4 package jalview.ext.jmol;
6 import static org.junit.Assert.*;
8 import java.util.Vector;
10 import jalview.datamodel.Alignment;
11 import jalview.datamodel.AlignmentI;
12 import jalview.datamodel.SequenceI;
14 import org.junit.Test;
20 public class PDBFileWithJmolTest
24 public void test() throws Exception
26 PDBFileWithJmol jtest=new PDBFileWithJmol("./examples/1GAQ.txt", jalview.io.AppletFormatAdapter.FILE);
27 Vector<SequenceI> seqs=jtest.getSeqs();
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)
32 AlignmentI al = new Alignment(new SequenceI[] { sq});
33 if (!al.isNucleotide())
35 assertTrue("No secondary structure assigned for protein sequence.",sq.getAnnotation()!=null && sq.getAnnotation().length>=1 && sq.getAnnotation()[0].hasIcons);