Example usage for java.io File getAbsolutePath

List of usage examples for java.io File getAbsolutePath

Introduction

In this page you can find the example usage for java.io File getAbsolutePath.

Prototype

public String getAbsolutePath() 

Source Link

Document

Returns the absolute pathname string of this abstract pathname.

Usage

From source file:edu.ucdenver.ccp.nlp.ae.dict_util.GeneInfoToDictionary.java

public static void main(String args[]) {

    BasicConfigurator.configure();/*from   w ww . ja  va  2  s . co  m*/

    if (args.length < 2) {
        usage();
    } else {
        try {
            File geneFile = new File(args[0]);
            File outputFile = new File(args[1]);
            if (!geneFile.canRead()) {
                System.out.println("can't read input file;" + geneFile.getAbsolutePath());
                usage();
                System.exit(-2);
            }
            if (outputFile.exists() && !outputFile.canWrite()) {
                System.out.println("can't write output file;" + outputFile.getAbsolutePath());
                usage();
                System.exit(-3);
            }

            logger.warn("running with: " + geneFile.getAbsolutePath());
            GeneInfoToDictionary converter = new GeneInfoToDictionary(geneFile);
            converter.convert(geneFile, outputFile);
        } catch (Exception e) {
            System.out.println("error:" + e);
            e.printStackTrace();
            System.exit(-1);
        }
    }
}

From source file:act.installer.reachablesexplorer.PatentFinder.java

public static void main(String[] args) throws Exception {
    CLIUtil cliUtil = new CLIUtil(Loader.class, HELP_MESSAGE, OPTION_BUILDERS);
    CommandLine cl = cliUtil.parseCommandLine(args);

    String host = cl.getOptionValue(OPTION_DB_HOST, DEFAULT_HOST);
    Integer port = Integer.parseInt(cl.getOptionValue(OPTION_DB_PORT, DEFAULT_PORT.toString()));
    String targetDB = cl.getOptionValue(OPTION_TARGET_DB, DEFAULT_TARGET_DATABASE);
    String collection = cl.getOptionValue(OPTION_TARGET_REACHABLES_COLLECTION, DEFAULT_TARGET_COLLECTION);
    LOGGER.info("Connecting to %s:%d/%s, using collection %s", host, port, targetDB, collection);

    Loader loader = new Loader(host, port, UNUSED_SOURCE_DB, targetDB, collection, UNUSED_SEQUENCES_COLLECTION,
            UNUSED_ASSETS_DIR);//w  w w .  j  a va  2s  . com

    File indexesTopDir = new File(cl.getOptionValue(OPTION_PATENT_INDEX_DIR, DEFAULT_PATENT_INDEX_LOCATION));
    if (!indexesTopDir.exists() || !indexesTopDir.isDirectory()) {
        cliUtil.failWithMessage("Index top-level directory at %s is not a directory",
                indexesTopDir.getAbsolutePath());
    }

    LOGGER.info("Using index top level dir: %s", indexesTopDir.getAbsolutePath());

    PatentFinder finder = new PatentFinder();
    try (Searcher searcher = Searcher.Factory.getInstance().build(indexesTopDir)) {
        finder.run(loader, searcher);
    }
}

From source file:com.amazonaws.services.kinesis.clientlibrary.proxies.util.KinesisLocalFileDataCreator.java

/** Creates a new temp file populated with fake Kinesis data records.
 * @param args Expects 5 args: numShards, shardPrefix, numRecordsPerShard, startingSequenceNumber, fileNamePrefix
 *//* ww w  .j a v a  2s  .c o  m*/
// CHECKSTYLE:OFF MagicNumber
// CHECKSTYLE:IGNORE UncommentedMain FOR NEXT 2 LINES
public static void main(String[] args) {
    int numShards = 1;
    String shardIdPrefix = "shardId";
    int numRecordsPerShard = 17;
    BigInteger startingSequenceNumber = new BigInteger("99");
    String fileNamePrefix = "kinesisFakeRecords";

    try {
        if ((args.length != 0) && (args.length != 5)) {
            // Temporary util code, so not providing detailed usage feedback.
            System.out.println("Unexpected number of arguments.");
            System.exit(0);
        }

        if (args.length == 5) {
            numShards = Integer.parseInt(args[0]);
            shardIdPrefix = args[1];
            numRecordsPerShard = Integer.parseInt(args[2]);
            startingSequenceNumber = new BigInteger(args[3]);
            fileNamePrefix = args[4];
        }

