test/jalview/analysis/AlignmentUtilsTests.java

   1 package jalview.analysis;
   2
   3 import org.junit.Test;
   4
   5 import jalview.datamodel.Alignment;
   6 import jalview.datamodel.AlignmentI;
   7 import jalview.datamodel.Sequence;
   8 import jalview.datamodel.SequenceI;
   9 import jalview.io.AppletFormatAdapter;
  10
  11 public class AlignmentUtilsTests
  12 {
  13   public static Sequence ts=new Sequence("short","ASDASDASDASDASDASDASDASDASDASDASDASDASD");
  14   @Test
  15   public void testExpandFlanks()
  16   {
  17     AlignmentI al = new Alignment(new Sequence[] {});
  18     for (int i=4;i<14;i+=3)
  19     {
  20       SequenceI s1=ts.deriveSequence().getSubSequence(i, i+7);
  21       al.addSequence(s1);
  22     }
  23     System.out.println(new AppletFormatAdapter().formatSequences("Clustal", al, true));
  24     for (int flnk=-1;flnk<25; flnk++)
  25     {
  26       System.out.println("\nFlank size: "+flnk);
  27       System.out.println(new AppletFormatAdapter().formatSequences("Clustal", AlignmentUtils.expandContext(al, flnk), true));
  28     }
  29   }
  30 }