Examples of AlFormatter

Examples of net.sourceforge.align.formatter.AlFormatter

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    }

    filter = FilterDecorators.decorate(filter);

    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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Examples of net.sourceforge.align.formatter.AlFormatter

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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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Examples of net.sourceforge.align.formatter.AlFormatter

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      throw new MissingParameterException("class");
    }
    Formatter formatter;
    if (cls.equals("al")) {
      Writer writer = getSingleWriter(commandLine);
      formatter = new AlFormatter(writer);
    } else if (cls.equals("txt")) {
      if (commandLine.getArgs().length != 2) {
        throw new WrongArgumentCountException("2", commandLine.getArgs().length);
      }
      String sourceFileName = commandLine.getArgs()[0];
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Examples of net.sourceforge.align.formatter.AlFormatter

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      sourceAlgorithm = new NullModifyAlgorithm();
    } else {
      throw new UnknownParameterException("part");
    }
   
    Formatter formatter = new AlFormatter(getOut());
   
    Filter filter = new Modifier(sourceAlgorithm, targetAlgorithm);
    filter = FilterDecorators.decorate(filter);

    if (alignmentList == null) {
      alignmentList = parser.parse();
    }
   
    alignmentList = filter.apply(alignmentList);
    formatter.format(alignmentList);
  }
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Examples of net.sourceforge.align.formatter.AlFormatter

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    }
   
    filter = FilterDecorators.decorate(filter);
   
    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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Examples of net.sourceforge.align.formatter.AlFormatter

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      alignmentList = parser.parse();
      AlignAlgorithm algorithm = createAlgorithm(commandLine, alignmentList);
      filter = new Aligner(algorithm);
    }
    filter = FilterDecorators.decorate(filter);
    Formatter formatter = new AlFormatter(getOut());
    if (alignmentList == null) {
      alignmentList = parser.parse();
    }
    alignmentList = filter.apply(alignmentList);
    formatter.format(alignmentList);
  }
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