test/jalview/analysis/AlignmentUtilsTests.java

   1 package jalview.analysis;
   2
   3 import static org.junit.Assert.assertTrue;
   4
   5 import org.junit.Test;
   6
   7 import jalview.datamodel.Alignment;
   8 import jalview.datamodel.AlignmentI;
   9 import jalview.datamodel.Sequence;
  10 import jalview.datamodel.SequenceI;
  11 import jalview.io.AppletFormatAdapter;
  12
  13 public class AlignmentUtilsTests
  14 {
  15   public static Sequence ts=new Sequence("short","ASDASDASDASDASDASDASDASDASDASDASDASDASD");
  16   @Test
  17   public void testExpandFlanks()
  18   {
  19     AlignmentI al = new Alignment(new Sequence[] {});
  20     for (int i=4;i<14;i+=3)
  21     {
  22       SequenceI s1=ts.deriveSequence().getSubSequence(i, i+7);
  23       al.addSequence(s1);
  24     }
  25     System.out.println(new AppletFormatAdapter().formatSequences("Clustal", al, true));
  26     for (int flnk=-1;flnk<25; flnk++)
  27     {
  28       AlignmentI exp;
  29       System.out.println("\nFlank size: "+flnk);
  30       System.out.println(new AppletFormatAdapter().formatSequences("Clustal", exp=AlignmentUtils.expandContext(al, flnk), true));
  31       if (flnk==-1) {
  32         for (SequenceI sq:exp.getSequences())
  33       {
  34           String ung = sq.getSequenceAsString().replaceAll("-+", "");
  35           assertTrue("Flanking sequence not the same as original dataset sequence.\n"+ung+"\n"+sq.getDatasetSequence().getSequenceAsString(),ung.equalsIgnoreCase(sq.getDatasetSequence().getSequenceAsString()));
  36       }
  37       }
  38     }
  39   }
  40 }