test/jalview/io/AnnotatedPDBFileInputTest.java

   1 package jalview.io;
   2
   3 import static org.junit.Assert.assertNotNull;
   4 import static org.junit.Assert.assertTrue;
   5 import jalview.datamodel.AlignmentAnnotation;
   6 import jalview.datamodel.AlignmentI;
   7 import jalview.gui.AlignFrame;
   8
   9 import org.junit.Before;
  10 import org.junit.Test;
  11
  12 public class AnnotatedPDBFileInputTest
  13 {
  14
  15   AlignmentI al;
  16
  17   @Before
  18   public void setup() throws Exception
  19   {
  20     FileLoader loader = new FileLoader(false);
  21     AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
  22             FormatAdapter.FILE);
  23     al = af.getViewport().getAlignment();
  24   }
  25
  26   @Test
  27   public void checkAnnotationWiring()
  28   {
  29     assertTrue(al.getAlignmentAnnotation() != null);
  30     // verify that all sequence annotation is doubly referenced
  31     for (AlignmentAnnotation aa : al.getAlignmentAnnotation())
  32     {
  33       if (aa.sequenceRef != null)
  34       {
  35         assertTrue(al.getSequences().contains(aa.sequenceRef));
  36         assertNotNull(aa.sequenceRef.getAnnotation());
  37         boolean found = false;
  38         for (AlignmentAnnotation sqan : aa.sequenceRef.getAnnotation())
  39         {
  40           if (sqan == aa)
  41           {
  42             found = true;
  43             break;
  44           }
  45         }
  46         assertTrue(
  47                 "Couldn't find sequence associated annotation "
  48                         + aa.label
  49                         + " on the sequence it is associated with.\nSequence associated editing will fail.",
  50                 found);
  51       }
  52     }
  53   }
  54 }