test/jalview/ext/jmol/PDBFileWithJmolTest.java

   1 /**
   2  *
   3  */
   4 package jalview.ext.jmol;
   5
   6 import static org.junit.Assert.*;
   7
   8 import java.util.Vector;
   9
  10 import jalview.datamodel.Alignment;
  11 import jalview.datamodel.AlignmentI;
  12 import jalview.datamodel.SequenceI;
  13
  14 import org.junit.Test;
  15
  16 /**
  17  * @author jimp
  18  *
  19  */
  20 public class PDBFileWithJmolTest
  21 {
  22
  23   @Test
  24   public void test() throws Exception
  25   {
  26     PDBFileWithJmol jtest=new PDBFileWithJmol("./examples/1GAQ.txt", jalview.io.AppletFormatAdapter.FILE);
  27     Vector<SequenceI> seqs=jtest.getSeqs();
  28
  29     assertTrue("No sequences extracted from testfile\n"+(jtest.hasWarningMessage() ? jtest.getWarningMessage(): "(No warnings raised)"), seqs!=null && seqs.size()>0);
  30     for (SequenceI sq:seqs)
  31     {
  32       AlignmentI al = new Alignment(new SequenceI[] { sq});
  33       if (!al.isNucleotide())
  34       {
  35         assertTrue("No secondary structure assigned for protein sequence.",sq.getAnnotation()!=null && sq.getAnnotation().length>=1 && sq.getAnnotation()[0].hasIcons);
  36       }
  37     }
  38   }
  39
  40 }