From: Jim Procter <jprocter@dundee.ac.uk>
Date: Wed, 12 Nov 2014 12:37:12 +0000 (+0000)
Subject: JAL-674 note about broken .transfer method (expect this to disappear in future!)
X-Git-Tag: Release_2_8_2b1^2~36^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=392d163b8c1cc1f731fb667a5300eb7f751ea395;p=jalview.git

JAL-674 note about broken .transfer method (expect this to disappear in future!)
---

diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index cbc2c00..e0033e1 100644
--- a/src/jalview/structure/StructureMapping.java
+++ b/src/jalview/structure/StructureMapping.java
@@ -133,7 +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)
     {