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;
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;
}
}
+ 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()