TargetIDOnly || !LCMS1.ReadPeakCluster()) { LCMS1.PeakClusterDetection(); } if (pepXMLfile.exists()) { LCMS1.AssignQuant(false); LCMS1.IDsummary.ExportPepID(outputfolder); } time = System.currentTimeMillis() - time; logger.info(LCMS1.ParentmzXMLName + " 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)))); LCMS1.BaseClearAllPeaks(); LCMS1.SetSpectrumParser(null); LCMS1.IDsummary = null; LCMS1 = null; System.gc(); } else if (mode == 2) { LCMSID IDsummary = new LCMSID("", "", ""); logger.info("Parsing all pepXML files in " + pepXMLPath + "...."); for (File file : pepXMLfolder.listFiles()) { if (file.getName().toLowerCase().endsWith("pep.xml") || file.getName().toLowerCase().endsWith("pepxml")) { PepXMLParser pepXMLParser = new PepXMLParser(IDsummary, file.getAbsolutePath(), MinProb); } } HashMap<String, LCMSID> LCMSIDMap = IDsummary.GetLCMSIDFileMap(); ExecutorService executorPool = null; executorPool = Executors.newFixedThreadPool(NoFile); logger.info("Processing all mzXML files in " + mzXMLPath + "...."); for (File file : mzXMLfolder.listFiles()) { if (file.getName().toLowerCase().endsWith("mzxml")) { LCMSID id = LCMSIDMap.get(FilenameUtils.getBaseName(file.getName())); if (id == null || id.PSMList == null) { logger.warn("No IDs found in :" + FilenameUtils.getBaseName(file.getName()) + ". Quantification for this file is skipped"); continue; } if (!id.PSMList.isEmpty()) { MS1TargetQuantThread thread = new MS1TargetQuantThread(file, id, NoCPUs, outputfolder, param); executorPool.execute(thread); } } } LCMSIDMap.clear(); LCMSIDMap = null; IDsummary = null; executorPool.shutdown(); try { executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS); } catch (InterruptedException e) { logger.info("interrupted.."); } if (outputfolder == null | outputfolder.equals("")) { outputfolder = mzXMLPath; } logger.info("Merging PSM files.."); File output = new File(outputfolder); FileWriter writer = new FileWriter(output.getAbsolutePath() + "/PSM_merge.csv"); boolean header = false; for (File csvfile : output.listFiles()) { if (csvfile.getName().toLowerCase().endsWith("_psms.csv")) { BufferedReader outreader = new BufferedReader(new FileReader(csvfile)); String outline = outreader.readLine(); if (!header) { writer.write(outline + "\n"); header = true; } while ((outline = outreader.readLine()) != null) { writer.write(outline + "\n"); } outreader.close(); csvfile.delete(); } } writer.close(); } logger.info("MS1 quant module is complete."); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:org.apache.cxf.cwiki.SiteExporter.java
public static void main(String[] args) throws Exception { Authenticator.setDefault(new Authenticator() { protected PasswordAuthentication getPasswordAuthentication() { return new PasswordAuthentication(userName, password.toCharArray()); }// w w w .j a v a2 s. com }); ListIterator<String> it = Arrays.asList(args).listIterator(); List<String> files = new ArrayList<String>(); boolean forceAll = false; int maxThreads = -1; while (it.hasNext()) { String s = it.next(); if ("-debug".equals(s)) { debug = true; } else if ("-user".equals(s)) { userName = it.next(); } else if ("-password".equals(s)) { password = it.next(); } else if ("-d".equals(s)) { rootOutputDir = new File(it.next()); } else if ("-force".equals(s)) { forceAll = true; } else if ("-svn".equals(s)) { svn = true; } else if ("-commit".equals(s)) { commit = true; } else if ("-maxThreads".equals(s)) { maxThreads = Integer.parseInt(it.next()); } else if (s != null && s.length() > 0) { files.add(s); } } List<SiteExporter> exporters = new ArrayList<SiteExporter>(); for (String file : files) { exporters.add(new SiteExporter(file, forceAll)); } List<SiteExporter> modified = new ArrayList<SiteExporter>(); for (SiteExporter exporter : exporters) { if (exporter.initialize()) { modified.add(exporter); } } // render stuff only if needed if (!modified.isEmpty()) { setSiteExporters(exporters); if (maxThreads <= 0) { maxThreads = modified.size(); } ExecutorService executor = Executors.newFixedThreadPool(maxThreads, new ThreadFactory() { public Thread newThread(Runnable r) { Thread t = new Thread(r); t.setDaemon(true); return t; } }); List<Future<?>> futures = new ArrayList<Future<?>>(modified.size()); for (SiteExporter exporter : modified) { futures.add(executor.submit(exporter)); } for (Future<?> t : futures) { t.get(); } } if (commit) { File file = FileUtils.createTempFile("svncommit", "txt"); FileWriter writer = new FileWriter(file); writer.write(svnCommitMessage.toString()); writer.close(); callSvn(rootOutputDir, "commit", "-F", file.getAbsolutePath(), rootOutputDir.getAbsolutePath()); svnCommitMessage.setLength(0); } }
From source file:ch.kostceco.tools.kostsimy.KOSTSimy.java
/** Die Eingabe besteht aus 2 Parameter: [0] Original-Ordner [1] Replica-Ordner * //from w w w . jav a2s . c om * @param args * @throws IOException */ public static void main(String[] args) throws IOException { ApplicationContext context = new ClassPathXmlApplicationContext("classpath:config/applicationContext.xml"); // Zeitstempel Start java.util.Date nowStart = new java.util.Date(); java.text.SimpleDateFormat sdfStart = new java.text.SimpleDateFormat("dd.MM.yyyy HH:mm:ss"); String ausgabeStart = sdfStart.format(nowStart); KOSTSimy kostsimy = (KOSTSimy) context.getBean("kostsimy"); File configFile = new File("configuration" + File.separator + "kostsimy.conf.xml"); // Ueberprfung des Parameters (Log-Verzeichnis) String pathToLogfile = kostsimy.getConfigurationService().getPathToLogfile(); File directoryOfLogfile = new File(pathToLogfile); if (!directoryOfLogfile.exists()) { directoryOfLogfile.mkdir(); } // Im Logverzeichnis besteht kein Schreibrecht if (!directoryOfLogfile.canWrite()) { System.out.println( kostsimy.getTextResourceService().getText(ERROR_LOGDIRECTORY_NOTWRITABLE, directoryOfLogfile)); System.exit(1); } if (!directoryOfLogfile.isDirectory()) { System.out.println(kostsimy.getTextResourceService().getText(ERROR_LOGDIRECTORY_NODIRECTORY)); System.exit(1); } // Ist die Anzahl Parameter (2) korrekt? if (args.length > 3) { System.out.println(kostsimy.getTextResourceService().getText(ERROR_PARAMETER_USAGE)); System.exit(1); } File origDir = new File(args[0]); File repDir = new File(args[1]); File logDatei = null; logDatei = origDir; // Informationen zum Arbeitsverzeichnis holen String pathToWorkDir = kostsimy.getConfigurationService().getPathToWorkDir(); /* Nicht vergessen in "src/main/resources/config/applicationContext-services.xml" beim * entsprechenden Modul die property anzugeben: <property name="configurationService" * ref="configurationService" /> */ // Konfiguration des Loggings, ein File Logger wird zustzlich erstellt LogConfigurator logConfigurator = (LogConfigurator) context.getBean("logconfigurator"); String logFileName = logConfigurator.configure(directoryOfLogfile.getAbsolutePath(), logDatei.getName()); File logFile = new File(logFileName); // Ab hier kann ins log geschrieben werden... LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_HEADER)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_START, ausgabeStart)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_END)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_INFO)); System.out.println("KOST-Simy"); System.out.println(""); if (!origDir.exists()) { // Das Original-Verzeichnis existiert nicht LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_NOORIGDIR, origDir.getAbsolutePath()))); System.out .println(kostsimy.getTextResourceService().getText(ERROR_NOORIGDIR, origDir.getAbsolutePath())); System.exit(1); } if (!repDir.exists()) { // Das Replica-Verzeichnis existiert nicht LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_NOREPDIR1, repDir.getAbsolutePath()))); System.out .println(kostsimy.getTextResourceService().getText(ERROR_NOREPDIR1, repDir.getAbsolutePath())); System.exit(1); } File xslOrig = new File("resources" + File.separator + "kost-simy.xsl"); File xslCopy = new File(directoryOfLogfile.getAbsolutePath() + File.separator + "kost-simy.xsl"); if (!xslCopy.exists()) { Util.copyFile(xslOrig, xslCopy); } // Informationen zur prozentualen Stichprobe holen String randomTest = kostsimy.getConfigurationService().getRandomTest(); /* Nicht vergessen in "src/main/resources/config/applicationContext-services.xml" beim * entsprechenden Modul die property anzugeben: <property name="configurationService" * ref="configurationService" /> */ int iRandomTest = 100; try { iRandomTest = Integer.parseInt(randomTest); } catch (Exception ex) { // unzulaessige Eingabe --> 50 wird gesetzt iRandomTest = 50; } if (iRandomTest > 100 || iRandomTest < 1) { // unzulaessige Eingabe --> 50 wird gesetzt iRandomTest = 50; } File tmpDir = new File(pathToWorkDir); /* bestehendes Workverzeichnis Abbruch wenn nicht leer, da am Schluss das Workverzeichnis * gelscht wird und entsprechend bestehende Dateien gelscht werden knnen */ if (tmpDir.exists()) { if (tmpDir.isDirectory()) { // Get list of file in the directory. When its length is not zero the folder is not empty. String[] files = tmpDir.list(); if (files.length > 0) { LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_WORKDIRECTORY_EXISTS, pathToWorkDir))); System.out.println( kostsimy.getTextResourceService().getText(ERROR_WORKDIRECTORY_EXISTS, pathToWorkDir)); System.exit(1); } } } // Im Pfad keine Sonderzeichen Programme knnen evtl abstrzen String patternStr = "[^!#\\$%\\(\\)\\+,\\-_\\.=@\\[\\]\\{\\}\\~:\\\\a-zA-Z0-9 ]"; Pattern pattern = Pattern.compile(patternStr); String name = tmpDir.getAbsolutePath(); String[] pathElements = name.split("/"); for (int i = 0; i < pathElements.length; i++) { String element = pathElements[i]; Matcher matcher = pattern.matcher(element); boolean matchFound = matcher.find(); if (matchFound) { LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name))); System.out.println(kostsimy.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name)); System.exit(1); } } // die Anwendung muss mindestens unter Java 6 laufen String javaRuntimeVersion = System.getProperty("java.vm.version"); if (javaRuntimeVersion.compareTo("1.6.0") < 0) { LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_WRONG_JRE))); System.out.println(kostsimy.getTextResourceService().getText(ERROR_WRONG_JRE)); System.exit(1); } // bestehendes Workverzeichnis wieder anlegen if (!tmpDir.exists()) { tmpDir.mkdir(); File origDirTmp = new File(tmpDir.getAbsolutePath() + File.separator + "orig"); File repDirTmp = new File(tmpDir.getAbsolutePath() + File.separator + "rep"); origDirTmp.mkdir(); repDirTmp.mkdir(); } // Im workverzeichnis besteht kein Schreibrecht if (!tmpDir.canWrite()) { LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_WORKDIRECTORY_NOTWRITABLE, tmpDir))); System.out.println(kostsimy.getTextResourceService().getText(ERROR_WORKDIRECTORY_NOTWRITABLE, tmpDir)); System.exit(1); } // Im Pfad keine Sonderzeichen --> Absturzgefahr name = origDir.getAbsolutePath(); pathElements = name.split("/"); for (int i = 0; i < pathElements.length; i++) { String element = pathElements[i]; Matcher matcher = pattern.matcher(element); boolean matchFound = matcher.find(); if (matchFound) { LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name))); System.out.println(kostsimy.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name)); System.exit(1); } } name = repDir.getAbsolutePath(); pathElements = name.split("/"); for (int i = 0; i < pathElements.length; i++) { String element = pathElements[i]; Matcher matcher = pattern.matcher(element); boolean matchFound = matcher.find(); if (matchFound) { LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name))); System.out.println(kostsimy.