Package gem

Examples of gem.PlotForTissue2$Group

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      abuilder.withName("dictionaryType").withMinimum(1).withMaximum(1).create()).withDescription(
      "The dictionary file type (text|sequencefile)").withShortName("dt").create();
    Option helpOpt = obuilder.withLongName("help").withDescription("Print out help").withShortName("h")
        .create();
   
    Group group = gbuilder.withName("Options").withOption(dictOpt).withOption(outOpt).withOption(wordOpt)
        .withOption(inputOpt).withOption(dictTypeOpt).create();
    try {
      Parser parser = new Parser();
      parser.setGroup(group);
      CommandLine cmdLine = parser.parse(args);
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      .withArgument(
          argumentBuilder.withName("defaultCategory").withMaximum(1).withDefault("unknown")
          .create())
      .withDescription("the default category value to use").create();

    Group normalArgs = new GroupBuilder().withOption(help)
        .withOption(quiet).withOption(auc).withOption(scores)
        .withOption(confusion).withOption(inputFileOption)
        .withOption(modelFileOption).withOption(defaultCagetoryOption).create();

    Parser parser = new Parser();
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    Option analyzerOpt = obuilder.withLongName("analyzer").withRequired(false).withArgument(
      abuilder.withName("analyzer").withMinimum(1).withMaximum(1).create()).withDescription(
      "The analyzer to use, must have a no argument constructor").withShortName("a").create();
    Option helpOpt = DefaultOptionCreator.helpOption();
   
    Group group = gbuilder.withName("Options").withOption(categoriesOpt).withOption(dirInputPathOpt)
        .withOption(dirOutputPathOpt).withOption(exactMatchOpt).withOption(analyzerOpt).withOption(helpOpt)
        .create();
   
    Parser parser = new Parser();
    parser.setGroup(group);
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    Option allOpt = obuilder.withLongName("all")
        .withDescription("If set, Select all files. Default is false").withShortName("all").create();
   
    Option helpOpt = DefaultOptionCreator.helpOption();
   
    Group group = gbuilder.withName("Options").withOption(categoriesOpt).withOption(dirInputPathOpt)
        .withOption(dirOutputPathOpt).withOption(exactMatchOpt).withOption(allOpt).withOption(helpOpt)
        .create();
   
    Parser parser = new Parser();
    parser.setGroup(group);
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          + "  Expressed as an integer between 0 and 100. Default is 99.").withShortName("x").create();

    Option helpOpt = obuilder.withLongName("help").withDescription("Print out help").withShortName("h")
        .create();

    Group group = gbuilder.withName("Options").withOption(inputOpt).withOption(idFieldOpt).withOption(
      outputOpt).withOption(delimiterOpt).withOption(helpOpt).withOption(fieldOpt).withOption(maxOpt)
        .withOption(dictOutOpt).withOption(powerOpt).withOption(outWriterOpt).withOption(maxDFPercentOpt)
        .withOption(weightOpt).withOption(minDFOpt).create();

    try {
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    }

    Variable v = ds.findVariable("time_offset");
    v.addAttribute(new Attribute( "units", "seconds since "+dfo.toDateTimeString(start)));

    Group root = ds.getRootGroup();
    root.addAttribute(new Attribute( "Convention", "Suomi-Station-CDM"));   
    ds.finish();
  }
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  public void testEosMetadata() {
    //NetcdfFile ncfile = TestH5.open("c:/data/hdf5/HIRDLS/HIRDLS2_v0.3.1-aIrix-c3_2003d106.h5");
    NetcdfFile ncfile = TestH5.open(testDir +"HIRDLS2-Aura73p_b029_2000d275.he5");

    Group root = ncfile.getRootGroup();
    Group g = root.findGroup("HDFEOS INFORMATION");
    Variable dset = g.findVariable("StructMetadata.0");
    assert(null != dset );
    assert(dset.getDataType() == DataType.CHAR);

    // read entire array
    Array A;
    try {
      A = dset.read();
    }
    catch (IOException e) {
      System.err.println("ERROR reading file");
      assert(false);
      return;
    }
    assert(A.getRank() == 1);
    assert (A instanceof ArrayChar);

    ArrayChar ca = (ArrayChar) A;
    String sval = ca.getString();
    System.out.println(dset.getFullName());
    System.out.println(" Length = "+sval.length());
    System.out.println(" Value = "+sval);

    ////////////////
    dset = g.findVariable("coremetadata.0");
    assert(null != dset );
    assert(dset.getDataType() == DataType.CHAR);

    // read entire array
    try {
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    public int doAct(String filename) throws IOException {
      NetcdfFile ncfile = null;

      try {
        ncfile = NetcdfFile.open(filename);
        Group root = ncfile.getRootGroup();
        Group g = root.findGroup("HDFEOS INFORMATION");
        if (g == null) g = ncfile.getRootGroup();

        Variable dset = g.findVariable("StructMetadata.0");
        if (dset != null) {
          System.out.println("EOS file=" + filename);
          return 1;
        }
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    public void setSearchPath(final String... groupNames) {
        final Group[] groups = new Group[groupNames.length];
        int count = 0;
        for (final String name : groupNames) {
            if (name != null) {
                final Group group = file.findGroup(name);
                if (group == null) {
                    continue; // Group not found - do not increment the counter.
                }
                groups[count] = group;
            }
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     */
    @Override
    public String[] getSearchPath() {
        final String[] path = new String[groups.length];
        for (int i=0; i<path.length; i++) {
            final Group group = groups[i];
            if (group != null) {
                path[i] = group.getShortName();
            }
        }
        return path;
    }
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