Merge branch 'develop' into Release_2_9_0b1_Branch

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index ab11089..95141e6 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -957,6 +957,12 @@ public class AlignmentAnnotation
 
   }
 
+  /**
+   * When positional annotation and a sequence reference is present, clears and
+   * resizes the annotations array to the current alignment width, and adds
+   * annotation according to aligned positions of the sequenceRef given by
+   * sequenceMapping.
+   */
   public void adjustForAlignment()
   {
     if (sequenceRef == null)
@@ -980,18 +986,20 @@ public class AlignmentAnnotation
     int position;
     Annotation[] temp = new Annotation[aSize];
     Integer index;
-
-    for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
+    if (sequenceMapping != null)
     {
-      index = new Integer(a);
-      if (sequenceMapping.containsKey(index))
+      for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
       {
-        position = sequenceRef.findIndex(a) - 1;
+        index = new Integer(a);
+        Annotation annot = sequenceMapping.get(index);
+        if (annot != null)
+        {
+          position = sequenceRef.findIndex(a) - 1;
 
-        temp[position] = sequenceMapping.get(index);
+          temp[position] = annot;
+        }
       }
     }
-
     annotations = temp;
   }
 
@@ -1028,11 +1036,11 @@ public class AlignmentAnnotation
   }
 
   /**
-   * Associate this annotion with the aligned residues of a particular sequence.
-   * sequenceMapping will be updated in the following way: null sequenceI -
-   * existing mapping will be discarded but annotations left in mapped
-   * positions. valid sequenceI not equal to current sequenceRef: mapping is
-   * discarded and rebuilt assuming 1:1 correspondence TODO: overload with
+   * Associate this annotation with the aligned residues of a particular
+   * sequence. sequenceMapping will be updated in the following way: null
+   * sequenceI - existing mapping will be discarded but annotations left in
+   * mapped positions. valid sequenceI not equal to current sequenceRef: mapping
+   * is discarded and rebuilt assuming 1:1 correspondence TODO: overload with
    * parameter to specify correspondence between current and new sequenceRef
    * 
    * @param sequenceI