JAL-3489 ensure all chains mapped when loading local multimeric PDB file

[jalview.git] / src / jalview / gui / AssociatePdbFileWithSeq.java

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index fe0aedf..c68914c 100644 (file)
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -28,8 +28,6 @@ import jalview.io.StructureFile;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 
-import javax.swing.JOptionPane;
-
 /**
  * GUI related routines for associating PDB files with sequences
  * 
@@ -40,19 +38,24 @@ public class AssociatePdbFileWithSeq
 {
 
   /**
-   * assocate the given PDB file with
+   * Associates the given file as a PDB structure for the given sequence.
    * 
    * @param choice
+   * @param file
    * @param sequence
+   * @param prompt
+   * @param ssmp
+   * @param forViewer
+   * @return
    */
   public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
           SequenceI sequence, boolean prompt,
-          StructureSelectionManagerProvider ssmp)
+          StructureSelectionManagerProvider ssmp, boolean forViewer)
   {
     PDBEntry entry = new PDBEntry();
     StructureFile pdbfile = null;
     pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
-            .setMapping(false, new SequenceI[]
+            .setMapping(forViewer, new SequenceI[]
             { sequence }, null, choice, file);
     if (pdbfile == null)
     {