Package net.sourceforge.align.formatter

Examples of net.sourceforge.align.formatter.Formatter.format()

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    Parser parser = new AlParser(getIn());
    Formatter formatter = new AlFormatter(getOut());
    List<Alignment> alignmentList = parser.parse();
    alignmentList = filter.apply(alignmentList);
    formatter.format(alignmentList);
  }

}
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      } else {
        throw new UnknownParameterException("class");
      }
      Formatter formatter = new AlFormatter(getOut());
      formatter.format(alignmentList);
    } catch (IOException e) {
      throw new IORuntimeException(e);
    }
  }
}
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    } else {
      throw new UnknownParameterException("class");
    }
    Parser parser = new AlParser(getIn());
    List<Alignment> alignmentList = parser.parse();
    formatter.format(alignmentList);
  }
 
  private Writer getSingleWriter(CommandLine commandLine) {
    Writer writer;
    if (commandLine.getArgs().length == 0) {
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    if (alignmentList == null) {
      alignmentList = parser.parse();
    }
   
    alignmentList = filter.apply(alignmentList);
    formatter.format(alignmentList);
  }
 
  private Pair<ModifyAlgorithm, ModifyAlgorithm> createUnifyRareWordsAlgorithms(
      CommandLine commandLine, List<Alignment> alignmentList) {
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    Parser parser = new AlParser(getIn());
    Formatter formatter = new AlFormatter(getOut());
    List<Alignment> alignmentList = parser.parse();
    alignmentList = filter.apply(alignmentList);
    formatter.format(alignmentList);
  }

  private List<Alignment> loadAlignmentList(String fileName) {
    Reader reader = getReader(getFileInputStream(fileName));
    Parser parser = new AlParser(reader);
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    Formatter formatter = new AlFormatter(getOut());
    if (alignmentList == null) {
      alignmentList = parser.parse();
    }
    alignmentList = filter.apply(alignmentList);
    formatter.format(alignmentList);
  }
 
  private AlignAlgorithm createAlgorithm(CommandLine commandLine,
      List<Alignment> alignmentList) {
    String cls = commandLine.getOptionValue('c');
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        List<Alignment> leftGroup = leftIterator.next();
        List<Alignment> rightGroup = rightIterator.next();
       
        getErr().println("< left alignments");
        getErr().println();
        formatter.format(leftGroup);
        getErr().println();
        getErr().println();

        getErr().println("> right alignments");
        getErr().println();
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        getErr().println();
        getErr().println();

        getErr().println("> right alignments");
        getErr().println();
        formatter.format(rightGroup);
        getErr().println();
        getErr().println();

        getErr().println();
       
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