import static org.junit.Assert.assertNotEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
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 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;
+
public class AnnotatedPDBFileInputTest
{
AlignmentI al;
- String pdbStr = "examples/2GIS.pdb";
+ String pdbStr = "examples/1gaq.txt";
String pdbId;
@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
}
}
+ /**
+ * Check sequence features have been added
+ */
+ @Test
+ 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
public void checkAnnotationWiring()
{
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());