        File file = KinesisLocalFileDataCreator.generateTempDataFile(numShards, shardIdPrefix,
                numRecordsPerShard, startingSequenceNumber, fileNamePrefix);
        System.out.println("Created fake kinesis records in file: " + file.getAbsolutePath());
    } catch (Exception e) {
        // CHECKSTYLE:IGNORE IllegalCatch FOR NEXT -1 LINES
        System.out.println("Caught Exception: " + e);
    }

}

From source file:com.act.lcms.db.analysis.FeedingAnalysis.java

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());//from www.j  a va 2 s .c  om
    }

    CommandLine cl = null;
    try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
    } catch (ParseException e) {
        System.err.format("Argument parsing failed: %s\n", e.getMessage());
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    if (cl.hasOption("help")) {
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        return;
    }

    File lcmsDir = new File(cl.getOptionValue(OPTION_DIRECTORY));
    if (!lcmsDir.isDirectory()) {
        System.err.format("File at %s is not a directory\n", lcmsDir.getAbsolutePath());
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    try (DB db = DB.openDBFromCLI(cl)) {
        System.out.format("Loading/updating LCMS scan files into DB\n");
        ScanFile.insertOrUpdateScanFilesInDirectory(db, lcmsDir);

        System.out.format("Running feeding analysis\n");
        performFeedingAnalysis(db, cl.getOptionValue(OPTION_DIRECTORY), cl.getOptionValue(OPTION_ION_NAME),
                cl.getOptionValue(OPTION_SEARCH_MZ), cl.getOptionValue(OPTION_PLATE_BARCODE),
                cl.getOptionValue(OPTION_FEEDING_STRAIN_OR_CONSTRUCT),
                cl.getOptionValue(OPTION_FEEDING_EXTRACT), cl.getOptionValue(OPTION_FEEDING_FED_CHEMICAL),
                cl.getOptionValue(OPTION_OUTPUT_PREFIX), "pdf");
    }
}

From source file:edu.cmu.lti.oaqa.knn4qa.apps.LuceneIndexer.java

public static void main(String[] args) {
    Options options = new Options();

    options.addOption(CommonParams.ROOT_DIR_PARAM, null, true, CommonParams.ROOT_DIR_DESC);
    options.addOption(CommonParams.SUB_DIR_TYPE_PARAM, null, true, CommonParams.SUB_DIR_TYPE_DESC);
    options.addOption(CommonParams.MAX_NUM_REC_PARAM, null, true, CommonParams.MAX_NUM_REC_DESC);
    options.addOption(CommonParams.SOLR_FILE_NAME_PARAM, null, true, CommonParams.SOLR_FILE_NAME_DESC);
    options.addOption(CommonParams.OUT_INDEX_PARAM, null, true, CommonParams.OUT_MINDEX_DESC);

    CommandLineParser parser = new org.apache.commons.cli.GnuParser();

    try {/*from   ww  w  .  jav  a2  s  .  c  om*/
        CommandLine cmd = parser.parse(options, args);

        String rootDir = null;

        rootDir = cmd.getOptionValue(CommonParams.ROOT_DIR_PARAM);

        if (null == rootDir)
            Usage("Specify: " + CommonParams.ROOT_DIR_DESC, options);

