X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAssociatePdbFileWithSeq.java;h=b2689be6c5a29a7344f3ca006d8e4160bec0ec15;hb=5640ec0623c6d1205e62f9fe15292f32bfdab7d9;hp=7073d03fff1a16789382f6898480f7fa39a2b01e;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index 7073d03..b2689be 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 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.
  * 
@@ -23,12 +23,12 @@ 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.StructureImportSettings.TFType;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 
-import javax.swing.JOptionPane;
-
 /**
  * GUI related routines for associating PDB files with sequences
  * 
@@ -44,15 +44,25 @@ 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)
   {
+    return associatePdbWithSeq(choice, file, sequence, prompt, ssmp,
+            TFType.DEFAULT, null, false);
+  }
+
+  public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
+          SequenceI sequence, boolean prompt,
+          StructureSelectionManagerProvider ssmp, TFType tft,
+          String paeFilename, boolean doXferSettings)
+  {
     PDBEntry entry = new PDBEntry();
-    StructureFile pdbfile = null;
-    pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
-            .setMapping(false, new SequenceI[] { sequence }, null, choice,
-                    protocol);
+    StructureFile pdbfile = StructureSelectionManager
+            .getStructureSelectionManager(ssmp)
+            .setMapping(false, new SequenceI[]
+            { sequence }, null, choice, file, tft, paeFilename,
+                    doXferSettings);
     if (pdbfile == null)
     {
       // stacktrace already thrown so just return
@@ -64,11 +74,11 @@ public class AssociatePdbFileWithSeq
 
       if (prompt)
       {
-        reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
+        reply = JvOptionPane.showInternalInputDialog(Desktop.desktop,
                 MessageManager
                         .getString("label.couldnt_find_pdb_id_in_file"),
                 MessageManager.getString("label.no_pdb_id_in_file"),
-                JOptionPane.QUESTION_MESSAGE);
+                JvOptionPane.QUESTION_MESSAGE);
       }
       if (reply == null)
       {
@@ -87,9 +97,14 @@ public class AssociatePdbFileWithSeq
     {
       entry.setFile(choice);
       sequence.getDatasetSequence().addPDBId(entry);
+      entry.setStructureFile(pdbfile);
       StructureSelectionManager.getStructureSelectionManager(ssmp)
               .registerPDBEntry(entry);
     }
+    if (tft != null)
+      entry.setProperty("TFType", tft.name());
+    if (paeFilename != null)
+      entry.setProperty("PAEFile", paeFilename);
     return entry;
   }
 }