X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAssociatePdbFileWithSeq.java;h=b2689be6c5a29a7344f3ca006d8e4160bec0ec15;hb=5640ec0623c6d1205e62f9fe15292f32bfdab7d9;hp=420e2cbf7a0891ffa9ead3a5c95e2d247e81aa3a;hpb=692669611f7244598bd34df92e8a3e5cbaf9bd2e;p=jalview.git

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index 420e2cb..b2689be 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -49,19 +49,20 @@ public class AssociatePdbFileWithSeq
           StructureSelectionManagerProvider ssmp)
   {
     return associatePdbWithSeq(choice, file, sequence, prompt, ssmp,
-            TFType.DEFAULT, null);
+            TFType.DEFAULT, null, false);
   }
 
   public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
           SequenceI sequence, boolean prompt,
           StructureSelectionManagerProvider ssmp, TFType tft,
-          String paeFilename)
+          String paeFilename, boolean doXferSettings)
   {
     PDBEntry entry = new PDBEntry();
     StructureFile pdbfile = StructureSelectionManager
             .getStructureSelectionManager(ssmp)
             .setMapping(false, new SequenceI[]
-            { sequence }, null, choice, file, tft, paeFilename);
+            { sequence }, null, choice, file, tft, paeFilename,
+                    doXferSettings);
     if (pdbfile == null)
     {
       // stacktrace already thrown so just return
@@ -96,9 +97,9 @@ public class AssociatePdbFileWithSeq
     {
       entry.setFile(choice);
       sequence.getDatasetSequence().addPDBId(entry);
+      entry.setStructureFile(pdbfile);
       StructureSelectionManager.getStructureSelectionManager(ssmp)
               .registerPDBEntry(entry);
-      entry.setStructureFile(pdbfile);
     }
     if (tft != null)
       entry.setProperty("TFType", tft.name());