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.structures.models.AAStructureBindingModel;
+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;
public class JalviewChimeraView
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private JalviewStructureDisplayI chimeraViewer;
/**
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- Jalview.main(new String[] {
- "-noquestionnaire -nonews -props",
+ Jalview.main(new String[] { "-noquestionnaire", "-nonews", "-props",
"test/jalview/ext/rbvi/chimera/testProps.jvprops" });
Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
ViewerType.CHIMERA.name());
Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
ViewerType.CHIMERA.name());
Cache.setProperty("MAP_WITH_SIFTS", "true");
+ // TODO this should not be necessary!
+ SiftsSettings.setMapWithSifts(true);
}
/**
@AfterMethod(alwaysRun = true)
public void tearDownAfterTest() throws Exception
{
+ SiftsClient.setMockSiftsFile(null);
if (chimeraViewer != null)
{
chimeraViewer.closeViewer(true);
}
/**
- * Load 1GAQ and view the first structure for which a PDB id is found
+ * Load 1GAQ and view the first structure for which a PDB id is found. Note no
+ * network connection is needed - PDB file is read locally, SIFTS fetch fails
+ * so mapping falls back to Needleman-Wunsch - ok for this test.
*/
- @Test(groups = { "External", "Network" })
+ // External as local install of Chimera required
+ @Test(groups = { "External" })
public void testSingleSeqViewChimera()
{
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");
.getStructureSelectionManager());
chimeraViewer = structureViewer.viewStructures(pdbEntry,
new SequenceI[] { sq }, af.getCurrentView().getAlignPanel());
+ JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
+ .getBinding();
+
/*
* Wait for viewer load thread to complete
*/
- while (!chimeraViewer.getBinding().isFinishedInit())
+ while (!binding.isFinishedInit())
{
try
{
{
}
}
+
+ assertTrue(binding.isChimeraRunning(), "Failed to start Chimera");
+
assertEquals(chimeraViewer.getBinding().getPdbCount(), 1);
chimeraViewer.closeViewer(true);
chimeraViewer = null;
/**
* Test for writing Jalview features as attributes on mapped residues in
- * Chimera
+ * 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
- // Network as fetch from PDB/SIFTS is involved TODO mock this
- @Test(groups = { "External", "Network" })
- public void testTransferFeatures()
+ @Test(groups = { "External" })
+ public void testTransferFeatures() throws IOException, SiftsException
{
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");
* need a Uniprot dbref for SIFTS mapping to work!!
*/
sq.addDBRef(new DBRefEntry("UNIPROT", "0", "P16972", null));
- PDBEntry pdbEntry = new PDBEntry("4ZHO", null, null, null);
- // addPDBId() doesn't (yet) delegate to dataset sequence if there is one!
- sq.getDatasetSequence().addPDBId(pdbEntry);
+
+ /*
+ * 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[] { sq }, af.getCurrentView().getAlignPanel());
- AAStructureBindingModel binding = chimeraViewer.getBinding();
+ 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);
/*
* (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");
assertEquals(mappings.length, 2);
assertEquals(mappings[0].getChain(), "A");
assertEquals(mappings[0].getPDBResNum(53), 2);
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
- ((JalviewChimeraBinding) binding).sendFeaturesToChimera(af
- .getViewport().getAlignPanel());
+ binding.sendFeaturesToViewer(af.getViewport().getAlignPanel());
/*
* give Chimera time to open the commands file and execute it
/*
* ask Chimera for its residue attribute names
*/
- List<String> reply = ((JalviewChimeraBinding) binding)
- .sendChimeraCommand("list resattr", true);
+ List<String> reply = binding.sendChimeraCommand("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"));
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
* ask Chimera for residues with an attribute
* 91 and 96 on sequence --> residues 40 and 45 on chains A and B
*/
- reply = ((JalviewChimeraBinding) binding).sendChimeraCommand(
+ reply = binding.sendChimeraCommand(
"list resi att jv_metal_ion_binding_site", true);
assertEquals(reply.size(), 4);
assertTrue(reply
* check attributes with score values
* sequence positions 62 and 65 --> residues 11 and 14 on chains A and B
*/
- reply = ((JalviewChimeraBinding) binding).sendChimeraCommand(
- "list resi att jv_kd", true);
+ reply = binding.sendChimeraCommand("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 = ((JalviewChimeraBinding) binding).sendChimeraCommand(
+ reply = binding.sendChimeraCommand(
"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"));
+ SiftsClient.setMockSiftsFile(null);
+ 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