X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGStructureViewer.java;h=418e4132178c295b016144e256db43fbdcd1a143;hb=e1a435a213f105bac3ea0258c6fe26f11df2a392;hp=d8f3f611877d68b663879ed6b6939809469b8865;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git

diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index d8f3f61..418e413 100644
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -28,7 +28,10 @@ import java.awt.BorderLayout;
 import java.awt.GridLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.List;
 
+import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JMenu;
@@ -37,8 +40,8 @@ import javax.swing.JMenuItem;
 import javax.swing.JPanel;
 import javax.swing.JRadioButtonMenuItem;
 
-public abstract class GStructureViewer extends JInternalFrame implements
-        JalviewStructureDisplayI, ColourChangeListener
+public abstract class GStructureViewer extends JInternalFrame
+        implements JalviewStructureDisplayI, ColourChangeListener
 {
   // private AAStructureBindingModel bindingModel;
 
@@ -54,6 +57,8 @@ public abstract class GStructureViewer extends JInternalFrame implements
 
   protected JMenuItem alignStructs;
 
+  protected JCheckBoxMenuItem showAlignmentOnly;
+
   protected JMenuItem fitToWindow;
 
   protected JRadioButtonMenuItem seqColour;
@@ -93,7 +98,8 @@ public abstract class GStructureViewer extends JInternalFrame implements
     fileMenu.setText(MessageManager.getString("action.file"));
 
     savemenu = new JMenu();
-    savemenu.setActionCommand(MessageManager.getString("action.save_image"));
+    savemenu.setActionCommand(
+            MessageManager.getString("action.save_image"));
     savemenu.setText(MessageManager.getString("action.save_as"));
 
     JMenuItem pdbFile = new JMenuItem();
@@ -170,8 +176,8 @@ public abstract class GStructureViewer extends JInternalFrame implements
       }
     });
     alignStructs = new JMenuItem();
-    alignStructs.setText(MessageManager
-            .getString("label.superpose_structures"));
+    alignStructs.setText(
+            MessageManager.getString("label.superpose_structures"));
     alignStructs.addActionListener(new ActionListener()
     {
       @Override
@@ -266,4 +272,27 @@ public abstract class GStructureViewer extends JInternalFrame implements
   {
 
   }
+
+  /**
+   * Saves the selected entries in the 'View Chain' menu into a list. Entries are
+   * formatted as "pdbid:chainid". Only the selected chains should be drawn in the
+   * structure display.
+   */
+  protected void setSelectedChains()
+  {
+    List<String> chains = new ArrayList<>();
+    for (int i = 0; i < chainMenu.getItemCount(); i++)
+    {
+      JMenuItem menuItem = chainMenu.getItem(i);
+      if (menuItem instanceof JCheckBoxMenuItem)
+      {
+        JCheckBoxMenuItem item = (JCheckBoxMenuItem) menuItem;
+        if (item.isSelected())
+        {
+          chains.add(item.getText());
+        }
+      }
+    }
+    getBinding().setChainsToShow(chains);
+  }
 }