List of usage examples for java.lang String trim
public String trim()
From source file:edu.cmu.tetrad.cli.search.FgsDiscrete.java
/** * @param args the command line arguments */// w ww. j a va2 s. com public static void main(String[] args) { if (args == null || args.length == 0 || Args.hasLongOption(args, "help")) { Args.showHelp("fgs-discrete", MAIN_OPTIONS); return; } parseArgs(args); System.out.println("================================================================================"); System.out.printf("FGS Discrete (%s)%n", DateTime.printNow()); System.out.println("================================================================================"); String argInfo = createArgsInfo(); System.out.println(argInfo); LOGGER.info("=== Starting FGS Discrete: " + Args.toString(args, ' ')); LOGGER.info(argInfo.trim().replaceAll("\n", ",").replaceAll(" = ", "=")); Set<String> excludedVariables = (excludedVariableFile == null) ? Collections.EMPTY_SET : getExcludedVariables(); runPreDataValidations(excludedVariables, System.err); DataSet dataSet = readInDataSet(excludedVariables); runOptionalDataValidations(dataSet, System.err); Path outputFile = Paths.get(dirOut.toString(), outputPrefix + ".txt"); try (PrintStream writer = new PrintStream( new BufferedOutputStream(Files.newOutputStream(outputFile, StandardOpenOption.CREATE)))) { String runInfo = createOutputRunInfo(excludedVariables, dataSet); writer.println(runInfo); String[] infos = runInfo.trim().replaceAll("\n\n", ";").split(";"); for (String s : infos) { LOGGER.info(s.trim().replaceAll("\n", ",").replaceAll(":,", ":").replaceAll(" = ", "=")); } Graph graph = runFgsDiscrete(dataSet, writer); writer.println(); writer.println(graph.toString()); if (graphML) { writeOutGraphML(graph, Paths.get(dirOut.toString(), outputPrefix + "_graph.txt")); } } catch (IOException exception) { LOGGER.error("FGS Discrete failed.", exception); System.err.printf("%s: FGS Discrete failed.%n", DateTime.printNow()); System.out.println("Please see log file for more information."); System.exit(-128); } System.out.printf("%s: FGS Discrete finished! Please see %s for details.%n", DateTime.printNow(), outputFile.getFileName().toString()); LOGGER.info(String.format("FGS Discrete finished! Please see %s for details.", outputFile.getFileName().toString())); }
From source file:com.kactech.otj.examples.App_otj.java
@SuppressWarnings("unchecked") public static void main(String[] args) throws Exception { String command = null;//from w ww . ja va2 s.co m String hisacct = null; String hisacctName = null; String hisacctAsset = null; String asset = null; String assetName = null; List<String> argList = null; boolean newAccount = false; File dir = null; ConnectionInfo connection = null; List<ScriptFilter> filters = null; CommandLineParser parser = new GnuParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (Exception e) { System.err.println("Command-line parsing error: " + e.getMessage()); help(); System.exit(-1); } if (cmd.hasOption('h')) { help(); System.exit(0); } @SuppressWarnings("unchecked") List<String> list = cmd.getArgList(); if (list.size() > 1) { System.err.println("only one command is supported, you've typed " + list); help(); System.exit(-1); } if (list.size() > 0) command = list.get(0).trim(); List<SampleAccount> accounts = ExamplesUtils.getSampleAccounts(); if (cmd.hasOption('s')) { String v = cmd.getOptionValue('s').trim(); connection = ExamplesUtils.findServer(v); if (connection == null) { System.err.println("unknown server: " + v); System.exit(-1); } } else { connection = ExamplesUtils.findServer(DEF_SERVER_NAME); if (connection == null) { System.err.println("default server not found server: " + DEF_SERVER_NAME); System.exit(-1); } } if (cmd.hasOption('t')) { String v = cmd.getOptionValue('t'); for (SampleAccount ac : accounts) if (ac.accountName.startsWith(v)) { hisacct = ac.accountID; hisacctName = ac.accountName; hisacctAsset = ac.assetID; break; } if (hisacct == null) if (mayBeValid(v)) hisacct = v; else { System.err.println("invalid hisacct: " + v); System.exit(-1); } } if (cmd.hasOption('p')) { String v = cmd.getOptionValue('p'); for (SampleAccount ac : accounts) if (ac.assetName.startsWith(v)) { asset = ac.assetID; assetName = ac.assetName; break; } if (asset == null) if (mayBeValid(v)) asset = v; else { System.err.println("invalid asset: " + v); System.exit(-1); } } if (cmd.hasOption('a')) { String v = cmd.getOptionValue('a'); argList = new ArrayList<String>(); boolean q = false; StringBuilder b = new StringBuilder(); for (int i = 0; i < v.length(); i++) { char c = v.charAt(i); if (c == '"') { if (q) { argList.add(b.toString()); b = null; q = false; continue; } if (b != null) argList.add(b.toString()); b = new StringBuilder(); q = true; continue; } if (c == ' ' || c == '\t') { if (q) { b.append(c); continue; } if (b != null) argList.add(b.toString()); b = null; continue; } if (b == null) b = new StringBuilder(); b.append(c); } if (b != null) argList.add(b.toString()); if (q) { System.err.println("unclosed quote in args: " + v); System.exit(-1); } } dir = new File(cmd.hasOption('d') ? cmd.getOptionValue('d') : DEF_CLIENT_DIR); if (cmd.hasOption('x')) del(dir); newAccount = cmd.hasOption('n'); if (cmd.hasOption('f')) { filters = new ArrayList<ScriptFilter>(); ScriptEngineManager manager = new ScriptEngineManager(); ScriptEngine engine = manager.getEngineByName("JavaScript"); Compilable compilingEngine = (Compilable) engine; for (String fn : cmd.getOptionValue('f').split(",")) { fn = fn.trim(); if (fn.isEmpty()) continue; fn += ".js"; Reader r = null; try { r = new InputStreamReader(new FileInputStream(new File("filters", fn)), Utils.UTF8); } catch (Exception e) { try { r = new InputStreamReader( App_otj.class.getResourceAsStream("/com/kactech/otj/examples/filters/" + fn)); } catch (Exception e2) { } } if (r == null) { System.err.println("filter not found: " + fn); System.exit(-1); } else