From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 3 Jul 2017 14:39:09 +0000 (+0100)
Subject: Merge branch 'develop' into bug/JAL-147scrollWrappedView
X-Git-Tag: Release_2_10_3b1~132^2~57
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2c50a2864785391e69940a9381d0ee5c5a6ea538;hp=-c;p=jalview.git

Merge branch 'develop' into bug/JAL-147scrollWrappedView
---

2c50a2864785391e69940a9381d0ee5c5a6ea538
diff --combined src/jalview/viewmodel/AlignmentViewport.java
index 0cdba1e,9a08a2b..1e094fd
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@@ -405,7 -405,6 +405,7 @@@ public abstract class AlignmentViewpor
    public void setWrapAlignment(boolean state)
    {
      viewStyle.setWrapAlignment(state);
 +    ranges.setWrappedMode(state);
    }
  
    /**
@@@ -2871,4 -2870,45 +2871,45 @@@
    {
      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;
+   }
  }