JAL-2629 add ability to add background frequencies to a HMM

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 702773b..8c87aa0 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -34,10 +34,12 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.HiddenColumns;
 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;
@@ -56,6 +58,8 @@ import jalview.util.UrlLink;
 import java.awt.Color;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.io.IOException;
+import java.net.MalformedURLException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.BitSet;
@@ -161,6 +165,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   JMenuItem sequenceFeature = new JMenuItem();
 
+
   JMenuItem textColour = new JMenuItem();
 
   JMenu jMenu1 = new JMenu();
@@ -417,8 +422,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
      * currently selected sequence (if there is one):
      */
     final List<SequenceI> selectedSequence = (seq == null
-            ? Collections.<SequenceI> emptyList()
-            : Arrays.asList(seq));
+            ? Collections.<SequenceI> emptyList() : Arrays.asList(seq));
+
     buildAnnotationTypesMenus(seqShowAnnotationsMenu,
             seqHideAnnotationsMenu, selectedSequence);
     configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
@@ -531,6 +536,36 @@ 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()
@@ -655,7 +690,8 @@ 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())