JAL-4307 View->Ligands submenu, implementation for Jmol and documentation

[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 dc18369..c8ce3cd 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -26,6 +26,8 @@ import java.awt.event.ComponentListener;
 import java.io.File;
 import java.net.URL;
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.StringTokenizer;
@@ -41,6 +43,8 @@ import org.jmol.api.JmolViewer;
 import org.jmol.c.CBK;
 import org.jmol.viewer.Viewer;
 
+import com.google.common.collect.Lists;
+
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.FeatureSettingsModelI;
@@ -184,7 +188,25 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   // End StructureListener
   // //////////////////////////
-
+  
+  ////////////////////////////
+  // HETATM get
+  //
+  
+  @Override
+  public List<String> getHetatmNames()
+  {
+    HashMap<String,String> hetlist=new HashMap();
+    for (int mc=0;mc<jmolViewer.ms.mc; mc++)
+    {
+      Map<String,String> hets = jmolViewer.ms.getHeteroList(mc);
+      hetlist.putAll(hets);
+    }
+    return Arrays.asList(hetlist.keySet().toArray(new String[0]));
+  }
+  //
+  ////////////////////////////
+  
   @Override
   public float[][] functionXY(String functionName, int x, int y)
   {