Example usage for java.io File getName

Introduction

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

Prototype

public String getName()

Source Link

Document

Returns the name of the file or directory denoted by this abstract pathname.

Usage

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

public static void main(String[] args) throws Exception {
    PrintStream hier_out = null;/* ww  w  .ja v a 2  s.c o  m*/
    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 String getFileExtensionName(File f) {
    if (f.getName().indexOf(".") == -1) {
        return "";
    } else {//from w  w  w  . ja  v a2  s  . co  m
        return f.getName().substring(f.getName().length() - 3, f.getName().length());
    }
}

From source file:Main.java

private static boolean isJarFile(File file) {
    return file.getName().contains(JAR_FILE_EXT);
}

From source file:Main.java

public static boolean isTargz(File f) {
    return f.getName().endsWith("tar.gz");
}

From source file:Main.java

public static String getFilename(File file) {
    return file.getName().replace(".epub", "");
}

From source file:Main.java

private final static boolean looksLikeImage(File src) {
    String n = src.getName().toLowerCase();
    return (n.endsWith(".jpg") || n.endsWith(".png") || n.endsWith(".gif"));
}

From source file:Main.java

public static boolean isOGMFile(File f) {
    return isOGMFile(f.getName());
}

From source file:Main.java

public static boolean isOGGFile(File in) {
    return isOGGFile(in.getName());
}

From source file:Main.java

public static boolean isVideo(File file) {
    return isVideo(file.getName());
}

From source file:Main.java

public static boolean isM4AFile(File in) {
    return isM4AFile(in.getName());
}