'Update to Covariaton color scheme' merge; JAL-580

[jalview.git] / src / jalview / datamodel / SequenceGroup.java

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index f045555..d253560 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -440,7 +440,9 @@ public class SequenceGroup
   }
 
   /**
-   * Add s to this sequence group
+   * Add s to this sequence group. If aligment sequence is already contained in
+   * group, it will not be added again, but recalculation may happen if the flag
+   * is set.
    * 
    * @param s
    *          alignment sequence to be added
@@ -794,9 +796,12 @@ public class SequenceGroup
   {
     return getSequencesInOrder(al, true);
   }
+
   /**
-   * return an array representing the intersection of the group with al, optionally returning an array the size of al.getHeight() 
-   * where nulls mark the non-intersected sequences
+   * return an array representing the intersection of the group with al,
+   * optionally returning an array the size of al.getHeight() where nulls mark
+   * the non-intersected sequences
+   * 
    * @param al
    * @param trim
    * @return null or array
@@ -993,6 +998,18 @@ public class SequenceGroup
   private boolean showConsensusHistogram;
 
   /**
+   * set this alignmentAnnotation object as the one used to render consensus annotation
+   * @param aan
+   */
+  public void setConsensus(AlignmentAnnotation aan)
+  {
+    if (consensus==null)
+    {
+      consensus=aan;
+    }
+  }
+  
+  /**
    * 
    * @return automatically calculated consensus row
    */
@@ -1021,6 +1038,17 @@ public class SequenceGroup
   }
 
   /**
+   * set this alignmentAnnotation object as the one used to render consensus annotation
+   * @param aan
+   */
+  public void setConservationRow(AlignmentAnnotation aan)
+  {
+    if (conservation==null)
+    {
+      conservation=aan;
+    }
+  }
+  /**
    * get the conservation annotation row for this group
    * 
    * @return autoCalculated annotation row