merge from 2_4_Release branch

[jalview.git] / src / MCview / AppletPDBViewer.java

diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java
index fc8478d..8299abc 100755 (executable)
--- a/src/MCview/AppletPDBViewer.java
+++ b/src/MCview/AppletPDBViewer.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program 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 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program 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 this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -25,23 +25,18 @@ import jalview.appletgui.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
 
-
-public class AppletPDBViewer
-    extends EmbmenuFrame implements ActionListener, ItemListener
+public class AppletPDBViewer extends EmbmenuFrame implements
+        ActionListener, ItemListener
 {
   AppletPDBCanvas pdbcanvas;
 
-  public AppletPDBViewer(PDBEntry pdbentry,
-                         SequenceI[] seq,
-                         String [] chains,
-                         AlignmentPanel ap,
-                         String protocol)
+  public AppletPDBViewer(PDBEntry pdbentry, SequenceI[] seq,
+          String[] chains, AlignmentPanel ap, String protocol)
   {
     try
     {
       jbInit();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -51,26 +46,23 @@ public class AppletPDBViewer
     embedMenuIfNeeded(pdbcanvas);
     add(pdbcanvas, BorderLayout.CENTER);
 
-    StringBuffer title = new StringBuffer(seq[0].getName()
-                                          + ":"
-                                          + pdbcanvas.pdbentry.getFile());
+    StringBuffer title = new StringBuffer(seq[0].getName() + ":"
+            + pdbcanvas.pdbentry.getFile());
 
     jalview.bin.JalviewLite.addFrame(this, title.toString(), 400, 400);
 
   }
 
-
-
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == mapping)
     {
-      jalview.appletgui.CutAndPasteTransfer cap
-          = new jalview.appletgui.CutAndPasteTransfer(false, null);
+      jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
+              false, null);
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500,
-                                       600);
+      jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping",
+              500, 600);
       cap.setText(pdbcanvas.mappingDetails.toString());
 
     }
@@ -138,7 +130,7 @@ public class AppletPDBViewer
     }
     else if (evt.getSource() == wire)
     {
-          pdbcanvas.wire = !pdbcanvas.wire;
+      pdbcanvas.wire = !pdbcanvas.wire;
     }
     else if (evt.getSource() == depth)
     {
@@ -152,8 +144,7 @@ public class AppletPDBViewer
     pdbcanvas.repaint();
   }
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     setMenuBar(jMenuBar1);
     fileMenu.setLabel("File");
@@ -196,7 +187,8 @@ public class AppletPDBViewer
     jMenuBar1.add(fileMenu);
     jMenuBar1.add(coloursMenu);
     jMenuBar1.add(viewMenu);
-    fileMenu.add(mapping); ;
+    fileMenu.add(mapping);
+    ;
 
     coloursMenu.add(seqButton);
     coloursMenu.add(chain);
@@ -217,32 +209,48 @@ public class AppletPDBViewer
   }
 
   MenuBar jMenuBar1 = new MenuBar();
+
   Menu fileMenu = new Menu();
+
   Menu coloursMenu = new Menu();
+
   MenuItem mapping = new MenuItem();
+
   CheckboxGroup bg = new CheckboxGroup();
+
   CheckboxMenuItem wire = new CheckboxMenuItem();
+
   CheckboxMenuItem depth = new CheckboxMenuItem();
+
   CheckboxMenuItem zbuffer = new CheckboxMenuItem();
 
   MenuItem charge = new MenuItem();
+
   MenuItem hydro = new MenuItem();
+
   MenuItem chain = new MenuItem();
+
   MenuItem seqButton = new MenuItem();
 
   CheckboxMenuItem allchains = new CheckboxMenuItem();
+
   Menu viewMenu = new Menu();
+
   MenuItem turn = new MenuItem();
+
   MenuItem strand = new MenuItem();
+
   MenuItem helix = new MenuItem();
+
   MenuItem taylor = new MenuItem();
+
   MenuItem zappo = new MenuItem();
-  MenuItem buried = new MenuItem();
-  MenuItem user = new MenuItem();
 
+  MenuItem buried = new MenuItem();
 
-//End StructureListener
-////////////////////////////
+  MenuItem user = new MenuItem();
 
+  // End StructureListener
+  // //////////////////////////
 
 }