JAL-3551 working proof of concept of Jalview driving PyMOL

[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 93ed555..30c23af 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
+++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
@@ -41,6 +41,7 @@ import jalview.gui.StructureViewer;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
+import jalview.structure.StructureCommand;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
 import jalview.ws.sifts.SiftsClient;
@@ -290,7 +291,8 @@ public class JalviewChimeraView
     /*
      * ask Chimera for its residue attribute names
      */
-    List<String> reply = binding.executeCommand("list resattr", true);
+    List<String> reply = binding
+            .executeCommand(new StructureCommand("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"));
@@ -307,7 +309,8 @@ public class JalviewChimeraView
      * 91 and 96 on sequence --> residues 40 and 45 on chains A and B
      */
     reply = binding.executeCommand(
-            "list resi att jv_metal_ion_binding_site", true);
+            new StructureCommand("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"));
@@ -322,7 +325,8 @@ public class JalviewChimeraView
      * check attributes with score values
      * sequence positions 62 and 65 --> residues 11 and 14 on chains A and B
      */
-    reply = binding.executeCommand("list resi att jv_kd", true);
+    reply = binding.executeCommand(
+            new StructureCommand("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"));
@@ -333,7 +337,8 @@ public class JalviewChimeraView
      * list residues with positive kd score 
      */
     reply = binding.executeCommand(
-            "list resi spec :*/jv_kd>0 attr jv_kd", true);
+            new StructureCommand("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"));