JAL-2602 pulled up identical methods to base class

[jalview.git] / src / jalview / appletgui / AlignViewport.java

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index a894d0b..1d2c4bc 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -230,46 +230,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   }
 
-  /**
-   * get the consensus sequence as displayed under the PID consensus annotation
-   * row.
-   * 
-   * @return consensus sequence as a new sequence object
-   */
-  public SequenceI getConsensusSeq()
-  {
-    if (consensus == null)
-    {
-      updateConsensus(null);
-    }
-    if (consensus == null)
-    {
-      return null;
-    }
-    StringBuilder seqs = new StringBuilder(consensus.annotations.length);
-    for (int i = 0; i < consensus.annotations.length; i++)
-    {
-      Annotation annotation = consensus.annotations[i];
-      if (annotation != null)
-      {
-        String description = annotation.description;
-        if (description != null && description.startsWith("["))
-        {
-          // consensus is a tie - just pick the first one
-          seqs.append(annotation.description.charAt(1));
-        }
-        else
-        {
-          seqs.append(annotation.displayCharacter);
-        }
-      }
-    }
-    SequenceI sq = new Sequence("Consensus", seqs.toString());
-    sq.setDescription("Percentage Identity Consensus "
-            + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
-    return sq;
-  }
-
   java.awt.Frame nullFrame;
 
   protected FeatureSettings featureSettings = null;