import jalview.schemes.*;\r
import javax.swing.*;\r
import java.awt.event.*;\r
-\r
+import jalview.io.*;\r
+import MCview.*;\r
\r
public class PopupMenu extends JPopupMenu\r
{\r
JMenu residueMenu = new JMenu();\r
JMenuItem annotateResidue = new JMenuItem();\r
\r
- SequenceI sequence;\r
+ Sequence sequence;\r
JMenuItem unGroupMenuItem = new JMenuItem();\r
+ JMenuItem pdbMenuItem = new JMenuItem();\r
\r
- public PopupMenu(AlignmentPanel ap, SequenceI seq)\r
+ public PopupMenu(AlignmentPanel ap, Sequence seq)\r
{\r
///////////////////////////////////////////////////////////\r
// If this is activated from the sequence panel, the user may want to\r
unGroupMenuItem_actionPerformed(e);\r
}\r
});\r
+ pdbMenuItem.setText("View PDB structure");\r
+ pdbMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ pdbMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
add(groupMenu);\r
this.add(sequenceMenu);\r
this.add(residueMenu);\r
defineMenu.add(conservationMenuItem);\r
\r
sequenceMenu.add(sequenceName);\r
+ sequenceMenu.add(pdbMenuItem);\r
residueMenu.add(annotateResidue);\r
\r
noColourmenuItem.setText("None");\r
ap.av.setRubberbandGroup(null);\r
ap.RefreshPanels();\r
}\r
+\r
+ void pdbMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if(sequence.getPDBId()==null)\r
+ return;\r
+\r
+ try\r
+ {\r
+ EBIFetchClient ebi = new EBIFetchClient();\r
+ String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);\r
+\r
+ PDBfile pdb = new PDBfile(result);\r
+ sequence.setPDBfile(pdb);\r
+\r
+ ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).isVisible = true;\r
+ ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).sequence = sequence;\r
+ // ( (PDBChain)pdb.chains.elementAt(sequence.maxchain)).colourBySequence();\r
+\r
+ rotCanvas rc = new rotCanvas(pdb);\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(rc);\r
+ Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
}\r