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name)); System.exit(1); } } LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_IMAGE1)); float count = 0; int countNio = 0; int countIo = 0; float countVal = 0; int countNotVal = 0; float percentage = (float) 0.0; if (!origDir.isDirectory()) { // TODO: Bildervergleich zweier Dateien --> erledigt --> nur Marker if (repDir.isDirectory()) { // Das Replica-ist ein Verzeichnis, aber Original eine Datei LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_NOREPDIR2, repDir.getAbsolutePath()))); System.out.println( kostsimy.getTextResourceService().getText(ERROR_NOREPDIR2, repDir.getAbsolutePath())); System.exit(1); } boolean compFile = compFile(origDir, logFileName, directoryOfLogfile, repDir, tmpDir); float statIo = 0; int statNio = 0; float statUn = 0; if (compFile) { statIo = 100; } else { statNio = 100; } LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_IMAGE2)); LOGGER.logError( kostsimy.getTextResourceService().getText(MESSAGE_XML_STATISTICS, statIo, statNio, statUn)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_LOGEND)); // Zeitstempel End java.util.Date nowEnd = new java.util.Date(); java.text.SimpleDateFormat sdfEnd = new java.text.SimpleDateFormat("dd.MM.yyyy HH:mm:ss"); String ausgabeEnd = sdfEnd.format(nowEnd); ausgabeEnd = "<End>" + ausgabeEnd + "</End>"; Util.valEnd(ausgabeEnd, logFile); Util.amp(logFile); // Die Konfiguration hereinkopieren try { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setValidating(false); factory.setExpandEntityReferences(false); Document docConfig = factory.newDocumentBuilder().parse(configFile); NodeList list = docConfig.getElementsByTagName("configuration"); Element element = (Element) list.item(0); Document docLog = factory.newDocumentBuilder().parse(logFile); Node dup = docLog.importNode(element, true); docLog.getDocumentElement().appendChild(dup); FileWriter writer = new FileWriter(logFile); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ElementToStream(docLog.getDocumentElement(), baos); String stringDoc2 = new String(baos.toByteArray()); writer.write(stringDoc2); writer.close(); // Der Header wird dabei leider verschossen, wieder zurck ndern String newstring = kostsimy.getTextResourceService().getText(MESSAGE_XML_HEADER); String oldstring = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><KOSTSimyLog>"; Util.oldnewstring(oldstring, newstring, logFile); } catch (Exception e) { LOGGER.logError( "<Error>" + kostsimy.getTextResourceService().getText(ERROR_XML_UNKNOWN, e.getMessage())); System.out.println("Exception: " + e.getMessage()); } if (compFile) { // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } // Validierte Datei valide System.exit(0); } else { // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } // Fehler in Validierte Datei --> invalide System.exit(2); } } else { // TODO: Bildervergleich zweier Verzeichnisse --> in Arbeit --> nur Marker if (!repDir.isDirectory()) { // Das Replica-ist eine Datei, aber Original ein Ordner LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_NOREPDIR3, repDir.getAbsolutePath()))); System.out.println( kostsimy.getTextResourceService().getText(ERROR_NOREPDIR3, repDir.getAbsolutePath())); System.exit(1); } Map<String, File> fileMap = Util.getFileMap(origDir, false); Set<String> fileMapKeys = fileMap.keySet(); boolean other = false; for (Iterator<String> iterator = fileMapKeys.iterator(); iterator.hasNext();) { String entryName = iterator.next(); File newFile = fileMap.get(entryName); if (!newFile.isDirectory()) { origDir = newFile; count = count + 1; if ((origDir.getAbsolutePath().toLowerCase().endsWith(".pdf") || origDir.getAbsolutePath().toLowerCase().endsWith(".pdfa") || origDir.getAbsolutePath().toLowerCase().endsWith(".tif") || origDir.getAbsolutePath().toLowerCase().endsWith(".tiff") || origDir.getAbsolutePath().toLowerCase().endsWith(".jpeg") || origDir.getAbsolutePath().toLowerCase().endsWith(".jpg") || origDir.getAbsolutePath().toLowerCase().endsWith(".jpe") || origDir.getAbsolutePath().toLowerCase().endsWith(".jp2") || origDir.getAbsolutePath().toLowerCase().endsWith(".gif") || origDir.getAbsolutePath().toLowerCase().endsWith(".png") || origDir.getAbsolutePath().toLowerCase().endsWith(".bmp"))) { percentage = 100 / count * countVal; if (percentage < iRandomTest) { // if ( 100 / count * (countVal + 1) <= iRandomTest ) { countVal = countVal + 1; String origWithOutExt = FilenameUtils.removeExtension(origDir.getName()); File repFile = new File( repDir.getAbsolutePath() + File.separator + origWithOutExt + ".pdf"); if (!repFile.exists()) { repFile = new File( repDir.getAbsolutePath() + File.separator + origWithOutExt + ".pdfa"); if (!repFile.exists()) { repFile = new File( repDir.getAbsolutePath() + File.separator + origWithOutExt + ".tif"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".tiff"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".jpeg"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".jpg"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".jpe"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".jp2"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".gif"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".png"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".bmp"); if (!repFile.exists()) { other = true; LOGGER.logError(kostsimy .getTextResourceService() .getText(MESSAGE_XML_VALERGEBNIS)); LOGGER.logError(kostsimy .getTextResourceService() .getText(MESSAGE_XML_COMPFILE, origDir)); LOGGER.logError(kostsimy .getTextResourceService().getText( MESSAGE_XML_VALERGEBNIS_NOTVALIDATED)); LOGGER.logError( kostsimy.getTextResourceService() .getText(ERROR_NOREP, origDir.getName())); LOGGER.logError(kostsimy .getTextResourceService().getText( MESSAGE_XML_VALERGEBNIS_CLOSE)); } } } } } } } } } } } if (!other) { boolean compFile = compFile(origDir, logFileName, directoryOfLogfile, repFile, tmpDir); if (compFile) { // Vergleich bestanden countIo = countIo + 1; } else { // Vergleich nicht bestanden countNio = countNio + 1; } } } else { countNotVal = countNotVal + 1; LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS)); LOGGER.logError( kostsimy.getTextResourceService().getText(MESSAGE_XML_COMPFILE, origDir)); LOGGER.logError(kostsimy.getTextResourceService() .getText(MESSAGE_XML_VALERGEBNIS_NOTVALIDATED)); LOGGER.logError( kostsimy.