JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
+ JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
+
JMenu editMenu = new JMenu();
JMenuItem cut = new JMenuItem();
{
conservationMenuItem.setSelected(true);
}
-
+ displayNonconserved.setSelected(sg.getShowunconserved());
showText.setSelected(sg.getDisplayText());
showColourText.setSelected(sg.getColourText());
showBoxes.setSelected(sg.getDisplayBoxes());
if (links != null && links.size() > 0)
{
JMenu linkMenu = new JMenu("Link");
-
+ Vector linkset = new Vector();
for (int i = 0; i < links.size(); i++)
{
String link = links.elementAt(i).toString();
{ urlLink.getTarget() });
// collect id string too
String id = seq.getName();
+ String descr = seq.getDescription();
+ if (descr!=null && descr.length()<1)
+ {
+ descr = null;
+ }
+
if (dbr != null)
{
for (int r = 0; r < dbr.length; r++)
{
for (int u = 0; u < urls.length; u += 2)
{
- addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
+ if (!linkset.contains(urls[u]+"|"+urls[u+1]))
+ {
+ linkset.addElement(urls[u]+"|"+urls[u+1]);
+ addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
+ }
}
}
}
{
for (int u = 0; u < urls.length; u += 2)
{
- addshowLink(linkMenu, label, urls[u + 1]);
+ if (!linkset.contains(urls[u]+"|"+urls[u+1]))
+ {
+ linkset.addElement(urls[u]+"|"+urls[u+1]);
+ addshowLink(linkMenu, label, urls[u + 1]);
+ }
+ }
+ }
+ }
+ // Create urls from description but only for URL links which are regex links
+ if (descr != null && urlLink.getRegexReplace()!=null)
+ {
+ // create link for this URL from description where regex matches
+ String[] urls = urlLink.makeUrls(descr, true);
+ if (urls != null)
+ {
+ for (int u = 0; u < urls.length; u += 2)
+ {
+ if (!linkset.contains(urls[u]+"|"+urls[u+1]))
+ {
+ linkset.addElement(urls[u]+"|"+urls[u+1]);
+ addshowLink(linkMenu, label, urls[u + 1]);
+ }
}
}
}
}
else
{
- // Add a non-dynamic link
- addshowLink(linkMenu, label, urlLink.getUrl_prefix());
+ if (!linkset.contains(label+"|"+urlLink.getUrl_prefix()))
+ {
+ linkset.addElement(label+"|"+urlLink.getUrl_prefix());
+ // Add a non-dynamic link
+ addshowLink(linkMenu, label, urlLink.getUrl_prefix());
+ }
}
}
if (sequence != null)
showColourText_actionPerformed();
}
});
+ displayNonconserved.setText("Show Nonconserved");
+ displayNonconserved.setState(true);
+ displayNonconserved.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showNonconserved_actionPerformed();
+ }
+ });
editMenu.setText("Edit");
cut.setText("Cut");
cut.addActionListener(new ActionListener()
jMenu1.add(showText);
jMenu1.add(showColourText);
jMenu1.add(outline);
+ jMenu1.add(displayNonconserved);
structureMenu.add(pdbMenu);
structureMenu.add(viewStructureMenu);
// structureMenu.add(colStructureMenu);
});
}
+ protected void showNonconserved_actionPerformed()
+ {
+ getGroup().setShowunconserved(displayNonconserved.isSelected());
+ refresh();
+ }
+
/**
- * DOCUMENT ME!
+ * call to refresh view after settings change
*/
void refresh()
{
}
ap.av.hideSequence(hseqs);
+ ap.av.sendSelection();
}
public void copy_actionPerformed()
if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
features, true, ap))
{
- ap.alignFrame.showSeqFeatures.setSelected(true);
- ap.av.setShowSequenceFeatures(true);
+ ap.alignFrame.setShowSeqFeatures(true);
ap.highlightSearchResults(null);
}
}