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 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;
public class AnnotatedPDBFileInputTest
AlignmentI al;
+ String pdbStr = "examples/1gaq.txt";
+
+ String pdbId;
+
@Before
public void setup() throws Exception
{
FileLoader loader = new FileLoader(false);
- AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
+ AlignFrame af = loader.LoadFileWaitTillLoaded(pdbStr,
FormatAdapter.FILE);
al = af.getViewport().getAlignment();
+ pdbId = ((PDBEntry) al.getSequenceAt(0).getDatasetSequence().getPDBId()
+ .get(0)).getId();
}
@Test
}
@Test
+ public void checkPDBannotationSource()
+ {
+
+ for (SequenceI asq : al.getSequences())
+ {
+ for (AlignmentAnnotation aa : asq.getAnnotation())
+ {
+
+ System.out.println("CalcId: " + aa.getCalcId());
+ assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+ }
+ }
+ }
+
+ /**
+ * 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()
{
assertTrue(al.getAlignmentAnnotation() != null);
}
}
}
+
+ /**
+ * @throws java.lang.Exception
+ */
+ @BeforeClass
+ public static void setUpBeforeClass() throws Exception
+ {
+ jalview.bin.Jalview.main(new String[]
+ { "-props", "test/src/jalview/io/testProps.jvprops" });
+ }
+
+ /**
+ * @throws java.lang.Exception
+ */
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception
+ {
+ jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+
+ }
+
+ @Test
+ public void testJalviewProjectRelocationAnnotation() throws Exception
+ {
+
+ String inFile = "examples/1gaq.txt";
+ String tfile = File.createTempFile("JalviewTest", ".jvp")
+ .getAbsolutePath();
+ AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+ inFile, FormatAdapter.FILE);
+ assertTrue("Didn't read input file " + inFile, af != null);
+ assertTrue("Failed to store as a project.",
+ af.saveAlignment(tfile, "Jalview"));
+ af.closeMenuItem_actionPerformed(true);
+ af = null;
+ af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
+ FormatAdapter.FILE);
+ assertTrue("Failed to import new project", af != null);
+ for (SequenceI asq : af.getViewport().getAlignment().getSequences())
+ {
+ SequenceI sq = asq;
+ while (sq.getDatasetSequence() != null)
+ {
+ sq = sq.getDatasetSequence();
+ }
+ assertNotNull(sq.getPDBId());
+ assertEquals("Expected only one PDB ID", sq.getPDBId().size(), 1);
+ for (PDBEntry pdbentry : (Vector<PDBEntry>) sq.getPDBId())
+ {
+ System.err.println("PDB Entry " + pdbentry.getId() + " "
+ + pdbentry.getFile());
+ boolean exists = false, found = false;
+ for (AlignmentAnnotation ana : sq.getAnnotation())
+ {
+ System.err.println("CalcId " + ana.getCalcId());
+ if (ana.getCalcId() != null
+ && MCview.PDBfile.isCalcIdHandled(ana.getCalcId()))
+ {
+ exists = true;
+ if (MCview.PDBfile.isCalcIdForFile(ana,
+ pdbentry.getId()))
+ {
+ found = true;
+ }
+ }
+ }
+ if (exists)
+ {
+ assertTrue("Couldn't find any annotation for " + pdbentry.getId()
+ + " (file handle " + pdbentry.getFile() + ")", found);
+ }
+ }
+ }
+ }
}