/**
 * 
 */
package jalview.ext.jmol;

import static org.junit.Assert.*;

import java.util.Vector;

import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;

import org.junit.Test;

/**
 * @author jimp
 *
 */
public class PDBFileWithJmolTest
{

  @Test
  public void test() throws Exception
  {
    PDBFileWithJmol jtest=new PDBFileWithJmol("./examples/1GAQ.txt", jalview.io.AppletFormatAdapter.FILE);
    Vector<SequenceI> seqs=jtest.getSeqs();
    
    assertTrue("No sequences extracted from testfile\n"+(jtest.hasWarningMessage() ? jtest.getWarningMessage(): "(No warnings raised)"), seqs!=null && seqs.size()>0);
    for (SequenceI sq:seqs)
    {
      AlignmentI al = new Alignment(new SequenceI[] { sq});
      if (!al.isNucleotide())
      {
        assertTrue("No secondary structure assigned for protein sequence.",sq.getAnnotation()!=null && sq.getAnnotation().length>=1 && sq.getAnnotation()[0].hasIcons);
      }
    }
  }

}