Example usage for java.io File getParentFile

List of usage examples for java.io File getParentFile

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Introduction

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

Prototype

public File getParentFile()

Source Link

Document

Returns the abstract pathname of this abstract pathname's parent, or null if this pathname does not name a parent directory.

Usage

From source file:ee.ria.xroad.asyncdb.AsyncDBIntegrationTest.java

/**
 *
 *
 * @param args//w  w  w  . j  a v  a2s . co  m
 *            - use 'preservedb' to retain directory structure for further
 *            investigation
 * @throws Exception - when running integration test fails.
 */
public static void main(String[] args) throws Exception {
    File provider = new File(AsyncDBTestUtil.getProviderDirPath());
    File logFile = new File(AsyncDBTestUtil.getAsyncLogFilePath());
    if (provider.exists() || logFile.exists()) {
        throw new IntegrationTestFailedException(
                "Directory '" + AsyncDBTestUtil.DB_FILEPATH + "' and file '" + AsyncDBTestUtil.LOG_FILEPATH
                        + "' must not be present in the beginning of integration test, delete it!");
    }

    File logDir = logFile.getParentFile();
    logDir.mkdirs();

    boolean preserveDB = false;
    if (args.length > 0) {
        preserveDB = "preservedb".equalsIgnoreCase(args[0]);
        LOG.warn("Preserving DB file tree after test, be sure to remove them later by yourself!");
    }

    long freeFileDescriptorsAtBeginning = SystemMetrics.getFreeFileDescriptorCount();

    try {

        addRequestToNonExistentProvider();
        addRequestToExistentProvider();
        markSecondRequestAsRemoved();
        restoreSecondRequest();
        getAllMessageQueues();
        sendFirstRequestSuccessfully();
        sendSecondRequestUnsuccessfully();
        resetSendCountOfSecondRequest();
        skipNotSendingRequest();
        revertWritingFailure();

        // Test cases from real life
        removeCorruptRequestAndSendNext();
    } finally {
        validateFileDescriptors(freeFileDescriptorsAtBeginning);

        if (!preserveDB) {
            FileUtils.deleteDirectory(new File(AsyncDBTestUtil.getProviderDirPath()));
            FileUtils.deleteDirectory(logDir);
        }
    }

    LOG.info("Integration test of ASYNC-DB accomplished successfully.");
}

From source file:acmi.l2.clientmod.l2_version_switcher.Main.java

public static void main(String[] args) {
    if (args.length != 3 && args.length != 4) {
        System.out.println("USAGE: l2_version_switcher.jar host game version <--splash> <filter>");
        System.out.println("EXAMPLE: l2_version_switcher.jar " + L2.NCWEST_HOST + " " + L2.NCWEST_GAME
                + " 1 \"system\\*\"");
        System.out.println(//from w ww  . j av  a2 s  . c o  m
                "         l2_version_switcher.jar " + L2.PLAYNC_TEST_HOST + " " + L2.PLAYNC_TEST_GAME + " 48");
        System.exit(0);
    }

    List<String> argsList = new ArrayList<>(Arrays.asList(args));
    String host = argsList.get(0);
    String game = argsList.get(1);
    int version = Integer.parseInt(argsList.get(2));
    Helper helper = new Helper(host, game, version);
    boolean available = false;

    try {
        available = helper.isAvailable();
    } catch (IOException e) {
        System.err.print(e.getClass().getSimpleName());
        if (e.getMessage() != null) {
            System.err.print(": " + e.getMessage());
        }

        System.err.println();
    }

    System.out.println(String.format("Version %d available: %b", version, available));
    if (!available) {
        System.exit(0);
    }

    List<FileInfo> fileInfoList = null;
    try {
        fileInfoList = helper.getFileInfoList();
    } catch (IOException e) {
        System.err.println("Couldn\'t get file info map");
        System.exit(1);
    }

    boolean splash = argsList.remove("--splash");
    if (splash) {
        Optional<FileInfo> splashObj = fileInfoList.stream()
                .filter(fi -> fi.getPath().contains("sp_32b_01.bmp")).findAny();
        if (splashObj.isPresent()) {
            try (InputStream is = new FilterInputStream(
                    Util.getUnzipStream(helper.getDownloadStream(splashObj.get().getPath()))) {
                @Override
                public int read() throws IOException {
                    int b = super.read();
                    if (b >= 0)
                        b ^= 0x36;
                    return b;
                }

