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;
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.
}
}
+ 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()
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())