List of usage examples for java.io File getName
public String getName()
From source file:mzmatch.ipeak.align.CowCoda.java
@SuppressWarnings("unchecked") public static void main(String args[]) { final String lbl_mcq = "mcq"; try {/* ww w.j a v a 2s.com*/ Tool.init(); // parse the commandline options final Options options = new Options(); CmdLineParser cmdline = new CmdLineParser(options); // check whether we need to show the help cmdline.parse(args); if (options.help) { Tool.printHeader(System.out, application, version); cmdline.printUsage(System.out, ""); return; } if (options.verbose) { Tool.printHeader(System.out, application, version); cmdline.printOptions(); } // check the command-line parameters int filetype = JFreeChartTools.PDF; { if (options.ppm == -1) { System.err.println("[ERROR]: the ppm-value needs to be set."); System.exit(0); } if (options.order == -1) { System.err.println("[ERROR]: the order for the polynomial fit needs to be set."); System.exit(0); } if (options.maxrt == -1) { System.err.println("[ERROR]: the maximum retention time shift is not set."); System.exit(0); } if (options.image != null) { String extension = options.image.substring(options.image.lastIndexOf('.') + 1); if (extension.toLowerCase().equals("png")) filetype = JFreeChartTools.PNG; else if (extension.toLowerCase().equals("pdf")) filetype = JFreeChartTools.PDF; else { System.err.println( "[ERROR]: file extension of the image file needs to be either PDF or PNG."); System.exit(0); } } // if the output directories do not exist, create them if (options.output != null) Tool.createFilePath(options.output, true); if (options.image != null) Tool.createFilePath(options.image, true); if (options.selection != null) Tool.createFilePath(options.selection, true); } // load the data if (options.verbose) System.out.println("Loading the data"); double maxrt = 0; Vector<ParseResult> data = new Vector<ParseResult>(); Vector<IPeakSet<IPeak>> matchdata = new Vector<IPeakSet<IPeak>>(); for (String file : options.input) { System.out.println("- " + new File(file).getName()); // load the mass chromatogram data ParseResult result = PeakMLParser.parse(new FileInputStream(file), true); data.add(result); // select the best mass chromatograms Vector<IPeak> selection = new Vector<IPeak>(); for (IPeak peak : (IPeakSet<IPeak>) result.measurement) { maxrt = Math.max(maxrt, maxRT(peak)); double mcq = codaDW(peak); peak.addAnnotation(lbl_mcq, Double.toString(mcq), Annotation.ValueType.DOUBLE); if (mcq >= options.codadw) selection.add(peak); } // keep track of the selected mass chromatograms int id = options.input.indexOf(file); IPeakSet<IPeak> peakset = new IPeakSet<IPeak>(selection); peakset.setMeasurementID(id); for (IPeak mc : peakset) mc.setMeasurementID(id); matchdata.add(peakset); } // match the selection together if (options.verbose) System.out.println("Matching the data"); Vector<IPeakSet<IPeak>> matches = IPeak.match((Vector) matchdata, options.ppm, new IPeak.MatchCompare<IPeak>() { public double distance(IPeak peak1, IPeak peak2) { double diff = Math.abs(peak1.getRetentionTime() - peak2.getRetentionTime()); if (diff > options.maxrt) return -1; Signal signal1 = new Signal(peak1.getSignal()); signal1.normalize(); Signal signal2 = new Signal(peak2.getSignal()); signal2.normalize(); double offset = bestOffSet(peak1, peak2, options.maxrt); for (int i = 0; i < signal2.getSize(); ++i) signal2.getX()[i] += offset; double correlation = signal2 .pearsonsCorrelation(signal1)[Statistical.PEARSON_CORRELATION]; if (correlation < 0.5) return -1; // the match-function optimizes toward 0 (it's a distance) return 1 - correlation; } }); // filter out all incomplete sets Vector<IPeakSet<IPeak>> valids = new Vector<IPeakSet<IPeak>>(); for (IPeakSet<IPeak> set : matches) { if (set.size() < options.input.size()) continue; valids.add((IPeakSet) set); } // calculate the alignment factors if (options.verbose) System.out.println("Calculating the alignment factors"); double medians[] = new double[valids.size() + 2]; DataFrame.Double dataframe = new DataFrame.Double(valids.size() + 2, options.input.size()); medians[0] = 0; medians[medians.length - 1] = maxrt; for (int i = 0; i < options.input.size(); ++i) { dataframe.set(0, i, 0.1); dataframe.set(dataframe.getNrRows() - 1, i, 0); } for (int matchid = 0; matchid < valids.size(); ++matchid) { IPeakSet<IPeak> match = valids.get(matchid); // find the most central double offsets[][] = new double[match.size()][match.size()]; for (int i = 0; i < match.size(); ++i) for (int j = i + 1; j < match.size(); ++j) { offsets[i][j] = bestOffSet(match.get(i), match.get(j), options.maxrt); offsets[j][i] = -offsets[i][j]; } int besti = 0; double bestabssum = Double.MAX_VALUE; for (int i = 0; i < match.size(); ++i) { double abssum = 0; for (int j = 0; j < match.size(); ++j) abssum += Math.abs(offsets[i][j]); if (abssum < bestabssum) { besti = i; bestabssum = abssum; } } for (int i = 0; i < match.size(); ++i) dataframe.set(matchid + 1, match.get(i).getMeasurementID(), (i == besti ? 