public static LinkedHashMap < String , ProteinSequence > readGenbankProteinSequence ( InputStream inStream ) throws Exception { GenbankReader < ProteinSequence , AminoAcidCompound > GenbankReader = new GenbankReader < ProteinSequence , AminoAcidCompound > ( inStream , new GenericGenbankHeaderParser < ProteinSequence , AminoAcidCompound > ( ) , new ProteinSequenceCreator ( AminoAcidCompoundSet . getAminoAcidCompoundSet ( ) ) ) ; return GenbankReader . process ( ) ; }
Read a Genbank file containing amino acids with setup that would handle most cases . User is responsible for closing InputStream because you opened it