X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=bed10a1d09841453881aadef0953e7eb57461e6d;hb=c1cbfffa52f43d3b0dd74eca5e7d4e30af3b83dc;hp=dc8f72b78c35cd63fee4a65aa7e678c02202b9aa;hpb=81d90a3969ade80091512d829a4fd2850d85b7bc;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index dc8f72b..bed10a1 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -172,6 +172,7 @@ public class AlignFrame
     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
                                   HistoryItem.HIDE));
     restoreHistoryItem(hi);
+    resetAllColourSchemes();
   }
 
   protected void redoMenuItem_actionPerformed(ActionEvent e)
@@ -180,6 +181,7 @@ public class AlignFrame
     restoreHistoryItem(hi);
     updateEditMenuBar();
     viewport.updateConsensus();
+    resetAllColourSchemes();
     alignPanel.repaint();
     alignPanel.repaint();
   }
@@ -420,6 +422,7 @@ public class AlignFrame
         viewport.alignment.getWidth();
         viewport.updateConservation();
         viewport.updateConsensus();
+        resetAllColourSchemes();
         alignPanel.repaint();
       }
 
@@ -488,6 +491,7 @@ public class AlignFrame
     }
     viewport.updateConservation();
     viewport.updateConsensus();
+    resetAllColourSchemes();
     alignPanel.repaint();
 
   }
@@ -557,7 +561,7 @@ public class AlignFrame
           viewport.alignment.deleteGroup(sg);
         }
       }
-
+      resetAllColourSchemes();
       alignPanel.repaint();
     }
   }
@@ -585,7 +589,7 @@ public class AlignFrame
           viewport.alignment.deleteGroup(sg);
         }
       }
-
+      resetAllColourSchemes();
       alignPanel.repaint();
     }
 
@@ -608,7 +612,7 @@ public class AlignFrame
 
     viewport.updateConservation();
     viewport.updateConsensus();
-    resetAllClustalSchemes();
+    resetAllColourSchemes();
     alignPanel.repaint();
   }
 
@@ -660,14 +664,32 @@ public class AlignFrame
     }
 
     viewport.setStartRes(seq.findIndex(startRes)-1);
-    resetAllClustalSchemes();
     viewport.updateConservation();
     viewport.updateConsensus();
+    resetAllColourSchemes();
     alignPanel.repaint();
   }
 
-  void resetAllClustalSchemes()
+  void resetAllColourSchemes()
   {
+    ColourSchemeI cs = viewport.globalColourScheme;
+    if(cs!=null)
+    {
+        cs.setConsensus(viewport.vconsensus);
+        if(cs.conservationApplied())
+        {
+          Alignment al = (Alignment) viewport.alignment;
+          Conservation c = new Conservation("All",
+                                            ResidueProperties.propHash, 3,
+                                            al.getSequences(), 0,
+                                            al.getWidth() - 1);
+          c.calculate();
+          c.verdict(false, viewport.ConsPercGaps);
+
+          cs.setConservation(c);
+        }
+    }
+
     if(viewport.getGlobalColourScheme()!=null
        && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)
     {
@@ -680,10 +702,13 @@ public class AlignFrame
     for(s=0; s<sSize; s++)
     {
       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
-      if(sg.cs instanceof ClustalxColourScheme)
+      if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
       {
         ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
       }
+
+      sg.recalcConservation();
+
     }
   }