JAL-2431 show cDNA consensus after New View in split frame

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index cf6a901..c7bce10 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2744,6 +2744,14 @@ 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);
@@ -3359,7 +3367,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void modifyPID_actionPerformed()
   {
     SliderPanel.setPIDSliderSource(alignPanel,
-            viewport.getViewportColourScheme(), alignPanel.getViewName());
+            viewport.getResidueShading(), alignPanel.getViewName());
     SliderPanel.showPIDSlider();
   }
 
@@ -3370,7 +3378,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void modifyConservation_actionPerformed()
   {
     SliderPanel.setConservationSlider(alignPanel,
-            viewport.getViewportColourScheme(), alignPanel.getViewName());
+            viewport.getResidueShading(), alignPanel.getViewName());
     SliderPanel.showConservationSlider();
   }
 
@@ -3382,7 +3390,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     modifyConservation.setEnabled(selected);
     viewport.setConservationSelected(selected);
-    viewport.getViewportColourScheme().setConservationApplied(selected);
+    viewport.getResidueShading().setConservationApplied(selected);
 
     changeColour(viewport.getGlobalColourScheme());
     if (selected)
@@ -3405,7 +3413,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.setAbovePIDThreshold(selected);
     if (!selected)
     {
-      viewport.getViewportColourScheme().setThreshold(0,
+      viewport.getResidueShading().setThreshold(0,
               viewport.isIgnoreGapsConsensus());
     }
 
@@ -4838,7 +4846,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (viewport.getConservationSelected())
     {
       SliderPanel.setConservationSlider(alignPanel,
-              viewport.getViewportColourScheme(), alignPanel.getViewName());
+              viewport.getResidueShading(), alignPanel.getViewName());
     }
     else
     {
@@ -4847,7 +4855,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (viewport.getAbovePIDThreshold())
     {
       SliderPanel.setPIDSliderSource(alignPanel,
-              viewport.getViewportColourScheme(), alignPanel.getViewName());
+              viewport.getResidueShading(), alignPanel.getViewName());
     }
     else
     {