try { CompiledScript compiled = compilingEngine.compile(r); ScriptFilter sf = new ScriptFilter(compiled); filters.add(sf); } catch (Exception ex) { System.err.println("error while loading " + fn + ": " + ex); System.exit(-1); } } } System.out.println("server: " + connection.getEndpoint() + " " + connection.getID()); System.out.println("command: '" + command + "'"); System.out.println("args: " + argList); System.out.println("hisacct: " + hisacct); System.out.println("hisacctName: " + hisacctName); System.out.println("hisacctAsset: " + hisacctAsset); System.out.println("asset: " + asset); System.out.println("assetName: " + assetName); if (asset != null && hisacctAsset != null && !asset.equals(hisacctAsset)) { System.err.println("asset differs from hisacctAsset"); System.exit(-1); } EClient client = new EClient(dir, connection); client.setAssetType(asset != null ? asset : hisacctAsset); client.setCreateNewAccount(newAccount); if (filters != null) client.setFilters(filters); try { Utils.init(); Client.DEBUG_JSON = true; client.init(); if ("balance".equals(command)) System.out.println("Balance: " + client.getAccount().getBalance().getAmount()); else if ("acceptall".equals(command)) client.processInbox(); else if ("transfer".equals(command)) { if (hisacct == null) System.err.println("please specify --hisacct"); else { int idx = argList != null ? argList.indexOf("amount") : -1; if (idx < 0) System.err.println("please specify amount"); else if (idx == argList.size()) System.err.println("amount argument needs value"); else { Long amount = -1l; try { amount = new Long(argList.get(idx + 1)); } catch (Exception e) { } if (amount <= 0) System.err.println("invalid amount"); else { client.notarizeTransaction(hisacct, amount); } } } } else if ("reload".equals(command)) client.reloadState(); else if ("procnym".equals(command)) client.processNymbox(); } finally { client.saveState(); client.close(); } }
From source file:ExecSQL.java
public static void main(String args[]) { try {// w w w .j av a2 s . c om Scanner in; if (args.length == 0) in = new Scanner(System.in); else in = new Scanner(new File(args[0])); Connection conn = getConnection(); try { Statement stat = conn.createStatement(); while (true) { if (args.length == 0) System.out.println("Enter command or EXIT to exit:"); if (!in.hasNextLine()) return; String line = in.nextLine(); if (line.equalsIgnoreCase("EXIT")) return; if (line.trim().endsWith(";")) // remove trailing semicolon { line = line.trim(); line = line.substring(0, line.length() - 1); } try { boolean hasResultSet = stat.execute(line); if (hasResultSet) showResultSet(stat); } catch (SQLException ex) { for (Throwable e : ex) e.printStackTrace(); } } } finally { conn.close(); } } catch (SQLException e) { for (Throwable t : e) t.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } }
From source file:com.sustainalytics.crawlerfilter.PDFTitleGeneration.java
/** * Driver method for the class/*from w ww .jav a 2s . c o m*/ * @param args contains the file path and name */ public static void main(String[] args) { showBanner(); File pdfFile = new File(args[0]); initiateLogger(pdfFile); File textFile = new File(FilenameUtils.removeExtension(args[0]) + ".txt"); String title = extractTitle(pdfFile); String creationDate = extractDate(pdfFile); String content = null; try { content = FileUtils.readFileToString(textFile); } catch (IOException e) { logger.info("Error reading PDF content\n"); } String digest = getDocumentDigest(content.trim()); String finalTitle = makeTitle(title, creationDate, digest); renameFile(pdfFile, textFile, finalTitle); }
From source file:edu.cmu.lti.oaqa.knn4qa.apps.FilterTranTable.java
public static void main(String[] args) { Options options = new Options(); options.addOption(INPUT_PARAM, null, true, INPUT_DESC); options.addOption(OUTPUT_PARAM, null, true, OUTPUT_DESC); options.addOption(CommonParams.MEM_FWD_INDEX_PARAM, null, true, CommonParams.MEM_FWD_INDEX_DESC); options.addOption(CommonParams.GIZA_ITER_QTY_PARAM, null, true, CommonParams.GIZA_ITER_QTY_PARAM); options.addOption(CommonParams.GIZA_ROOT_DIR_PARAM, null, true, CommonParams.GIZA_ROOT_DIR_PARAM); options.addOption(CommonParams.MIN_PROB_PARAM, null, true, CommonParams.MIN_PROB_DESC); options.addOption(CommonParams.MAX_WORD_QTY_PARAM, null, true, CommonParams.MAX_WORD_QTY_PARAM); CommandLineParser parser = new org.apache.commons.cli.GnuParser(); try {/* ww w . j a v a 2s. c o m*/ CommandLine cmd = parser.parse(options, args); String outputFile = null; outputFile = cmd.getOptionValue(OUTPUT_PARAM); if (null == outputFile) { Usage("Specify 'A name of the output file'", options); } String gizaRootDir = cmd.getOptionValue(CommonParams.GIZA_ROOT_DIR_PARAM); if (null == gizaRootDir) { Usage("Specify '" + CommonParams.GIZA_ROOT_DIR_DESC + "'", options); } String gizaIterQty = cmd.getOptionValue(CommonParams.GIZA_ITER_QTY_PARAM); if (null == gizaIterQty) { Usage("Specify '" + CommonParams.GIZA_ITER_QTY_DESC + "'", options); } float minProb = 0; String tmpf = cmd.getOptionValue(CommonParams.MIN_PROB_PARAM); if (tmpf != null) { minProb = Float.parseFloat(tmpf); } int maxWordQty = Integer.MAX_VALUE; String tmpi = cmd.getOptionValue(CommonParams.MAX_WORD_QTY_PARAM); if (null != tmpi) { maxWordQty = Integer.parseInt(tmpi); } String memFwdIndxName = cmd.getOptionValue(CommonParams.MEM_FWD_INDEX_PARAM); if (null == memFwdIndxName) { Usage("Specify '" + CommonParams.MEM_FWD_INDEX_DESC + "'", options); } System.out.println("Filtering index: " + memFwdIndxName + " max # of frequent words: " + maxWordQty + " min. probability:" + minProb); VocabularyFilterAndRecoder filter = new FrequentIndexWordFilterAndRecoder(memFwdIndxName, maxWordQty); String srcVocFile = CompressUtils.findFileVariant(gizaRootDir + "/source.vcb"); System.out.println("Source vocabulary file: " + srcVocFile); GizaVocabularyReader srcVoc = new GizaVocabularyReader(srcVocFile, filter); String