BioJava:CookBook:Phylo:ProfileToMSA

From BioJava

       MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound> multipleSequenceAlignment= new MultipleSequenceAlignment <ProteinSequence, AminoAcidCompound>();
       List<AlignedSequence<ProteinSequence,AminoAcidCompound>> alSeq=profile.getAlignedSequences();
       Sequence<AminoAcidCompound> seq;
       ProteinSequence pSeq;
       for (int i=0; i<alSeq.size(); i++){
     
           seq=alSeq.get(i);
           pSeq=new ProteinSequence(seq.getSequenceAsString(),seq.getCompoundSet());
           pSeq.setAccession(seq.getAccession());
           multipleSequenceAlignment.addAlignedSequence(pSeq);
              
       }