                @Override
                public int read(byte[] b, int off, int len) throws IOException {
                    int r = super.read(b, off, len);
                    if (r >= 0) {
                        for (int i = 0; i < r; i++)
                            b[off + i] ^= 0x36;
                    }
                    return r;
                }
            }) {
                new DataInputStream(is).readFully(new byte[28]);
                BufferedImage bi = ImageIO.read(is);

                JFrame frame = new JFrame("Lineage 2 [" + version + "] " + splashObj.get().getPath());
                frame.setContentPane(new JComponent() {
                    {
                        setPreferredSize(new Dimension(bi.getWidth(), bi.getHeight()));
                    }

                    @Override
                    protected void paintComponent(Graphics g) {
                        g.drawImage(bi, 0, 0, null);
                    }
                });
                frame.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
                frame.pack();
                frame.setLocationRelativeTo(null);
                frame.setVisible(true);
            } catch (IOException e) {
                e.printStackTrace();
            }
        } else {
            System.out.println("Splash not found");
        }
        return;
    }

    String filter = argsList.size() > 3 ? separatorsToSystem(argsList.get(3)) : null;

    File l2Folder = new File(System.getProperty("user.dir"));
    List<FileInfo> toUpdate = fileInfoList.parallelStream().filter(fi -> {
        String filePath = separatorsToSystem(fi.getPath());

        if (filter != null && !wildcardMatch(filePath, filter, IOCase.INSENSITIVE))
            return false;
        File file = new File(l2Folder, filePath);

        try {
            if (file.exists() && file.length() == fi.getSize() && Util.hashEquals(file, fi.getHash())) {
                System.out.println(filePath + ": OK");
                return false;
            }
        } catch (IOException e) {
            System.out.println(filePath + ": couldn't check hash: " + e);
            return true;
        }

        System.out.println(filePath + ": need update");
        return true;
    }).collect(Collectors.toList());

    List<String> errors = Collections.synchronizedList(new ArrayList<>());
    ExecutorService executor = Executors.newFixedThreadPool(16);
    CompletableFuture[] tasks = toUpdate.stream().map(fi -> CompletableFuture.runAsync(() -> {
        String filePath = separatorsToSystem(fi.getPath());
        File file = new File(l2Folder, filePath);

        File folder = file.getParentFile();
        if (!folder.exists()) {
            if (!folder.mkdirs()) {
                errors.add(filePath + ": couldn't create parent dir");
                return;
            }
        }

        try (InputStream input = Util
                .getUnzipStream(new BufferedInputStream(helper.getDownloadStream(fi.getPath())));
                OutputStream output = new BufferedOutputStream(new FileOutputStream(file))) {
            byte[] buffer = new byte[Math.min(fi.getSize(), 1 << 24)];
            int pos = 0;
            int r;
            while ((r = input.read(buffer, pos, buffer.length - pos)) >= 0) {
                pos += r;
                if (pos == buffer.length) {
                    output.write(buffer, 0, pos);
                    pos = 0;
                }
            }
            if (pos != 0) {
                output.write(buffer, 0, pos);
            }
            System.out.println(filePath + ": OK");
        } catch (IOException e) {
            String msg = filePath + ": FAIL: " + e.getClass().getSimpleName();
            if (e.getMessage() != null) {
                msg += ": " + e.getMessage();
            }
            errors.add(msg);
        }
    }, executor)).toArray(CompletableFuture[]::new);
    CompletableFuture.allOf(tasks).thenRun(() -> {
        for (String err : errors)
            System.err.println(err);
        executor.shutdown();
    });
}

