import charite.christo.strap.StrapProtein; import charite.christo.strap.BiojavaSequence2StrapProtein; import org.biojava.bio.seq.GappedSequence; import org.biojava.bio.seq.ProteinTools; import static java.lang.System.*; /* java DemoBiojavaSequence2StrapProtein If you want to add strap-functionality to your biojava project you might need to turn Biojava sequence objects into strap objects. BiojavaSequence2StrapProtein is a class that extends StrapProtein. Protein objects are constructed with a Biojava gapped sequence object. */ public class DemoBiojavaSequence2StrapProtein { public static void main(String[] argv){ try { /* prepare a Biojava GappedSequence-object for testing */ GappedSequence gs=ProteinTools.createGappedProteinSequence("asdfgfghk","name"); gs.addGapsInSource(3,10); out.println("gs.addGapsInSource(3,10); Inserts a gap after the 2nd and before the 3rd residue"); out.println("In STRAP residue indices start with zero but in Biojava with one."); out.println(gs.seqString()); /* conversion to Strap */ StrapProtein p=new BiojavaSequence2StrapProtein(gs); /* check whether the sequence is OK */ out.print("p.getResidueType()="+p.getResidueTypeAsString()); out.print("p.getGappedSequence()="+p.getGappedSequenceAsString()); } catch(Exception e){ e.printStackTrace(out);} exit(0); } }