code: public static AFPChain fastaFileToAfpChain(File fastaFile, Structure structure1, Structure structure2)
  			throws IOException, StructureException {
  		InputStream inStream = new FileInputStream(fastaFile);
  		SequenceCreatorInterface<AminoAcidCompound> creator = new CasePreservingProteinSequenceCreator(
  				AminoAcidCompoundSet.getAminoAcidCompoundSet());
  		SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound> headerParser = new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>();
  		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
  				inStream, headerParser, creator);
  		LinkedHashMap<String, ProteinSequence> sequences = fastaReader.process();
  		inStream.close();
  		return fastaToAfpChain(sequences, structure1, structure2);
  	}
docs: Reads the file {@code fastaFile}, expecting exactly two sequences which give a pairwise alignment. Uses this and two structures to create an AFPChain corresponding to the alignment. Uses a
  {@link CasePreservingProteinSequenceCreator} and assumes that a residue is aligned if and only if it is given by an uppercase letter.
  
  @see #fastaToAfpChain(ProteinSequence, ProteinSequence, Structure, Structure)
  @throws IOException
  @throws StructureException