        String outputDirName = cmd.getOptionValue(CommonParams.OUT_INDEX_PARAM);

        if (null == outputDirName)
            Usage("Specify: " + CommonParams.OUT_MINDEX_DESC, options);

        String subDirTypeList = cmd.getOptionValue(CommonParams.SUB_DIR_TYPE_PARAM);

        if (null == subDirTypeList || subDirTypeList.isEmpty())
            Usage("Specify: " + CommonParams.SUB_DIR_TYPE_DESC, options);

        String solrFileName = cmd.getOptionValue(CommonParams.SOLR_FILE_NAME_PARAM);
        if (null == solrFileName)
            Usage("Specify: " + CommonParams.SOLR_FILE_NAME_DESC, options);

        int maxNumRec = Integer.MAX_VALUE;

        String tmp = cmd.getOptionValue(CommonParams.MAX_NUM_REC_PARAM);

        if (tmp != null) {
            try {
                maxNumRec = Integer.parseInt(tmp);
                if (maxNumRec <= 0) {
                    Usage("The maximum number of records should be a positive integer", options);
                }
            } catch (NumberFormatException e) {
                Usage("The maximum number of records should be a positive integer", options);
            }
        }

        File outputDir = new File(outputDirName);
        if (!outputDir.exists()) {
            if (!outputDir.mkdirs()) {
                System.out.println("couldn't create " + outputDir.getAbsolutePath());
                System.exit(1);
            }
        }
        if (!outputDir.isDirectory()) {
            System.out.println(outputDir.getAbsolutePath() + " is not a directory!");
            System.exit(1);
        }
        if (!outputDir.canWrite()) {
            System.out.println("Can't write to " + outputDir.getAbsolutePath());
            System.exit(1);
        }

        String subDirs[] = subDirTypeList.split(",");

        int docNum = 0;

        // No English analyzer here, all language-related processing is done already,
        // here we simply white-space tokenize and index tokens verbatim.
        Analyzer analyzer = new WhitespaceAnalyzer();
        FSDirectory indexDir = FSDirectory.open(outputDir);
        IndexWriterConfig indexConf = new IndexWriterConfig(analyzer.getVersion(), analyzer);

        System.out.println("Creating a new Lucene index, maximum # of docs to process: " + maxNumRec);
        indexConf.setOpenMode(OpenMode.CREATE);
        IndexWriter indexWriter = new IndexWriter(indexDir, indexConf);

        for (int subDirId = 0; subDirId < subDirs.length && docNum < maxNumRec; ++subDirId) {
            String inputFileName = rootDir + "/" + subDirs[subDirId] + "/" + solrFileName;

            System.out.println("Input file name: " + inputFileName);

            BufferedReader inpText = new BufferedReader(
                    new InputStreamReader(CompressUtils.createInputStream(inputFileName)));
            String docText = XmlHelper.readNextXMLIndexEntry(inpText);

            for (; docText != null && docNum < maxNumRec; docText = XmlHelper.readNextXMLIndexEntry(inpText)) {
                ++docNum;
                Map<String, String> docFields = null;

                Document luceneDoc = new Document();

                try {
                    docFields = XmlHelper.parseXMLIndexEntry(docText);
                } catch (Exception e) {
                    System.err.println(String.format("Parsing error, offending DOC #%d:\n%s", docNum, docText));
                    System.exit(1);
                }

                String id = docFields.get(UtilConst.TAG_DOCNO);

                if (id == null) {
                    System.err.println(String.format("No ID tag '%s', offending DOC #%d:\n%s",
                            UtilConst.TAG_DOCNO, docNum, docText));
                }

                luceneDoc.add(new StringField(UtilConst.TAG_DOCNO, id, Field.Store.YES));

                for (Map.Entry<String, String> e : docFields.entrySet())
                    if (!e.getKey().equals(UtilConst.TAG_DOCNO)) {
                        luceneDoc.add(new TextField(e.getKey(), e.getValue(), Field.Store.YES));
                    }
                indexWriter.addDocument(luceneDoc);
                if (docNum % 1000 == 0)
                    System.out.println("Indexed " + docNum + " docs");
            }
            System.out.println("Indexed " + docNum + " docs");
        }

        indexWriter.commit();
        indexWriter.close();

