spike branch updated from latest features/JAL-2446

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 86e1144..835371f 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -39,7 +39,6 @@ import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.ResidueShader;
@@ -311,44 +310,6 @@ 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;
-    }
-    StringBuffer seqs = new StringBuffer();
-    for (int i = 0; i < consensus.annotations.length; i++)
-    {
-      if (consensus.annotations[i] != null)
-      {
-        if (consensus.annotations[i].description.charAt(0) == '[')
-        {
-          seqs.append(consensus.annotations[i].description.charAt(1));
-        }
-        else
-        {
-          seqs.append(consensus.annotations[i].displayCharacter);
-        }
-      }
-    }
-
-    SequenceI sq = new Sequence("Consensus", seqs.toString());
-    sq.setDescription("Percentage Identity Consensus "
-            + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
-    return sq;
-  }
-
   boolean validCharWidth;
 
   /**