JAL-1620 version bump and release notes

[jalview.git] / src / jalview / appletgui / APopupMenu.java

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index d98e2aa..57e2674 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -20,19 +20,43 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.MessageManager;
-import jalview.util.UrlLink;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.commands.ChangeCaseCommand;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.SequenceAnnotationReport;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.util.MessageManager;
+import jalview.util.UrlLink;
+
+import java.awt.CheckboxMenuItem;
+import java.awt.Frame;
+import java.awt.Menu;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.Vector;
 
 public class APopupMenu extends java.awt.PopupMenu implements
         ActionListener, ItemListener
@@ -549,7 +573,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
       if (sg != null)
       {
         if (seq == null)
+        {
           seq = (Sequence) sg.getSequenceAt(0);
+        }
 
         EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
                 sg.getStartRes(), sg.getEndRes() + 1), null,
@@ -559,8 +585,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
         if (dialog.accept)
         {
-          EditCommand editCommand = new EditCommand("Edit Sequences",
-                  EditCommand.REPLACE, dialog.getName().replace(' ',
+          EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),
+                  Action.REPLACE, dialog.getName().replace(' ',
                           ap.av.getGapCharacter()),
                   sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
                   sg.getStartRes(), sg.getEndRes() + 1,
@@ -672,9 +698,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
     // TODO consider using getSequenceSelection instead here
 
     cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
-            e.getActionCommand(),
-            new Alignment(ap.av.getSelectionAsNewSequence()),
-            ap.av.showJVSuffix));
+            e.getActionCommand(), 
+            ap.av.showJVSuffix, ap.av, true));
 
   }
 
@@ -743,11 +768,15 @@ public class APopupMenu extends java.awt.PopupMenu implements
       PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement();
 
       if (ap.av.applet.jmolAvailable)
+      {
         new jalview.appletgui.AppletJmol(entry, new Sequence[]
         { seq }, null, ap, AppletFormatAdapter.URL);
+      }
       else
+      {
         new MCview.AppletPDBViewer(entry, new Sequence[]
         { seq }, null, ap, AppletFormatAdapter.URL);
+      }
 
     }
     else
@@ -837,34 +866,34 @@ public class APopupMenu extends java.awt.PopupMenu implements
     colourMenu.add(abovePIDColour);
     colourMenu.add(conservationMenuItem);
 
-    noColourmenuItem.setLabel("None");
+    noColourmenuItem.setLabel(MessageManager.getString("label.none"));
     noColourmenuItem.addActionListener(this);
 
-    clustalColour.setLabel("Clustalx colours");
+    clustalColour.setLabel(MessageManager.getString("label.clustalx_colours"));
     clustalColour.addActionListener(this);
-    zappoColour.setLabel("Zappo");
+    zappoColour.setLabel(MessageManager.getString("label.zappo"));
     zappoColour.addActionListener(this);
-    taylorColour.setLabel("Taylor");
+    taylorColour.setLabel(MessageManager.getString("label.taylor"));
     taylorColour.addActionListener(this);
-    hydrophobicityColour.setLabel("Hydrophobicity");
+    hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
     hydrophobicityColour.addActionListener(this);
-    helixColour.setLabel("Helix propensity");
+    helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
     helixColour.addActionListener(this);
-    strandColour.setLabel("Strand propensity");
+    strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
     strandColour.addActionListener(this);
-    turnColour.setLabel("Turn propensity");
+    turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
     turnColour.addActionListener(this);
-    buriedColour.setLabel("Buried Index");
+    buriedColour.setLabel(MessageManager.getString("label.buried_index"));
     buriedColour.addActionListener(this);
-    abovePIDColour.setLabel("Above % Identity");
+    abovePIDColour.setLabel(MessageManager.getString("label.above_identity_percentage"));
 
-    userDefinedColour.setLabel("User Defined");
+    userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
     userDefinedColour.addActionListener(this);
-    PIDColour.setLabel("Percentage Identity");
+    PIDColour.setLabel(MessageManager.getString("action.percentage_identity"));
     PIDColour.addActionListener(this);
     BLOSUM62Colour.setLabel("BLOSUM62");
     BLOSUM62Colour.addActionListener(this);
-    conservationMenuItem.setLabel("Conservation");
+    conservationMenuItem.setLabel(MessageManager.getString("label.conservation"));
 
     editMenu.add(copy);
     copy.addActionListener(this);