From source file:edu.msu.cme.rdp.readseq.utils.SequenceTrimmer.java

public static void main(String[] args) throws IOException {
    Options options = new Options();
    options.addOption("r", "ref-seq", true,
            "Trim points are given as positions in a reference sequence from this file");
    options.addOption("i", "inclusive", false, "Trim points are inclusive");
    options.addOption("l", "length", true, "Minimum length of sequence after trimming");
    options.addOption("f", "filled-ratio", true,
            "Minimum ratio of filled model positions of sequence after trimming");
    options.addOption("o", "out", true, "Write sequences to directory (default=cwd)");
    options.addOption("s", "stats", true, "Write stats to file");

    PrintWriter statsOut = new PrintWriter(new NullWriter());
    boolean inclusive = false;
    int minLength = 0;
    int minTrimmedLength = 0;
    int maxNs = 0;
    int maxTrimNs = 0;

    int trimStart = 0;
    int trimStop = 0;
    Sequence refSeq = null;//from  w w  w  .  j  a  v a 2 s .com
    float minFilledRatio = 0;

    int expectedModelPos = -1;
    String[] inputFiles = null;
    File outdir = new File(".");
    try {
        CommandLine line = new PosixParser().parse(options, args);

        if (line.hasOption("ref-seq")) {
            refSeq = readRefSeq(new File(line.getOptionValue("ref-seq")));
        }

        if (line.hasOption("inclusive")) {
            inclusive = true;
        }

        if (line.hasOption("length")) {
            minLength = Integer.valueOf(line.getOptionValue("length"));
        }

        if (line.hasOption("filled-ratio")) {
            minFilledRatio = Float.valueOf(line.getOptionValue("filled-ratio"));
        }

        if (line.hasOption("out")) {
            outdir = new File(line.getOptionValue("out"));
            if (!outdir.isDirectory()) {
                outdir = outdir.getParentFile();
                System.err.println("Output option is not a directory, using " + outdir + " instead");
            }
        }

        if (line.hasOption("stats")) {
            statsOut = new PrintWriter(line.getOptionValue("stats"));
        }

        args = line.getArgs();

        if (args.length < 3) {
            throw new Exception("Unexpected number of arguments");
        }

        trimStart = Integer.parseInt(args[0]);
        trimStop = Integer.parseInt(args[1]);
        inputFiles = Arrays.copyOfRange(args, 2, args.length);

        if (refSeq != null) {
            expectedModelPos = SeqUtils.getMaskedBySeqString(refSeq.getSeqString()).length();
            trimStart = translateCoord(trimStart, refSeq, CoordType.seq, CoordType.model);
            trimStop = translateCoord(trimStop, refSeq, CoordType.seq, CoordType.model);
        }

    } catch (Exception e) {
        new HelpFormatter().printHelp("SequenceTrimmer <trim start> <trim stop> <aligned file> ...", options);
        System.err.println("Error: " + e.getMessage());
    }

    System.err.println("Starting sequence trimmer");
    System.err.println("*  Input files:           " + Arrays.asList(inputFiles));
    System.err.println("*  Minimum Length:        " + minLength);
    System.err.println("*  Trim point inclusive?: " + inclusive);
    System.err.println("*  Trim points:           " + trimStart + "-" + trimStop);
    System.err.println("*  Min filled ratio:      " + minFilledRatio);
    System.err.println("*  refSeq:                "
            + ((refSeq == null) ? "model" : refSeq.getSeqName() + " " + refSeq.getDesc()));

    Sequence seq;
    SeqReader reader;
    TrimStats stats;

    writeStatsHeader(statsOut);

    FastaWriter seqWriter;
    File in;
    for (String infile : inputFiles) {
        in = new File(infile);
        reader = new SequenceReader(in);
        seqWriter = new FastaWriter(new File(outdir, "trimmed_" + in.getName()));

        while ((seq = reader.readNextSequence()) != null) {
            if (seq.getSeqName().startsWith("#")) {
                seqWriter.writeSeq(seq.getSeqName(), "", trimMetaSeq(seq.getSeqString(), trimStart, trimStop));
                continue;
            }

            stats = getStats(seq, trimStart, trimStop);
            boolean passed = didSeqPass(stats, minLength, minTrimmedLength, maxNs, maxTrimNs, minFilledRatio);
            writeStats(statsOut, seq.getSeqName(), stats, passed);
            if (passed) {
                seqWriter.writeSeq(seq.getSeqName(), seq.getDesc(), new String(stats.trimmedBases));
            }
        }

        reader.close();
        seqWriter.close();
    }

    statsOut.close();
}

From source file:at.newmedialab.ldpath.template.LDTemplate.java

public static void main(String[] args) {
    Options options = buildOptions();//from   w ww.j  a v  a 2s .c  o  m

