JAL-2344 use .equals() to compare FileFormatI objects

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

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 9ba50ca..e295dfb 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -1,10 +1,30 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.gui;
 
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
 import jalview.jbgui.GStructureViewer;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
@@ -132,6 +152,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     this.ap = alp;
   }
 
+  @Override
   public AlignmentPanel[] getAllAlignmentPanels()
   {
     AlignmentPanel[] t, list = new AlignmentPanel[0];
@@ -271,6 +292,7 @@ public abstract class StructureViewerBase extends GStructureViewer
         // queue.
         new Thread(new Runnable()
         {
+          @Override
           public void run()
           {
             while (worker != null && worker.isAlive() && _started)
@@ -391,7 +413,7 @@ public abstract class StructureViewerBase extends GStructureViewer
      * create the mappings
      */
     apanel.getStructureSelectionManager().setMapping(seq, chains,
-            pdbFilename, AppletFormatAdapter.FILE);
+            pdbFilename, DataSourceType.FILE);
 
     /*
      * alert the FeatureRenderer to show new (PDB RESNUM) features