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_CLOSE)); } } else { countNotVal = countNotVal + 1; LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_COMPFILE, origDir)); LOGGER.logError( kostsimy.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_NOTVALIDATED)); LOGGER.logError( kostsimy.getTextResourceService().getText(ERROR_INCORRECTFILEENDING, origDir)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_CLOSE)); } } } if (countNio == 0 && countIo == 0) { // keine Dateien verglichen LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_INCORRECTFILEENDINGS)); System.out.println(kostsimy.getTextResourceService().getText(ERROR_INCORRECTFILEENDINGS)); } float statIo = 100 / (float) count * (float) countIo; float statNio = 100 / (float) count * (float) countNio; float statUn = 100 - statIo - statNio; LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_IMAGE2)); LOGGER.logError( kostsimy.getTextResourceService().getText(MESSAGE_XML_STATISTICS, statIo, statNio, statUn)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_LOGEND)); // Zeitstempel End java.util.Date nowEnd = new java.util.Date(); java.text.SimpleDateFormat sdfEnd = new java.text.SimpleDateFormat("dd.MM.yyyy HH:mm:ss"); String ausgabeEnd = sdfEnd.format(nowEnd); ausgabeEnd = "<End>" + ausgabeEnd + "</End>"; Util.valEnd(ausgabeEnd, logFile); Util.amp(logFile); // Die Konfiguration hereinkopieren try { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setValidating(false); factory.setExpandEntityReferences(false); Document docConfig = factory.newDocumentBuilder().parse(configFile); NodeList list = docConfig.getElementsByTagName("configuration"); Element element = (Element) list.item(0); Document docLog = factory.newDocumentBuilder().parse(logFile); Node dup = docLog.importNode(element, true); docLog.getDocumentElement().appendChild(dup); FileWriter writer = new FileWriter(logFile); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ElementToStream(docLog.getDocumentElement(), baos); String stringDoc2 = new String(baos.toByteArray()); writer.write(stringDoc2); writer.close(); // Der Header wird dabei leider verschossen, wieder zurck ndern String newstring = kostsimy.getTextResourceService().getText(MESSAGE_XML_HEADER); String oldstring = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><KOSTSimyLog>"; Util.oldnewstring(oldstring, newstring, logFile); } catch (Exception e) { LOGGER.logError( "<Error>" + kostsimy.getTextResourceService().getText(ERROR_XML_UNKNOWN, e.getMessage())); System.out.println("Exception: " + e.getMessage()); } if (countNio == 0 && countIo == 0) { // keine Dateien verglichen bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } System.exit(1); } else if (countNio == 0) { // bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } // alle Validierten Dateien valide System.exit(0); } else { // bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } // Fehler in Validierten Dateien --> invalide System.exit(2); } if (tmpDir.exists()) { Util.deleteDir(tmpDir); tmpDir.deleteOnExit(); } } }
From source file:DIA_Umpire_Quant.DIA_Umpire_ProtQuant.java
/** * @param args the command line arguments *///from www . j a v a 2 s . c om public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println( "DIA-Umpire protein quantitation module (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_PortQuant.jar diaumpire_module.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_orotquant.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 Combined_Prot = ""; boolean DefaultProtFiltering = true; float Freq = 0f; int TopNPep = 6; int TopNFrag = 6; String FilterWeight = "GW"; float MinWeight = 0.9f; TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); HashMap<String, File> AssignFiles = new HashMap<>(); boolean ExportSaint = false; boolean SAINT_MS1 = false; boolean SAINT_MS2 = true; HashMap<String, String[]> BaitList = new HashMap<>(); HashMap<String, String> BaitName = new HashMap<>(); HashMap<String, String[]> ControlList = new HashMap<>(); HashMap<String, String> ControlName = 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 "Combined_Prot": { Combined_Prot = value; break; } case "DefaultProtFiltering": { DefaultProtFiltering = Boolean.parseBoolean(value); break; } case "DecoyPrefix": { if (!"".equals(value)) { tandemPara.DecoyPrefix = value; } break; } case "ProteinFDR": { tandemPara.ProtFDR = Float.parseFloat(value); break; } case "FilterWeight": { FilterWeight = value; break; } case "MinWeight": { MinWeight = Float.parseFloat(value); break; } case "TopNFrag": { TopNFrag = Integer.parseInt(value); break; } case "TopNPep": { TopNPep = Integer.parseInt(value); break; } case "Freq": { Freq = Float.parseFloat(value); break; } //<editor-fold defaultstate="collapsed" desc="SaintOutput"> case "ExportSaintInput": { ExportSaint = Boolean.parseBoolean(value); break; } case "QuantitationType": { switch (value) { case "MS1": { SAINT_MS1 = true; SAINT_MS2 = false; break; } case "MS2": { SAINT_MS1 = false; SAINT_MS2 = true; break; } case "BOTH": { SAINT_MS1 = true; SAINT_MS2 = true; break; } } break; } // case "BaitInputFile": { // SaintBaitFile = value; // break; // } // case "PreyInputFile": { // SaintPreyFile = value; // break; // } // case "InterationInputFile": { // SaintInteractionFile = value; // break; // } default: { if (type.startsWith("BaitName_")) { BaitName.put(type.substring(9), value); } if (type.startsWith("BaitFile_")) { BaitList.put(type.substring(9), value.split("\t")); } if (type.startsWith("ControlName_")) { ControlName.put(type.substring(12), value); } if (type.startsWith("ControlFile_")) { ControlList.put(type.substring(12), value.split("\t")); } break; } //</editor-fold> } } } //</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); } //Check if the prot.xml file can be found if (!new File(Combined_Prot).exists()) { Logger.getRootLogger().info("ProtXML file: " + Combined_Prot + " cannot be found, the export protein summary table will be empty."); } LCMSID protID = null; //Parse prot.xml and generate protein master list given an FDR if (Combined_Prot != null && !Combined_Prot.equals("")) { protID = LCMSID.ReadLCMSIDSerialization(Combined_Prot); if (!"".equals(Combined_Prot) && protID == null) { protID = new LCMSID(Combined_Prot, tandemPara.DecoyPrefix, tandemPara.FastaPath); ProtXMLParser protxmlparser = new ProtXMLParser(protID, Combined_Prot, 0f); //Use DIA-Umpire default protein FDR calculation if (DefaultProtFiltering) { protID.RemoveLowLocalPWProtein(0.8f); protID.RemoveLowMaxIniProbProtein(0.9f); protID.FilterByProteinDecoyFDRUsingMaxIniProb(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } //Get protein FDR calculation without other filtering else { protID.FilterByProteinDecoyFDRUsingLocalPW(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } protID.LoadSequence(); protID.WriteLCMSIDSerialization(Combined_Prot); } Logger.getRootLogger().info("Protein No.:" + protID.ProteinList.size()); } HashMap<String, HashMap<String, FragmentPeak>> IDSummaryFragments = new HashMap<>(); //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.ClearAssignPeakCluster(); FileList.add(DiaFile); HashMap<String, FragmentPeak> FragMap = new HashMap<>(); IDSummaryFragments.put(FilenameUtils.getBaseName(mzXMLFile), FragMap); } } } //<editor-fold defaultstate="collapsed" desc="Peptide and fragment selection"> Logger.getRootLogger().info("Peptide and fragment selection across the whole dataset"); ArrayList<LCMSID> SummaryList = new ArrayList<>(); for (DIAPack diafile : FileList) { if (protID != null) { //Generate protein list according to mapping of peptide ions for each DIA file to the master protein list diafile.IDsummary.GenerateProteinByRefIDByPepSeq(protID, true); diafile.IDsummary.ReMapProPep(); } if ("GW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByGroupWeight(); } else if ("PepW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByWeight(); } SummaryList.add(diafile.IDsummary); } FragmentSelection fragselection = new FragmentSelection(SummaryList); fragselection.freqPercent = Freq; fragselection.GeneratePepFragScoreMap(); fragselection.GenerateTopFragMap(TopNFrag); fragselection.GenerateProtPepScoreMap(MinWeight); fragselection.GenerateTopPepMap(TopNPep); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Writing general reports"> ExportTable export = new ExportTable(WorkFolder, SummaryList, IDSummaryFragments, protID, fragselection); export.Export(TopNPep, TopNFrag, Freq); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="//<editor-fold defaultstate="collapsed" desc="Generate SAINT input files"> if (ExportSaint && protID != null) { HashMap<String, DIAPack> Filemap = new HashMap<>(); for (DIAPack DIAfile : FileList) { Filemap.put(DIAfile.GetBaseName(), DIAfile); } FileWriter baitfile = new FileWriter(WorkFolder + "SAINT_Bait_" + DateTimeTag.GetTag() + ".txt"); FileWriter preyfile = new FileWriter(WorkFolder + "SAINT_Prey_" + DateTimeTag.GetTag() + ".txt"); FileWriter interactionfileMS1 = null; FileWriter interactionfileMS2 = null; if (SAINT_MS1) { interactionfileMS1 = new FileWriter( WorkFolder + "SAINT_Interaction_MS1_" + DateTimeTag.GetTag() + ".txt"); } if (SAINT_MS2) { interactionfileMS2 = new FileWriter( WorkFolder + "SAINT_Interaction_MS2_" + DateTimeTag.GetTag() + ".txt"); } HashMap<String, String> PreyID = new HashMap<>(); for (String samplekey : ControlName.keySet()) { String name = ControlName.get(samplekey); for (String file : ControlList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "C\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } for (String samplekey : BaitName.keySet()) { String name = BaitName.get(samplekey); for (String file : BaitList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "T\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } baitfile.close(); if (SAINT_MS1) { interactionfileMS1.close(); } if (SAINT_MS2) { interactionfileMS2.close(); } for (String AccNo : PreyID.keySet()) { preyfile.write(AccNo + "\t" + PreyID.get(AccNo) + "\n"); } preyfile.close(); } //</editor-fold> Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:com.amalto.workbench.utils.XSDParser.java
