X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureMapping.java;h=a62f1aea7413e5d7ad770d01b8aa207869ea95cf;hb=4bba61a3c701f83bdcb6707c4d9f17a1f5faaa04;hp=923633152e0821d559fcfe1c27ddcff78bda1334;hpb=e0172c233914b64dc561b0a3b0d9aad850e99efc;p=jalview.git

diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index 9236331..a62f1ae 100644
--- a/src/jalview/structure/StructureMapping.java
+++ b/src/jalview/structure/StructureMapping.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -64,6 +64,11 @@ public class StructureMapping
     return pdbid;
   }
 
+  /**
+   * 
+   * @param seqpos
+   * @return 0 or corresponding atom number for the sequence position
+   */
   public int getAtomNum(int seqpos)
   {
     if (mapping.length > seqpos)
@@ -76,6 +81,11 @@ public class StructureMapping
     }
   }
 
+  /**
+   * 
+   * @param seqpos
+   * @return 0 or the corresponding residue number for the sequence position
+   */
   public int getPDBResNum(int seqpos)
   {
     if (mapping.length > seqpos)
@@ -88,6 +98,11 @@ public class StructureMapping
     }
   }
 
+  /**
+   * 
+   * @param pdbResNum
+   * @return -1 or the corresponding sequence position for a pdb residue number
+   */
   public int getSeqPos(int pdbResNum)
   {
     for (int i = 0; i < mapping.length; i++)
@@ -106,11 +121,30 @@ public class StructureMapping
    * 
    * @param ana
    * @return the copy that was remapped to the mapped sequence
+   * @note this method will create a copy and add it to the dataset sequence for
+   *       the mapped sequence as well as the mapped sequence (if it is not a
+   *       dataset sequence).
    */
   public AlignmentAnnotation transfer(AlignmentAnnotation ana)
   {
     AlignmentAnnotation ala_copy = new AlignmentAnnotation(ana);
-    ala_copy.remap(sequence, mapping, 0, -1, 1);
+    SequenceI ds = sequence;
+    while (ds.getDatasetSequence() != null)
+    {
+      ds = ds.getDatasetSequence();
+    }
+    // need to relocate annotation from pdb coordinates to local sequence
+    // -1,-1 doesn't look at pdbresnum but fails to remap sequence positions...
+
+    ala_copy.remap(ds, mapping, -1, -1, 0);
+    ds.addAlignmentAnnotation(ala_copy);
+    if (ds != sequence)
+    {
+      // mapping wasn't to an original dataset sequence, so we make a copy on
+      // the mapped sequence too
+      ala_copy = new AlignmentAnnotation(ala_copy);
+      sequence.addAlignmentAnnotation(ala_copy);
+    }
     return ala_copy;
   }
 }