use local reference for current target frame as set by JAL-451

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

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index f045555..7bb9670 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