From 734d0e761fda32cebaae59c370c5d64e1e8c99e8 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 15 Mar 2017 16:31:28 +0000
Subject: [PATCH] JAL-2431 show cDNA consensus after New View in split frame

---
 src/jalview/gui/AlignFrame.java              |    8 ++++++++
 src/jalview/gui/AlignmentPanel.java          |   22 ++++++++++++++++++++++
 src/jalview/gui/AnnotationLabels.java        |   26 ++------------------------
 src/jalview/viewmodel/AlignmentViewport.java |    8 +++++---
 4 files changed, 37 insertions(+), 27 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b5fc817..c7bce10 100644
--- 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);
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index e61b042..f7a1d2c 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1875,4 +1875,26 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     return this.dontScrollComplement;
   }
+
+  /**
+   * Redraw sensibly.
+   * 
+   * @adjustHeight if true, try to recalculate panel height for visible
+   *               annotations
+   */
+  protected void refresh(boolean adjustHeight)
+  {
+    validateAnnotationDimensions(adjustHeight);
+    addNotify();
+    if (adjustHeight)
+    {
+      // sort, repaint, update overview
+      paintAlignment(true);
+    }
+    else
+    {
+      // lightweight repaint
+      repaint();
+    }
+  }
 }
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 4b774d6..c9535d0 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -292,33 +292,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
     }
 
-    refresh(fullRepaint);
+    ap.refresh(fullRepaint);
 
   }
 
   /**
-   * Redraw sensibly.
-   * 
-   * @adjustHeight if true, try to recalculate panel height for visible
-   *               annotations
-   */
-  protected void refresh(boolean adjustHeight)
-  {
-    ap.validateAnnotationDimensions(adjustHeight);
-    ap.addNotify();
-    if (adjustHeight)
-    {
-      // sort, repaint, update overview
-      ap.paintAlignment(true);
-    }
-    else
-    {
-      // lightweight repaint
-      ap.repaint();
-    }
-  }
-
-  /**
    * DOCUMENT ME!
    * 
    * @param e
@@ -420,7 +398,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             // ann.visible = false;
             // }
             // }
-            refresh(true);
+            ap.refresh(true);
           }
         });
         pop.add(hideType);
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 0c470fe..6dcf26d 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1898,10 +1898,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   /**
-   * If this is a protein alignment and there are mappings to cDNA, add the cDNA
-   * consensus annotation.
+   * If this is a protein alignment and there are mappings to cDNA, adds the
+   * cDNA consensus annotation and returns true, else returns false.
    */
-  public void initComplementConsensus()
+  public boolean initComplementConsensus()
   {
     if (!alignment.isNucleotide())
     {
@@ -1928,9 +1928,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
                   "PID for cDNA", new Annotation[1], 0f, 100f,
                   AlignmentAnnotation.BAR_GRAPH);
           initConsensus(complementConsensus);
+          return true;
         }
       }
     }
+    return false;
   }
 
   private void initConsensus(AlignmentAnnotation aa)
-- 
1.7.10.2