X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAppletPDBCanvas.java;h=9cfb4ea21e77906f453c895cfc4b97f9f8cb982e;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=dc69f43cd88925fb25e9f346c9d1a4dd231545cc;hpb=43b415c68805f3dec44a6ddc666d52220483c120;p=jalview.git

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index dc69f43..9cfb4ea 100644
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,18 @@
  */
 package MCview;
 
+import jalview.analysis.AlignSeq;
+import jalview.appletgui.AlignmentPanel;
+import jalview.appletgui.FeatureRenderer;
+import jalview.appletgui.SequenceRenderer;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureListener;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+
 import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.Event;
@@ -37,18 +49,6 @@ import java.io.PrintStream;
 import java.util.List;
 import java.util.Vector;
 
-import jalview.analysis.AlignSeq;
-import jalview.appletgui.AlignmentPanel;
-import jalview.appletgui.FeatureRenderer;
-import jalview.appletgui.SequenceRenderer;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.structure.AtomSpec;
-import jalview.structure.StructureListener;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.MessageManager;
-
 public class AppletPDBCanvas extends Panel implements MouseListener,
         MouseMotionListener, StructureListener
 {
@@ -189,11 +189,9 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     {
 
       mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
-              + pdb.chains.elementAt(i).sequence
-                      .getSequenceAsString());
+              + pdb.chains.elementAt(i).sequence.getSequenceAsString());
       mappingDetails.append("\nNo of residues = "
-              + pdb.chains.elementAt(i).residues.size()
-              + "\n\n");
+              + pdb.chains.elementAt(i).residues.size() + "\n\n");
 
       // Now lets compare the sequences to get
       // the start and end points.
@@ -201,8 +199,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
       // TODO: DNa/Pep switch
       AlignSeq as = new AlignSeq(sequence,
               pdb.chains.elementAt(i).sequence,
-              pdb.chains.elementAt(i).isNa ? AlignSeq.DNA
-                      : AlignSeq.PEP);
+              pdb.chains.elementAt(i).isNa ? AlignSeq.DNA : AlignSeq.PEP);
       as.calcScoreMatrix();
       as.traceAlignment();
       PrintStream ps = new PrintStream(System.out)
@@ -1113,8 +1110,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
   // /StructureListener
   public String[] getPdbFile()
   {
-    return new String[]
-    { pdbentry.getFile() };
+    return new String[] { pdbentry.getFile() };
   }
 
   String lastMessage;