JAL-2422 pull-up refactoring of structure commands (continued)

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

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 22876a4..a92fe77 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -48,7 +48,6 @@ import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
-import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JInternalFrame;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
@@ -339,27 +338,6 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   /**
-   * Show only the selected chain(s) in the viewer
-   */
-  @Override
-  void showSelectedChains()
-  {
-    List<String> toshow = new ArrayList<>();
-    for (int i = 0; i < chainMenu.getItemCount(); i++)
-    {
-      if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
-      {
-        JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
-        if (item.isSelected())
-        {
-          toshow.add(item.getText());
-        }
-      }
-    }
-    jmb.showChains(toshow);
-  }
-
-  /**
    * Close down this instance of Jalview's Chimera viewer, giving the user the
    * option to close the associated Chimera window (process). They may wish to
    * keep it open until they have had an opportunity to save any work.
@@ -604,7 +582,7 @@ public class ChimeraViewFrame extends StructureViewerBase
       String chid = new String(
               pdb.getId() + ":" + pdb.getChains().elementAt(i).id);
       jmb.getChainNames().add(chid);
-      jmb.getChainFile().put(chid, file);
+      jmb.addChainFile(chid, file);
     }
   }