code: public static LinkedHashMap<String, ProteinSequence> readFastaProteinSequence(
  			File file) throws IOException {
  		FileInputStream inStream = new FileInputStream(file);
  		LinkedHashMap<String, ProteinSequence> proteinSequences = readFastaProteinSequence(inStream);
  		inStream.close();
  		return proteinSequences;
  	}
docs: Read a fasta file containing amino acids with setup that would handle most
  cases.
  
  @param file
  @return
  @throws IOException