X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;fp=src%2Fjalview%2Fgui%2FAlignViewport.java;h=80b3134369befaaefb97f5cfc5dc4a30c655f102;hb=a474ac9fbd7de4a6e77b3c445ea0205d3854af0f;hp=a44afa372af83745880ba19391ad06a606d8b2e6;hpb=05a1420df55d0f180ce3c0337133e9be98a643b7;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index a44afa3..80b3134 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -478,11 +478,6 @@ public class AlignViewport implements SelectionSource
   private boolean shownpfeats;
 
   /**
-   * consensus annotation includes all percentage for all symbols in column
-   */
-  private boolean includeAllConsensusSymbols = true;
-
-  /**
    * trigger update of conservation annotation
    */
   public void updateConservation(final AlignmentPanel ap)
@@ -558,10 +553,8 @@ public class AlignViewport implements SelectionSource
 
         hconsensus = new Hashtable[aWidth];
         AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment
-                .getWidth(), hconsensus, includeAllConsensusSymbols);
-        AAFrequency.completeConsensus(consensus, hconsensus, 0, aWidth,
-                ignoreGapsInConsensusCalculation,
-                includeAllConsensusSymbols);
+                .getWidth(), hconsensus, true);
+        updateAnnotation(true);
 
         if (globalColourScheme != null)
         {
@@ -584,6 +577,26 @@ public class AlignViewport implements SelectionSource
         ap.paintAlignment(true);
       }
     }
+
+    /**
+     * update the consensus annotation from the sequence profile data using
+     * current visualization settings.
+     */
+    public void updateAnnotation()
+    {
+      updateAnnotation(false);
+  }
+
+    protected void updateAnnotation(boolean immediate)
+    {
+      if (immediate
+              || (!updatingConsensus && consensus != null && hconsensus != null))
+      {
+        AAFrequency.completeConsensus(consensus, hconsensus, 0,
+                hconsensus.length, ignoreGapsInConsensusCalculation,
+                showSequenceLogo);
+      }
+    }
   }
 
   /**
@@ -2207,6 +2220,16 @@ public class AlignViewport implements SelectionSource
    */
   public void setShowSequenceLogo(boolean showSequenceLogo)
   {
+    if (showSequenceLogo != this.showSequenceLogo)
+    {
+      // TODO: decouple settings setting from calculation when refactoring
+      // annotation update method from alignframe to viewport
+      this.showSequenceLogo = showSequenceLogo;
+      if (consensusThread != null)
+      {
+        consensusThread.updateAnnotation();
+      }
+    }
     this.showSequenceLogo = showSequenceLogo;
   }
 
@@ -2254,24 +2277,6 @@ public class AlignViewport implements SelectionSource
   }
 
   /**
-   * @return the includeAllConsensusSymbols
-   */
-  public boolean isIncludeAllConsensusSymbols()
-  {
-    return includeAllConsensusSymbols;
-  }
-
-  /**
-   * @param includeAllConsensusSymbols
-   *          the includeAllConsensusSymbols to set
-   */
-  public void setIncludeAllConsensusSymbols(
-          boolean includeAllConsensusSymbols)
-  {
-    this.includeAllConsensusSymbols = includeAllConsensusSymbols;
-  }
-
-  /**
    * 
    * @return flag to indicate if the consensus histogram should be rendered by
    *         default