/** * Print a simple type definition for the document. * //from ww w . jav a 2 s. c om * @param xsdSimpleTypeDefinition a simple type definition in the schema for schema. */ /* * public void printSimpleTypeDefinition( XSDSimpleTypeDefinition xsdSimpleTypeDefinition) { if * (xsdSimpleTypeDefinition == null) { } else if (xsdSimpleTypeDefinition.getEffectiveEnumerationFacet() != null) { * List value = xsdSimpleTypeDefinition.getEffectiveEnumerationFacet() .getValue(); if (value.size() > 1) { * System.out.print("("); } for (Iterator enumerators = value.iterator(); enumerators.hasNext();) { String * enumerator = enumerators.next().toString(); System.out.print("<em>"); System.out.print(enumerator); * System.out.print("</em>"); if (enumerators.hasNext()) { System.out.print(" | "); } } if (value.size() > * 1) { System.out.print(")"); } } else if (xsdSimpleTypeDefinition.getElement() != null && * xsdSimpleTypeDefinition.getElement().hasAttribute( XSDConstants.ID_ATTRIBUTE)) { System.out.print("<a href='#" + * xsdSimpleTypeDefinition.getName() + "-simple-type'>"); System.out.print(xsdSimpleTypeDefinition.getName()); * System.out.print("</a>"); } else if (XSDVariety.UNION_LITERAL == xsdSimpleTypeDefinition .getVariety()) { * System.out.print("("); for (Iterator members = xsdSimpleTypeDefinition .getMemberTypeDefinitions().iterator(); * members.hasNext();) { XSDSimpleTypeDefinition memberTypeDefinition = (XSDSimpleTypeDefinition) members .next(); * printSimpleTypeDefinition(memberTypeDefinition); if (members.hasNext()) { System.out.print(" | "); } } * System.out.print(")"); } else if (XSDVariety.UNION_LITERAL == xsdSimpleTypeDefinition .getVariety()) { * System.out.print("List of "); printSimpleTypeDefinition(xsdSimpleTypeDefinition * .getItemTypeDefinition()); } else if (xsdSimpleTypeDefinition.getName() != null) { if * ("public".equals(xsdSimpleTypeDefinition.getName())) { System.out.print("<a target='Part2' href='" + * XSDConstants.PART2 + "#anyURI'>anyURI</a> "); System.out.print("<a target='Errata' href='" + errata + * "#pfipublic'><em>public</em></a>"); } else { System.out.print("<b><em>"); * System.out.print(xsdSimpleTypeDefinition.getName()); System.out.print("</em></b>"); } } else if * (xsdSimpleTypeDefinition.getEffectivePatternFacet() != null) { // * System.out.print(xsdSimpleTypeDefinition.getEffectivePatternFacet().getLexicalValue()); * * System.out.print("<em>"); System.out.print("<a target='Part1' href='" + XSDConstants.PART1 + * "#coss-identity-constraint'>"); System.out.print("a restricted xpath expression"); System.out.print("</a>"); * System.out.print("</em>"); } else { System.out.print("***"); } } */ public static void main(String args[]) { try { /* * String xsd = ""; FileInputStream fis = new FileInputStream( * "/home/bgrieder/workspace/XCBL35/XCBL35.xsd"); BufferedReader br = new BufferedReader(new * InputStreamReader(fis, "utf-8")); String line; while ((line = br.readLine()) != null) xsd += line + "\n"; * * XSDParser parser = new XSDParser(); parser.loadAndPrint(xsd); */ FileWriter fw = new FileWriter("/tmp/xcb35sr.xsd"); //$NON-NLS-1$ Resource.Factory.Registry.INSTANCE.getExtensionToFactoryMap().put("xsd", new XSDResourceFactoryImpl()); //$NON-NLS-1$ String xsdFile = "/home/bgrieder/workspace/XCBL35/XCBL35.xsd"; //$NON-NLS-1$ ResourceSet resourceSet = new ResourceSetImpl(); XSDResourceImpl xsdResource = (XSDResourceImpl) resourceSet.getResource(URI.createFileURI(xsdFile), true); /* * XSDResourceImpl res = new XSDResourceImpl(URI.createFileURI(xsdFile)); */ XSDSchema xsdSchema = xsdResource.getSchema(); String header = "<xsd:schema " + "elementFormDefault=\"qualified\" " //$NON-NLS-1$ //$NON-NLS-2$ + "targetNamespace=\"rrn:org.xcbl:schemas/xcbl/v3_5/xcbl35.xsd\" " //$NON-NLS-1$ + "xmlns=\"rrn:org.xcbl:schemas/xcbl/v3_5/xcbl35.xsd\" " //$NON-NLS-1$ + "xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\">"; //$NON-NLS-1$ fw.write(header); Iterator it = xsdSchema.getElementDeclarations().iterator(); for (; it.hasNext();) { XSDElementDeclaration elementDeclaration = (XSDElementDeclaration) it.next(); // if ("Order".equals(elementDeclaration.getName())) { fw.write(Util.nodeToString(elementDeclaration.getElement()) .replaceAll("xmlns:xsd=\"http:\\/\\/www\\.w3\\.org\\/2001\\/XMLSchema\"", "")); //$NON-NLS-1$ //$NON-NLS-2$ // } } it = xsdSchema.getTypeDefinitions().iterator(); for (; it.hasNext();) { XSDTypeDefinition typedef = (XSDTypeDefinition) it.next(); fw.write(Util.nodeToString(typedef.getElement())); } String footer = "</xsd:schema>"; //$NON-NLS-1$ fw.write(footer); fw.close(); } catch (Exception e) { log.error(e.getMessage(), e); } }
From source file:model.experiments.tuningRuns.CompetitiveAveragingGridSearch.java
public static void main(String[] args) throws IOException { FileWriter writer;/* = new FileWriter(Paths.get("runs", "tunings","averaging", "averagingTuning.csv").toFile()); /*from w ww . ja v a2 s . c om*/ for(float hrWeight= .1f; hrWeight<1f;hrWeight= round(hrWeight+.1f,1)) for(float salesWeight= .1f; salesWeight<1f;salesWeight= round(salesWeight+.1f,1)) for(PriceAverager.NoTradingDayPolicy hrPolicy : PriceAverager.NoTradingDayPolicy.values()) for(PriceAverager.NoTradingDayPolicy salesPolicy : PriceAverager.NoTradingDayPolicy.values()) { final CompetitiveAveragingResult r = exponentialRuns(hrWeight, hrPolicy, salesWeight, salesPolicy,20); final String line = hrWeight + "," + hrPolicy + "," + salesWeight + "," + salesPolicy + "," + r.getPrice() + "," + r.getQuantity() + "," + r.getStd(); System.out.println(line); writer.write(line+"\n"); } */ writer = new FileWriter(Paths.get("runs", "tunings", "averaging", "intervalTuning.csv").toFile()); for (float hrWeight = .1f; hrWeight < 1f; hrWeight = round(hrWeight + .1f, 1)) for (float salesWeight = .1f; salesWeight < 1f; salesWeight = round(salesWeight + .1f, 1)) { final CompetitiveAveragingResult r = intervalRuns(hrWeight, salesWeight); final String line = hrWeight + "," + salesWeight + "," + r.getPrice() + "," + r.getQuantity() + "," + r.getStd(); System.out.println(line); writer.write(line + "\n"); writer.flush(); } writer.close(); writer = new FileWriter(Paths.get("runs", "tunings", "averaging", "weightedAveragingTuning.csv").toFile()); for (int hrDays = 1; hrDays <= 10; hrDays++) for (int salesDays = 1; salesDays <= 10; salesDays++) for (boolean hrDecorated : new boolean[] { false, true }) for (boolean salesDecorated : new boolean[] { false, true }) { final CompetitiveAveragingResult r = weightedRun(hrDays, salesDays, hrDecorated, salesDecorated); final String line = hrDays + "," + salesDays + "," + hrDecorated + "," + salesDecorated + "," + r.getPrice() + "," + r.getQuantity() + "," + r.getStd(); System.out.println(line); writer.write(line + "\n"); writer.flush(); } writer = new FileWriter(Paths.get("runs", "tunings", "averaging", "doesSpeedMatters.csv").toFile()); /* for(int speed=1; speed<100; speed++) { final CompetitiveAveragingResult r = exponentialRuns(.8f, PriceAverager.NoTradingDayPolicy.COUNT_AS_LAST_CLOSING_PRICE, .8f, PriceAverager.NoTradingDayPolicy.COUNT_AS_LAST_CLOSING_PRICE, speed); final String line = speed + "," + r.getPrice() + "," + r.getQuantity() + "," + r.getStd(); System.out.println(line); writer.write(line+"\n"); } */ }