    } catch (ParseException e) {
        Usage("Cannot parse arguments", options);
    } catch (Exception e) {
        System.err.println("Terminating due to an exception: " + e);
        System.exit(1);
    }

}

From source file:gov.lanl.adore.djatoka.DjatokaCompress.java

/**
 * Uses apache commons cli to parse input args. Passes parsed
 * parameters to ICompress implementation.
 * @param args command line parameters to defined input,output,etc.
 */// www .  j a  v a  2 s.co  m
public static void main(String[] args) {
    // create the command line parser
    CommandLineParser parser = new PosixParser();

    // create the Options
    Options options = new Options();
    options.addOption("i", "input", true, "Filepath of the input file or dir.");
    options.addOption("o", "output", true, "Filepath of the output file or dir.");
    options.addOption("r", "rate", true, "Absolute Compression Ratio");
    options.addOption("s", "slope", true,
            "Used to generate relative compression ratio based on content characteristics.");
    options.addOption("y", "Clayers", true, "Number of quality levels.");
    options.addOption("l", "Clevels", true, "Number of DWT levels (reolution levels).");
    options.addOption("v", "Creversible", true, "Use Reversible Wavelet");
    options.addOption("c", "Cprecincts", true, "Precinct dimensions");
    options.addOption("p", "props", true, "Compression Properties File");
    options.addOption("d", "Corder", true, "Progression order");
    options.addOption("g", "ORGgen_plt", true, "Enables insertion of packet length information in the header");
    options.addOption("t", "ORGtparts", true, "Division of each tile's packets into tile-parts");
    options.addOption("b", "Cblk", true, "Codeblock Size");
    options.addOption("a", "AltImpl", true, "Alternate ICompress Implemenation");

    try {
        if (args.length == 0) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("gov.lanl.adore.djatoka.DjatokaCompress", options);
            System.exit(0);
        }

        // parse the command line arguments
        CommandLine line = parser.parse(options, args);
        String input = line.getOptionValue("i");
        String output = line.getOptionValue("o");

        String propsFile = line.getOptionValue("p");
        DjatokaEncodeParam p;
        if (propsFile != null) {
            Properties props = IOUtils.loadConfigByPath(propsFile);
            p = new DjatokaEncodeParam(props);
        } else
            p = new DjatokaEncodeParam();
        String rate = line.getOptionValue("r");
        if (rate != null)
            p.setRate(rate);
        String slope = line.getOptionValue("s");
        if (slope != null)
            p.setSlope(slope);
        String Clayers = line.getOptionValue("y");
        if (Clayers != null)
            p.setLayers(Integer.parseInt(Clayers));
        String Clevels = line.getOptionValue("l");
        if (Clevels != null)
            p.setLevels(Integer.parseInt(Clevels));
        String Creversible = line.getOptionValue("v");
        if (Creversible != null)
            p.setUseReversible(Boolean.parseBoolean(Creversible));
        String Cprecincts = line.getOptionValue("c");
        if (Cprecincts != null)
            p.setPrecincts(Cprecincts);
        String Corder = line.getOptionValue("d");
        if (Corder != null)
            p.setProgressionOrder(Corder);
        String ORGgen_plt = line.getOptionValue("g");
        if (ORGgen_plt != null)
            p.setInsertPLT(Boolean.parseBoolean(ORGgen_plt));
        String Cblk = line.getOptionValue("b");
        if (Cblk != null)
            p.setCodeBlockSize(Cblk);
        String alt = line.getOptionValue("a");