dstVocFile = CompressUtils.findFileVariant(gizaRootDir + "/target.vcb"); System.out.println("Target vocabulary file: " + dstVocFile); GizaVocabularyReader dstVoc = new GizaVocabularyReader(CompressUtils.findFileVariant(dstVocFile), filter); String inputFile = CompressUtils.findFileVariant(gizaRootDir + "/output.t1." + gizaIterQty); BufferedReader finp = new BufferedReader( new InputStreamReader(CompressUtils.createInputStream(inputFile))); BufferedWriter fout = new BufferedWriter( new OutputStreamWriter(CompressUtils.createOutputStream(outputFile))); try { String line; int prevSrcId = -1; int wordQty = 0; long addedQty = 0; long totalQty = 0; boolean isNotFiltered = false; for (totalQty = 0; (line = finp.readLine()) != null;) { ++totalQty; // Skip empty lines line = line.trim(); if (line.isEmpty()) continue; GizaTranRec rec = new GizaTranRec(line); if (rec.mSrcId != prevSrcId) { ++wordQty; } if (totalQty % REPORT_INTERVAL_QTY == 0) { System.out.println(String.format( "Processed %d lines (%d source word entries) from '%s', added %d lines", totalQty, wordQty, inputFile, addedQty)); } // isNotFiltered should be set after procOneWord if (rec.mSrcId != prevSrcId) { if (rec.mSrcId == 0) isNotFiltered = true; else { String wordSrc = srcVoc.getWord(rec.mSrcId); isNotFiltered = filter == null || (wordSrc != null && filter.checkWord(wordSrc)); } } prevSrcId = rec.mSrcId; if (rec.mProb >= minProb && isNotFiltered) { String wordDst = dstVoc.getWord(rec.mDstId); if (filter == null || (wordDst != null && filter.checkWord(wordDst))) { fout.write(String.format(rec.mSrcId + " " + rec.mDstId + " " + rec.mProb)); fout.newLine(); addedQty++; } } } System.out.println( String.format("Processed %d lines (%d source word entries) from '%s', added %d lines", totalQty, wordQty, inputFile, addedQty)); } finally { finp.close(); fout.close(); } } catch (ParseException e) { Usage("Cannot parse arguments", options); } catch (Exception e) { e.printStackTrace(); System.err.println("Terminating due to an exception: " + e); System.exit(1); } }
From source file:com.github.andreax79.meca.Main.java
@SuppressWarnings("static-access") public static void main(String[] args) { // create the command line parser CommandLineParser parser = new PosixParser(); // create the Options Options options = new Options(); options.addOption("X", "suppress-output", false, "don't create the output file"); OptionGroup boundariesOptions = new OptionGroup(); boundariesOptions.addOption(new Option("P", "periodic", false, "periodic boundaries (default)")); boundariesOptions.addOption(new Option("F", "fixed", false, "fixed-value boundaries")); boundariesOptions.addOption(new Option("A", "adiabatic", false, "adiabatic boundaries")); boundariesOptions.addOption(new Option("R", "reflective", false, "reflective boundaries")); options.addOptionGroup(boundariesOptions); OptionGroup colorOptions = new OptionGroup(); colorOptions.addOption(new Option("bn", "black-white", false, "black and white color scheme (default)")); colorOptions.addOption(new Option("ca", "activation-color", false, "activation color scheme")); colorOptions.addOption(new Option("co", "omega-color", false, "omega color scheme")); options.addOptionGroup(colorOptions); options.addOption(OptionBuilder.withLongOpt("rule").withDescription("rule number (required)").hasArg() .withArgName("rule").create()); options.addOption(OptionBuilder.withLongOpt("width").withDescription("space width (required)").hasArg() .withArgName("width").create()); options.addOption(OptionBuilder.withLongOpt("steps").withDescription("number of steps (required)").hasArg() .withArgName("steps").create()); options.addOption(OptionBuilder.withLongOpt("alpha").withDescription("memory factor (default 0)").hasArg() .withArgName("alpha").create()); options.addOption(OptionBuilder.withLongOpt("pattern").withDescription("inititial pattern").hasArg() .withArgName("pattern").create()); options.addOption("s", "single-seed", false, "single cell seed"); options.addOption("si", "single-seed-inverse", false, "all 1 except one cell"); options.addOption(OptionBuilder.withLongOpt("update-patter") .withDescription("update patter (valid values are " + UpdatePattern.validValues() + ")").hasArg() .withArgName("updatepatter").create()); // test/*from ww w. j ava 2 s .c o m*/ // args = new String[]{ "--rule=10", "--steps=500" , "--width=60", "-P" , "-s" }; try { // parse the command line arguments CommandLine line = parser.parse(options, args); if (!line.hasOption("rule")) throw new ParseException("no rule number (use --rule=XX)"); int rule; try { rule = Integer.parseInt(line.getOptionValue("rule")); if (rule < 0 || rule > 15) throw new ParseException("invalid rule number"); } catch (NumberFormatException ex) { throw new ParseException("invalid rule number"); } if (!line.hasOption("width")) throw new ParseException("no space width (use --width=XX)"); int width; try { width = Integer.parseInt(line.getOptionValue("width")); if (width < 1) throw new ParseException("invalid width"); } catch (NumberFormatException ex) { throw new ParseException("invalid width"); } if (!line.hasOption("steps")) throw new ParseException("no number of steps (use --steps=XX)"); int steps; try { steps = Integer.parseInt(line.getOptionValue("steps")); if (width < 1) throw new ParseException("invalid number of steps"); } catch (NumberFormatException ex) { throw new ParseException("invalid number of steps"); } double alpha = 0; if (line.hasOption("alpha")) { try { alpha = Double.parseDouble(line.getOptionValue("alpha")); if (alpha < 0 || alpha > 1) throw new ParseException("invalid alpha"); } catch (NumberFormatException ex) { throw new ParseException("invalid alpha"); } } String pattern = null; if (line.hasOption("pattern")) { pattern = line.getOptionValue("pattern"); if (pattern != null) pattern = pattern.trim(); } if (line.hasOption("single-seed")) pattern = "S"; else