JAL-1933 gap value as description; minor formatting

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

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index 5c55d48..1cce3ff 100644 (file)
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -119,7 +119,8 @@ public class ConsensusThread extends AlignCalcWorker
     AlignmentAnnotation consensus = getConsensusAnnotation();
     consensus.annotations = new Annotation[aWidth];
     AlignmentAnnotation gap = getGapAnnotation();
-    if (gap!=null) {
+    if (gap != null)
+    {
       gap.annotations = new Annotation[aWidth];
     }
   }
@@ -132,8 +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);
@@ -221,29 +222,26 @@ 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,
+  /**
+   * 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);
-
   }
 
   /**