X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=9208e5e4308cdc979b721448a9bf8c9b480f3be8;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=2791ffc17e40b492ed2aa55e6ffd37b23d73094e;hpb=6288934c2b3c469369bfb8ee09fea627dafd7776;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 2791ffc..9208e5e 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -433,7 +433,8 @@ public class AlignViewport implements SelectionSource
     showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED",
             false);
     sortByTree = jalview.bin.Cache.getDefault("SORT_BY_TREE", false);
-    followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS", true); 
+    followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS",
+            true);
   }
 
   /**
@@ -477,11 +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)
@@ -557,10 +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)
         {
@@ -583,6 +577,27 @@ 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)
+    {
+      // TODO: make calls thread-safe, so if another thread calls this method, it will either return or wait until one calculation is finished.
+      if (immediate
+              || (!updatingConsensus && consensus != null && hconsensus != null))
+      {
+        AAFrequency.completeConsensus(consensus, hconsensus, 0,
+                hconsensus.length, ignoreGapsInConsensusCalculation,
+                showSequenceLogo);
+      }
+    }
   }
 
   /**
@@ -2206,6 +2221,16 @@ 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;
   }
 
@@ -2253,24 +2278,6 @@ 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