X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGStructureViewer.java;h=66cd8f24196aa76a171cdf28110dafc5f334c7da;hb=e34c8452beda2cf80c2a3224f236d3096db69ae9;hp=83d85906fc6c7b5843999a465ec57d75d6c0e8db;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index 83d8590..66cd8f2 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;
@@ -54,6 +57,10 @@ public abstract class GStructureViewer extends JInternalFrame
 
   protected JMenuItem alignStructs;
 
+  protected JCheckBoxMenuItem showAlignmentOnly;
+
+  protected JCheckBoxMenuItem hideHiddenRegions;
+
   protected JMenuItem fitToWindow;
 
   protected JRadioButtonMenuItem seqColour;
@@ -267,4 +274,27 @@ public abstract class GStructureViewer extends JInternalFrame
   {
 
   }
+
+  /**
+   * 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);
+  }
 }