code: public static String toFatCat(MultipleAlignment alignment) {
  
  		// Initialize the String and put the summary information
  		StringWriter fatcat = new StringWriter();
  		fatcat.append(alignment.toString() + "\n\n");
  
  		// Get the alignment sequences and the mapping
  		List<Integer> mapSeqToStruct = new ArrayList<Integer>();
  		List<String> alnSequences = MultipleAlignmentTools
  				.getSequenceAlignment(alignment, mapSeqToStruct);
  
  		// Get the String of the Block Numbers for Position
  		String blockNumbers = "";
  		for (int pos = 0; pos < alnSequences.get(0).length(); pos++) {
  			int blockNr = MultipleAlignmentTools.getBlockForSequencePosition(
  					alignment, mapSeqToStruct, pos);
  			if (blockNr != -1) {
  				blockNumbers = blockNumbers.concat(String.valueOf(blockNr + 1));
  			} else
  				blockNumbers = blockNumbers.concat(" ");
  		}
  
  		// Write the Sequence Alignment
  		for (int str = 0; str < alignment.size(); str++) {
  			if (str < 9) {
  				fatcat.append("Chain 0" + (str + 1) + ": "
  						+ alnSequences.get(str) + "\n");
  			} else {
  				fatcat.append("Chain " + (str + 1) + ": "
  						+ alnSequences.get(str) + "\n");
  			}
  			if (str != alignment.size() - 1) {
  				fatcat.append("          " + blockNumbers + "\n");
  			}
  		}
  		return fatcat.toString();
  	}
docs: Converts the {@link MultipleAlignment} into a FatCat String format.
  Includes summary information about the alignment in the top and a
  multiple sequence alignment at the bottom.
  
  @param alignment
  MultipleAlignment
  @return String multiple sequence alignment in FASTA format
  @see MultipleAlignmentTools#getSequenceAlignment(MultipleAlignment)