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.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+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;
+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
{
AlignmentI al;
- String pdbStr = "examples/2GIS.pdb";
+ String pdbStr = "examples/1gaq.txt";
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()
{
{
System.out.println("CalcId: " + aa.getCalcId());
- assertTrue(MCview.PDBfile.isCalcIdForFile(aa.getCalcId(), pdbId));
+ assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
}
}
}
- @Test
+ /**
+ * Check sequence features have been added
+ */
+ @Test(groups ={ "Functional" })
+ public void checkPDBSequenceFeatures()
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ StructureMapping[] mappings = ssm.getMapping("1gaq");
+ // suspect we really want to make assertions on sequence features
+ // in these mappings' sequencess
+ /*
+ * 1GAQ/A
+ */
+ SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
+ assertEquals(296, sf.length);
+ assertEquals("RESNUM", sf[0].getType());
+ assertEquals("GLU:19 1gaqA", sf[0].getDescription());
+ assertEquals("RESNUM", sf[295].getType());
+ assertEquals("TYR:314 1gaqA", sf[295].getDescription());
+
+ /*
+ * 1GAQ/B
+ */
+ sf = al.getSequenceAt(1).getSequenceFeatures();
+ assertEquals(98, sf.length);
+ assertEquals("RESNUM", sf[0].getType());
+ assertEquals("ALA:1 1gaqB", sf[0].getDescription());
+ assertEquals("RESNUM", sf[97].getType());
+ assertEquals("ALA:98 1gaqB", sf[97].getDescription());
+
+ /*
+ * 1GAQ/C
+ */
+ sf = al.getSequenceAt(2).getSequenceFeatures();
+ assertEquals(296, sf.length);
+ assertEquals("RESNUM", sf[0].getType());
+ assertEquals("GLU:19 1gaqC", sf[0].getDescription());
+ assertEquals("RESNUM", sf[295].getType());
+ assertEquals("TYR:314 1gaqC", sf[295].getDescription());
+ }
+
+ @Test(groups ={ "Functional" })
public void checkAnnotationWiring()
{
assertTrue(al.getAlignmentAnnotation() != null);
}
- @Test
+ @Test(groups ={ "Functional" })
public void testJalviewProjectRelocationAnnotation() throws Exception
{
- String inFile = "examples/2GIS.pdb";
+ String inFile = "examples/1gaq.txt";
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
}
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());
&& MCview.PDBfile.isCalcIdHandled(ana.getCalcId()))
{
exists = true;
- if (MCview.PDBfile.isCalcIdForFile(ana.getCalcId(),
+ if (MCview.PDBfile.isCalcIdForFile(ana,
pdbentry.getId()))
{
found = true;