X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAssociatePdbFileWithSeq.java;h=c9951f54ed60cc74ca9921e5e52c04a7c9242f4c;hb=051cab343aed415a342a787e10ebd075f05243f6;hp=1247ace9732076bfc5e80b5f33ebc811ce4c79fd;hpb=6d7ab37f37b09174ec61fee301aed6057ef86605;p=jalview.git

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index 1247ace..c9951f5 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -23,11 +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
  * 
@@ -43,15 +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, true);
+  }
+
+  public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
+          SequenceI sequence, boolean prompt,
+          StructureSelectionManagerProvider ssmp, TFType tft,
+          String paeFilename, boolean doXferSettings)
+  {
     PDBEntry entry = new PDBEntry();
-    MCview.PDBfile 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
@@ -63,11 +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)
       {
@@ -88,7 +99,12 @@ public class AssociatePdbFileWithSeq
       sequence.getDatasetSequence().addPDBId(entry);
       StructureSelectionManager.getStructureSelectionManager(ssmp)
               .registerPDBEntry(entry);
+      entry.setStructureFile(pdbfile);
     }
+    if (tft != null)
+      entry.setProperty("TFType", tft.name());
+    if (paeFilename != null)
+      entry.setProperty("PAEFile", paeFilename);
     return entry;
   }
 }