import java.net.URL;
import java.util.ArrayList;
import java.util.List;
 
import org.biojava3.alignment.Alignments;
import org.biojava3.alignment.template.Profile;
import org.biojava3.core.sequence.ProteinSequence;
import org.biojava3.core.sequence.compound.AminoAcidCompound;
import org.biojava3.core.sequence.io.FastaReaderHelper;
import org.biojava3.core.util.ConcurrencyTools;
 
public class CookbookMSA {
 
    public static void main(String[] args) {
        String[] ids = new String[] {"Q21691", "Q21495", "O48771"};
        try {
            multipleSequenceAlignment(ids);
        } catch (Exception e){
            e.printStackTrace();
        }
    }
 
    private static void multipleSequenceAlignment(String[] ids) throws Exception {
        List<ProteinSequence> lst = new ArrayList<ProteinSequence>();
        for (String id : ids) {
            lst.add(getSequenceForId(id));
        }
        Profile<ProteinSequence, AminoAcidCompound> profile = Alignments.getMultipleSequenceAlignment(lst);
        System.out.printf("Clustalw:%n%s%n", profile);
        ConcurrencyTools.shutdown();
    }
 
    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;
    }
 
}