import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertTrue;
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+import java.util.Vector;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
import jalview.api.FeatureRenderer;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
+import jalview.structure.StructureCommand;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.ws.sifts.SiftsClient;
import jalview.ws.sifts.SiftsException;
import jalview.ws.sifts.SiftsSettings;
-import java.io.File;
-import java.io.IOException;
-import java.util.List;
-import java.util.Vector;
-
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
@Test(singleThreaded = true)
public class JalviewChimeraView
{
@Test(groups = { "External" })
public void testSingleSeqViewChimera()
{
+
String inFile = "examples/1gaq.txt";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
DataSourceType.FILE);
/*
* Wait for viewer load thread to complete
*/
- while (!binding.isFinishedInit())
+ do
{
try
{
} catch (InterruptedException e)
{
}
- }
+ } while (!binding.isFinishedInit() || !chimeraViewer.isVisible());
- assertTrue(binding.isChimeraRunning(), "Failed to start Chimera");
+ assertTrue(binding.isViewerRunning(), "Failed to start Chimera");
assertEquals(chimeraViewer.getBinding().getPdbCount(), 1);
+ assertTrue(chimeraViewer.hasViewerActionsMenu());
+
+ // now add another sequence and bind to view
+ //
+ AlignmentI al = af.getViewport().getAlignment();
+ PDBEntry xpdb = al.getSequenceAt(0).getPDBEntry("1GAQ");
+ sq = new Sequence("1GAQ", al.getSequenceAt(0).getSequence(25, 95).toString());
+ al.addSequence(sq);
+ structureViewer.viewStructures(new PDBEntry[] { xpdb }, new SequenceI[] { sq }, af.getCurrentView().getAlignPanel());
+
+ /*
+ * Wait for viewer load thread to complete
+ */
+ do
+ {
+ try {
+ Thread.sleep(1500);
+ } catch (InterruptedException q) {};
+ } while (!binding.isLoadingFinished());
+
+ // still just one PDB structure shown
+ assertEquals(chimeraViewer.getBinding().getPdbCount(), 1);
+ // and the viewer action menu should still be visible
+ assertTrue(chimeraViewer.hasViewerActionsMenu());
+
chimeraViewer.closeViewer(true);
chimeraViewer = null;
return;
}
} while (!binding.isFinishedInit());
- assertTrue(binding.isChimeraRunning(), "Failed to launch Chimera");
+ assertTrue(binding.isViewerRunning(), "Failed to launch Chimera");
assertEquals(binding.getPdbCount(), 1);
/*
* ask Chimera for its residue attribute names
*/
- List<String> reply = binding.sendChimeraCommand("list resattr", true);
+ List<String> reply = binding
+ .executeCommand(new StructureCommand("list resattr"), true);
// prefixed and sanitised attribute names for Jalview features:
assertTrue(reply.contains("resattr jv_domain"));
assertTrue(reply.contains("resattr jv_metal_ion_binding_site"));
* ask Chimera for residues with an attribute
* 91 and 96 on sequence --> residues 40 and 45 on chains A and B
*/
- reply = binding.sendChimeraCommand(
- "list resi att jv_metal_ion_binding_site", true);
+ reply = binding.executeCommand(
+ new StructureCommand("list resi att jv_metal_ion_binding_site"),
+ true);
assertEquals(reply.size(), 4);
assertTrue(reply
.contains("residue id #0:40.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
* check attributes with score values
* sequence positions 62 and 65 --> residues 11 and 14 on chains A and B
*/
- reply = binding.sendChimeraCommand("list resi att jv_kd", true);
+ reply = binding.executeCommand(
+ new StructureCommand("list resi att jv_kd"), true);
assertEquals(reply.size(), 4);
assertTrue(reply.contains("residue id #0:11.A jv_kd -2.1 index 11"));
assertTrue(reply.contains("residue id #0:14.A jv_kd 3.6 index 14"));
/*
* list residues with positive kd score
*/
- reply = binding.sendChimeraCommand(
- "list resi spec :*/jv_kd>0 attr jv_kd", true);
+ reply = binding.executeCommand(
+ new StructureCommand("list resi spec :*/jv_kd>0 attr jv_kd"),
+ true);
assertEquals(reply.size(), 2);
assertTrue(reply.contains("residue id #0:14.A jv_kd 3.6 index 14"));
assertTrue(reply.contains("residue id #0:14.B jv_kd 3.6 index 14"));
}
} while (!binding.isFinishedInit());
- assertTrue(binding.isChimeraRunning(), "Failed to launch Chimera");
+ assertTrue(binding.isViewerRunning(), "Failed to launch Chimera");
assertEquals(binding.getPdbCount(), 1);
/*
- * 'perform' menu action to copy visible features to
- * attributes in Chimera
+ * 'perform' menu action to copy Chimera attributes
+ * to features in Jalview
*/
// TODO rename and pull up method to binding interface
// once functionality is added for Jmol as well
binding.copyStructureAttributesToFeatures("phi", af.getViewport()
.getAlignPanel());
fr.setVisible("phi");
- List<SequenceFeature> fs = fer2Arath.getFeatures().findFeatures(54, 54);
- assertEquals(fs.size(), 3);
- /*
- * order of returned features is not guaranteed
- */
- assertTrue("RESNUM".equals(fs.get(0).getType())
- || "RESNUM".equals(fs.get(1).getType())
- || "RESNUM".equals(fs.get(2).getType()));
+ List<SequenceFeature> fs = fer2Arath.getFeatures().findFeatures(54, 54,
+ "phi");
+ assertEquals(fs.size(), 2);
assertTrue(fs.contains(new SequenceFeature("phi", "A", 54, 54,
-131.0713f, "Chimera")));
assertTrue(fs.contains(new SequenceFeature("phi", "B", 54, 54,
int res, String featureType)
{
String where = "at position " + res;
- List<SequenceFeature> fs = seq.getFeatures().findFeatures(res, res);
+ List<SequenceFeature> fs = seq.getFeatures().findFeatures(res, res,
+ featureType);
- assertEquals(fs.size(), 2, where);
- assertEquals(fs.get(0).getType(), "RESNUM", where);
- SequenceFeature sf = fs.get(1);
+ assertEquals(fs.size(), 1, where);
+ SequenceFeature sf = fs.get(0);
assertEquals(sf.getType(), featureType, where);
assertEquals(sf.getFeatureGroup(), "Chimera", where);
assertEquals(sf.getDescription(), "True", where);
git://source.jalview.org / jalview.git / blobdiff