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

[jalview.git] / src / jalview / structures / models / AAStructureBindingModel.java

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 4b11494..55955a8 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -26,6 +26,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.BitSet;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
@@ -884,14 +885,7 @@ public abstract class AAStructureBindingModel
       {
         for (int s : cs.getSelected())
         {
-          if (hiddenCols == null)
-          {
             matched.set(s);
-          }
-          else
-          {
-            matched.set(hiddenCols.visibleToAbsoluteColumn(s));
-          }
         }
       }
       else
@@ -2013,4 +2007,18 @@ public abstract class AAStructureBindingModel
   {
     return 0;
   }
+
+  public List<String> getHetatmNames() {
+    return Collections.EMPTY_LIST;
+  }
+  /**
+   * Generates and executes a command to show the given hetatm types as CPK
+   * 
+   * @param toShow - one or more of strings from getHetatmNames
+   */
+  public void showHetatms(List<String> toShow)
+  {
+    executeCommands(commandGenerator.showHetatms(toShow), false, "Adjusting hetatm visibility");
+  }
+
 }