    CommandLineParser parser = new PosixParser();
    try {
        CommandLine cmd = parser.parse(options, args);

        Level logLevel = Level.WARN;

        if (cmd.hasOption("loglevel")) {
            String logLevelName = cmd.getOptionValue("loglevel");
            if ("DEBUG".equals(logLevelName.toUpperCase())) {
                logLevel = Level.DEBUG;
            } else if ("INFO".equals(logLevelName.toUpperCase())) {
                logLevel = Level.INFO;
            } else if ("WARN".equals(logLevelName.toUpperCase())) {
                logLevel = Level.WARN;
            } else if ("ERROR".equals(logLevelName.toUpperCase())) {
                logLevel = Level.ERROR;
            } else {
                log.error("unsupported log level: {}", logLevelName);
            }
        }

        if (logLevel != null) {
            for (String logname : new String[] { "at", "org", "net", "com" }) {

                ch.qos.logback.classic.Logger logger = (ch.qos.logback.classic.Logger) LoggerFactory
                        .getLogger(logname);
                logger.setLevel(logLevel);
            }
        }

        File template = null;
        if (cmd.hasOption("template")) {
            template = new File(cmd.getOptionValue("template"));
        }

        GenericSesameBackend backend;
        if (cmd.hasOption("store")) {
            backend = new LDPersistentBackend(new File(cmd.getOptionValue("store")));
        } else {
            backend = new LDMemoryBackend();
        }

        Resource context = null;
        if (cmd.hasOption("context")) {
            context = backend.getRepository().getValueFactory().createURI(cmd.getOptionValue("context"));
        }

        BufferedWriter out = null;
        if (cmd.hasOption("out")) {
            File of = new File(cmd.getOptionValue("out"));
            if (of.canWrite()) {
                out = new BufferedWriter(new FileWriter(of));
            } else {
                log.error("cannot write to output file {}", of);
                System.exit(1);
            }
        } else {
            out = new BufferedWriter(new OutputStreamWriter(System.out));
        }

        if (backend != null && context != null && template != null) {
            TemplateEngine<Value> engine = new TemplateEngine<Value>(backend);

            engine.setDirectoryForTemplateLoading(template.getParentFile());
            engine.processFileTemplate(context, template.getName(), out);
            out.flush();
            out.close();
        }

        if (backend instanceof LDPersistentBackend) {
            ((LDPersistentBackend) backend).shutdown();
        }

    } catch (ParseException e) {
        System.err.println("invalid arguments");
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("LDQuery", options, true);
    } catch (FileNotFoundException e) {
        System.err.println("file or program could not be found");
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("LDQuery", options, true);
    } catch (IOException e) {
        System.err.println("could not access file");
        e.printStackTrace(System.err);
    } catch (TemplateException e) {
        System.err.println("error while processing template");
        e.printStackTrace(System.err);
    }

}

From source file:edu.oregonstate.eecs.mcplan.abstraction.PairDataset.java

/**
 * @param args/*  w  ww  .j  a va  2s.c  o  m*/
 */
public static void main(final String[] args) {
    int idx = 0;
    final String single_filename = args[idx++];
    System.out.println("single_filename = " + single_filename);
    final String keyword = args[idx++];
    System.out.println("keyword = " + keyword);
    final int seed = Integer.parseInt(args[idx++]);
    System.out.println("seed = " + seed);
    final int max_pairwise_instances = Integer.parseInt(args[idx++]);
    System.out.println("max_pairwise_instances = " + max_pairwise_instances);

    final File single_file = new File(single_filename);
    System.out.println("Opening '" + single_file.getAbsolutePath() + "'");
    assert (single_file.exists());
    final Instances single = WekaUtil.readLabeledDataset(single_file);
    final ArrayList<Attribute> single_attributes = WekaUtil.extractAttributes(single);

    final InstanceCombiner combiner;
    if ("difference".equals(keyword)) {
        combiner = new DifferenceFeatures(single_attributes);
    } else if ("symmetric".equals(keyword)) {
        combiner = new SymmetricFeatures(single_attributes);
    } else {
        throw new IllegalArgumentException("Unknown keyword '" + keyword + "'");
    }