0 : offsets[i][besti])); medians[matchid + 1] = match.get(besti).getRetentionTime(); dataframe.setRowName(matchid, Double.toString(match.get(besti).getRetentionTime())); } double minmedian = Statistical.min(medians); double maxmedian = Statistical.max(medians); // calculate for each profile the correction function PolynomialFunction functions[] = new PolynomialFunction[valids.size()]; for (int i = 0; i < options.input.size(); ++i) functions[i] = PolynomialFunction.fit(options.order, medians, dataframe.getCol(i)); // make a nice plot out of the whole thing if (options.verbose) System.out.println("Writing results"); if (options.image != null) { org.jfree.data.xy.XYSeriesCollection dataset = new org.jfree.data.xy.XYSeriesCollection(); JFreeChart linechart = ChartFactory.createXYLineChart(null, "Retention Time (seconds)", "offset", dataset, PlotOrientation.VERTICAL, true, // legend false, // tooltips false // urls ); // setup the colorkey Colormap colormap = new Colormap(Colormap.EXCEL); // get the structure behind the graph XYPlot plot = (XYPlot) linechart.getPlot(); XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) plot.getRenderer(); // setup the plot area linechart.setBackgroundPaint(java.awt.Color.WHITE); linechart.setBorderVisible(false); linechart.setAntiAlias(true); plot.setBackgroundPaint(java.awt.Color.WHITE); plot.setDomainGridlinesVisible(true); plot.setRangeGridlinesVisible(true); // create the datasets for (int i = 0; i < options.input.size(); ++i) { org.jfree.data.xy.XYSeries series = new org.jfree.data.xy.XYSeries(dataframe.getColName(i)); org.jfree.data.xy.XYSeries function = new org.jfree.data.xy.XYSeries( dataframe.getColName(i) + "-function"); dataset.addSeries(series); dataset.addSeries(function); renderer.setSeriesPaint(dataset.getSeriesCount() - 1, new java.awt.Color(colormap.getColor(i))); renderer.setSeriesPaint(dataset.getSeriesCount() - 2, new java.awt.Color(colormap.getColor(i))); renderer.setSeriesLinesVisible(dataset.getSeriesCount() - 2, false); renderer.setSeriesShapesVisible(dataset.getSeriesCount() - 2, true); // add the data-points for (int j = 0; j < valids.size(); ++j) series.add(medians[j], dataframe.get(j, i)); for (double x = minmedian; x < maxmedian; ++x) function.add(x, functions[i].getY(x)); } dataset.removeAllSeries(); for (int i = 0; i < options.input.size(); ++i) { Function function = functions[i]; org.jfree.data.xy.XYSeries series = new org.jfree.data.xy.XYSeries(dataframe.getColName(i)); dataset.addSeries(series); renderer.setSeriesPaint(i, new java.awt.Color(colormap.getColor(i))); renderer.setSeriesLinesVisible(i, false); renderer.setSeriesShapesVisible(i, true); // add the data-points for (int j = 0; j < valids.size(); ++j) series.add(medians[j], dataframe.get(j, i) - function.getY(medians[j])); } JFreeChartTools.writeAs(filetype, new FileOutputStream(options.image), linechart, 800, 500); } // save the selected if (options.selection != null) { Header header = new Header(); // set the number of peaks to be stored header.setNrPeaks(valids.size()); // create a set for the measurements SetInfo set = new SetInfo("", SetInfo.SET); header.addSetInfo(set); // create the measurement infos for (int i = 0; i < options.input.size(); ++i) { String file = options.input.get(i); // create the measurement info MeasurementInfo measurement = new MeasurementInfo(i, data.get(i).header.getMeasurementInfo(0)); measurement.addFileInfo(new FileInfo(file, file)); header.addMeasurementInfo(measurement); // add the file to the set set.addChild(new SetInfo(file, SetInfo.SET, i)); } // write the data PeakMLWriter.write(header, (Vector) valids, null, new GZIPOutputStream(new FileOutputStream(options.selection)), null); } // correct the values with the found function and save them for (int i = 0; i < options.input.size(); ++i) { Function function = functions[i]; ParseResult result = data.get(i); IPeakSet<MassChromatogram<Peak>> peakset = (IPeakSet<MassChromatogram<Peak>>) result.measurement; for (IPeak peak : peakset) align(peak, function); File filename = new File(options.input.get(i)); String name = filename.getName(); PeakMLWriter.write(result.header, (Vector) peakset.getPeaks(), null, new GZIPOutputStream(new FileOutputStream(options.output + "/" + name)), null); } } catch (Exception e) { Tool.unexpectedError(e, application); } }
From source file:de.tudarmstadt.ukp.csniper.resbuild.stuff.BncCheckDocuments.java
