*/
package jalview.gui;
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Hashtable;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPopupMenu;
+import javax.swing.JRadioButtonMenuItem;
+
import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.Conservation;
import jalview.util.MessageManager;
import jalview.util.UrlLink;
-import java.awt.Color;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Hashtable;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-import java.util.Vector;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JPopupMenu;
-import javax.swing.JRadioButtonMenuItem;
-
/**
* DOCUMENT ME!
*
JMenu jMenu1 = new JMenu();
- JMenu structureMenu = new JMenu();
+ JMenuItem structureMenu = new JMenuItem();
JMenu viewStructureMenu = new JMenu();
new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
new PDBEntry[reppdb.size()]);
final JMenuItem gpdbview, rpdbview;
- if (pdbe.size() == 1)
- {
- structureMenu.add(gpdbview = new JMenuItem(MessageManager
- .formatMessage("label.view_structure_for", new Object[]
- { sqass.getDisplayId(false) })));
- }
- else
- {
- structureMenu.add(gpdbview = new JMenuItem(MessageManager
- .formatMessage("label.view_all_structures", new Object[]
- { new Integer(pdbe.size()).toString() })));
- }
- gpdbview.setToolTipText(MessageManager
- .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
- gpdbview.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- new StructureViewer(ap.getStructureSelectionManager())
- .viewStructures(ap, pe, ap.av.collateForPDB(pe));
- }
- });
- if (reppdb.size() > 1 && reppdb.size() < pdbe.size())
- {
- structureMenu.add(rpdbview = new JMenuItem(MessageManager
- .formatMessage(
- "label.view_all_representative_structures",
- new Object[]
- { new Integer(reppdb.size()).toString() })));
- rpdbview.setToolTipText(MessageManager
- .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
- rpdbview.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- new StructureViewer(ap.getStructureSelectionManager())
- .viewStructures(ap, pr, ap.av.collateForPDB(pr));
- }
- });
- }
+ // if (pdbe.size() == 1)
+ // {
+ // structureMenu.add(gpdbview = new JMenuItem(MessageManager
+ // .formatMessage("label.view_structure_for", new String[]
+ // { sqass.getDisplayId(false) })));
+ // }
+ // else
+ // {
+ // structureMenu.add(gpdbview = new JMenuItem(MessageManager
+ // .formatMessage("label.view_all_structures", new String[]
+ // { new Integer(pdbe.size()).toString() })));
+ // }
+ // gpdbview.setToolTipText(MessageManager
+ // .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
+ // gpdbview.addActionListener(new ActionListener()
+ // {
+ //
+ // @Override
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // new StructureViewer(ap.getStructureSelectionManager())
+ // .viewStructures(ap, pe, ap.av.collateForPDB(pe));
+ // }
+ // });
+ // if (reppdb.size() > 1 && reppdb.size() < pdbe.size())
+ // {
+ // structureMenu.add(rpdbview = new JMenuItem(MessageManager
+ // .formatMessage(
+ // "label.view_all_representative_structures",
+ // new String[]
+ // { new Integer(reppdb.size()).toString() })));
+ // rpdbview.setToolTipText(MessageManager
+ // .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
+ // rpdbview.addActionListener(new ActionListener()
+ // {
+ //
+ // @Override
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // new StructureViewer(ap.getStructureSelectionManager())
+ // .viewStructures(ap, pr, ap.av.collateForPDB(pr));
+ // }
+ // });
+ // }
}
}
else
}
});
jMenu1.setText(MessageManager.getString("label.group"));
- structureMenu.setText(MessageManager.getString("label.structure"));
+ // structureMenu.setText(MessageManager.getString("label.structure"));
+ structureMenu.setText(MessageManager.getString("label.view_structure"));
+ structureMenu.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ SequenceI[] selectedSeqs = new SequenceI[]
+ { sequence };
+ if (ap.av.getSelectionGroup() != null)
+ {
+ selectedSeqs = ap.av.getSequenceSelection();
+ }
+ new StructureChooser(selectedSeqs, sequence, ap);
+ }
+ });
+
viewStructureMenu.setText(MessageManager
.getString("label.view_structure"));
// colStructureMenu.setText("Colour By Structure");
jMenu1.add(showColourText);
jMenu1.add(outline);
jMenu1.add(displayNonconserved);
- structureMenu.add(pdbMenu);
- structureMenu.add(viewStructureMenu);
+ // structureMenu.add(pdbMenu);
+ // structureMenu.add(viewStructureMenu);
// structureMenu.add(colStructureMenu);
noColourmenuItem.setText(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
}
cap.setText("<html>" + contents.toString() + "</html>");
- Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage(
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
"label.sequence_details_for",
(sequences.length == 1 ? new Object[]
{ sequences[0].getDisplayId(true) } : new Object[]