    //      final String pair_name = FilenameUtils.getBaseName( single_filename )
    //                         + "_" + keyword + "_" + max_pairwise_instances;
    final RandomGenerator rng = new MersenneTwister(seed);
    System.out.println("Making dataset...");
    final Instances pair_instances = makePairDataset(rng, max_pairwise_instances, single, combiner);
    System.out.println("Writing dataset...");
    WekaUtil.writeDataset(single_file.getParentFile(), pair_instances);
}

From source file:com.zarkonnen.longan.Main.java

public static void main(String[] args) throws IOException {
    // Use Apache Commons CLI (packaged into the Jar) to parse command line options.
    Options options = new Options();
    Option helpO = OptionBuilder.withDescription("print help").create("h");
    Option versionO = OptionBuilder.withDescription("print version").create("v");
    Option outputO = OptionBuilder.withDescription("output file").withLongOpt("out").hasArg()
            .withArgName("file").create("o");
    Option formatO = OptionBuilder
            .withDescription("output format: one of plaintext (default) and visualize (debug output in png)")
            .hasArg().withArgName("format").withLongOpt("format").create();
    Option serverO = OptionBuilder.withDescription("launches server mode: Server mode reads "
            + "command line strings one per line exactly as above. If no output file is "
            + "specified, returns a line containing the number of output lines before the "
            + "output. If there is an error, returns a single line with the error message. "
            + "Shut down server by sending \"quit\".").withLongOpt("server").create();
    Option openCLO = OptionBuilder
            .withDescription(/*  ww w. j  a v  a  2 s  .co  m*/
                    "enables use of the graphics card to " + "support the OCR system. Defaults to true.")
            .withLongOpt("enable-opencl").hasArg().withArgName("enabled").create();
    options.addOption(helpO);
    options.addOption(versionO);
    options.addOption(outputO);
    options.addOption(formatO);
    options.addOption(serverO);
    options.addOption(openCLO);
    CommandLineParser clp = new GnuParser();
    try {
        CommandLine line = clp.parse(options, args);
        if (line.hasOption("h")) {
            new HelpFormatter().printHelp(INVOCATION, options);
            System.exit(0);
        }
        if (line.hasOption("v")) {
            System.out.println(Longan.VERSION);
            System.exit(0);
        }
        boolean enableOpenCL = true;
        if (line.hasOption("enable-opencl")) {
            enableOpenCL = line.getOptionValue("enable-opencl").toLowerCase().equals("true")
                    || line.getOptionValue("enable-opencl").equals("1");
        }
        if (line.hasOption("server")) {
            Longan longan = Longan.getDefaultImplementation(enableOpenCL);
            BufferedReader inputR = new BufferedReader(new InputStreamReader(System.in));
            while (true) {
                String input = inputR.readLine();
                if (input.trim().equals("quit")) {
                    return;
                }
                String[] args2 = splitInput(input);
                Options o2 = new Options();
                o2.addOption(outputO);
                o2.addOption(formatO);
                try {
                    line = clp.parse(o2, args2);

                    File outFile = null;
                    if (line.hasOption("o")) {
                        outFile = new File(line.getOptionValue("o"));
                    }

                    ResultConverter format = FORMATS.get(line.getOptionValue("format", "plaintext"));
                    if (format != DEFAULT_FORMAT && outFile == null) {
                        System.out.println("You must specify an output file for non-plaintext output.");
                        continue;
                    }

                    if (line.getArgList().isEmpty()) {
                        System.out.println("Please specify an input image.");
                        continue;
                    }
                    if (line.getArgList().size() > 1) {
                        System.err.println("Please specify one input image at a time");
                        continue;
                    }

