import jalview.io.AppletFormatAdapter;
import java.io.IOException;
+import java.util.List;
import org.testng.annotations.Test;
public class PDBfileTest
{
- @Test
+ @Test(groups ={ "Functional" })
public void testIsRna()
{
SequenceI seq = new Sequence("Seq1", "CGAU");
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testParse() throws IOException
{
/*
assertTrue(chainD.sequence.getSequenceAsString().startsWith("ATYNVK"));
assertTrue(chainD.sequence.getSequenceAsString().endsWith("KEEELT"));
assertEquals("3W5V|D", chainD.sequence.getName());
+
+ /*
+ * verify PDB-related data in parsed sequences
+ */
+ List<SequenceI> seqs = pf.getSeqs();
+ assertEquals(4, seqs.size());
+ assertEquals("3W5V|A", seqs.get(0).getName());
+ assertEquals("3W5V|B", seqs.get(1).getName());
+ assertEquals("3W5V|C", seqs.get(2).getName());
+ assertEquals("3W5V|D", seqs.get(3).getName());
+ assertEquals(1, seqs.get(0).getPDBId().size());
+ PDBEntry pdbe = seqs.get(0).getPDBId().get(0);
+ assertEquals("A", pdbe.getChainCode());
+ assertEquals("3W5V", pdbe.getId());
+ assertEquals(PDBEntry.Type.PDB.toString(), pdbe.getType());
}
/**
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testParse_withAnnotations_noSS() throws IOException
{
PDBfile pf = new PDBfile(true, false, false, "examples/3W5V.pdb",
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testParse_withJmol_noAnnotations() throws IOException
{
PDBfile pf = new PDBfile(false, true, false, "examples/3W5V.pdb",
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testParse_withJmolAddAlignmentAnnotations()
throws IOException
{
* @throws IOException
*/
- @Test(enabled = false)
+ @Test(groups =
+ { "Functional" }, enabled = false)
public void testParse_withAnnotate3D() throws IOException
{
// TODO requires a mock for Annotate3D processing
private AlignmentAnnotation[] getAlignmentAnnotations(PDBfile pf)
{
AlignmentI al = new Alignment(pf.getSeqsAsArray());
- pf.addAnnotations((Alignment) al);
+ pf.addAnnotations(al);
return al.getAlignmentAnnotation();
}
}