import static org.junit.Assert.assertNotEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
+
+import java.io.File;
+
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
-import java.io.File;
-import java.util.Vector;
-
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
-
public class AnnotatedPDBFileInputTest
{
@Before
public void setup() throws Exception
{
+ Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("ADD_SS_ANN",
+ Boolean.TRUE.toString());
FileLoader loader = new FileLoader(false);
AlignFrame af = loader.LoadFileWaitTillLoaded(pdbStr,
FormatAdapter.FILE);
al = af.getViewport().getAlignment();
- pdbId = ((PDBEntry) al.getSequenceAt(0).getDatasetSequence().getPDBId()
- .get(0)).getId();
+ pdbId = al.getSequenceAt(0).getDatasetSequence().getPDBId()
+ .get(0).getId();
}
@Test
}
assertNotNull(sq.getPDBId());
assertEquals("Expected only one PDB ID", sq.getPDBId().size(), 1);
- for (PDBEntry pdbentry : (Vector<PDBEntry>) sq.getPDBId())
+ for (PDBEntry pdbentry : sq.getPDBId())
{
System.err.println("PDB Entry " + pdbentry.getId() + " "
+ pdbentry.getFile());