From source file:DIA_Umpire_Quant.DIA_Umpire_Quant.java
/** * @param args the command line arguments */// w w w .j av a 2 s . c o m public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println("DIA-Umpire quantitation with targeted re-extraction analysis (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, it should be like: java -jar -Xmx10G DIA_Umpire_Quant.jar diaumpire_quant.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_quant.log"); } catch (Exception e) { } try { 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 UserMod = ""; String Combined_Prot = ""; String InternalLibID = ""; String ExternalLibPath = ""; String ExternalLibDecoyTag = "DECOY"; boolean DefaultProtFiltering = true; boolean DataSetLevelPepFDR = false; float ProbThreshold = 0.99f; float ExtProbThreshold = 0.99f; float Freq = 0f; int TopNPep = 6; int TopNFrag = 6; float MinFragMz = 200f; String FilterWeight = "GW"; float MinWeight = 0.9f; float RTWindow_Int = -1f; float RTWindow_Ext = -1f; TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); HashMap<String, File> AssignFiles = new HashMap<>(); boolean InternalLibSearch = false; boolean ExternalLibSearch = false; boolean ExportSaint = false; boolean SAINT_MS1 = false; boolean SAINT_MS2 = true; HashMap<String, String[]> BaitList = new HashMap<>(); HashMap<String, String> BaitName = new HashMap<>(); HashMap<String, String[]> ControlList = new HashMap<>(); HashMap<String, String> ControlName = 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 "TargetedExtraction": { InternalLibSearch = Boolean.parseBoolean(value); break; } case "InternalLibSearch": { InternalLibSearch = Boolean.parseBoolean(value); break; } case "ExternalLibSearch": { ExternalLibSearch = Boolean.parseBoolean(value); break; } case "Path": { WorkFolder = value; break; } case "path": { WorkFolder = value; break; } case "Thread": { NoCPUs = Integer.parseInt(value); break; } case "Fasta": { tandemPara.FastaPath = value; break; } case "Combined_Prot": { Combined_Prot = value; break; } case "DefaultProtFiltering": { DefaultProtFiltering = Boolean.parseBoolean(value); break; } case "DecoyPrefix": { if (!"".equals(value)) { tandemPara.DecoyPrefix = value; } break; } case "UserMod": { UserMod = value; break; } case "ProteinFDR": { tandemPara.ProtFDR = Float.parseFloat(value); break; } case "PeptideFDR": { tandemPara.PepFDR = Float.parseFloat(value); break; } case "DataSetLevelPepFDR": { DataSetLevelPepFDR = Boolean.parseBoolean(value); break; } case "InternalLibID": { InternalLibID = value; break; } case "ExternalLibPath": { ExternalLibPath = value; break; } case "ExtProbThreshold": { ExtProbThreshold = Float.parseFloat(value); break; } case "RTWindow_Int": { RTWindow_Int = 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; } case "ProbThreshold": { ProbThreshold = Float.parseFloat(value); break; } case "ReSearchProb": { //ReSearchProb = Float.parseFloat(value); break; } case "FilterWeight": { FilterWeight = value; break; } case "MinWeight": { MinWeight = Float.parseFloat(value); break; } case "TopNFrag": { TopNFrag = Integer.parseInt(value); break; } case "TopNPep": { TopNPep = Integer.parseInt(value); break; } case "Freq": { Freq = Float.parseFloat(value); break; } case "MinFragMz": { MinFragMz = Float.parseFloat(value); break; } //<editor-fold defaultstate="collapsed" desc="SaintOutput"> case "ExportSaintInput": { ExportSaint = Boolean.parseBoolean(value); break; } case "QuantitationType": { switch (value) { case "MS1": { SAINT_MS1 = true; SAINT_MS2 = false; break; } case "MS2": { SAINT_MS1 = false; SAINT_MS2 = true; break; } case "BOTH": { SAINT_MS1 = true; SAINT_MS2 = true; break; } } break; } // case "BaitInputFile": { // SaintBaitFile = value; // break; // } // case "PreyInputFile": { // SaintPreyFile = value; // break; // } // case "InterationInputFile": { // SaintInteractionFile = value; // break; // } default: { if (type.startsWith("BaitName_")) { BaitName.put(type.substring(9), value); } if (type.startsWith("BaitFile_")) { BaitList.put(type.substring(9), value.split("\t")); } if (type.startsWith("ControlName_")) { ControlName.put(type.substring(12), value); } if (type.startsWith("ControlFile_")) { ControlList.put(type.substring(12), value.split("\t")); } break; } //</editor-fold> } } } //</editor-fold> //Initialize PTM manager using compomics library PTMManager.GetInstance(); if (!UserMod.equals("")) { PTMManager.GetInstance().ImportUserMod(UserMod); } //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); } //Check if the prot.xml file can be found if (!new File(Combined_Prot).exists()) { Logger.getRootLogger().info("ProtXML file: " + Combined_Prot + " cannot be found, the export protein summary table will be empty."); } LCMSID protID = null; //Parse prot.xml and generate protein master list given an FDR if (Combined_Prot != null && !Combined_Prot.equals("")) { protID = LCMSID.ReadLCMSIDSerialization(Combined_Prot); if (!"".equals(Combined_Prot) && protID == null) { protID = new LCMSID(Combined_Prot, tandemPara.DecoyPrefix, tandemPara.FastaPath); ProtXMLParser