public static void main(String[] args) throws IOException { boolean enabled = false; for (File f : FileUtils.listFiles(new File(BASE), new String[] { "xml" }, true)) { BufferedInputStream bis = null; try {//from w ww.j a va 2s.com bis = new BufferedInputStream(new FileInputStream(f)); int c; StringBuilder sb = new StringBuilder(); while ((c = bis.read()) != '>') { if (enabled) { if (c == '"') { enabled = false; break; } else { sb.append((char) c); } } if (c == '"') { enabled = true; } } String name = f.getName().substring(0, 3); String id = sb.toString(); if (!name.equals(id)) { System.out.println("Name is [" + name + "], but ID is [" + id + "]."); } } catch (IOException e) { e.printStackTrace(); } finally { IOUtils.closeQuietly(bis); } } }
From source file:com.interflora.ftp.SampleFTPS.java
public static final void main(String[] args) { boolean storeFile = true, binaryTransfer = false, error = false, listFiles = false, listNames = false, hidden = false;//from w w w.ja v a2 s . co m boolean localActive = false, useEpsvWithIPv4 = false, feat = false, printHash = false; boolean mlst = false, mlsd = false; boolean lenient = false; long keepAliveTimeout = -1; int controlKeepAliveReplyTimeout = -1; int minParams = 5; // listings require 3 params String protocol = "TLS,false"; // SSL protocol String doCommand = null; String trustmgr = "all"; String proxyHost = null; int proxyPort = 80; String proxyUser = null; String proxyPassword = null; //sample : rose-misc01.hyd.ftd.untd.com rosedev test123 /TestSftp C:/Users/skarin/Desktop/RosePaths.txt //172.16.160.70 demand quevfoc5 /TestSftp C:/Users/skarin/Desktop/RosePaths.txt int base = 0; for (base = 0; base < args.length; base++) { if (args[base].equals("-s")) { storeFile = true; } else if (args[base].equals("-a")) { localActive = true; } else if (args[base].equals("-b")) { binaryTransfer = true; } else if (args[base].equals("-c")) { doCommand = args[++base]; minParams = 3; } else if (args[base].equals("-d")) { mlsd = true; minParams = 3; } else if (args[base].equals("-e")) { useEpsvWithIPv4 = true; } else if (args[base].equals("-f")) { feat = true; minParams = 3; } else if (args[base].equals("-h")) { hidden = true; } else if (args[base].equals("-k")) { keepAliveTimeout = Long.parseLong(args[++base]); } else if (args[base].equals("-l")) { listFiles = true; minParams = 3; } else if (args[base].equals("-L")) { lenient = true; } else if (args[base].equals("-n")) { listNames = true; minParams = 3; } else if (args[base].equals("-p")) { protocol = args[++base]; } else if (args[base].equals("-t")) { mlst = true; minParams = 3; } else if (args[base].equals("-w")) { controlKeepAliveReplyTimeout = Integer.parseInt(args[++base]); } else if (args[base].equals("-T")) { trustmgr = args[++base]; } else if (args[base].equals("-PrH")) { proxyHost = args[++base]; String parts[] = proxyHost.split(":"); if (parts.length == 2) { proxyHost = parts[0]; proxyPort = Integer.parseInt(parts[1]); } } else if (args[base].equals("-PrU")) { proxyUser = args[++base]; } else if (args[base].equals("-PrP")) { proxyPassword = args[++base]; } else if (args[base].equals("-#")) { printHash = true; } else { break; } } int remain = args.length - base; if (remain < minParams) // server, user, pass, remote, local [protocol] { System.err.println(USAGE); System.exit(1); } String server = args[base++]; int port = 0; String parts[] = server.split(":"); if (parts.length == 2) { server = parts[0]; port = Integer.parseInt(parts[1]); } String username = args[base++]; String password = args[base++]; String remote = null; if (args.length - base > 0) { remote = args[base++]; } String local = null; if (args.length - base > 0) { local = args[base++]; } final FTPClient ftp; if (protocol == null) { if (proxyHost != null) { System.out.println("Using HTTP proxy server: " + proxyHost); ftp = new FTPHTTPClient(proxyHost, proxyPort, proxyUser, proxyPassword); } else { ftp = new FTPClient(); } } else { FTPSClient ftps; if (protocol.equals("true")) { ftps = new FTPSClient(true); } else if (protocol.equals("false")) { ftps = new FTPSClient(false); } else { String prot[] = protocol.split(","); if (prot.length == 1) { // Just protocol ftps = new FTPSClient(protocol); } else { // protocol,true|false ftps = new FTPSClient(prot[0], Boolean.parseBoolean(prot[1])); } } ftp = ftps; if ("all".equals(trustmgr)) { ftps.setTrustManager(TrustManagerUtils.getAcceptAllTrustManager()); } else if ("valid".equals(trustmgr)) { ftps.setTrustManager(TrustManagerUtils.getValidateServerCertificateTrustManager()); } else if ("none".equals(trustmgr)) { ftps.setTrustManager(null); } /* try{ //ftps.setFileType(FTP.ASCII_FILE_TYPE); ftps.execPBSZ(0); // Set protection buffer size ftps.execPROT("C"); // Set data channel protection to private }catch(IOException ex ){ex.printStackTrace();}; */ } // System.out.println("After I/O Exception"); if (printHash) { ftp.setCopyStreamListener(createListener()); } if (keepAliveTimeout >= 0) { ftp.setControlKeepAliveTimeout(keepAliveTimeout); } if (controlKeepAliveReplyTimeout >= 0) { ftp.setControlKeepAliveReplyTimeout(controlKeepAliveReplyTimeout); } ftp.setListHiddenFiles(hidden); // suppress login details ftp.addProtocolCommandListener(new PrintCommandListener(new PrintWriter(System.out), true)); try { int reply; if (port > 0) { ftp.connect(server, port); } else { System.out.println("Trying to Connect to the server \t" + server); ftp.connect(server); } System.out.println("Connected to " + server + " on " + (port > 0 ? port : ftp.getDefaultPort())); // After connection attempt, you should check the reply code to verify // success. reply = ftp.getReplyCode(); if (!FTPReply.isPositiveCompletion(reply)) { ftp.disconnect(); System.err.println("FTP server refused connection."); System.exit(1); } } catch (IOException e) { if (ftp.isConnected()) { try { ftp.disconnect(); } catch (IOException f) { // do nothing } } System.err.println("Could not connect to server."); e.printStackTrace(); System.exit(1); } __main: try { if (!ftp.login(username, password)) { ftp.logout(); error = true; break __main; } System.out.println("Remote system is " + ftp.getSystemType()); if (binaryTransfer) { ftp.setFileType(FTP.BINARY_FILE_TYPE); } // Use passive mode as default because most of us are // behind firewalls these days. if (localActive) { ftp.enterLocalActiveMode(); } else { ftp.enterLocalPassiveMode(); } ftp.setUseEPSVwithIPv4(useEpsvWithIPv4); if (storeFile) { //InputStream input; File fname = new File(local); FileInputStream input = new FileInputStream(fname); String localfilename = fname.getName(); System.out.println("Local file name " + localfilename); ftp.storeFile(remote + "/test/" + localfilename, input); input.close(); } else if (listFiles) { if (lenient) { FTPClientConfig config = new FTPClientConfig(); config.setLenientFutureDates(true); ftp.configure(config); } for (FTPFile f : ftp.listFiles(remote)) { System.out.println(f.getRawListing()); System.out.println(f.toFormattedString()); } } else if (mlsd) { for (FTPFile f : ftp.mlistDir(remote)) { System.out.println(f.getRawListing()); System.out.println(f.toFormattedString()); } } else if (mlst) { FTPFile f = ftp.mlistFile(remote); if (f != null) { System.out.println(f.toFormattedString()); } } else if (listNames) { for (String s : ftp.listNames(remote)) { System.out.println(s); } } else if (feat) { // boolean feature check if (remote != null) { // See if the command is present if (ftp.hasFeature(remote)) { System.out.println("Has feature: " + remote); } else { if (FTPReply.isPositiveCompletion(ftp.getReplyCode())) { System.out.println("FEAT " + remote + " was not detected"); } else { System.out.println("Command failed: " + ftp.getReplyString()); } } // Strings feature check String[] features = ftp.featureValues(remote); if (features != null) { for (String f : features) { System.out.println("FEAT " + remote + "=" + f + "."); } } else { if (FTPReply.isPositiveCompletion(ftp.getReplyCode())) { System.out.println("FEAT " + remote + " is not present"); } else { System.out.println("Command failed: " + ftp.getReplyString()); } } } else { if (ftp.features()) { // Command listener has already printed the output } else { System.out.println("Failed: " + ftp.getReplyString()); } } } else if (doCommand != null) { if (ftp.doCommand(doCommand, remote)) { // Command listener has already printed the output // for(String s : ftp.getReplyStrings()) { // System.out.println(s); // } } else { System.out.println("Failed: " + ftp.getReplyString()); } } else { OutputStream output; output = new FileOutputStream(local); ftp.retrieveFile(remote, output); output.close(); } ftp.noop(); // check that control connection is working OK ftp.logout(); } catch (FTPConnectionClosedException e) { error = true; System.err.println("Server closed connection."); e.printStackTrace(); } catch (IOException e) { error = true; e.printStackTrace(); } finally { if (ftp.isConnected()) { try { ftp.disconnect(); } catch (IOException f) { // do nothing } } } System.exit(error ? 1 : 0); }
From source file:de.tudarmstadt.ukp.experiments.dip.wp1.documents.Step8GoldDataAggregator.java
public static void main(String[] args) throws Exception { String inputDir = args[0] + "/"; // output dir File outputDir = new File(args[1]); File turkersConfidence = new File(args[2]); if (outputDir.exists()) { outputDir.delete();//from w w w . java2 s . com } outputDir.mkdir(); List<String> annotatorsIDs = new ArrayList<>(); // for (File f : FileUtils.listFiles(new File(inputDir), new String[] { "xml" }, false)) { // QueryResultContainer queryResultContainer = QueryResultContainer // .fromXML(FileUtils.readFileToString(f, "utf-8")); // for (QueryResultContainer.SingleRankedResult rankedResults : queryResultContainer.rankedResults) { // for (QueryResultContainer.MTurkRelevanceVote relevanceVote : rankedResults.mTurkRelevanceVotes) { // if (!annotatorsIDs.contains(relevanceVote.turkID)) // annotatorsIDs.add(relevanceVote.turkID); // } // } // } HashMap<String, Integer> countVotesForATurker = new HashMap<>(); // creates temporary file with format for mace // Hashmap annotations: key is the id of a document and a sentence // Value is an array votes[] of turkers decisions: true or false (relevant or not) // the length of this array equals the number of annotators in List<String> annotatorsIDs. // If an annotator worked on the task his decision is written in the array otherwise the value is NULL // key: queryID + clueWebID + sentenceID // value: true and false annotations TreeMap<String, Annotations> annotations = new TreeMap<>(); for (File f : FileUtils.listFiles(new File(inputDir), new String[] { "xml" }, false)) { QueryResultContainer queryResultContainer = QueryResultContainer .fromXML(FileUtils.readFileToString(f, "utf-8")); System.out.println("Reading " + f.getName()); for (QueryResultContainer.SingleRankedResult rankedResults : queryResultContainer.rankedResults) { String documentID = rankedResults.clueWebID; for (QueryResultContainer.MTurkRelevanceVote relevanceVote : rankedResults.mTurkRelevanceVotes) { Integer turkerID; if (!annotatorsIDs.contains(relevanceVote.turkID)) { annotatorsIDs.add(relevanceVote.turkID); turkerID = annotatorsIDs.size() - 1; } else { turkerID = annotatorsIDs.indexOf(relevanceVote.turkID); } Integer count = countVotesForATurker.get(relevanceVote.turkID); if (count == null) { count = 0; } count++; countVotesForATurker.put(relevanceVote.turkID, count); String id; List<Integer> trueVotes; List<Integer> falseVotes; for (QueryResultContainer.SingleSentenceRelevanceVote singleSentenceRelevanceVote : relevanceVote.singleSentenceRelevanceVotes) if (!"".equals(singleSentenceRelevanceVote.sentenceID)) { id = f.getName() + "_" + documentID + "_" + singleSentenceRelevanceVote.sentenceID; Annotations turkerVotes = annotations.get(id); if (turkerVotes == null) { trueVotes = new ArrayList<>(); falseVotes = new ArrayList<>(); turkerVotes = new Annotations(trueVotes, falseVotes); } trueVotes = turkerVotes.trueAnnotations; falseVotes = turkerVotes.falseAnnotations; if ("true".equals(singleSentenceRelevanceVote.relevant)) { // votes[turkerID] = true; trueVotes.add(turkerID); } else if ("false".equals(singleSentenceRelevanceVote.relevant)) { // votes[turkerID] = false; falseVotes.add(turkerID); } else { throw new IllegalStateException("Annotation value of sentence " + singleSentenceRelevanceVote.sentenceID + " in " + rankedResults.clueWebID + " equals " + singleSentenceRelevanceVote.relevant); } try { int allVotesCount = trueVotes.size() + falseVotes.size(); if (allVotesCount > 5) { System.err.println(id + " doesn't have 5 annotators: true: " + trueVotes.size() + " false: " + falseVotes.size()); // nasty hack, we're gonna strip some data; true votes first /* we can't do that, it breaks something down the line int toRemove = allVotesCount - 5; if (trueVotes.size() >= toRemove) { trueVotes = trueVotes .subList(0, trueVotes.size() - toRemove); } else if ( falseVotes.size() >= toRemove) { falseVotes = falseVotes .subList(0, trueVotes.size() - toRemove); } */ System.err.println("Adjusted: " + id + " doesn't have 5 annotators: true: " + trueVotes.size() + " false: " + falseVotes.size()); } } catch (IllegalStateException e) { e.printStackTrace(); } turkerVotes.trueAnnotations = trueVotes; turkerVotes.falseAnnotations = falseVotes; annotations.put(id, turkerVotes); } else { throw new IllegalStateException( "Empty Sentence ID in " + f.getName() + " for turker " + turkerID); } } } } File tmp = printHashMap(annotations, annotatorsIDs.size()); String file = TEMP_DIR + "/" + tmp.getName(); MACE.main(new String[] { "--prefix", file }); //gets the keys of the documents and sentences ArrayList<String> lines = (ArrayList<String>) FileUtils.readLines(new File(file + ".prediction")); int i = 0; TreeMap<String, TreeMap<String, ArrayList<HashMap<String, String>>>> ids = new TreeMap<>(); ArrayList<HashMap<String, String>> sentences; if (lines.size() != annotations.size()) { throw new IllegalStateException( "The size of prediction file is " + lines.size() + "but expected " + annotations.size()); } for (Map.Entry entry : annotations.entrySet()) { //1001.xml_clueweb12-1905wb-13-07360_8783 String key = (String) entry.getKey(); String[] IDs = key.split("_"); if (IDs.length > 2) { String queryID = IDs[0]; String clueWebID = IDs[1]; String sentenceID = IDs[2]; TreeMap<String, ArrayList<HashMap<String, String>>> clueWebIDs = ids.get(queryID); if (clueWebIDs == null) { clueWebIDs = new TreeMap<>(); } sentences = clueWebIDs.get(clueWebID); if (sentences == null) { sentences = new ArrayList<>(); } HashMap<String, String> sentence = new HashMap<>(); sentence.put(sentenceID, lines.get(i)); sentences.add(sentence); clueWebIDs.put(clueWebID, sentences); ids.put(queryID, clueWebIDs); } else { throw new IllegalStateException("Wrong ID " + key); } i++; } for (Map.Entry entry : ids.entrySet()) { TreeMap<Integer, String> value = (TreeMap<Integer, String>) entry.getValue(); String queryID = (String) entry.getKey(); QueryResultContainer queryResultContainer = QueryResultContainer .fromXML(FileUtils.readFileToString(new File(inputDir, queryID), "utf-8")); for (QueryResultContainer.SingleRankedResult rankedResults : queryResultContainer.rankedResults) { for (Map.Entry val : value.entrySet()) { String clueWebID = (String) val.getKey(); if (clueWebID.equals(rankedResults.clueWebID)) { List<QueryResultContainer.SingleSentenceRelevanceVote> goldEstimatedLabels = new ArrayList<>(); List<QueryResultContainer.SingleSentenceRelevanceVote> turkersVotes = new ArrayList<>(); int size = 0; int hitSize = 0; String hitID = ""; for (QueryResultContainer.MTurkRelevanceVote vote : rankedResults.mTurkRelevanceVotes) { if (!hitID.equals(vote.hitID)) { hitID = vote.hitID; hitSize = vote.singleSentenceRelevanceVotes.size(); size = size + hitSize; turkersVotes.addAll(vote.singleSentenceRelevanceVotes); } else { if (vote.singleSentenceRelevanceVotes.size() != hitSize) { hitSize = vote.singleSentenceRelevanceVotes.size(); size = size + hitSize; turkersVotes.addAll(vote.singleSentenceRelevanceVotes); } } } ArrayList<HashMap<String, String>> sentenceList = (ArrayList<HashMap<String, String>>) val .getValue(); if (sentenceList.size() != turkersVotes.size()) { try { throw new IllegalStateException("Expected size of annotations is " + turkersVotes.size() + "but found " + sentenceList.size() + " for document " + rankedResults.clueWebID + " in " + queryID); } catch (IllegalStateException ex) { ex.printStackTrace(); } } for (QueryResultContainer.SingleSentenceRelevanceVote s : turkersVotes) { String valSentence = null; for (HashMap<String, String> anno : sentenceList) { if (anno.keySet().contains(s.sentenceID)) { valSentence = anno.get(s.sentenceID); } } QueryResultContainer.SingleSentenceRelevanceVote singleSentenceVote = new QueryResultContainer.SingleSentenceRelevanceVote(); singleSentenceVote.sentenceID = s.sentenceID; if (("false").equals(valSentence)) { singleSentenceVote.relevant = "false"; } else if (("true").equals(valSentence)) { singleSentenceVote.relevant = "true"; } else { throw new IllegalStateException("Annotation value of sentence " + singleSentenceVote.sentenceID + " equals " + val.getValue()); } goldEstimatedLabels.add(singleSentenceVote); } rankedResults.goldEstimatedLabels = goldEstimatedLabels; } } } File outputFile = new File(outputDir, queryID); FileUtils.writeStringToFile(outputFile, queryResultContainer.toXML(), "utf-8"); System.out.println("Finished " + outputFile); } ArrayList<String> annotators = (ArrayList<String>) FileUtils.readLines(new File(file + ".competence")); FileWriter fileWriter; StringBuilder sb = new StringBuilder(); for (int j = 0; j < annotatorsIDs.size(); j++) { String[] s = annotators.get(0).split("\t"); Float score = Float.parseFloat(s[j]); String turkerID = annotatorsIDs.get(j); System.out.println(turkerID + " " + score + " " + countVotesForATurker.get(turkerID)); sb.append(turkerID).append(" ").append(score).append(" ").append(countVotesForATurker.get(turkerID)) .append("\n"); } fileWriter = new FileWriter(turkersConfidence); fileWriter.append(sb.toString()); fileWriter.close(); }
From source file:WriteIndex.java
/** * @param args/* w ww .j a v a 2s. c om*/ */ public static void main(String[] args) throws IOException { File docs = new File("documents"); File indexDir = new File(INDEX_DIRECTORY); Directory directory = FSDirectory.open(indexDir); Analyzer analyzer = new StandardAnalyzer(Version.LUCENE_35); IndexWriterConfig conf = new IndexWriterConfig(Version.LUCENE_35, analyzer); IndexWriter writer = new IndexWriter(directory, conf); writer.deleteAll(); for (File file : docs.listFiles()) { Metadata metadata = new Metadata(); ContentHandler handler = new BodyContentHandler(); ParseContext context = new ParseContext(); Parser parser = new AutoDetectParser(); InputStream stream = new FileInputStream(file); try { parser.parse(stream, handler, metadata, context); } catch (TikaException e) { e.printStackTrace(); } catch (SAXException e) { e.printStackTrace(); } finally { stream.close(); } String text = handler.toString(); String fileName = file.getName(); Document doc = new Document(); doc.add(new Field("file", fileName, Store.YES, Index.NO)); for (String key : metadata.names()) { String name = key.toLowerCase(); String value = metadata.get(key); if (StringUtils.isBlank(value)) { continue; } if ("keywords".equalsIgnoreCase(key)) { for (String keyword : value.split(",?(\\s+)")) { doc.add(new Field(name, keyword, Store.YES, Index.NOT_ANALYZED)); } } else if ("title".equalsIgnoreCase(key)) { doc.add(new Field(name, value, Store.YES, Index.ANALYZED)); } else { doc.add(new Field(name, fileName, Store.YES, Index.NOT_ANALYZED)); } } doc.add(new Field("text", text, Store.NO, Index.ANALYZED)); writer.addDocument(doc); } writer.commit(); writer.deleteUnusedFiles(); System.out.println(writer.maxDoc() + " documents written"); }
