+ } while (!binding.isFinishedInit());
+
+ assertTrue(binding.isChimeraRunning(), "Failed to launch Chimera");
+
+ assertEquals(binding.getPdbCount(), 1);
+
+ /*
+ * check mapping is (sequence) 53-145 to (structure) 2-94 A/B
+ * (or possibly 52-145 to 1-94 - see JAL-2319)
+ */
+ StructureSelectionManager ssm = binding.getSsm();
+ 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);
+ assertEquals(mappings[0].getPDBResNum(145), 94);
+ assertEquals(mappings[1].getChain(), "B");
+ assertEquals(mappings[1].getPDBResNum(53), 2);
+ assertEquals(mappings[1].getPDBResNum(145), 94);
+
+ /*
+ * now add some features to FER2_ARATH
+ */
+ // feature on a sequence region not mapped to structure:
+ sq.addSequenceFeature(new SequenceFeature("transit peptide",
+ "chloroplast", 1, 51, Float.NaN, null));
+ // feature on a region mapped to structure:
+ sq.addSequenceFeature(new SequenceFeature("domain",
+ "2Fe-2S ferredoxin-type", 55, 145, Float.NaN, null));
+ // on sparse positions of the sequence
+ sq.addSequenceFeature(new SequenceFeature("metal ion-binding site",
+ "Iron-Sulfur (2Fe-2S)", 91, 91, Float.NaN, null));
+ sq.addSequenceFeature(new SequenceFeature("metal ion-binding site",
+ "Iron-Sulfur (2Fe-2S)", 96, 96, Float.NaN, null));
+ // on a sequence region that is partially mapped to structure:
+ sq.addSequenceFeature(new SequenceFeature("helix", null, 50, 60,
+ Float.NaN, null));
+ // and again:
+ sq.addSequenceFeature(new SequenceFeature("chain", null, 50, 70,
+ Float.NaN, null));
+ // add numeric valued features - score is set as attribute value
+ sq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 62,
+ 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
+ */
+ af.setShowSeqFeatures(true);
+ FeatureRenderer fr = af.getFeatureRenderer();
+ fr.setVisible("transit peptide");
+ fr.setVisible("domain");
+ fr.setVisible("metal ion-binding site");
+ fr.setVisible("helix");
+ fr.setVisible("kd");
+ fr.setVisible("RESNUM");
+
+ /*
+ * '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.sendFeaturesToViewer(af.getViewport().getAlignPanel());
+
+ /*
+ * give Chimera time to open the commands file and execute it
+ */
+ try
+ {
+ Thread.sleep(1000);
+ } catch (InterruptedException e)
+ {
+ }
+
+ /*
+ * ask Chimera for its residue attribute names
+ */
+ 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
+ assertFalse(reply.contains("resattr jv_chain"));
+
+ /*
+ * 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);
+ assertEquals(reply.size(), 4);
+ assertTrue(reply
+ .contains("residue id #0:40.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
+ assertTrue(reply
+ .contains("residue id #0:45.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 45"));
+ assertTrue(reply
+ .contains("residue id #0:40.B jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
+ assertTrue(reply
+ .contains("residue id #0:45.B jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 45"));
+
+ /*
+ * 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);
+ 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"));
+ assertTrue(reply.contains("residue id #0:11.B jv_kd -2.1 index 11"));
+ assertTrue(reply.contains("residue id #0:14.B 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);
+ 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)