Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 4469b43..49542db 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -20,6 +20,8 @@
  */
 package jalview.gui;
 
+import java.util.Locale;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.event.ActionEvent;
@@ -64,11 +66,13 @@ import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.MappedFeatures;
 import jalview.datamodel.PDBEntry;
+import jalview.datamodel.ResidueCount;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.io.CountReader;
 import jalview.io.FileFormatI;
 import jalview.io.FileFormats;
 import jalview.io.FormatAdapter;
@@ -87,6 +91,9 @@ import jalview.util.StringUtils;
 import jalview.util.UrlLink;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
+import java.io.IOException;
+import java.net.MalformedURLException;
+
 /**
  * The popup menu that is displayed on right-click on a sequence id, or in the
  * sequence alignment.
@@ -545,6 +552,36 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         }
       }
 
+      if (seq.hasHMMProfile())
+      {
+        menuItem = new JMenuItem(MessageManager
+                .getString("action.add_background_frequencies"));
+        menuItem.addActionListener(new ActionListener()
+        {
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            try
+            {
+              ResidueCount counts = CountReader.getBackgroundFrequencies(ap,
+                      seq);
+              if (counts != null)
+              {
+                seq.getHMM().setBackgroundFrequencies(counts);
+                ap.alignFrame.buildColourMenu();
+              }
+            } catch (MalformedURLException e1)
+            {
+              e1.printStackTrace();
+            } catch (IOException e1)
+            {
+              e1.printStackTrace();
+            }
+          }
+        });
+        add(menuItem);
+      }
+
       menuItem = new JMenuItem(
               MessageManager.getString("action.hide_sequences"));
       menuItem.addActionListener(new ActionListener()
@@ -669,7 +706,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         buildGroupURLMenu(sg, groupLinks);
       }
       // Add a 'show all structures' for the current selection
-      Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
+      Hashtable<String, PDBEntry> pdbe = new Hashtable<>();
+      Hashtable<String, PDBEntry> reppdb = new Hashtable<>();
 
       SequenceI sqass = null;
       for (SequenceI sq : alignPanel.av.getSequenceSelection())
@@ -1125,7 +1163,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         for (int d = 0; d < nd; d++)
         {
           DBRefEntry e = dbr.get(d);
-          String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
+          String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(Locale.ROOT);
           Object[] sarray = commonDbrefs.get(src);
           if (sarray == null)
           {
@@ -1171,7 +1209,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       boolean usingNames = false;
       // Now see which parts of the group apply for this URL
       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
-      Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
+      Object[] idset = commonDbrefs.get(ltarget.toUpperCase(Locale.ROOT));
       String[] seqstr, ids; // input to makeUrl
       if (idset != null)
       {