        ICompress jp2 = new KduCompressExe();
        if (alt != null)
            jp2 = (ICompress) Class.forName(alt).newInstance();
        if (new File(input).isDirectory() && new File(output).isDirectory()) {
            ArrayList<File> files = IOUtils.getFileList(input, new SourceImageFileFilter(), false);
            for (File f : files) {
                long x = System.currentTimeMillis();
                File outFile = new File(output, f.getName().substring(0, f.getName().indexOf(".")) + ".jp2");
                compress(jp2, f.getAbsolutePath(), outFile.getAbsolutePath(), p);
                report(f.getAbsolutePath(), x);
            }
        } else {
            long x = System.currentTimeMillis();
            File f = new File(input);
            if (output == null)
                output = f.getName().substring(0, f.getName().indexOf(".")) + ".jp2";
            if (new File(output).isDirectory())
                output = output + f.getName().substring(0, f.getName().indexOf(".")) + ".jp2";
            compress(jp2, input, output, p);
            report(input, x);
        }
    } catch (ParseException e) {
        logger.error("Parse exception:" + e.getMessage(), e);
    } catch (DjatokaException e) {
        logger.error("djatoka Compression exception:" + e.getMessage(), e);
    } catch (InstantiationException e) {
        logger.error("Unable to initialize alternate implemenation:" + e.getMessage(), e);
    } catch (Exception e) {
        logger.error("An exception occured:" + e.getMessage(), e);
    }
}

From source file:net.minecraftforge.fml.common.patcher.GenDiffSet.java

public static void main(String[] args) throws IOException {
    String sourceJar = args[0]; //Clean Vanilla jar minecraft.jar or minecraft_server.jar
    String targetDir = args[1]; //Directory containing obfed output classes, typically mcp/reobf/minecraft
    String deobfData = args[2]; //Path to FML's deobfusication_data.lzma
    String outputDir = args[3]; //Path to place generated .binpatch
    String killTarget = args[4]; //"true" if we should destroy the target file if it generated a successful .binpatch

    LogManager.getLogger("GENDIFF").log(Level.INFO,
            String.format("Creating patches at %s for %s from %s", outputDir, sourceJar, targetDir));
    Delta delta = new Delta();
    FMLDeobfuscatingRemapper remapper = FMLDeobfuscatingRemapper.INSTANCE;
    remapper.setupLoadOnly(deobfData, false);
    JarFile sourceZip = new JarFile(sourceJar);
    boolean kill = killTarget.equalsIgnoreCase("true");

    File f = new File(outputDir);
    f.mkdirs();//  w ww. ja  v  a2  s. c  o m

    for (String name : remapper.getObfedClasses()) {
        //            Logger.getLogger("GENDIFF").info(String.format("Evaluating path for data :%s",name));
        String fileName = name;
        String jarName = name;
        if (RESERVED_NAMES.contains(name.toUpperCase(Locale.ENGLISH))) {
            fileName = "_" + name;
        }
        File targetFile = new File(targetDir, fileName.replace('/', File.separatorChar) + ".class");
        jarName = jarName + ".class";
        if (targetFile.exists()) {
            String sourceClassName = name.replace('/', '.');
            String targetClassName = remapper.map(name).replace('/', '.');
            JarEntry entry = sourceZip.getJarEntry(jarName);
            byte[] vanillaBytes = toByteArray(sourceZip, entry);
            byte[] patchedBytes = Files.toByteArray(targetFile);

            byte[] diff = delta.compute(vanillaBytes, patchedBytes);

            ByteArrayDataOutput diffOut = ByteStreams.newDataOutput(diff.length + 50);
            // Original name
            diffOut.writeUTF(name);
            // Source name
            diffOut.writeUTF(sourceClassName);
            // Target name
            diffOut.writeUTF(targetClassName);
            // exists at original
            diffOut.writeBoolean(entry != null);
            if (entry != null) {
                diffOut.writeInt(Hashing.adler32().hashBytes(vanillaBytes).asInt());
            }
            // length of patch
            diffOut.writeInt(diff.length);
            // patch
            diffOut.write(diff);

