import java.net.URL;
import org.biojava3.alignment.Alignments;
import org.biojava3.alignment.SimpleGapPenalty;
import org.biojava3.alignment.SubstitutionMatrixHelper;
import org.biojava3.alignment.Alignments.PairwiseSequenceAlignerType;
import org.biojava3.alignment.template.GapPenalty;
import org.biojava3.alignment.template.PairwiseSequenceAligner;
import org.biojava3.alignment.template.SequencePair;
import org.biojava3.alignment.template.SubstitutionMatrix;
import org.biojava3.core.sequence.ProteinSequence;
import org.biojava3.core.sequence.compound.AminoAcidCompound;
import org.biojava3.core.sequence.io.FastaReaderHelper;

public class DemoAlignProteins {

    public static void main(String[] args) {

        try {
            String uniprotID1 = "P69905";
            String uniprotID2 = "P68871";

            ProteinSequence s1 = getSequenceForId(uniprotID1);
            ProteinSequence s2 = getSequenceForId(uniprotID2);

            SubstitutionMatrix<AminoAcidCompound> matrix = SubstitutionMatrixHelper.getBlosum65();

            GapPenalty penalty = new SimpleGapPenalty();

            short gop = 8;
            short extend = 1;
            penalty.setOpenPenalty(gop);
            penalty.setExtensionPenalty(extend);


            PairwiseSequenceAligner<ProteinSequence, AminoAcidCompound=""> smithWaterman =
                    Alignments.getPairwiseAligner(s1, s2, PairwiseSequenceAlignerType.LOCAL, penalty, matrix);

            SequencePair<ProteinSequence, AminoAcidCompound=""> pair = smithWaterman.getPair();


            System.out.println(pair.toString(60));

        } catch (Exception e){
            e.printStackTrace();
        }
    }

    private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {
        URL uniprotFasta = new URL(String.format("http://www.uniprot.org/uniprot/%s.fasta", uniProtId));
        ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);
        System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());
        return seq;
    }

}