package jalview.io;

import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.gui.AlignFrame;

import org.junit.Before;
import org.junit.Test;

public class AnnotatedPDBFileInputTest
{

  AlignmentI al;

  @Before
  public void setup() throws Exception
  {
    FileLoader loader = new FileLoader(false);
    AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
            FormatAdapter.FILE);
    al = af.getViewport().getAlignment();
  }

  @Test
  public void checkAnnotationWiring()
  {
    assertTrue(al.getAlignmentAnnotation() != null);
    // verify that all sequence annotation is doubly referenced
    for (AlignmentAnnotation aa : al.getAlignmentAnnotation())
    {
      if (aa.sequenceRef != null)
      {
        assertTrue(al.getSequences().contains(aa.sequenceRef));
        assertNotNull(aa.sequenceRef.getAnnotation());
        boolean found = false;
        for (AlignmentAnnotation sqan : aa.sequenceRef.getAnnotation())
        {
          if (sqan == aa)
          {
            found = true;
            break;
          }
        }
        assertTrue(
                "Couldn't find sequence associated annotation "
                        + aa.label
                        + " on the sequence it is associated with.\nSequence associated editing will fail.",
                found);
      }
    }
  }
}