package org.biojava.nbio.alignment;

import java.net.URL; import java.util.ArrayList; import java.util.List;

import org.biojava.nbio.alignment.Alignments; import
org.biojava.nbio.alignment.template.Profile; import
org.biojava.nbio.core.sequence.ProteinSequence; import
org.biojava.nbio.core.sequence.compound.AminoAcidCompound; import
org.biojava.nbio.core.sequence.io.FastaReaderHelper; import
org.biojava.nbio.core.util.ConcurrencyTools;

public class CookbookMSA {

   public static void main(String[] args) {  
       String[] ids = new String[] {"Q21691", "A8WS47", "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;  
   }

}