                    File inFile = new File((String) line.getArgList().get(0));

                    if (!inFile.exists()) {
                        System.out.println("The input image does not exist.");
                        continue;
                    }

                    try {
                        Result result = longan.process(ImageIO.read(inFile));
                        if (outFile == null) {
                            String txt = DEFAULT_FORMAT.convert(result);
                            System.out.println(numNewlines(txt) + 1);
                            System.out.print(txt);
                        } else {
                            if (outFile.getAbsoluteFile().getParentFile() != null
                                    && !outFile.getAbsoluteFile().getParentFile().exists()) {
                                outFile.getParentFile().mkdirs();
                            }
                            FileOutputStream fos = new FileOutputStream(outFile);
                            try {
                                format.write(result, fos);
                            } finally {
                                fos.close();
                            }
                        }
                    } catch (Exception e) {
                        System.out.println("Processing error: " + exception(e));
                    }
                } catch (ParseException e) {
                    System.out.println("Input not recognized: " + exception(e));
                }
            } // End server loop
        } else {
            // Single invocation
            File outFile = null;
            if (line.hasOption("o")) {
                outFile = new File(line.getOptionValue("o"));
            }

            ResultConverter format = FORMATS.get(line.getOptionValue("format", "plaintext"));
            if (format != DEFAULT_FORMAT && outFile == null) {
                System.err.println("You must specify an output file for non-plaintext output.");
                System.exit(1);
            }

            if (line.getArgList().isEmpty()) {
                System.err.println("Please specify an input image.");
                new HelpFormatter().printHelp(INVOCATION, options);
                System.exit(1);
            }
            if (line.getArgList().size() > 1) {
                System.err.println("Please specify one input image only. To process multiple "
                        + "images, use server mode.");
                System.exit(1);
            }
            File inFile = new File((String) line.getArgList().get(0));

            if (!inFile.exists()) {
                System.err.println("The input image does not exist.");
                System.exit(1);
            }

            try {
                Result result = Longan.getDefaultImplementation(enableOpenCL).process(ImageIO.read(inFile));
                if (outFile == null) {
                    String txt = DEFAULT_FORMAT.convert(result);
                    System.out.print(txt);
                } else {
                    if (outFile.getAbsoluteFile().getParentFile() != null
                            && !outFile.getAbsoluteFile().getParentFile().exists()) {
                        outFile.getParentFile().mkdirs();
                    }
                    FileOutputStream fos = new FileOutputStream(outFile);
                    try {
                        format.write(format.convert(result), fos);
                    } finally {
                        fos.close();
                    }
                }
            } catch (Exception e) {
                System.err.println("Processing error: " + exception(e));
                System.exit(1);
            }
        }
    } catch (ParseException e) {
        System.err.println("Parsing command line input failed: " + exception(e));
        System.exit(1);
    }
}

From source file:edu.msu.cme.rdp.multicompare.Main.java

public static void main(String[] args) throws Exception {
    PrintStream hier_out = null;//from www. ja v  a  2s  .c om
    PrintWriter assign_out = new PrintWriter(new NullWriter());
    PrintStream bootstrap_out = null;
    File hier_out_filename = null;
    String propFile = null;
    File biomFile = null;
    File metadataFile = null;
    PrintWriter shortseq_out = null;
    List<MCSample> samples = new ArrayList();
    ClassificationResultFormatter.FORMAT format = ClassificationResultFormatter.FORMAT.allRank;
    float conf = CmdOptions.DEFAULT_CONF;
    String gene = null;
    int min_bootstrap_words = Classifier.MIN_BOOTSTRSP_WORDS;

    try {
        CommandLine line = new PosixParser().parse(options, args);

