Merge branch 'feature/JAL-3551Pymol' into develop

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 038ca48..eee48df 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -39,7 +39,9 @@ import org.jmol.api.JmolViewer;
 import org.jmol.c.CBK;
 import org.jmol.viewer.Viewer;
 
+import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
+import jalview.api.SequenceRenderer;
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
@@ -52,6 +54,7 @@ import jalview.structure.StructureCommand;
 import jalview.structure.StructureCommandI;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
+import javajs.util.BS;
 
 public abstract class JalviewJmolBinding extends AAStructureBindingModel
         implements JmolStatusListener, JmolSelectionListener,
@@ -115,7 +118,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   private String jmolScript(String script)
   {
     Cache.log.debug(">>Jmol>> " + script);
-    String s = jmolViewer.scriptWait(script);
+    String s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH
     Cache.log.debug("<<Jmol<< " + s);
 
     return s;
@@ -595,6 +598,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     modelFileNames = null;
     boolean notifyLoaded = false;
     String[] modelfilenames = getStructureFiles();
+    if (modelfilenames == null)
+    {
+      // Jmol is still loading files!
+      return;
+    }
     // first check if we've lost any structures
     if (oldmodels != null && oldmodels.length > 0)
     {
@@ -997,4 +1005,23 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   {
     return ".spt";
   }
+
+  @Override
+  public void selectionChanged(BS arg0)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel avp)
+  {
+    return new jalview.gui.SequenceRenderer(avp.getAlignViewport());
+  }
+
+  @Override
+  public String getHelpURL()
+  {
+    return "http://wiki.jmol.org"; // BH 2018
+  }
 }