JAL-2137 create 1:1 mapping between model and query sequence

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index c104fb2..3bb41c4 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -36,6 +36,7 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
+import jalview.structure.StructureSelectionManager;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -1306,7 +1307,11 @@ public class AnnotationFile
       }
       else
       {
-        // assume 1:1 - so synthesise sequences to use to construct mapping ?
+        // assume 1:1 - so synthesise sequences to use to construct mapping
+        StructureFile pdbf = StructureSelectionManager
+                .getStructureSelectionManager().setMapping(false,
+                        new SequenceI[] { refSeq2.getDatasetSequence() },
+                        null, modelPath, modelProt);
         refSeq2.getDatasetSequence().addPDBId(modelpe);
         if (templateSeq == null && tPw != null)
         {