Merge branch 'develop' into feature/JAL-244_Automatically_adjust_left_margin_to_avoid...

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

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index d53ddc8..c9951f5 100644 (file)
--- 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
  * 
@@ -43,31 +44,41 @@ 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)
+    StructureFile pdbfile = StructureSelectionManager
+            .getStructureSelectionManager(ssmp)
             .setMapping(false, new SequenceI[]
-            { sequence }, null, choice, protocol);
+            { sequence }, null, choice, file, tft, paeFilename,
+                    doXferSettings);
     if (pdbfile == null)
     {
       // stacktrace already thrown so just return
       return null;
     }
-    if (pdbfile.id == null)
+    if (pdbfile.getId() == null)
     {
       String reply = null;
 
       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)
       {
@@ -78,8 +89,9 @@ public class AssociatePdbFileWithSeq
     }
     else
     {
-      entry.setId(pdbfile.id);
+      entry.setId(pdbfile.getId());
     }
+    entry.setType(PDBEntry.Type.FILE);
 
     if (pdbfile != null)
     {
@@ -87,7 +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;
   }
 }