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.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.ws.sifts.SiftsClient;
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");
{
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");
* (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");
62, -2.1f, null));
sq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 65,
65, 3.6f, null));
+ sq.addSequenceFeature(new SequenceFeature("RESNUM", "ALA: 2 4zhoA",
+ 53, 53, Float.NaN, null));
/*
* set all features visible except for chain
fr.setVisible("metal ion-binding site");
fr.setVisible("helix");
fr.setVisible("kd");
+ fr.setVisible("RESNUM");
/*
* 'perform' menu action to copy visible features to
*/
// TODO rename and pull up method to binding interface
// once functionality is added for Jmol as well
- binding.sendFeaturesToChimera(af.getViewport().getAlignPanel());
+ binding.sendFeaturesToViewer(af.getViewport().getAlignPanel());
/*
* give Chimera time to open the commands file and execute it
assertTrue(reply.contains("resattr jv_metal_ion_binding_site"));
assertTrue(reply.contains("resattr jv_helix"));
assertTrue(reply.contains("resattr jv_kd"));
+ assertTrue(reply.contains("resattr jv_RESNUM"));
// feature is not on a mapped region - no attribute created
assertFalse(reply.contains("resattr jv_transit_peptide"));
// feature is not visible - no attribute created
chimeraViewer.closeViewer(true);
chimeraViewer = null;
}
+
+ /**
+ * Test for creating Jalview features from attributes on mapped residues in
+ * Chimera. Note this uses local copies of PDB and SIFTS file, no network
+ * connection required.
+ *
+ * @throws IOException
+ * @throws SiftsException
+ */
+ // External as this requires a local install of Chimera
+ @Test(groups = { "External" })
+ public void testGetAttributes() throws IOException, SiftsException
+ {
+ String inFile = "examples/uniref50.fa";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+ DataSourceType.FILE);
+ assertNotNull(af, "Failed to create AlignFrame");
+ SequenceI fer2Arath = af.getViewport().getAlignment()
+ .findName("FER2_ARATH");
+ assertNotNull(fer2Arath, "Didn't find FER2_ARATH");
+
+ /*
+ * need a Uniprot dbref for SIFTS mapping to work!!
+ */
+ fer2Arath.addDBRef(new DBRefEntry("UNIPROT", "0", "P16972", null));
+
+ /*
+ * use local test PDB and SIFTS files
+ */
+ String pdbFilePath = new File(
+ "test/jalview/ext/rbvi/chimera/4zho.pdb").getPath();
+ PDBEntry pdbEntry = new PDBEntry("4ZHO", null, null, pdbFilePath);
+ String siftsFilePath = new File(
+ "test/jalview/ext/rbvi/chimera/4zho.xml.gz")
+ .getPath();
+ SiftsClient.setMockSiftsFile(new File(siftsFilePath));
+
+ StructureViewer structureViewer = new StructureViewer(af.getViewport()
+ .getStructureSelectionManager());
+ chimeraViewer = structureViewer.viewStructures(pdbEntry,
+ new SequenceI[] { fer2Arath }, af.getCurrentView()
+ .getAlignPanel());
+
+ JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
+ .getBinding();
+ do
+ {
+ try
+ {
+ Thread.sleep(500);
+ } catch (InterruptedException e)
+ {
+ }
+ } while (!binding.isFinishedInit());
+
+ assertTrue(binding.isChimeraRunning(), "Failed to launch Chimera");
+
+ assertEquals(binding.getPdbCount(), 1);
+
+ /*
+ * 'perform' menu action to copy visible features to
+ * attributes in Chimera
+ */
+ // TODO rename and pull up method to binding interface
+ // once functionality is added for Jmol as well
+ binding.copyStructureAttributesToFeatures("isHelix", af.getViewport()
+ .getAlignPanel());
+
+ /*
+ * verify 22 residues have isHelix feature
+ * (may merge into ranges in future)
+ */
+ af.setShowSeqFeatures(true);
+ FeatureRenderer fr = af.getFeatureRenderer();
+ fr.setVisible("isHelix");
+ for (int res = 75; res <= 83; res++)
+ {
+ checkFeaturesAtRes(fer2Arath, fr, res, "isHelix");
+ }
+ for (int res = 117; res <= 123; res++)
+ {
+ checkFeaturesAtRes(fer2Arath, fr, res, "isHelix");
+ }
+ for (int res = 129; res <= 131; res++)
+ {
+ checkFeaturesAtRes(fer2Arath, fr, res, "isHelix");
+ }
+ for (int res = 143; res <= 145; res++)
+ {
+ checkFeaturesAtRes(fer2Arath, fr, res, "isHelix");
+ }
+
+ /*
+ * fetch a numeric valued attribute
+ */
+ 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()));
+ 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
+ */
+ SiftsClient.setMockSiftsFile(null);
+ chimeraViewer.closeViewer(true);
+ chimeraViewer = null;
+ }
+
+ /**
+ * Helper method to verify new feature at a sequence position
+ *
+ * @param seq
+ * @param fr
+ * @param res
+ * @param featureType
+ */
+ protected void checkFeaturesAtRes(SequenceI seq, FeatureRenderer fr,
+ int res, String featureType)
+ {
+ String where = "at position " + res;
+ List<SequenceFeature> fs = seq.getFeatures().findFeatures(res, res);
+
+ assertEquals(fs.size(), 2, where);
+ assertEquals(fs.get(0).getType(), "RESNUM", where);
+ SequenceFeature sf = fs.get(1);
+ assertEquals(sf.getType(), featureType, where);
+ assertEquals(sf.getFeatureGroup(), "Chimera", where);
+ assertEquals(sf.getDescription(), "True", where);
+ assertEquals(sf.getScore(), Float.NaN, where);
+ }
}
git://source.jalview.org / jalview.git / blobdiff