public static String toFASTA(MultipleAlignment alignment) {

		// Get the alignment sequences
		List<String> alnSequences = MultipleAlignmentTools
				.getSequenceAlignment(alignment);

		String fasta = "";
		for (int st = 0; st < alignment.size(); st++) {
			// Add the structure identifier as the head of the FASTA
			fasta += ">" + alignment.getEnsemble().getStructureIdentifiers().get(st).getIdentifier()
					+ "\n" + alnSequences.get(st) + "\n";
		}
		return fasta;
	}
public static String toFASTA ( MultipleAlignment alignment ) { List < String > alnSequences = MultipleAlignmentTools . getSequenceAlignment ( alignment ) ; String fasta = "" ; for ( int st = 0 ; st < alignment . size ( ) ; st ++ ) { fasta += ">" + alignment . getEnsemble ( ) . getStructureIdentifiers ( ) . get ( st ) . getIdentifier ( ) + "\n" + alnSequences . get ( st ) + "\n" ; } return fasta ; }
Converts the {@link MultipleAlignment} into a multiple sequence alignment
String in FASTA format.

@param alignment
MultipleAlignment
@return String multiple sequence alignment in FASTA format
@see MultipleAlignmentTools#getSequenceAlignment(MultipleAlignment)