/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+ // protected JRadioButtonMenuItem covariationColour = new
+ // JRadioButtonMenuItem();
+
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
JMenuItem sequenceName = new JMenuItem();
- Sequence sequence;
+ SequenceI sequence;
JMenuItem unGroupMenuItem = new JMenuItem();
* @param links
* @param groupLinks
*/
- public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links,
+ public PopupMenu(final AlignmentPanel ap, final SequenceI seq, Vector links,
Vector groupLinks)
{
// /////////////////////////////////////////////////////////
colours.add(userDefinedColour);
colours.add(PIDColour);
colours.add(BLOSUM62Colour);
+ colours.add(purinePyrimidineColour);
+ // colours.add(covariationColour);
for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
{
}
else
{
+ if (ap.av.alignment.isNucleotide() == false)
+ {
structureMenu.remove(viewStructureMenu);
+ }
// structureMenu.remove(colStructureMenu);
}
+ if (ap.av.alignment.isNucleotide() == true)
+ {
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (aa[i].getRNAStruc() != null)
+ {
+ final String rnastruc = aa[i].getRNAStruc();
+
+ menuItem = new JMenuItem();
+ menuItem.setText("RNA structure - consensus");
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ new AppVarna(seq.getSequenceAsString(), rnastruc, seq
+ .getName(), ap);
+ }
+ });
+ viewStructureMenu.add(menuItem);
+ }
+ }
+
+ // SequenceFeatures[] test = seq.getSequenceFeatures();
+
+ if (seq.getAnnotation() != null)
+ {
+ AlignmentAnnotation seqAnno[] = seq.getAnnotation();
+ for (int i = 0; i < seqAnno.length; i++)
+ {
+ if (seqAnno[i].getRNAStruc() != null)
+ {
+ final String rnastruc = seqAnno[i].getRNAStruc();
+
+ // TODO: make rnastrucF a bit more nice
+ menuItem = new JMenuItem();
+ menuItem.setText("RNA structure - "+seq.getName());
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: VARNA does'nt print gaps in the sequence
+ new AppVarna(seq.getSequenceAsString(), rnastruc, seq
+ .getName(), ap);
+ }
+ });
+ viewStructureMenu.add(menuItem);
+ }
+ }
+ }
+
+
+ }
+
menuItem = new JMenuItem("Hide Sequences");
menuItem.addActionListener(new java.awt.event.ActionListener()
{
{
clustalColour.setSelected(true);
}
+ else if (sg.cs instanceof PurinePyrimidineColourScheme)
+ {
+ purinePyrimidineColour.setSelected(true);
+ }
+ /*
+ * else if (sg.cs instanceof CovariationColourScheme) {
+ * covariationColour.setSelected(true); }
+ */
else
{
noColourmenuItem.setSelected(true);
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideMenuItem);
+ if (ap.getAlignment().isNucleotide()) {
+ colourMenu.add(purinePyrimidineColour);
+ }
+ // colourMenu.add(covariationColour);
colourMenu.add(userDefinedColour);
if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
BLOSUM62Colour_actionPerformed();
}
});
+ purinePyrimidineColour.setText("Purine/Pyrimidine");
+ purinePyrimidineColour
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ purinePyrimidineColour_actionPerformed();
+ }
+ });
+ /*
+ * covariationColour.addActionListener(new java.awt.event.ActionListener() {
+ * public void actionPerformed(ActionEvent e) {
+ * covariationColour_actionPerformed(); } });
+ */
+
conservationMenuItem.setText("Conservation");
conservationMenuItem
.addActionListener(new java.awt.event.ActionListener()
refresh();
}
+ protected void purinePyrimidineColour_actionPerformed()
+ {
+ getGroup().cs = new PurinePyrimidineColourScheme();
+ refresh();
+ }
+
+ /*
+ * protected void covariationColour_actionPerformed() { getGroup().cs = new
+ * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
+ */
/**
* DOCUMENT ME!
*
public void discoverPDB_actionPerformed()
{
- final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
+ final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new SequenceI[]
{ sequence }
: ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
Thread discpdb = new Thread(new Runnable()