Merge branch 'develop' into alpha/JAL-3362_Jalview_212_alpha

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 568f7f1..0fd5feb 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -60,10 +60,12 @@ 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.io.CountReader;
 import jalview.io.FileFormatI;
 import jalview.io.FileFormats;
 import jalview.io.FormatAdapter;
@@ -81,6 +83,9 @@ 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.
@@ -539,6 +544,36 @@ 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()
@@ -663,7 +698,8 @@ 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())