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.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
import jalview.gui.Preferences;
import jalview.gui.StructureViewer;
import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.DataSourceType;
import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
+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
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private JalviewStructureDisplayI chimeraViewer;
/**
{
String inFile = "examples/1gaq.txt";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
- FormatAdapter.FILE);
+ DataSourceType.FILE);
assertNotNull(af, "Failed to create AlignFrame");
SequenceI sq = af.getViewport().getAlignment().getSequenceAt(0);
assertEquals(sq.getName(), "1GAQ|A");
}
}
- assertTrue(binding.isChimeraRunning(), "Failed to start Chimera");
+ assertTrue(binding.isViewerRunning(), "Failed to start Chimera");
assertEquals(chimeraViewer.getBinding().getPdbCount(), 1);
chimeraViewer.closeViewer(true);
{
String inFile = "examples/uniref50.fa";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
- FormatAdapter.FILE);
+ DataSourceType.FILE);
assertNotNull(af, "Failed to create AlignFrame");
SequenceI sq = af.getViewport().getAlignment().findName("FER2_ARATH");
assertNotNull(sq, "Didn't find FER2_ARATH");
}
} while (!binding.isFinishedInit());
- assertTrue(binding.isChimeraRunning(), "Failed to launch Chimera");
+ assertTrue(binding.isViewerRunning(), "Failed to launch Chimera");
assertEquals(binding.getPdbCount(), 1);
* (or possibly 52-145 to 1-94 - see JAL-2319)
*/
StructureSelectionManager ssm = binding.getSsm();
- String pdbFile = binding.getPdbFile()[0];
+ String pdbFile = binding.getStructureFiles()[0];
StructureMapping[] mappings = ssm.getMapping(pdbFile);
assertTrue(mappings[0].getMappingDetailsOutput().contains("SIFTS"),
"Failed to perform SIFTS mapping");
/*
* 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"));
{
String inFile = "examples/uniref50.fa";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
- FormatAdapter.FILE);
+ DataSourceType.FILE);
assertNotNull(af, "Failed to create AlignFrame");
SequenceI fer2Arath = af.getViewport().getAlignment()
.findName("FER2_ARATH");
}
} 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 = fr.findFeaturesAtRes(fer2Arath, 54);
- assertEquals(fs.size(), 3);
- assertEquals(fs.get(0).getType(), "RESNUM");
- assertEquals(fs.get(1).getType(), "phi");
- assertEquals(fs.get(2).getType(), "phi");
- assertEquals(fs.get(1).getDescription(), "A"); // chain
- assertEquals(fs.get(2).getDescription(), "B");
- assertEquals(fs.get(1).getScore(), -131.0713f, 0.001f);
- assertEquals(fs.get(2).getScore(), -127.39512, 0.001f);
+ 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,
+ -127.39512f, "Chimera")));
/*
* tear down - also in AfterMethod
int res, String featureType)
{
String where = "at position " + res;
- List<SequenceFeature> fs = fr.findFeaturesAtRes(seq, res);
- assertEquals(fs.size(), 2, where);
- assertEquals(fs.get(0).getType(), "RESNUM", where);
- SequenceFeature sf = fs.get(1);
+ List<SequenceFeature> fs = seq.getFeatures().findFeatures(res, res,
+ featureType);
+
+ 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