From 7db0832b434e34aa682d38a896fbd3ad3ae2d217 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 30 Jun 2017 11:48:15 +0100
Subject: [PATCH] JAL-2602 pulled up identical methods to base class

---
 src/jalview/appletgui/AlignViewport.java     |   40 ------------------------
 src/jalview/gui/AlignViewport.java           |   43 --------------------------
 src/jalview/viewmodel/AlignmentViewport.java |   41 ++++++++++++++++++++++++
 3 files changed, 41 insertions(+), 83 deletions(-)

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index a894d0b..1d2c4bc 100644
--- 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;
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 288f261..835371f 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -34,13 +34,11 @@ import jalview.commands.CommandI;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 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;
@@ -312,47 +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++)
-    {
-      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(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;
-  }
-
   boolean validCharWidth;
 
   /**
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 107cdd4..9a08a2b 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -2870,4 +2870,45 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     return searchResults;
   }
+
+  /**
+   * 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++)
+    {
+      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(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;
+  }
 }
-- 
1.7.10.2