X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=8fb9b3720e9c66d327d4fc022c1c1b9fd5fedeb6;hb=27a5a96f40f4721c9b9024938547a997dbf16cf4;hp=65c4fefb7708b28983fc52ce07035cf744e46d69;hpb=c437fc72420baf7b045d417fb6cabcebe87987c5;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 65c4fef..8fb9b37 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -90,7 +90,6 @@ import java.awt.Label;
 import java.awt.Menu;
 import java.awt.MenuBar;
 import java.awt.MenuItem;
-import java.awt.MenuShortcut;
 import java.awt.Panel;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -2690,9 +2689,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     boolean selected = conservationMenuItem.getState();
     modifyConservation.setEnabled(selected);
     viewport.setConservationSelected(selected);
-
-    // viewport.setAbovePIDThreshold(false);
-    // abovePIDThreshold.setState(false);
+    viewport.getResidueShading().setConservationApplied(selected);
 
     changeColour(viewport.getGlobalColourScheme());
 
@@ -2711,8 +2708,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     boolean selected = abovePIDThreshold.getState();
     modifyPID.setEnabled(selected);
     viewport.setAbovePIDThreshold(selected);
-    // conservationMenuItem.setState(false);
-    // viewport.setConservationSelected(false);
+    if (!selected)
+    {
+      viewport.getResidueShading().setThreshold(0,
+              viewport.isIgnoreGapsConsensus());
+    }
 
     changeColour(viewport.getGlobalColourScheme());
 
@@ -4136,7 +4136,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       // register the association(s) and quit, don't create any windows.
       if (StructureSelectionManager.getStructureSelectionManager(applet)
-              .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
+              .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
       {
         System.err.println("Failed to map " + pdb.getFile() + " ("
                 + protocol + ") to any sequences");