            File target = new File(outputDir, targetClassName + ".binpatch");
            target.getParentFile().mkdirs();
            Files.write(diffOut.toByteArray(), target);
            Logger.getLogger("GENDIFF").info(String.format("Wrote patch for %s (%s) at %s", name,
                    targetClassName, target.getAbsolutePath()));
            if (kill) {
                targetFile.delete();
                Logger.getLogger("GENDIFF").info(String.format("  Deleted target: %s", targetFile.toString()));
            }
        }
    }
    sourceZip.close();
}

From source file:DIA_Umpire_Quant.DIA_Umpire_LCMSIDGen.java

/**
 * @param args the command line arguments
 *///  w ww .  jav  a 2 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(
                "=================================================================================================");
    }
}

From source file:com.timothyyip.face.FaceDetector.java

public static void main(String[] args) throws ImageReadException, IOException, ImageWriteException {

    Detector detector = new Detector("C:\\Code\\Java\\FaceDetector\\lib\\haarcascade_frontalface_default.xml");

    flickr.photoservice.flickrresponse.Rsp response = getFlickrPhotos();

    for (Photo photo : response.getPhotos().getPhoto()) {
        String timestamp = String.valueOf(Calendar.getInstance().getTimeInMillis());
        BufferedImage originalImage = getPhysicalFlickrImage(photo);

        if (originalImage != null) {
            File originalImageFile = new File(
                    "C:\\Code\\Java\\FaceDetector\\images\\original\\" + timestamp + ".jpg");

            //Sanselan.writeImage(originalImage, originalImageFile, ImageFormat.IMAGE_FORMAT_JPEG, null);
            ImageIO.write(originalImage, "JPG", originalImageFile);
            List<Rectangle> res = detector.getFaces(originalImageFile.getAbsolutePath(), 3, 1.25f, 0.1f, 1,
                    false);/*from  w w  w .j  av a 2  s  .c o  m*/

            for (Rectangle face : res) {
                BufferedImage faceImage = originalImage.getSubimage(face.x, face.y, face.width, face.height);

                Sanselan.writeImage(faceImage,
                        new File("C:\\Code\\Java\\FaceDetector\\images\\"
                                + String.valueOf(Calendar.getInstance().getTimeInMillis()) + ".png"),
                        ImageFormat.IMAGE_FORMAT_PNG, null);
            }

        }
    }
}

From source file:com.clank.launcher.Launcher.java

/**
 * Bootstrap.// www  .  j a va 2  s.  co m
 *
 * @param args args
 */
public static void main(String[] args) {
    SimpleLogFormatter.configureGlobalLogger();

    LauncherArguments options = new LauncherArguments();
    try {
        new JCommander(options, args);
    } catch (ParameterException e) {
        System.err.print(e.getMessage());
        System.exit(1);
        return;
    }

    Integer bsVersion = options.getBootstrapVersion();
    log.info(bsVersion != null ? "Bootstrap version " + bsVersion + " detected" : "Not bootstrapped");

    File dir = options.getDir();
    if (dir != null) {
        log.info("Using given base directory " + dir.getAbsolutePath());
    } else {
        dir = new File(".");
        log.info("Using current directory " + dir.getAbsolutePath());
    }

    final File baseDir = dir;

    SwingUtilities.invokeLater(new Runnable() {
        @Override
        public void run() {
            try {
                UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
                UIManager.getDefaults().put("SplitPane.border", BorderFactory.createEmptyBorder());
                Launcher launcher = new Launcher(baseDir);
                new LauncherFrame(launcher).setVisible(true);
            } catch (Throwable t) {
                log.log(Level.WARNING, "Load failure", t);
                SwingHelper.showErrorDialog(null,
                        "Uh oh! The updater couldn't be opened because a " + "problem was encountered.",
                        "Launcher error", t);
            }
        }
    });

}