if (line.hasOption("single-seed-inverse")) pattern = "SI"; UpdatePattern updatePatter = UpdatePattern.synchronous; if (line.hasOption("update-patter")) { try { updatePatter = UpdatePattern.getUpdatePattern(line.getOptionValue("update-patter")); } catch (IllegalArgumentException ex) { throw new ParseException(ex.getMessage()); } } Boundaries boundaries = Boundaries.periodic; if (line.hasOption("periodic")) boundaries = Boundaries.periodic; else if (line.hasOption("fixed")) boundaries = Boundaries.fixed; else if (line.hasOption("adiabatic")) boundaries = Boundaries.adiabatic; else if (line.hasOption("reflective")) boundaries = Boundaries.reflective; ColorScheme colorScheme = ColorScheme.noColor; if (line.hasOption("black-white")) colorScheme = ColorScheme.noColor; else if (line.hasOption("activation-color")) colorScheme = ColorScheme.activationColor; else if (line.hasOption("omega-color")) colorScheme = ColorScheme.omegaColor; Output output = Output.all; if (line.hasOption("suppress-output")) output = Output.noOutput; Main.drawRule(rule, width, boundaries, updatePatter, steps, alpha, pattern, output, colorScheme); } catch (ParseException ex) { System.err.println("Copyright (C) 2009 Andrea Bonomi - <andrea.bonomi@gmail.com>"); System.err.println(); System.err.println("https://github.com/andreax79/one-neighbor-binary-cellular-automata"); System.err.println(); System.err.println("This program is free software; you can redistribute it and/or modify it"); System.err.println("under the terms of the GNU General Public License as published by the"); System.err.println("Free Software Foundation; either version 2 of the License, or (at your"); System.err.println("option) any later version."); System.err.println(); System.err.println("This program is distributed in the hope that it will be useful, but"); System.err.println("WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY"); System.err.println("or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License"); System.err.println("for more details."); System.err.println(); System.err.println("You should have received a copy of the GNU General Public License along"); System.err.println("with this program; if not, write to the Free Software Foundation, Inc.,"); System.err.println("59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.)"); System.err.println(); System.err.println(ex.getMessage()); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("main", options); } catch (IOException ex) { System.err.println("IO exception:" + ex.getMessage()); } }
From source file:cht.Parser.java
public static void main(String[] args) throws IOException { // TODO get from google drive boolean isUnicode = false; boolean isRemoveInputFileOnComplete = false; int rowNum;//ww w. j av a 2 s . co m int colNum; Gson gson = new GsonBuilder().setPrettyPrinting().create(); Properties prop = new Properties(); try { prop.load(new FileInputStream("config.txt")); } catch (IOException ex) { ex.printStackTrace(); } String inputFilePath = prop.getProperty("inputFile"); String outputDirectory = prop.getProperty("outputDirectory"); System.out.println(outputDirectory); // optional String unicode = prop.getProperty("unicode"); String removeInputFileOnComplete = prop.getProperty("removeInputFileOnComplete"); inputFilePath = inputFilePath.trim(); outputDirectory = outputDirectory.trim(); if (unicode != null) { isUnicode = Boolean.parseBoolean(unicode.trim()); } if (removeInputFileOnComplete != null) { isRemoveInputFileOnComplete = Boolean.parseBoolean(removeInputFileOnComplete.trim()); } Writer out = null; FileInputStream in = null; final String newLine = System.getProperty("line.separator").toString(); final String separator = File.separator; try { in = new FileInputStream(inputFilePath); Workbook workbook = new XSSFWorkbook(in); Sheet sheet = workbook.getSheetAt(0); rowNum = sheet.getLastRowNum() + 1; colNum = sheet.getRow(0).getPhysicalNumberOfCells(); for (int j = 1; j < colNum; ++j) { String outputFilename = sheet.getRow(0).getCell(j).getStringCellValue(); // guess directory int slash = outputFilename.indexOf('/'); if (slash != -1) { // has directory outputFilename = outputFilename.substring(0, slash) + separator + outputFilename.substring(slash + 1); } String outputPath = FilenameUtils.concat(outputDirectory, outputFilename); System.out.println("--Writing " + outputPath); out = new OutputStreamWriter(new FileOutputStream(outputPath), "UTF-8"); TreeMap<String, Object> map = new TreeMap<String, Object>(); for (int i = 1; i < rowNum; i++) { try { String key = sheet.getRow(i).getCell(0).getStringCellValue(); //String value = ""; Cell tmp = sheet.getRow(i).getCell(j); if (tmp != null) { // not empty string! value = sheet.getRow(i).getCell(j).getStringCellValue(); } if (!key.equals("") && !key.startsWith("#") && !key.startsWith(".")) { value = isUnicode ? StringEscapeUtils.escapeJava(value) : value; int firstdot = key.indexOf("."); String keyName, keyAttribute; if (firstdot > 0) {// a.b.c.d keyName = key.substring(0, firstdot); // a keyAttribute = key.substring(firstdot + 1); // b.c.d TreeMap oldhash = null; Object old = null; if (map.get(keyName) != null) { old = map.get(keyName); if (old instanceof TreeMap == false) { System.out.println("different type of key:" + key); continue; } oldhash = (TreeMap) old; } else { oldhash = new TreeMap(); } int firstdot2 = keyAttribute.indexOf("."); String rootName, childName; if (firstdot2 > 0) {// c, d.f --> d, f rootName = keyAttribute.substring(0, firstdot2); childName = keyAttribute.substring(firstdot2 + 1); } else {// c, d -> d, null rootName = keyAttribute; childName = null; } TreeMap<String, Object> object = myPut(oldhash, rootName, childName); map.put(keyName, object); } else {// c, d -> d, null keyName = key; keyAttribute = null; // simple string mode map.put(key, value); } } } catch (Exception e) { // just ingore empty rows } } String json = gson.toJson(map); // output json out.write(json + newLine); out.close(); } in.close(); System.out.println("\n---Complete!---"); System.out.println("Read input file from " + inputFilePath); System.out.println(colNum - 1 + " output files ate generated at " + outputDirectory); System.out.println(rowNum + " records are generated for each output file."); System.out.println("output file is ecoded as unicode? " + (isUnicode ? "yes" : "no")); if (isRemoveInputFileOnComplete) { File input = new File(inputFilePath); input.deleteOnExit(); System.out.println("Deleted " + inputFilePath); } } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } finally { if (in != null) { in.close(); } } }