protxmlparser = new ProtXMLParser(protID, Combined_Prot, 0f); //Use DIA-Umpire default protein FDR calculation if (DefaultProtFiltering) { protID.RemoveLowLocalPWProtein(0.8f); protID.RemoveLowMaxIniProbProtein(0.9f); protID.FilterByProteinDecoyFDRUsingMaxIniProb(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } //Get protein FDR calculation without other filtering else { protID.FilterByProteinDecoyFDRUsingLocalPW(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } protID.LoadSequence(); protID.WriteLCMSIDSerialization(Combined_Prot); } Logger.getRootLogger().info("Protein No.:" + protID.ProteinList.size()); } HashMap<String, HashMap<String, FragmentPeak>> IDSummaryFragments = new HashMap<>(); //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()); String mzXMLFile = fileEntry.getAbsolutePath(); if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) { DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs); FileList.add(DiaFile); HashMap<String, FragmentPeak> FragMap = new HashMap<>(); IDSummaryFragments.put(FilenameUtils.getBaseName(mzXMLFile), FragMap); 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); } } } LCMSID combinePepID = null; if (DataSetLevelPepFDR) { combinePepID = LCMSID.ReadLCMSIDSerialization(WorkFolder + "combinePepID.SerFS"); if (combinePepID == null) { FDR_DataSetLevel fdr = new FDR_DataSetLevel(); fdr.GeneratePepIonList(FileList, tandemPara, WorkFolder + "combinePepID.SerFS"); combinePepID = fdr.combineID; combinePepID.WriteLCMSIDSerialization(WorkFolder + "combinePepID.SerFS"); } } //process each DIA file for quantification based on untargeted identifications for (DIAPack DiaFile : FileList) { long time = System.currentTimeMillis(); Logger.getRootLogger().info("Loading identification results " + DiaFile.Filename + "...."); //If the LCMSID serialization is found if (!DiaFile.ReadSerializedLCMSID()) { DiaFile.ParsePepXML(tandemPara, combinePepID); 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(DiaFile.Filename + " 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)))); } //<editor-fold defaultstate="collapsed" desc="Targete re-extraction using internal library"> Logger.getRootLogger().info( "================================================================================================="); if (InternalLibSearch && FileList.size() > 1) { Logger.getRootLogger().info("Module C: Targeted 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, 1.1f, 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> //<editor-fold defaultstate="collapsed" desc="Targeted re-extraction using external library"> //External library search if (ExternalLibSearch) { Logger.getRootLogger().info("Module C: 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, ProbThreshold, 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> //<editor-fold defaultstate="collapsed" desc="Peptide and fragment selection"> Logger.getRootLogger().info("Peptide and fragment selection across the whole dataset"); ArrayList<LCMSID> SummaryList = new ArrayList<>(); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); diafile.IDsummary.ClearAssignPeakCluster(); //diafile.IDsummary.ClearPSMs(); } if (protID != null) { //Generate protein list according to mapping of peptide ions for each DIA file to the master protein list diafile.IDsummary.GenerateProteinByRefIDByPepSeq(protID, true); diafile.IDsummary.ReMapProPep(); } if ("GW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByGroupWeight(); } else if ("PepW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByWeight(); } SummaryList.add(diafile.IDsummary); } FragmentSelection fragselection = new FragmentSelection(SummaryList); fragselection.freqPercent = Freq; fragselection.MinFragMZ = MinFragMz; fragselection.GeneratePepFragScoreMap(); fragselection.GenerateTopFragMap(TopNFrag); fragselection.GenerateProtPepScoreMap(MinWeight); fragselection.GenerateTopPepMap(TopNPep); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Writing general reports"> ExportTable export = new ExportTable(WorkFolder, SummaryList, IDSummaryFragments, protID, fragselection); export.Export(TopNPep, TopNFrag, Freq); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="//<editor-fold defaultstate="collapsed" desc="Generate SAINT input files"> if (ExportSaint && protID != null) { HashMap<String, DIAPack> Filemap = new HashMap<>(); for (DIAPack DIAfile : FileList) { Filemap.put(DIAfile.GetBaseName(), DIAfile); } FileWriter baitfile = new FileWriter(WorkFolder + "SAINT_Bait_" + DateTimeTag.GetTag() + ".txt"); FileWriter preyfile = new FileWriter(WorkFolder + "SAINT_Prey_" + DateTimeTag.GetTag() + ".txt"); FileWriter interactionfileMS1 = null; FileWriter interactionfileMS2 = null; if (SAINT_MS1) { interactionfileMS1 = new FileWriter( WorkFolder + "SAINT_Interaction_MS1_" + DateTimeTag.GetTag() + ".txt"); } if (SAINT_MS2) { interactionfileMS2 = new FileWriter( WorkFolder + "SAINT_Interaction_MS2_" + DateTimeTag.GetTag() + ".txt"); } HashMap<String, String> PreyID = new HashMap<>(); for (String samplekey : ControlName.keySet()) { String name = ControlName.get(samplekey); for (String file : ControlList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "C\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } for (String samplekey : BaitName.keySet()) { String name = BaitName.get(samplekey); for (String file : BaitList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "T\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } baitfile.close(); if (SAINT_MS1) { interactionfileMS1.close(); } if (SAINT_MS2) { interactionfileMS2.close(); } for (String AccNo : PreyID.keySet()) { preyfile.write(AccNo + "\t" + PreyID.get(AccNo) + "\n"); } preyfile.close(); } //</editor-fold> Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }