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(chainA.sequence.getSequenceAsString().endsWith("WNVEVY"));
assertEquals("3W5V|A", chainA.sequence.getName());
assertNull(chainA.sequence.getAnnotation());
- assertEquals(1, chainA.sequence.getPDBId().size());
- PDBEntry pdb = chainA.sequence.getPDBId().get(0);
+ assertEquals(1, chainA.sequence.getAllPDBEntries().size());
+ PDBEntry pdb = chainA.sequence.getAllPDBEntries().get(0);
assertEquals("A", pdb.getChainCode());
assertEquals("PDB", pdb.getType());
assertEquals("3W5V", pdb.getId());
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(1, seqs.get(0).getAllPDBEntries().size());
+ PDBEntry pdbe = seqs.get(0).getAllPDBEntries().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