X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAppletPDBViewer.java;h=adf833f7bdef5a4066f620753bf7f51be4f1261b;hb=refs%2Fheads%2Fbug%2FJAL-3806_mappingCoversCDS_reprise;hp=8a1c430d5cdf72bf44a72c39c4f0b7ba158af40a;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java
index 8a1c430..adf833f 100644
--- a/src/MCview/AppletPDBViewer.java
+++ b/src/MCview/AppletPDBViewer.java
@@ -1,38 +1,58 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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/>.
+ * 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 MCview;
 
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.appletgui.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.appletgui.AlignmentPanel;
+import jalview.appletgui.EmbmenuFrame;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
 import jalview.util.MessageManager;
 
-public class AppletPDBViewer extends EmbmenuFrame implements
-        ActionListener, ItemListener
+import java.awt.BorderLayout;
+import java.awt.CheckboxGroup;
+import java.awt.CheckboxMenuItem;
+import java.awt.Frame;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
+public class AppletPDBViewer extends EmbmenuFrame
+        implements ActionListener, ItemListener
 {
   AppletPDBCanvas pdbcanvas;
 
   public AppletPDBViewer(PDBEntry pdbentry, SequenceI[] seq,
-          String[] chains, AlignmentPanel ap, String protocol)
+          String[] chains, AlignmentPanel ap, DataSourceType protocol)
   {
     try
     {
@@ -47,13 +67,14 @@ public class AppletPDBViewer extends EmbmenuFrame implements
     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);
 
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == mapping)
@@ -62,8 +83,9 @@ public class AppletPDBViewer extends EmbmenuFrame implements
               false, null);
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.pdb_sequence_mapping"),
-              500, 600);
+      jalview.bin.JalviewLite.addFrame(frame,
+              MessageManager.getString("label.pdb_sequence_mapping"), 500,
+              600);
       cap.setText(pdbcanvas.mappingDetails.toString());
 
     }
@@ -123,6 +145,7 @@ public class AppletPDBViewer extends EmbmenuFrame implements
 
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == allchains)
@@ -162,26 +185,32 @@ public class AppletPDBViewer extends EmbmenuFrame implements
     zbuffer.addItemListener(this);
     charge.setLabel(MessageManager.getString("label.charge_cysteine"));
     charge.addActionListener(this);
-    hydro.setLabel(MessageManager.getString("label.hydrophobicity"));
+    hydro.setLabel(
+            MessageManager.getString("label.colourScheme_hydrophobic"));
     hydro.addActionListener(this);
     chain.setLabel(MessageManager.getString("action.by_chain"));
     chain.addActionListener(this);
     seqButton.setLabel(MessageManager.getString("action.by_sequence"));
     seqButton.addActionListener(this);
-    allchains.setLabel(MessageManager.getString("label.all_chains_visible"));
+    allchains
+            .setLabel(MessageManager.getString("label.all_chains_visible"));
     allchains.addItemListener(this);
     viewMenu.setLabel(MessageManager.getString("action.view"));
-    zappo.setLabel(MessageManager.getString("label.zappo"));
+    zappo.setLabel(MessageManager.getString("label.colourScheme_zappo"));
     zappo.addActionListener(this);
-    taylor.setLabel(MessageManager.getString("label.taylor"));
+    taylor.setLabel(MessageManager.getString("label.colourScheme_taylor"));
     taylor.addActionListener(this);
-    helix.setLabel(MessageManager.getString("label.helix_propensity"));
+    helix.setLabel(MessageManager
+            .getString("label.colourScheme_helix_propensity"));
     helix.addActionListener(this);
-    strand.setLabel(MessageManager.getString("label.strand_propensity"));
+    strand.setLabel(MessageManager
+            .getString("label.colourScheme_strand_propensity"));
     strand.addActionListener(this);
-    turn.setLabel(MessageManager.getString("label.turn_propensity"));
+    turn.setLabel(
+            MessageManager.getString("label.colourScheme_turn_propensity"));
     turn.addActionListener(this);
-    buried.setLabel(MessageManager.getString("label.buried_index"));
+    buried.setLabel(
+            MessageManager.getString("label.colourScheme_buried_index"));
     buried.addActionListener(this);
     user.setLabel(MessageManager.getString("action.user_defined"));
     user.addActionListener(this);