import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import java.io.IOException;
+import java.util.List;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.io.DataSourceType;
import jalview.structure.StructureImportSettings;
-import java.io.IOException;
-import java.util.List;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
public class PDBfileTest
{
assertEquals(0, chainA.seqend); // not set
assertEquals(18, chainA.sequence.getStart());
assertEquals(314, chainA.sequence.getEnd());
- assertTrue(chainA.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
+ assertTrue(
+ chainA.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY"));
assertEquals("3W5V|A", chainA.sequence.getName());
assertNull(chainA.sequence.getAnnotation());
PDBChain chainC = pf.getChains().get(2);
assertEquals(18, chainC.sequence.getStart());
assertEquals(314, chainC.sequence.getEnd());
- assertTrue(chainC.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
+ assertTrue(
+ chainC.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
assertTrue(chainC.sequence.getSequenceAsString().endsWith("WNVEVY"));
assertEquals("3W5V|C", chainC.sequence.getName());
* @throws IOException
*/
@Test(groups = { "Functional" })
- public void testParse_withJmolAddAlignmentAnnotations()
- throws IOException
+ public void testParse_withJmolAddAlignmentAnnotations() throws IOException
{
PDBfile pf = new PDBfile(true, true, false, "examples/3W5V.pdb",
DataSourceType.FILE);
for (int i = 0; i < 20; i++)
{
assertNull(anns[0].annotations[i]);
- assertEquals("E", anns[0].annotations[20].displayCharacter);
+ assertNull(anns[0].annotations[20].displayCharacter);
assertEquals('E', anns[0].annotations[20].secondaryStructure);
- assertEquals("E", anns[2].annotations[18].displayCharacter);
- assertEquals("H", anns[2].annotations[23].displayCharacter);
+ assertEquals('E', anns[2].annotations[18].secondaryStructure);
+ assertEquals('H', anns[2].annotations[23].secondaryStructure);
}
}