        if (line.hasOption(CmdOptions.OUTFILE_SHORT_OPT)) {
            assign_out = new PrintWriter(line.getOptionValue(CmdOptions.OUTFILE_SHORT_OPT));
        } else {
            throw new IllegalArgumentException("Require the output file for classification assignment");
        }
        if (line.hasOption(CmdOptions.HIER_OUTFILE_SHORT_OPT)) {
            hier_out_filename = new File(line.getOptionValue(CmdOptions.HIER_OUTFILE_SHORT_OPT));
            hier_out = new PrintStream(hier_out_filename);
        }
        if (line.hasOption(CmdOptions.BIOMFILE_SHORT_OPT)) {
            biomFile = new File(line.getOptionValue(CmdOptions.BIOMFILE_SHORT_OPT));
        }
        if (line.hasOption(CmdOptions.METADATA_SHORT_OPT)) {
            metadataFile = new File(line.getOptionValue(CmdOptions.METADATA_SHORT_OPT));
        }

        if (line.hasOption(CmdOptions.TRAINPROPFILE_SHORT_OPT)) {
            if (gene != null) {
                throw new IllegalArgumentException(
                        "Already specified the gene from the default location. Can not specify train_propfile");
            } else {
                propFile = line.getOptionValue(CmdOptions.TRAINPROPFILE_SHORT_OPT);
            }
        }
        if (line.hasOption(CmdOptions.FORMAT_SHORT_OPT)) {
            String f = line.getOptionValue(CmdOptions.FORMAT_SHORT_OPT);
            if (f.equalsIgnoreCase("allrank")) {
                format = ClassificationResultFormatter.FORMAT.allRank;
            } else if (f.equalsIgnoreCase("fixrank")) {
                format = ClassificationResultFormatter.FORMAT.fixRank;
            } else if (f.equalsIgnoreCase("filterbyconf")) {
                format = ClassificationResultFormatter.FORMAT.filterbyconf;
            } else if (f.equalsIgnoreCase("db")) {
                format = ClassificationResultFormatter.FORMAT.dbformat;
            } else if (f.equalsIgnoreCase("biom")) {
                format = ClassificationResultFormatter.FORMAT.biom;
            } else {
                throw new IllegalArgumentException(
                        "Not an valid output format, only allrank, fixrank, biom, filterbyconf and db allowed");
            }
        }
        if (line.hasOption(CmdOptions.GENE_SHORT_OPT)) {
            if (propFile != null) {
                throw new IllegalArgumentException(
                        "Already specified train_propfile. Can not specify gene any more");
            }
            gene = line.getOptionValue(CmdOptions.GENE_SHORT_OPT).toLowerCase();

            if (!gene.equals(ClassifierFactory.RRNA_16S_GENE) && !gene.equals(ClassifierFactory.FUNGALLSU_GENE)
                    && !gene.equals(ClassifierFactory.FUNGALITS_warcup_GENE)
                    && !gene.equals(ClassifierFactory.FUNGALITS_unite_GENE)) {
                throw new IllegalArgumentException(gene + " not found, choose from"
                        + ClassifierFactory.RRNA_16S_GENE + ", " + ClassifierFactory.FUNGALLSU_GENE + ", "
                        + ClassifierFactory.FUNGALITS_warcup_GENE + ", "
                        + ClassifierFactory.FUNGALITS_unite_GENE);
            }
        }
        if (line.hasOption(CmdOptions.MIN_BOOTSTRAP_WORDS_SHORT_OPT)) {
            min_bootstrap_words = Integer
                    .parseInt(line.getOptionValue(CmdOptions.MIN_BOOTSTRAP_WORDS_SHORT_OPT));
            if (min_bootstrap_words < Classifier.MIN_BOOTSTRSP_WORDS) {
                throw new IllegalArgumentException(CmdOptions.MIN_BOOTSTRAP_WORDS_LONG_OPT
                        + " must be at least " + Classifier.MIN_BOOTSTRSP_WORDS);
            }
        }
        if (line.hasOption(CmdOptions.BOOTSTRAP_SHORT_OPT)) {
            String confString = line.getOptionValue(CmdOptions.BOOTSTRAP_SHORT_OPT);
            try {
                conf = Float.valueOf(confString);
            } catch (NumberFormatException e) {
                throw new IllegalArgumentException("Confidence must be a decimal number");
            }

