X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=8d26d4f4e12480000057f13999dcb35a0d5d4adb;hb=5312252fee162e6bc9bf5ac355930e16f1776c53;hp=ab1ac0e1b533b8a208d859c7996dd24fb6e5d7c5;hpb=3965e9e3bc4ca05dcc82b8dc72c380f208c9a1e6;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ab1ac0e..8d26d4f 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -681,23 +681,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         case KeyEvent.VK_PAGE_UP:
           if (viewport.getWrapAlignment())
           {
-            alignPanel.scrollUp(true);
+            vpRanges.scrollUp(true);
           }
           else
           {
-            alignPanel.setScrollValues(vpRanges.getStartRes(),
-                    2 * vpRanges.getStartSeq() - vpRanges.getEndSeq());
+            vpRanges.pageUp();
           }
           break;
         case KeyEvent.VK_PAGE_DOWN:
           if (viewport.getWrapAlignment())
           {
-            alignPanel.scrollUp(false);
+            vpRanges.scrollUp(false);
           }
           else
           {
-            alignPanel.setScrollValues(vpRanges.getStartRes(),
-                    vpRanges.getEndSeq());
+            vpRanges.pageDown();
           }
           break;
         }
@@ -2750,6 +2748,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      */
     newap.av.replaceMappings(viewport.getAlignment());
 
+    /*
+     * start up cDNA consensus (if applicable) now mappings are in place
+     */
+    if (newap.av.initComplementConsensus())
+    {
+      newap.refresh(true); // adjust layout of annotations
+    }
+
     newap.av.viewName = getNewViewName(viewTitle);
 
     addAlignmentPanel(newap, true);
@@ -3327,7 +3333,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      */
     if (ResidueColourScheme.USER_DEFINED.equals(name))
     {
-      new UserDefinedColours(alignPanel, null);
+      new UserDefinedColours(alignPanel);
       return;
     }
 
@@ -3348,10 +3354,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void changeColour(ColourSchemeI cs)
   {
     // TODO: pull up to controller method
-    if (cs != null)
-    {
-      ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
-    }
+    ColourMenuHelper.setColourSelected(colourMenu, cs);
 
     viewport.setGlobalColourScheme(cs);
 
@@ -5700,10 +5703,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     colourMenu.add(annotationColour);
 
     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
-    String schemeName = colourScheme == null ? null : colourScheme
-            .getSchemeName();
-
-    ColourMenuHelper.setColourSelected(colourMenu, schemeName);
+    ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
   }
 }