From source file:com.github.ansell.shp.SHPDump.java
public static void main(String... args) throws Exception { final OptionParser parser = new OptionParser(); final OptionSpec<Void> help = parser.accepts("help").forHelp(); final OptionSpec<File> input = parser.accepts("input").withRequiredArg().ofType(File.class).required() .describedAs("The input SHP file"); final OptionSpec<File> output = parser.accepts("output").withRequiredArg().ofType(File.class).required() .describedAs("The output directory to use for debugging files"); final OptionSpec<String> outputPrefix = parser.accepts("prefix").withRequiredArg().ofType(String.class) .defaultsTo("shp-debug").describedAs("The output prefix to use for debugging files"); final OptionSpec<File> outputMappingTemplate = parser.accepts("output-mapping").withRequiredArg() .ofType(File.class).describedAs("The output mapping template file if it needs to be generated."); final OptionSpec<Integer> resolution = parser.accepts("resolution").withRequiredArg().ofType(Integer.class) .defaultsTo(2048).describedAs("The output image file resolution"); final OptionSpec<String> format = parser.accepts("format").withRequiredArg().ofType(String.class) .defaultsTo("png").describedAs("The output image format"); final OptionSpec<String> removeIfEmpty = parser.accepts("remove-if-empty").withRequiredArg() .ofType(String.class).describedAs( "The name of an attribute to remove if its value is empty before outputting the resulting shapefile. Use multiple times to specify multiple fields to check"); OptionSet options = null;/* www. ja va 2 s. c o m*/ try { options = parser.parse(args); } catch (final OptionException e) { System.out.println(e.getMessage()); parser.printHelpOn(System.out); throw e; } if (options.has(help)) { parser.printHelpOn(System.out); return; } final Path inputPath = input.value(options).toPath(); if (!Files.exists(inputPath)) { throw new FileNotFoundException("Could not find input SHP file: " + inputPath.toString()); } final Path outputPath = output.value(options).toPath(); if (!Files.exists(outputPath)) { throw new FileNotFoundException("Output directory does not exist: " + outputPath.toString()); } final Path outputMappingPath = options.has(outputMappingTemplate) ? outputMappingTemplate.value(options).toPath() : null; if (options.has(outputMappingTemplate) && Files.exists(outputMappingPath)) { throw new FileNotFoundException( "Output mapping template file already exists: " + outputMappingPath.toString()); } final Set<String> filterFields = ConcurrentHashMap.newKeySet(); if (options.has(removeIfEmpty)) { for (String nextFilterField : removeIfEmpty.values(options)) { System.out.println("Will filter field if empty value found: " + nextFilterField); filterFields.add(nextFilterField); } } if (!filterFields.isEmpty()) { System.out.println("Full set of filter fields: " + filterFields); } final String prefix = outputPrefix.value(options); FileDataStore store = FileDataStoreFinder.getDataStore(inputPath.toFile()); if (store == null) { throw new RuntimeException("Could not read the given input as an ESRI Shapefile: " + inputPath.toAbsolutePath().toString()); } for (String typeName : new LinkedHashSet<>(Arrays.asList(store.getTypeNames()))) { System.out.println(""); System.out.println("Type: " + typeName); SimpleFeatureSource featureSource = store.getFeatureSource(typeName); SimpleFeatureType schema = featureSource.getSchema(); Name outputSchemaName = new NameImpl(schema.getName().getNamespaceURI(), schema.getName().getLocalPart().replace(" ", "").replace("%20", "")); System.out.println("Replacing name on schema: " + schema.getName() + " with " + outputSchemaName); SimpleFeatureType outputSchema = SHPUtils.changeSchemaName(schema, outputSchemaName); List<String> attributeList = new ArrayList<>(); for (AttributeDescriptor attribute : schema.getAttributeDescriptors()) { System.out.println("Attribute: " + attribute.getName().toString()); attributeList.add(attribute.getName().toString()); } CsvSchema csvSchema = CSVUtil.buildSchema(attributeList); SimpleFeatureCollection collection = featureSource.getFeatures(); int featureCount = 0; Path nextCSVFile = outputPath.resolve(prefix + ".csv"); Path nextSummaryCSVFile = outputPath .resolve(prefix + "-" + outputSchema.getTypeName() + "-Summary.csv"); List<SimpleFeature> outputFeatureList = new CopyOnWriteArrayList<>(); try (SimpleFeatureIterator iterator = collection.features(); Writer bufferedWriter = Files.newBufferedWriter(nextCSVFile, StandardCharsets.UTF_8, StandardOpenOption.CREATE_NEW); SequenceWriter csv = CSVUtil.newCSVWriter(bufferedWriter, csvSchema);) { List<String> nextLine = new ArrayList<>(); while (iterator.hasNext()) { SimpleFeature feature = iterator.next(); featureCount++; if (featureCount <= 2) { System.out.println(""); System.out.println(feature.getIdentifier()); } else if (featureCount % 100 == 0) { System.out.print("."); } boolean filterThisFeature = false; for (AttributeDescriptor attribute : schema.getAttributeDescriptors()) { String featureString = Optional.ofNullable(feature.getAttribute(attribute.getName())) .orElse("").toString(); nextLine.add(featureString); if (filterFields.contains(attribute.getName().toString()) && featureString.trim().isEmpty()) { filterThisFeature = true; } if (featureString.length() > 100) { featureString = featureString.substring(0, 100) + "..."; } if (featureCount <= 2) { System.out.print(attribute.getName() + "="); System.out.println(featureString); } } if (!filterThisFeature) { outputFeatureList.add(SHPUtils.changeSchemaName(feature, outputSchema)); csv.write(nextLine); } nextLine.clear(); } } try (Reader csvReader = Files.newBufferedReader(nextCSVFile, StandardCharsets.UTF_8); Writer summaryOutput = Files.newBufferedWriter(nextSummaryCSVFile, StandardCharsets.UTF_8, StandardOpenOption.CREATE_NEW); final Writer mappingWriter = options.has(outputMappingTemplate) ? Files.newBufferedWriter(outputMappingPath) : NullWriter.NULL_WRITER) { CSVSummariser.runSummarise(csvReader, summaryOutput, mappingWriter, CSVSummariser.DEFAULT_SAMPLE_COUNT, false); } if (featureCount > 100) { System.out.println(""); } System.out.println(""); System.out.println("Feature count: " + featureCount); SimpleFeatureCollection outputCollection = new ListFeatureCollection(outputSchema, outputFeatureList); Path outputShapefilePath = outputPath.resolve(prefix + "-" + outputSchema.getTypeName() + "-dump"); if (!Files.exists(outputShapefilePath)) { Files.createDirectory(outputShapefilePath); } SHPUtils.writeShapefile(outputCollection, outputShapefilePath); // Create ZIP file from the contents to keep the subfiles together Path outputShapefileZipPath = outputPath .resolve(prefix + "-" + outputSchema.getTypeName() + "-dump.zip"); try (final OutputStream out = Files.newOutputStream(outputShapefileZipPath, StandardOpenOption.CREATE_NEW); final ZipOutputStream zip = new ZipOutputStream(out, StandardCharsets.UTF_8);) { Files.list(outputShapefilePath).forEachOrdered(Unchecked.consumer(e -> { zip.putNextEntry(new ZipEntry(e.getFileName().toString())); Files.copy(e, zip); zip.closeEntry(); })); } try (final OutputStream outputStream = Files.newOutputStream( outputPath.resolve(prefix + "." + format.value(options)), StandardOpenOption.CREATE_NEW);) { MapContent map = new MapContent(); map.setTitle(prefix + "-" + outputSchema.getTypeName()); Style style = SLD.createSimpleStyle(featureSource.getSchema()); Layer layer = new FeatureLayer(new CollectionFeatureSource(outputCollection), style); map.addLayer(layer); SHPUtils.renderImage(map, outputStream, resolution.value(options), format.value(options)); } } }
From source file:de.uniwue.info2.main.CommandLineInterpreter.java
@SuppressWarnings("static-access") public static void main(String[] args) { /*-------------------------------------------------------- */ /*---------------SETTING TARGET LANGUAGE------------------ */ /*-------------------------------------------------------- */ LanguageFactory languageFactory = new LanguageFactory(); CommandLine line = null;/*from ww w. j a va 2 s .c om*/ CommandLineParser parser = new BasicParser(); Options options = new Options(); // options to display in the help page Options options_short = new Options(); // add help option Option help_option = new Option(HELP_OPTION_SHORT, HELP_OPTION, false, HELP_DESCRIPTION); options.addOption(help_option); options_short.addOption(help_option); // add extended help option Option help2_option = new Option(HELP2_OPTION_SHORT, HELP2_OPTION, false, HELP2_DESCRIPTION); options.addOption(help2_option); options_short.addOption(help2_option); // add optional operations option options.addOption(new Option(OPTIONAL_OPTION_SHORT, OPTIONAL_OPTION, false, OPTIONAL_DESCRIPTION)); options.addOption(new Option(BIG_ENDIAN_OPTION_SHORT, BIG_ENDIAN_OPTION, false, BIG_ENDIAN_DESCRIPTION)); options.addOption( new Option(LITTLE_ENDIAN_OPTION_SHORT, LITTLE_ENDIAN_OPTION, false, LITTLE_ENDIAN_DESCRIPTION)); // add optional operations config option options.addOption(OptionBuilder.withLongOpt(OPTIONAL_FUNCTIONS_CONFIG_OPTION) .withArgName(OPTIONAL_FUNCTIONS_CONFIG_ARGUMENT) .withDescription(OPTIONAL_FUNCTIONS_CONFIG_DESCRIPTION).hasArg() .create(OPTIONAL_FUNCTIONS_CONFIG_SHORT)); // add dsl option Option dsl_option = OptionBuilder.withLongOpt(DSL_OPTION).withArgName(DSL_ARGUMENT) .withDescription(DSL_DESCRIPTION).hasArg().isRequired().create(DSL_OPTION_SHORT); options.addOption(dsl_option); options_short.addOption(dsl_option); // add output-folder option Option output_option = OptionBuilder.withLongOpt(OUTPUT_OPTION).isRequired().withArgName(OUTPUT_ARGUMENT) .withDescription(OUTPUT_DESCRIPTION).hasArg().create(OUTPUT_OPTION_SHORT); options.addOption(output_option); options_short.addOption(output_option); // count possible language-specifications short optionCounter = 1; // get all possible language-specifications from language-factory and iterate through them List<LanguageSpecification> lSpecs = languageFactory.getAvailableLanguageSpecifications_(); for (LanguageSpecification lSpec : lSpecs) { // get all possible unit-specifications for current language and iterate through them List<UnitTestLibrarySpecification> uSpecs = languageFactory .getAvailableUnitTestLibraries_(lSpec.getOptionName()); String languageDescriptionAll = LANGUAGE_SPECIFICATION + lSpec.getLanguageName(); String languageCounter = "s" + INDEX.format(optionCounter++); for (UnitTestLibrarySpecification uSpec : uSpecs) { // get all possible arithmetic-library-specifications for current language and iterate through // them List<ArithmeticLibrarySpecification> aSpecs = languageFactory .getAvailableArithmeticLibraries_(lSpec.getOptionName()); for (ArithmeticLibrarySpecification aSpec : aSpecs) { String languageDescription = "Generate unit-test for " + lSpec.getLanguageName() + "\n*[" + uSpec.getLibraryName() + " - " + uSpec.getVersion() + "]\n*[" + aSpec.getLibraryName() + " - " + aSpec.getVersion() + "]"; // if there is more than one option, generate suitable option-names and add them all to // commandline options if (uSpecs.size() > 1 || aSpecs.size() > 1) { options.addOption(OptionBuilder .withLongOpt(lSpec.getOptionName() + "_" + uSpec.getOptionName() + "_" + aSpec.getOptionName()) .withDescription(languageDescription).hasArg(false) .create("s" + INDEX.format(optionCounter++))); } else { // if there is only one option, use language-name as option-name languageDescriptionAll = languageDescription; } } // add specifications to options options.addOption(OptionBuilder.withLongOpt(lSpec.getOptionName()) .withDescription(languageDescriptionAll).hasArg(false).create(languageCounter)); } } /*-------------------------------------------------------- */ /*-------------------PARSE USER INPUT--------------------- */ /*-------------------------------------------------------- */ try { // manual search for help-arguments for (String arg : args) { arg = arg.trim().replace("-", ""); if (arg.equals(HELP_OPTION_SHORT) || arg.equals(HELP_OPTION)) { printHelp(options_short); return; } if (arg.equals(HELP2_OPTION_SHORT) || arg.equals(HELP2_OPTION)) { printExtendedHelp(options); return; } } // parse arguments line = parser.parse(options, args); File dsl_file = null; File output_folder = null; File optional_config = null; Properties optional_operations = null; Boolean optional = false; Boolean little_endian = null; ArrayList<String> optional_exceptions = new ArrayList<String>(); // if help-option found print help if (line.hasOption(HELP2_OPTION_SHORT) || args.length == 0) { printExtendedHelp(options); return; } // if help-option found print help if (line.hasOption(HELP_OPTION_SHORT) || args.length == 0) { System.out.println("\n"); printHelp(options_short); return; } if (line.hasOption(OPTIONAL_OPTION_SHORT)) { optional = true; } if (line.hasOption(LITTLE_ENDIAN_OPTION)) { little_endian = true; } if (line.hasOption(BIG_ENDIAN_OPTION)) { little_endian = false; } // if dsl-option found, check if file exists and is readable // print help if error occurs if (line.hasOption(DSL_OPTION_SHORT)) { dsl_file = new File(line.getOptionValue(DSL_OPTION_SHORT)); if (!dsl_file.exists()) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - DSL-file doesn't exist:\n" + dsl_file + "\n" + SEPERATOR + "\n"); printHelp(options_short); return; } else if (dsl_file.isDirectory()) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - DSL-file is a directory:\n" + dsl_file + "\n" + SEPERATOR + "\n"); printHelp(options_short); return; } else if (!dsl_file.canRead()) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - Need read-permission for DSL-file:\n" + dsl_file + "\n" + SEPERATOR + "\n"); printHelp(options_short); return; } } // if output-option found, check if folder exists and if write-permission was granted // print help if error occurs if (line.hasOption(OUTPUT_OPTION_SHORT)) { output_folder = new File(line.getOptionValue(OUTPUT_OPTION_SHORT)); if (!output_folder.exists()) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - Output-folder doesn't exist:\n" + output_folder + "\n" + SEPERATOR + "\n"); printHelp(options_short); return; } else if (!output_folder.isDirectory()) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - Output-folder is not a directory:\n" + output_folder + "\n" + SEPERATOR + "\n"); printHelp(options_short); return; } else if (!output_folder.canWrite() || !output_folder.canRead()) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - Missing permissions for output-folder:\n" + output_folder + "\n" + SEPERATOR + "\n"); printHelp(options_short); return; } } if (line.hasOption(OPTIONAL_FUNCTIONS_CONFIG_SHORT)) { optional_config = new File(line.getOptionValue(OPTIONAL_FUNCTIONS_CONFIG_OPTION)); if (!dsl_file.exists()) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - config-file doesn't exist:\n" + dsl_file + "\n" + SEPERATOR + "\n"); printExtendedHelp(options); return; } else if (dsl_file.isDirectory()) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - config-file is a directory:\n" + dsl_file + "\n" + SEPERATOR + "\n"); printExtendedHelp(options); return; } else if (!dsl_file.canRead()) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - Need read-permission for config-file:\n" + dsl_file + "\n" + SEPERATOR + "\n"); printExtendedHelp(options); return; } } if (optional_config != null) { optional_operations = new Properties(); BufferedInputStream stream = new BufferedInputStream(new FileInputStream(optional_config)); optional_operations.load(stream); stream.close(); String optional_prop = optional_operations.getProperty("GENERATE_OPTIONAL"); if (optional_prop != null) { if (optional_prop.trim().toLowerCase().equals("true")) { optional = true; } else if (optional_prop.trim().toLowerCase().equals("false")) { optional = false; } else if (!optional_prop.trim().isEmpty()) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - Syntax incorrect in config-file:\nUse \"true\" or \"false\" for \"GENERATE_OPTIONAL\"\n" + SEPERATOR + "\n"); printExtendedHelp(options); return; } } String exceptions = optional_operations.getProperty("EXCLUSIONS"); if (exceptions != null) { for (String exc : optional_operations.getProperty("EXCLUSIONS").split(";")) { optional_exceptions.add(exc.trim()); } } } /*-------------------------------------------------------- */ /*-------------------START GENERATING--------------------- */ /*-------------------------------------------------------- */ // instantiate generator for unit-tests TestcaseGenerator mainGenerator = new TestcaseGenerator(dsl_file, output_folder); boolean overrideDefaultSpecs = false; // check if user input contains a language-specifications // if user specified language, set overrideDefaultSpecs to true, so that only given specifications // are used for (int i = 1; i <= optionCounter; i++) { String opt = "s" + INDEX.format(i); if (line.hasOption(opt)) { LanguageSpecification targetSpecification = languageFactory .getLanguageSpecification(options.getOption(opt).getLongOpt()); String output = (GENERATING_DIALOG + targetSpecification.getLanguageName()); // finally generate unit-test for