JAL-1912 javadoc for adjustForAlignment stating current behaviour

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 01926dc..830dbc7 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 != null && 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;
   }