JAL-1503 update version in GPL header

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index f7e95b7..d992233 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -118,6 +118,7 @@ import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JButton;
+import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JEditorPane;
 import javax.swing.JInternalFrame;
 import javax.swing.JLabel;
@@ -3234,10 +3235,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
                 "Background");
-
         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
-        viewport.setGlobalColourScheme(cs);
       }
       else
       {
@@ -3944,23 +3942,30 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     calculateTree.removeAll();
     // build the calculate menu
+    
     for (final String type:new String[] {"NJ", "AV"})
     {
+      String treecalcnm = MessageManager.getString("label.tree_calc_"+type.toLowerCase());
       for (final Object pwtype: ResidueProperties.scoreMatrices.keySet())
       {
         JMenuItem tm = new JMenuItem();
         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
-        final String title="Calculate "+type+" using "+sm.getName();
-        tm.setText(title);// MessageManager.getString("label.neighbour_blosum62"));
-        tm
-                .addActionListener(new java.awt.event.ActionListener()
-                {
-                  public void actionPerformed(ActionEvent e)
-                  {
-                    NewTreePanel(type, (String) pwtype, title);
-                  }
-                });
-        calculateTree.add(tm);
+        if (sm.isProtein()==!viewport.getAlignment().isNucleotide())
+        {
+          String smn = MessageManager.getStringOrReturn(
+                  "label.score_model_", sm.getName());
+          final String title = MessageManager.formatMessage(
+                  "label.treecalc_title", treecalcnm, smn);
+          tm.setText(title);//
+          tm.addActionListener(new java.awt.event.ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              NewTreePanel(type, (String) pwtype, title);
+            }
+          });
+          calculateTree.add(tm);
+        }
 
       }
     }
@@ -4416,12 +4421,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
               this);
     }
-
-    if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
-    {
-      jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
-              webService, this);
-    }
   }
 
   /*
@@ -5198,6 +5197,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     rfetch.setToolTipText(MessageManager.getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));\r
     webService.add(rfetch);
 
+    final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(MessageManager.getString("option.trim_retrieved_seqs"));
+    trimrs.setToolTipText(MessageManager.getString("label.trim_retrieved_sequences"));
+    trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
+    trimrs.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e) {
+      trimrs.setSelected(trimrs.isSelected());
+      Cache.setProperty("TRIM_FETCHED_DATASET_SEQS", Boolean.valueOf(trimrs.isSelected()).toString());
+    };
+    });
+    rfetch.add(trimrs);
     JMenuItem fetchr = new JMenuItem(MessageManager.getString("label.standard_databases"));\r
     fetchr.setToolTipText(MessageManager.getString("label.fetch_embl_uniprot"));\r
     fetchr.addActionListener(new ActionListener()