Distinguish text-only output formats and others (.jar/.jvp)

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

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index f13bb35..c380e2f 100644 (file)
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -23,6 +23,8 @@ package jalview.gui;
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 
@@ -43,21 +45,21 @@ public class AssociatePdbFileWithSeq
    * @param choice
    * @param sequence
    */
-  public PDBEntry associatePdbWithSeq(String choice, String protocol,
+  public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
           SequenceI sequence, boolean prompt,
           StructureSelectionManagerProvider ssmp)
   {
     PDBEntry entry = new PDBEntry();
-    MCview.PDBfile pdbfile = null;
+    StructureFile pdbfile = null;
     pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
-            .setMapping(false, new SequenceI[]
-            { sequence }, null, choice, protocol);
+            .setMapping(false, new SequenceI[] { sequence }, null, choice,
+                    file);
     if (pdbfile == null)
     {
       // stacktrace already thrown so just return
       return null;
     }
-    if (pdbfile.id == null)
+    if (pdbfile.getId() == null)
     {
       String reply = null;
 
@@ -78,8 +80,9 @@ public class AssociatePdbFileWithSeq
     }
     else
     {
-      entry.setId(pdbfile.id);
+      entry.setId(pdbfile.getId());
     }
+    entry.setType(PDBEntry.Type.FILE);
 
     if (pdbfile != null)
     {