Esempio n. 1
0
  /**
   * Gets a detailed description for a given argument group.
   *
   * @param argumentDefinitionGroup The group of argument definitions to render.
   * @return A string giving detailed info about the contents of this group.
   */
  private String getDetailForGroup(ArgumentDefinitionGroup argumentDefinitionGroup) {
    if (argumentDefinitionGroup.allHidden()) return "";

    StringBuilder builder = new StringBuilder();
    Formatter formatter = new Formatter(builder);

    if (argumentDefinitionGroup.groupName != null
        && argumentDefinitionGroup.argumentDefinitions.size() != 0)
      builder.append(String.format("%nArguments for %s:%n", argumentDefinitionGroup.groupName));

    List<ArgumentDefinition> argumentDefinitions = new ArrayList<ArgumentDefinition>();
    for (ArgumentDefinition argumentDefinition : argumentDefinitionGroup.argumentDefinitions) {
      if (!argumentDefinition.isHidden) argumentDefinitions.add(argumentDefinition);
    }

    // Try to fit the entire argument definition across the screen, but impose an arbitrary cap of
    // 3/4 *
    // LINE_WIDTH in case the length of the arguments gets out of control.
    int argWidth =
        Math.min(
            findLongestArgumentCallingInfo(argumentDefinitions),
            (TextFormattingUtils.DEFAULT_LINE_WIDTH * 3) / 4 - FIELD_SEPARATION_WIDTH);
    int docWidth = TextFormattingUtils.DEFAULT_LINE_WIDTH - argWidth - FIELD_SEPARATION_WIDTH;

    for (ArgumentDefinition argumentDefinition : argumentDefinitions) {
      Iterator<String> wordWrappedArgs =
          TextFormattingUtils.wordWrap(getArgumentCallingInfo(argumentDefinition), argWidth)
              .iterator();
      Iterator<String> wordWrappedDoc =
          TextFormattingUtils.wordWrap(getArgumentDoc(argumentDefinition), docWidth).iterator();

      while (wordWrappedArgs.hasNext() || wordWrappedDoc.hasNext()) {
        String arg = wordWrappedArgs.hasNext() ? wordWrappedArgs.next() : "";
        String doc = wordWrappedDoc.hasNext() ? wordWrappedDoc.next() : "";

        String formatString = "%-" + argWidth + "s%" + FIELD_SEPARATION_WIDTH + "s%s%n";
        formatter.format(formatString, arg, "", doc);
      }
    }

    return builder.toString();
  }
Esempio n. 2
0
 /**
  * Creates a program record (@PG) tag
  *
  * @param toolkit the engine
  * @param walker the walker object (so we can extract the command line)
  * @param PROGRAM_RECORD_NAME the name for the PG tag
  * @return a program record for the tool
  */
 public static SAMProgramRecord createProgramRecord(
     GenomeAnalysisEngine toolkit, Object walker, String PROGRAM_RECORD_NAME) {
   final SAMProgramRecord programRecord = new SAMProgramRecord(PROGRAM_RECORD_NAME);
   final ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("StingText");
   try {
     final String version = headerInfo.getString("org.broadinstitute.sting.gatk.version");
     programRecord.setProgramVersion(version);
   } catch (MissingResourceException e) {
     // couldn't care less if the resource is missing...
   }
   programRecord.setCommandLine(
       toolkit.createApproximateCommandLineArgumentString(toolkit, walker));
   return programRecord;
 }
Esempio n. 3
0
  /**
   * Gets the synopsis: the actual command to run.
   *
   * @param runningInstructions Instructions on how to run hte application.
   * @param argumentGroups Program arguments sorted in order of definition group displays.
   * @return A synopsis line.
   */
  private String getSynopsis(
      String runningInstructions, List<ArgumentDefinitionGroup> argumentGroups) {
    // Build out the synopsis all as one long line.
    StringBuilder lineBuilder = new StringBuilder();
    Formatter lineFormatter = new Formatter(lineBuilder);

    lineFormatter.format("java %s", runningInstructions);

    for (ArgumentDefinitionGroup argumentGroup : argumentGroups) {
      for (ArgumentDefinition argumentDefinition : argumentGroup.argumentDefinitions) {
        if (argumentDefinition.isHidden) continue;
        lineFormatter.format(" ");
        if (!argumentDefinition.required) lineFormatter.format("[");
        if (argumentDefinition.shortName != null)
          lineFormatter.format("-%s", argumentDefinition.shortName);
        else lineFormatter.format("--%s", argumentDefinition.fullName);
        if (!argumentDefinition.isFlag) lineFormatter.format(" <%s>", argumentDefinition.fullName);
        if (!argumentDefinition.required) lineFormatter.format("]");
      }
    }

    // Word wrap the synopsis.
    List<String> wrappedSynopsis =
        TextFormattingUtils.wordWrap(
            lineBuilder.toString(), TextFormattingUtils.DEFAULT_LINE_WIDTH);

    String header = "usage: ";
    int headerLength = header.length();

    StringBuilder synopsisBuilder = new StringBuilder();
    Formatter synopsisFormatter = new Formatter(synopsisBuilder);
    for (String synopsisLine : wrappedSynopsis) {
      synopsisFormatter.format("%" + headerLength + "s%s%n", header, synopsisLine);
      header = "";
    }

    return synopsisBuilder.toString();
  }