code: public static LinkedHashMap<String, ProteinSequence> readFastaProteinSequence(
  			InputStream inStream) throws IOException {
  		FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
  				inStream,
  				new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
  				new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
  		return fastaReader.process();
  	}
docs: Read a fasta file containing amino acids with setup that would handle most
  cases. User is responsible for closing InputStream because you opened it
  
  @param inStream
  @return
  @throws IOException