JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 587e08a..8146237 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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;
@@ -32,20 +52,28 @@ public abstract class StructureViewerBase extends GStructureViewer
    * list of sequenceSet ids associated with the view
    */
   protected List<String> _aps = new ArrayList<String>();
+
   /**
    * list of alignment panels to use for superposition
    */
   protected Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
+
   /**
    * list of alignment panels that are used for colouring structures by aligned
    * sequences
    */
   protected Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
+
   private String viewId = null;
+
   private AlignmentPanel ap;
+
   protected boolean alignAddedStructures = false;
+
   protected boolean _started = false;
+
   protected boolean addingStructures = false;
+
   protected Thread worker = null;
 
   /**
@@ -60,7 +88,7 @@ public abstract class StructureViewerBase extends GStructureViewer
 
   public boolean isUsedforaligment(AlignmentPanel ap2)
   {
-  
+
     return (_alignwith != null) && _alignwith.contains(ap2);
   }
 
@@ -138,7 +166,7 @@ public abstract class StructureViewerBase extends GStructureViewer
         list = t;
       }
     }
-  
+
     return list;
   }
 
@@ -209,7 +237,8 @@ public abstract class StructureViewerBase extends GStructureViewer
     }
   }
 
-  public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, boolean enableColourBySeq)
+  public void useAlignmentPanelForColourbyseq(AlignmentPanel nap,
+          boolean enableColourBySeq)
   {
     useAlignmentPanelForColourbyseq(nap);
     getBinding().setColourBySequence(enableColourBySeq);
@@ -250,7 +279,8 @@ public abstract class StructureViewerBase extends GStructureViewer
    *          alignment
    * @param alignFrame
    */
-  protected void addStructure(final PDBEntry pdbentry, final SequenceI[] seqs, final String[] chains,
+  protected void addStructure(final PDBEntry pdbentry,
+          final SequenceI[] seqs, final String[] chains,
           final boolean align, final IProgressIndicator alignFrame)
   {
     if (pdbentry.getFile() == null)
@@ -268,7 +298,7 @@ public abstract class StructureViewerBase extends GStructureViewer
               try
               {
                 Thread.sleep(100 + ((int) Math.random() * 100));
-  
+
               } catch (Exception e)
               {
               }
@@ -299,12 +329,13 @@ public abstract class StructureViewerBase extends GStructureViewer
    * @param view
    * @return YES, NO or CANCEL JOptionPane code
    */
-  protected int chooseAlignStructureToViewer(String pdbId, StructureViewerBase view)
+  protected int chooseAlignStructureToViewer(String pdbId,
+          StructureViewerBase view)
   {
     int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
             MessageManager.formatMessage("label.add_pdbentry_to_view",
-                    new Object[]
-                    { pdbId, view.getTitle() }), MessageManager
+                    new Object[] { pdbId, view.getTitle() }),
+            MessageManager
                     .getString("label.align_to_existing_structure_view"),
             JOptionPane.YES_NO_CANCEL_OPTION);
     return option;
@@ -356,7 +387,7 @@ public abstract class StructureViewerBase extends GStructureViewer
         // NO_OPTION - offer the next viewer if any
       }
     }
-  
+
     /*
      * nothing offered and selected
      */
@@ -379,9 +410,9 @@ public abstract class StructureViewerBase extends GStructureViewer
     /*
      * create the mappings
      */
-    apanel.getStructureSelectionManager().setMapping(seq, chains, pdbFilename,
-            AppletFormatAdapter.FILE);
-  
+    apanel.getStructureSelectionManager().setMapping(seq, chains,
+            pdbFilename, AppletFormatAdapter.FILE);
+
     /*
      * alert the FeatureRenderer to show new (PDB RESNUM) features
      */
@@ -390,7 +421,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       apanel.getSeqPanel().seqCanvas.fr.featuresAdded();
       apanel.paintAlignment(true);
     }
-  
+
     /*
      * add the sequences to any other viewers (of the same type) for this pdb
      * file
@@ -411,7 +442,8 @@ public abstract class StructureViewerBase extends GStructureViewer
            */
           viewer.useAlignmentPanelForColourbyseq(apanel);
           viewer.buildActionMenu();
-          apanel.getStructureSelectionManager().sequenceColoursChanged(apanel);
+          apanel.getStructureSelectionManager().sequenceColoursChanged(
+                  apanel);
           break;
         }
       }
@@ -434,18 +466,20 @@ public abstract class StructureViewerBase extends GStructureViewer
     boolean finished = false;
     String alreadyMapped = apanel.getStructureSelectionManager()
             .alreadyMappedToFile(pdbId);
-  
+
     if (alreadyMapped != null)
     {
       /*
        * the PDB file is already loaded
        */
       int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-      MessageManager.formatMessage(
-              "label.pdb_entry_is_already_displayed", new Object[]
-              { pdbId }), MessageManager.formatMessage(
-              "label.map_sequences_to_visible_window", new Object[]
-              { pdbId }), JOptionPane.YES_NO_CANCEL_OPTION);
+              MessageManager.formatMessage(
+                      "label.pdb_entry_is_already_displayed",
+                      new Object[] { pdbId }), MessageManager
+                      .formatMessage(
+                              "label.map_sequences_to_visible_window",
+                              new Object[] { pdbId }),
+              JOptionPane.YES_NO_CANCEL_OPTION);
       if (option == JOptionPane.CANCEL_OPTION)
       {
         finished = true;