            if (conf < 0 || conf > 1) {
                throw new IllegalArgumentException("Confidence must be in the range [0,1]");
            }
        }
        if (line.hasOption(CmdOptions.SHORTSEQ_OUTFILE_SHORT_OPT)) {
            shortseq_out = new PrintWriter(line.getOptionValue(CmdOptions.SHORTSEQ_OUTFILE_SHORT_OPT));
        }
        if (line.hasOption(CmdOptions.BOOTSTRAP_OUTFILE_SHORT_OPT)) {
            bootstrap_out = new PrintStream(line.getOptionValue(CmdOptions.BOOTSTRAP_OUTFILE_SHORT_OPT));
        }

        if (format.equals(ClassificationResultFormatter.FORMAT.biom) && biomFile == null) {
            throw new IllegalArgumentException("biom format requires an input biom file");
        }
        if (biomFile != null) { // if input biom file provided, use biom format
            format = ClassificationResultFormatter.FORMAT.biom;
        }

        args = line.getArgs();
        for (String arg : args) {
            String[] inFileNames = arg.split(",");
            File inputFile = new File(inFileNames[0]);
            File idmappingFile = null;
            if (!inputFile.exists()) {
                throw new IllegalArgumentException("Failed to find input file \"" + inFileNames[0] + "\"");
            }
            if (inFileNames.length == 2) {
                idmappingFile = new File(inFileNames[1]);
                if (!idmappingFile.exists()) {
                    throw new IllegalArgumentException("Failed to find input file \"" + inFileNames[1] + "\"");
                }
            }

            MCSample nextSample = new MCSample(inputFile, idmappingFile);
            samples.add(nextSample);
        }
        if (propFile == null && gene == null) {
            gene = CmdOptions.DEFAULT_GENE;
        }
        if (samples.size() < 1) {
            throw new IllegalArgumentException("Require at least one sample files");
        }
    } catch (Exception e) {
        System.out.println("Command Error: " + e.getMessage());
        new HelpFormatter().printHelp(80, " [options] <samplefile>[,idmappingfile] ...", "", options, "");
        return;
    }

    MultiClassifier multiClassifier = new MultiClassifier(propFile, gene, biomFile, metadataFile);
    MultiClassifierResult result = multiClassifier.multiCompare(samples, conf, assign_out, format,
            min_bootstrap_words);
    assign_out.close();
    if (hier_out != null) {
        DefaultPrintVisitor printVisitor = new DefaultPrintVisitor(hier_out, samples);
        result.getRoot().topDownVisit(printVisitor);
        hier_out.close();
        if (multiClassifier.hasCopyNumber()) {
            // print copy number corrected counts
            File cn_corrected_s = new File(hier_out_filename.getParentFile(),
                    "cnadjusted_" + hier_out_filename.getName());
            PrintStream cn_corrected_hier_out = new PrintStream(cn_corrected_s);
            printVisitor = new DefaultPrintVisitor(cn_corrected_hier_out, samples, true);
            result.getRoot().topDownVisit(printVisitor);
            cn_corrected_hier_out.close();
        }
    }

    if (bootstrap_out != null) {
        for (MCSample sample : samples) {
            MCSamplePrintUtil.printBootstrapCountTable(bootstrap_out, sample);
        }
        bootstrap_out.close();
    }

    if (shortseq_out != null) {
        for (String id : result.getBadSequences()) {
            shortseq_out.write(id + "\n");
        }
        shortseq_out.close();
    }

}

From source file:Main.java

public static void makeDir(File dir) {
    if (!dir.getParentFile().exists()) {
        makeDir(dir.getParentFile());//ww w  .j a v a2 s .c  o  m
    }
    dir.mkdir();
}

From source file:Main.java

static void createParentDirs(File file) {
    File dir = file.getParentFile();
    if (dir != null && !dir.exists() && !dir.mkdirs())
        throw new IllegalStateException("Couldnt create " + dir);
}

From source file:Main.java

public static void mkFile(String filePath, boolean mkdir) throws Exception {
    File file = new File(filePath);
    file.getParentFile().mkdirs();
    file.createNewFile();//ww  w  .j  av a 2  s .  co m
    file = null;
}