JAL-3518 more extraction of ChimeraX commands as overrides

[jalview.git] / test / jalview / ext / rbvi / chimera / JalviewChimeraView.java

diff --git a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
index 29fd092..93ed555 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
+++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
@@ -39,6 +39,7 @@ 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.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
@@ -50,7 +51,6 @@ import java.io.File;
 import java.io.IOException;
 import java.util.List;
 import java.util.Vector;
-import jalview.io.DataSourceType;
 
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.AfterMethod;
@@ -290,7 +290,7 @@ public class JalviewChimeraView
     /*
      * 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"));
@@ -306,7 +306,7 @@ public class JalviewChimeraView
      * 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
@@ -322,7 +322,7 @@ public class JalviewChimeraView
      * 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"));
@@ -332,7 +332,7 @@ public class JalviewChimeraView
     /*
      * 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"));
@@ -402,8 +402,8 @@ public class JalviewChimeraView
     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
@@ -440,15 +440,13 @@ public class JalviewChimeraView
     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
@@ -470,10 +468,11 @@ public class JalviewChimeraView
           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);