From source file:ms1quant.MS1Quant.java
/** * @param args the command line arguments MS1Quant parameterfile *//*from ww w .j a v a 2 s. c om*/ 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:main.RankerOCR.java
/** * Command line interface for RankerOCR. * <p>/* w ww . j a va2 s . c o m*/ * <b>Command line input:</b> * <ul> * usage: java -jar Ranker-OCR [options] * </ul> * <b>Options list:</b> * <ul> * <li>-gui Launch a graphical user interface</li> * <li>-help Show the help</li> * <li>-indoc1 [arg] Set the file name of the original document</li> * <li>-indoc2 [arg] Set the file name of the document to compare</li> * <li>-ranker [arg] Set the ranker used for the comparison</li> * <li>-outdoc [arg] Set the document where write the results</li> * <li>-separator [arg] Set the delimiter char use in the CSV out file</li> * </ul> * <b>Return values are if error:</b> * <ul> * <li>(-1) The precision parameter is not a number.</li> * <li>(-2) The precision parameter is lower than 0.</li> * <li>(-3) The precision parameter is greater than 10.</li> * <li>(-11) The ranker name is wrong</li> * <li>(-21) The separator char is empty</li> * <li>(-22) The separator is not a char</li> * <li>(-31) File name doesn't exist</li> * <li>(-32) File name is not a file</li> * <li>(-33) Error when access to documents files</li> * <li>(-34) Output file can not be write</li> * <li>(-35) Output file can not be created</li> * <li>(-41) Error when parsing parameters</li> * <li>(-100) Internal error when creating the ranker. Please report a * bug</li> * <li>(-101) Internal error when get the ranker list. Please report a * bug.</li> * <li>(-102) Error when access to help file. Please report a bug.</li> * </ul> * <p> * @param args Argument array which can have the values from options list */ public static void main(String[] args) { //Parse command line CommandLineParser parser = new GnuParser(); try { CommandLine cmd = parser.parse(options, args); if (cmd.hasOption("help")) { showHelp(hf, options); } else if (cmd.hasOption("gui")) { display.DispalyRankerOCR.main(new String[] {}); } else if (cmd.hasOption("indoc1") && cmd.hasOption("indoc2") && cmd.hasOption("outdoc")) { //<editor-fold defaultstate="collapsed" desc="Rank documents"> //Prepare parameter Class ranker = evalRanker(cmd.getOptionValue("ranker", "SimpleRanker")); char separator = evalSeparator(cmd.getOptionValue("separator", "\t")); File f1 = evalInputFile(cmd.getOptionValue("indoc1", "")); File f2 = evalInputFile(cmd.getOptionValue("indoc2", "")); File f3 = evalOutputFile(cmd.getOptionValue("outdoc", ""), separator); //Read file String s1 = readInputDocText(f1); String s2 = readInputDocText(f2); //Compare file double percent = rankDocuments(s1, s2, ranker); //Write result String[] s = { Double.toString(percent), ranker.getSimpleName(), f1.getName(), f2.getName(), f1.getParent(), f2.getParent(), new Date().toString() }; writeOutpuDocCsv(f3, separator, s); //</editor-fold> } else { printFormated("java -jar Ranker-OCR [options] please type " + "-help for more info"); } } catch (ParseException ex) { printFormated(ex.getLocalizedMessage()); System.exit(-41); } }
From source file:eu.annocultor.utils.OntologySubtractor.java
public static void main(String[] args) throws Exception { boolean copy = checkNoCopyOption(args); if (args.length == 2 || args.length == 3) { File sourceDir = new File(args[0]); File destinationDir = new File(args[1]); checkSrcAndDstDirs(sourceDir, destinationDir); Collection<String> filesWithDeletedStatements = listNameStamsForFilesWithDeletedStatements(sourceDir); if (filesWithDeletedStatements.isEmpty()) { System.out.println(//from w ww . j a va 2 s . c o m "Did not found any file *.*.*.deleted.rdf with statements to be deleted. Do nothing and exit."); } else { System.out.println( "Found " + filesWithDeletedStatements.size() + " files with statements to be deleted"); System.out.println( "Copying all RDF files from " + sourceDir.getName() + " to " + destinationDir.getName()); if (copy) { copyRdfFiles(sourceDir, destinationDir); } sutractAll(sourceDir, destinationDir, filesWithDeletedStatements); } } else { for (Object string : IOUtils.readLines(new AutoCloseInputStream( OntologySubtractor.class.getResourceAsStream("/subtractor/readme.txt")))) { System.out.println(string.toString()); } } }
From source file:com.l2jfree.tools.ProjectSettingsSynchronizer.java
