JAL-3551 working proof of concept of Jalview driving PyMOL

[jalview.git] / src / jalview / gui / AppJmol.java

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 0768c00..4087e63 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -26,6 +26,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.gui.StructureViewer.ViewerType;
+import jalview.structure.StructureCommand;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.BrowserLauncher;
 import jalview.util.ImageMaker;
@@ -245,8 +246,8 @@ public class AppJmol extends StructureViewerBase
     {
       command = "";
     }
-    jmb.executeCommand(command, false);
-    jmb.executeCommand("set hoverDelay=0.1", false);
+    jmb.executeCommand(new StructureCommand(command), false);
+    jmb.executeCommand(new StructureCommand("set hoverDelay=0.1"), false);
     jmb.setFinishedInit(true);
   }
 
@@ -323,7 +324,7 @@ public class AppJmol extends StructureViewerBase
       cmd.append("loadingJalviewdata=true\nload APPEND ");
       cmd.append(filesString);
       cmd.append("\nloadingJalviewdata=null");
-      final String command = cmd.toString();
+      final StructureCommand command = new StructureCommand(cmd.toString());
       lastnotify = jmb.getLoadNotifiesHandled();
 
       try