import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.ext.rbvi.chimera.ChimeraCommands;
import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.AppletFormatAdapter;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.InputStream;
import java.io.PrintWriter;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.List;
import java.util.Random;
import java.util.Vector;
// TODO Auto-generated method stub
}
});
+
JMenuItem writeFeatures = new JMenuItem(
MessageManager.getString("label.create_chimera_attributes"));
writeFeatures.setToolTipText(MessageManager
}
});
viewerActionMenu.add(writeFeatures);
+
+ final JMenu fetchAttributes = new JMenu("Fetch Chimera attributes");
+ fetchAttributes
+ .setToolTipText("Copy Chimera attribute to Jalview feature");
+ fetchAttributes.addMouseListener(new MouseAdapter()
+ {
+
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ buildAttributesMenu(fetchAttributes);
+ }
+ });
+ viewerActionMenu.add(fetchAttributes);
+
+ }
+
+ /**
+ * Query Chimera for its residue attribute names and add them as items off the
+ * attributes menu
+ *
+ * @param attributesMenu
+ */
+ protected void buildAttributesMenu(JMenu attributesMenu)
+ {
+ List<String> atts = jmb.sendChimeraCommand("list resattr", true);
+ if (atts == null)
+ {
+ return;
+ }
+ attributesMenu.removeAll();
+ Collections.sort(atts);
+ for (String att : atts)
+ {
+ final String attName = att.split(" ")[1];
+
+ /*
+ * ignore 'jv_*' attributes, as these are Jalview features that have
+ * been transferred to residue attributes in Chimera!
+ */
+ if (!attName.startsWith(ChimeraCommands.NAMESPACE_PREFIX))
+ {
+ JMenuItem menuItem = new JMenuItem(attName);
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ getChimeraAttributes(attName);
+ }
+ });
+ attributesMenu.add(menuItem);
+ }
+ }
+ }
+
+ /**
+ * Read residues in Chimera with the given attribute name, and set as features
+ * on the corresponding sequence positions (if any)
+ *
+ * @param attName
+ */
+ protected void getChimeraAttributes(String attName)
+ {
+ jmb.copyStructureAttributesToFeatures(attName, getAlignmentPanel());
}
/**
*/
protected void sendFeaturesToChimera()
{
- jmb.sendFeaturesToChimera(getAlignmentPanel());
+ jmb.sendFeaturesToViewer(getAlignmentPanel());
}
/**