/*
* ask Chimera for its residue attribute names
*/
- List<String> reply = binding.sendChimeraCommand("list resattr", true);
+ List<String> reply = binding.executeCommand("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(
+ reply = binding.executeCommand(
"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 = binding.sendChimeraCommand("list resi att jv_kd", true);
+ reply = binding.executeCommand("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(
+ reply = binding.executeCommand(
"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"));
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);