Merge branch 'develop' into bug/JAL-2346annotationChoice

[jalview.git] / src / jalview / workers / ConsensusThread.java

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index 0c7e69a..284f1a1 100644 (file)
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -50,7 +50,8 @@ public class ConsensusThread extends AlignCalcWorker
     try
     {
       AlignmentAnnotation consensus = getConsensusAnnotation();
-      if (consensus == null || calcMan.isPending(this))
+      AlignmentAnnotation gap = getGapAnnotation();
+      if ((consensus == null && gap == null) || calcMan.isPending(this))
       {
         calcMan.workerComplete(this);
         return;
@@ -117,6 +118,11 @@ public class ConsensusThread extends AlignCalcWorker
   {
     AlignmentAnnotation consensus = getConsensusAnnotation();
     consensus.annotations = new Annotation[aWidth];
+    AlignmentAnnotation gap = getGapAnnotation();
+    if (gap != null)
+    {
+      gap.annotations = new Annotation[aWidth];
+    }
   }
 
   /**
@@ -127,8 +133,8 @@ public class ConsensusThread extends AlignCalcWorker
 
     SequenceI[] aseqs = getSequences();
     int width = alignment.getWidth();
-    ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0,
-            width, true);
+    ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0, width,
+            true);
 
     alignViewport.setSequenceConsensusHash(hconsensus);
     setColourSchemeConsensus(hconsensus);
@@ -165,6 +171,16 @@ public class ConsensusThread extends AlignCalcWorker
   }
 
   /**
+   * Get the Gap annotation for the alignment
+   * 
+   * @return
+   */
+  protected AlignmentAnnotation getGapAnnotation()
+  {
+    return alignViewport.getAlignmentGapAnnotation();
+  }
+
+  /**
    * update the consensus annotation from the sequence profile data using
    * current visualization settings.
    */
@@ -182,6 +198,11 @@ public class ConsensusThread extends AlignCalcWorker
             && hconsensus != null)
     {
       deriveConsensus(consensus, hconsensus);
+      AlignmentAnnotation gap = getGapAnnotation();
+      if (gap != null)
+      {
+        deriveGap(gap, hconsensus);
+      }
     }
   }
 
@@ -200,13 +221,29 @@ public class ConsensusThread extends AlignCalcWorker
 
     long nseq = getSequences().length;
     AAFrequency.completeConsensus(consensusAnnotation, hconsensus,
-            hconsensus.getStartColumn(),
-            hconsensus.getEndColumn() + 1,
+            hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
             alignViewport.isIgnoreGapsConsensus(),
             alignViewport.isShowSequenceLogo(), nseq);
   }
 
   /**
+   * Convert the computed consensus data into a gap annotation row for display.
+   * 
+   * @param gapAnnotation
+   *          the annotation to be populated
+   * @param hconsensus
+   *          the computed consensus data
+   */
+  protected void deriveGap(AlignmentAnnotation gapAnnotation,
+          ProfilesI hconsensus)
+  {
+    long nseq = getSequences().length;
+    AAFrequency.completeGapAnnot(gapAnnotation, hconsensus,
+            hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
+            nseq);
+  }
+
+  /**
    * Get the consensus data stored on the viewport.
    * 
    * @return