X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureMapping.java;fp=src%2Fjalview%2Fstructure%2FStructureMapping.java;h=e0033e165d0c1e67aa2caa24dcc37864b665ff2a;hb=f9cf34a5681f00ec37e1254f92c3be9cb6c37ee8;hp=e4749c9be07fbaec1a7cea84891ac0b55aed17e8;hpb=68c26e8852772be21fdb5b091fa9083d8cdb6eec;p=jalview.git

diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index e4749c9..e0033e1 100644
--- a/src/jalview/structure/StructureMapping.java
+++ b/src/jalview/structure/StructureMapping.java
@@ -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++)
@@ -118,7 +133,10 @@ public class StructureMapping
     {
       ds = ds.getDatasetSequence();
     }
-    ala_copy.remap(ds, mapping, 0, -1, 1);
+    // 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)
     {