public static void main(String[] args) throws IOException { final File src = new File(".").getCanonicalFile(); System.out.println("Copying from: " + src); System.out.println();//from ww w . j a va 2s . co m final List<File> destinations = new ArrayList<File>(); for (File dest : src.getParentFile().listFiles()) { if (dest.isHidden() || !dest.isDirectory()) continue; destinations.add(dest); System.out.println("Copying to: " + dest); } System.out.println(); // .project System.out.println(".project"); System.out.println("================================================================================"); { final List<String> lines = FileUtils.readLines(new File(src, ".project")); for (File dest : destinations) { lines.set(2, lines.get(2).replaceAll(src.getName(), dest.getName())); writeLines(dest, ".project", lines); lines.set(2, lines.get(2).replaceAll(dest.getName(), src.getName())); } } System.out.println(); // .classpath System.out.println(".classpath"); System.out.println("================================================================================"); { final List<String> lines = FileUtils.readLines(new File(src, ".classpath")); for (File dest : destinations) { if (dest.getName().endsWith("-main") || dest.getName().endsWith("-datapack")) { final ArrayList<String> tmp = new ArrayList<String>(); for (String line : lines) if (!line.contains("classpathentry")) tmp.add(line); writeLines(dest, ".classpath", tmp); continue; } writeLines(dest, ".classpath", lines); } } System.out.println(); // .settings System.out.println(".settings"); System.out.println("================================================================================"); for (File settingsFile : new File(src, ".settings").listFiles()) { if (settingsFile.getName().endsWith(".prefs")) { System.out.println(".settings/" + settingsFile.getName()); System.out.println( "--------------------------------------------------------------------------------"); final List<String> lines = FileUtils.readLines(settingsFile); if (lines.get(0).startsWith("#")) lines.remove(0); for (File dest : destinations) { writeLines(new File(dest, ".settings"), settingsFile.getName(), lines); } System.out.println(); } } System.out.println(); }
From source file:com.clustercontrol.agent.Agent.java
/** * ?//from w w w . j a v a 2 s . c o m * * @param args ?? */ public static void main(String[] args) throws Exception { // ? if (args.length != 1) { System.out.println("Usage : java Agent [Agent.properties File Path]"); System.exit(1); } try { // System m_log.info("starting Hinemos Agent..."); m_log.info("java.vm.version = " + System.getProperty("java.vm.version")); m_log.info("java.vm.vendor = " + System.getProperty("java.vm.vendor")); m_log.info("java.home = " + System.getProperty("java.home")); m_log.info("os.name = " + System.getProperty("os.name")); m_log.info("os.arch = " + System.getProperty("os.arch")); m_log.info("os.version = " + System.getProperty("os.version")); m_log.info("user.name = " + System.getProperty("user.name")); m_log.info("user.dir = " + System.getProperty("user.dir")); m_log.info("user.country = " + System.getProperty("user.country")); m_log.info("user.language = " + System.getProperty("user.language")); m_log.info("file.encoding = " + System.getProperty("file.encoding")); // System(SET) String limitKey = "jdk.xml.entityExpansionLimit"; // TODO JRE??????????????????? System.setProperty(limitKey, "0"); m_log.info(limitKey + " = " + System.getProperty(limitKey)); // TODO ???agentHome // ?????????? File file = new File(args[0]); agentHome = file.getParentFile().getParent() + "/"; m_log.info("agentHome=" + agentHome); // long startDate = HinemosTime.currentTimeMillis(); m_log.info("start date = " + new Date(startDate) + "(" + startDate + ")"); agentInfo.setStartupTime(startDate); // Agent?? m_log.info("Agent.properties = " + args[0]); // ? File scriptDir = new File(agentHome + "script/"); if (scriptDir.exists()) { File[] listFiles = scriptDir.listFiles(); if (listFiles != null) { for (File f : listFiles) { boolean ret = f.delete(); if (ret) { m_log.debug("delete script : " + f.getName()); } else { m_log.warn("delete script error : " + f.getName()); } } } else { m_log.warn("listFiles is null"); } } else { //???????? boolean ret = scriptDir.mkdir(); if (!ret) { m_log.warn("mkdir error " + scriptDir.getPath()); } } // queue? m_sendQueue = new SendQueue(); // Agent? Agent agent = new Agent(args[0]); //----------------- //-- //----------------- m_log.debug("exec() : create topic "); m_receiveTopic = new ReceiveTopic(m_sendQueue); m_receiveTopic.setName("ReceiveTopicThread"); m_log.info("receiveTopic start 1"); m_receiveTopic.start(); m_log.info("receiveTopic start 2"); // ? agent.exec(); m_log.info("Hinemos Agent started"); // ? agent.waitAwakeAgent(); } catch (Throwable e) { m_log.error("Agent.java: Runtime Exception Occurred. " + e.getClass().getName() + ", " + e.getMessage(), e); } }