protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
- // protected JRadioButtonMenuItem covariationColour = new
- // JRadioButtonMenuItem();
-
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
JMenuItem pdbFromFile = new JMenuItem();
- // JBPNote: Commented these out - Should add these services via the web
- // services menu system.
- // JMenuItem ContraFold = new JMenuItem();
-
- // JMenuItem RNAFold = new JMenuItem();
-
JMenuItem enterPDB = new JMenuItem();
JMenuItem discoverPDB = new JMenuItem();
JMenu viewStructureMenu = new JMenu();
- // JMenu colStructureMenu = new JMenu();
JMenuItem editSequence = new JMenuItem();
- // JMenuItem annotationMenuItem = new JMenuItem();
-
JMenu groupLinksMenu;
JMenuItem hideInsertions = new JMenuItem();
colours.add(BLOSUM62Colour);
colours.add(purinePyrimidineColour);
colours.add(RNAInteractionColour);
- // colours.add(covariationColour);
for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
{
{
structureMenu.remove(viewStructureMenu);
}
- // structureMenu.remove(colStructureMenu);
}
if (ap.av.getAlignment().isNucleotide() == true)
{
@Override
public void actionPerformed(ActionEvent e)
{
- // // System.out.println("1:"+structureLine);
- // System.out.println("1:sname" + seq.getName());
- // System.out.println("2:seq" + seq);
- //
- // // System.out.println("3:"+seq.getSequenceAsString());
- // System.out.println("3:strucseq" + rnastruc);
- // // System.out.println("4:struc"+seq.getRNA());
- // System.out.println("5:name" + seq.getName());
- // System.out.println("6:ap" + ap);
new AppVarna(structureLine, seq, seq.getSequenceAsString(),
rnastruc, seq.getName(), ap);
- // new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(),
- // seq.getName(), ap);
System.out.println("end");
}
});
}
}
- // SequenceFeatures[] test = seq.getSequenceFeatures();
if (seq.getAnnotation() != null)
{
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 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
if (urlset != null)
{
int type = urlLink.getGroupURLType() & 3;
- // System.out.println(urlLink.getGroupURLType()
- // +" "+((String[])urlset[3])[0]);
// first two bits ofurlLink type bitfield are sequenceids and sequences
// TODO: FUTURE: ensure the groupURL menu structure can be generalised
addshowLink(linkMenus[type], label
pdbFromFile_actionPerformed();
}
});
- // RNAFold.setText("From RNA Fold with predict2D");
- // RNAFold.addActionListener(new ActionListener()
- // {
- // public void actionPerformed(ActionEvent e)
- // {
- // try {
- // RNAFold_actionPerformed();
- // } catch (Exception e1) {
- // // TODO Auto-generated catch block
- // e1.printStackTrace();
- // }
- // }
- // });
- // ContraFold.setText("From Contra Fold with predict2D");
- // ContraFold.addActionListener(new ActionListener()
- // {
- // public void actionPerformed(ActionEvent e)
- // {
- // try {
- // ContraFold_actionPerformed();
- // } catch (Exception e1) {
- // // TODO Auto-generated catch block
- // e1.printStackTrace();
- // }
- // }
- // });
+
enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
enterPDB.addActionListener(new ActionListener()
{
}
});
jMenu1.setText(MessageManager.getString("label.group"));
- // structureMenu.setText(MessageManager.getString("label.structure"));
structureMenu.setText(MessageManager.getString("label.view_structure"));
structureMenu.addActionListener(new ActionListener()
{
if (ap.getAlignment().isNucleotide())
{
// JBPNote - commented since the colourscheme isn't functional
- // colourMenu.add(RNAInteractionColour);
colourMenu.add(purinePyrimidineColour);
}
- // colourMenu.add(covariationColour);
colourMenu.add(userDefinedColour);
if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
colourMenu.addSeparator();
colourMenu.add(abovePIDColour);
colourMenu.add(conservationMenuItem);
- // colourMenu.add(annotationMenuItem);
editMenu.add(copy);
editMenu.add(cut);
editMenu.add(editSequence);
jMenu1.add(showColourText);
jMenu1.add(outline);
jMenu1.add(displayNonconserved);
- // structureMenu.add(pdbMenu);
- // structureMenu.add(viewStructureMenu);
- // structureMenu.add(colStructureMenu);
noColourmenuItem.setText(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
}
- // JBNote: commented out - these won't be instantiated here...!
- // public void RNAFold_actionPerformed() throws Exception
- // {
- // Predict2D P2D = new Predict2D();
- // P2D.getStructure2DFromRNAFold("toto");
- // }
- //
- // public void ContraFold_actionPerformed() throws Exception
- // {
- // Predict2D P2D = new Predict2D();
- // P2D.getStructure2DFromContraFold("toto");
- // }
+
public void enterPDB_actionPerformed()
{
String id = JOptionPane.showInternalInputDialog(Desktop.desktop,