package jalview.io;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
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;
+import org.junit.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
public class AnnotatedPDBFileInputTest
{
String pdbId;
- @Before
+ @BeforeMethod
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
+ @Test(groups ={ "Functional" })
public void checkNoDuplicates()
{
// not strictly a requirement, but strange things may happen if multiple
{
for (int q = p + 1; q < avec.length; q++)
{
- assertNotEquals(
+ Assert.assertNotEquals(
"Found a duplicate annotation row " + avec[p].label,
avec[p], avec[q]);
}
}
}
- @Test
+ @Test(groups ={ "Functional" })
public void checkPDBannotationSource()
{
/**
* Check sequence features have been added
*/
- @Test
+ @Test(groups ={ "Functional" })
public void checkPDBSequenceFeatures()
{
StructureSelectionManager ssm = StructureSelectionManager
assertEquals("TYR:314 1gaqC", sf[295].getDescription());
}
- @Test
+ @Test(groups ={ "Functional" })
public void checkAnnotationWiring()
{
assertTrue(al.getAlignmentAnnotation() != null);
}
- @Test
+ @Test(groups ={ "Functional" })
public void testJalviewProjectRelocationAnnotation() throws Exception
{
}
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());