current language-specification boolean successful = mainGenerator.generateUnitTest(targetSpecification, optional, optional_exceptions, little_endian); if (successful) { System.out.println(output + "\n--> Successfully generated."); } else { System.err.println(output + "\n--> ERROR - see logfile"); } overrideDefaultSpecs = true; } } // skip, if user already defined one language-specification // if user did not define language-specification, generate unit-tests for all // possible language-specifications (default) if (!overrideDefaultSpecs) { for (int i = 0; i < lSpecs.size(); i++) { LanguageSpecification specification = languageFactory .getLanguageSpecification(lSpecs.get(i).getOptionName()); String output = INDEX.format(i + 1) + " - " + GENERATING_DIALOG + specification.getLanguageName(); // finally generate unit-test for current language-specification boolean successful = mainGenerator.generateUnitTest(specification, optional, optional_exceptions, little_endian); if (successful) { System.out.println(output + "\n--> Successfully generated."); } else { System.err.println(output + "\n--> ERROR - see logfile"); } } } } catch (ParseException | IOException p) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - WRONG ARGUMENTS:\n" + p.getMessage() + "\n" + SEPERATOR + "\n"); printHelp(options_short); System.out.println("\n"); } }
From source file:DIA_Umpire_Quant.DIA_Umpire_LCMSIDGen.java
/** * @param args the command line arguments */// w w w . j a v a2 s. c o m public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println("DIA-Umpire LCMSID geneartor (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_LCMSIDGen.jar diaumpire_module.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_lcmsidgen.log"); } catch (Exception e) { } Logger.getRootLogger().info("Version: " + UmpireInfo.GetInstance().Version); Logger.getRootLogger().info("Parameter file:" + args[0]); BufferedReader reader = new BufferedReader(new FileReader(args[0])); String line = ""; String WorkFolder = ""; int NoCPUs = 2; TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); HashMap<String, File> AssignFiles = new HashMap<>(); //<editor-fold defaultstate="collapsed" desc="Reading parameter file"> while ((line = reader.readLine()) != null) { line = line.trim(); Logger.getRootLogger().info(line); if (!"".equals(line) && !line.startsWith("#")) { //System.out.println(line); if (line.equals("==File list begin")) { do { line = reader.readLine(); line = line.trim(); if (line.equals("==File list end")) { continue; } else if (!"".equals(line)) { File newfile = new File(line); if (newfile.exists()) { AssignFiles.put(newfile.getAbsolutePath(), newfile); } else { Logger.getRootLogger().info("File: " + newfile + " does not exist."); } } } while (!line.equals("==File list end")); } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); String value = line.split("=")[1].trim(); switch (type) { case "Path": { WorkFolder = value; break; } case "path": { WorkFolder = value; break; } case "Thread": { NoCPUs = Integer.parseInt(value); break; } case "DecoyPrefix": { if (!"".equals(value)) { tandemPara.DecoyPrefix = value; } break; } case "PeptideFDR": { tandemPara.PepFDR = Float.parseFloat(value); break; } } } } //</editor-fold> //Initialize PTM manager using compomics library PTMManager.GetInstance(); //Generate DIA file list ArrayList<DIAPack> FileList = new ArrayList<>(); File folder = new File(WorkFolder); if (!folder.exists()) { Logger.getRootLogger().info("The path : " + WorkFolder + " cannot be found."); System.exit(1); } for (final File fileEntry : folder.listFiles()) { if (fileEntry.isFile() && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry.getAbsolutePath(), fileEntry); } if (fileEntry.isDirectory()) { for (final File fileEntry2 : fileEntry.listFiles()) { if (fileEntry2.isFile() && (fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry2.getAbsolutePath(), fileEntry2); } } } } Logger.getRootLogger().info("No. of files assigned :" + AssignFiles.size()); for (File fileEntry : AssignFiles.values()) { Logger.getRootLogger().info(fileEntry.getAbsolutePath()); } //process each DIA file to genearate untargeted identifications for (File fileEntry : AssignFiles.values()) { String mzXMLFile = fileEntry.getAbsolutePath(); if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) { long time = System.currentTimeMillis(); DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs); FileList.add(DiaFile); Logger.getRootLogger().info( "================================================================================================="); Logger.getRootLogger().info("Processing " + mzXMLFile); if (!DiaFile.LoadDIASetting()) { Logger.getRootLogger().info("Loading DIA setting failed, job is incomplete"); System.exit(1); } if (!DiaFile.LoadParams()) { Logger.getRootLogger().info("Loading parameters failed, job is incomplete"); System.exit(1); } Logger.getRootLogger().info("Loading identification results " + mzXMLFile + "...."); DiaFile.ParsePepXML(tandemPara, null); DiaFile.BuildStructure(); if (!DiaFile.MS1FeatureMap.ReadPeakCluster()) { Logger.getRootLogger().info("Loading peak and structure failed, job is incomplete"); System.exit(1); } DiaFile.MS1FeatureMap.ClearMonoisotopicPeakOfCluster(); //Generate mapping between index of precursor feature and pseudo MS/MS scan index DiaFile.GenerateClusterScanNomapping(); //Doing quantification DiaFile.AssignQuant(); DiaFile.ClearStructure(); DiaFile.IDsummary.ReduceMemoryUsage(); time = System.currentTimeMillis() - time; Logger.getRootLogger().info(mzXMLFile + " processed time:" + String.format("%d hour, %d min, %d sec", TimeUnit.MILLISECONDS.toHours(time), TimeUnit.MILLISECONDS.toMinutes(time) - TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(time)), TimeUnit.MILLISECONDS.toSeconds(time) - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(time)))); } Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); } }