X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAssociatePdbFileWithSeq.java;fp=src%2Fjalview%2Fgui%2FAssociatePdbFileWithSeq.java;h=fd89c503eac593533f0f48b2b0e970c90cd65ce8;hb=7e3a6674abdd31bf48e7e249a74eff50fd2ce589;hp=fe0aedfc79c99440d6f6d8f5e42c3093d3b859f7;hpb=156ab6ab1046c02dc327c2ac986afa336f0bbf3b;p=jalview.git

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index fe0aedf..fd89c50 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -25,11 +25,10 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
+import jalview.structure.StructureImportSettings.TFType;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 
-import javax.swing.JOptionPane;
-
 /**
  * GUI related routines for associating PDB files with sequences
  * 
@@ -49,11 +48,20 @@ public class AssociatePdbFileWithSeq
           SequenceI sequence, boolean prompt,
           StructureSelectionManagerProvider ssmp)
   {
+    return associatePdbWithSeq(choice, file, sequence, prompt, ssmp,
+            TFType.DEFAULT, null);
+  }
+
+  public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
+          SequenceI sequence, boolean prompt,
+          StructureSelectionManagerProvider ssmp, TFType tft,
+          String paeFilename)
+  {
     PDBEntry entry = new PDBEntry();
-    StructureFile pdbfile = null;
-    pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
+    StructureFile pdbfile = StructureSelectionManager
+            .getStructureSelectionManager(ssmp)
             .setMapping(false, new SequenceI[]
-            { sequence }, null, choice, file);
+            { sequence }, null, choice, file, tft, paeFilename);
     if (pdbfile == null)
     {
       // stacktrace already thrown so just return
@@ -90,6 +98,7 @@ public class AssociatePdbFileWithSeq
       sequence.getDatasetSequence().addPDBId(entry);
       StructureSelectionManager.getStructureSelectionManager(ssmp)
               .registerPDBEntry(entry);
+      entry.setStructureFile(pdbfile);
     }
     return entry;
   }