X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=7990a5cfb6afb30796bdb60f1e1ca6945d1f0611;hb=a7bda2e291fc5d01b6e3e43ba6215b78067beb5d;hp=9c3af271926de7b81ec0ebdfee51d7ca3084bc81;hpb=bc85369667c2665d81631e96f0701038f04f9bb3;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 9c3af27..7990a5c 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -245,6 +245,7 @@ public class AlignmentAnnotation
    * 
    * @see java.lang.Object#finalize()
    */
+  @Override
   protected void finalize() throws Throwable
   {
     sequenceRef = null;
@@ -957,10 +958,20 @@ 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 || sequenceMapping == null
-            || annotations == null)
+    if (sequenceRef == null)
+    {
+      return;
+    }
+
+    if (annotations == null)
     {
       return;
     }
@@ -976,18 +987,20 @@ 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;
   }
 
@@ -1024,11 +1037,11 @@ 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
@@ -1292,7 +1305,8 @@ public class AlignmentAnnotation
    * @note caller should add the remapped annotation to newref if they have not
    *       already
    */
-  public void remap(SequenceI newref, int[][] mapping, int from, int to,
+  public void remap(SequenceI newref, HashMap<Integer, int[]> mapping,
+          int from, int to,
           int idxoffset)
   {
     if (mapping != null)
@@ -1300,7 +1314,7 @@ public class AlignmentAnnotation
       Map<Integer, Annotation> old = sequenceMapping;
       Map<Integer, Annotation> remap = new HashMap<Integer, Annotation>();
       int index = -1;
-      for (int mp[] : mapping)
+      for (int mp[] : mapping.values())
       {
         if (index++ < 0)
         {