import charite.christo.strap.StrapProtein;
import charite.christo.strap.interfaces.AlignmentWriter;
import charite.christo.strap.ExportAlignment;
/*
  java   DemoAlignmentWriter
  The class ExportAlignment is an implementations of the interface AlignmentWriter.
  The alignment consists of proteins p0 and p1.
  Both proteins have a gapped sequence and a name which are used to produce an output in MSF-format.
*/
public class DemoAlignmentWriter {
    public static void main(String[] argv){
        /* Prepare proteins */
        final StrapProtein p0=new StrapProtein();
        final StrapProtein p1=new StrapProtein();
        p0.setGappedSequence("ASDFGHKL");
        p1.setGappedSequence("AS FGHKL");
        p0.setName("protein0");
        p1.setName("protein1");
        /* create an instance of AlignmentWriter */
        final AlignmentWriter alignmentWriter=new ExportAlignment();
        /* Set the proteins of the alignment */
        alignmentWriter.setProteins(p0,p1);

        final StringBuffer sb=new StringBuffer();
        /* obtain the MSF-text  */
        final long options=AlignmentWriter.MSF;
        alignmentWriter.getText(options,sb);
        System.out.println(sb);
        System.exit(0);
    }
}