import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.Conservation;
-import jalview.bin.Cache;
import jalview.commands.ChangeCaseCommand;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
urlLink = new UrlLink(link);
} catch (Exception foo)
{
- Cache.log.error("Exception for URLLink '" + link + "'", foo);
+ System.err.println("Exception for URLLink '" + link + "': "
+ + foo.getMessage());
continue;
}
if (!urlLink.isValid())
{
- Cache.log.error(urlLink.getInvalidMessage());
+ System.err.println(urlLink.getInvalidMessage());
continue;
}
addshowLinks(linkMenu, linkset.values());
+ // disable link menu if there are no valid entries
if (linkMenu.getItemCount() > 0)
{
- if (seq != null)
- {
- seqMenu.add(linkMenu);
- }
- else
- {
- add(linkMenu);
- }
+ linkMenu.setEnabled(true);
}
+ else
+ {
+ linkMenu.setEnabled(false);
+ }
+
+ if (seq != null)
+ {
+ seqMenu.add(linkMenu);
+ }
+ else
+ {
+ add(linkMenu);
+ }
+
}
private void addshowLinks(Menu linkMenu, Collection<List<String>> linkset)
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
- StringBuffer contents = new StringBuffer();
+ StringBuilder contents = new StringBuilder(128);
for (SequenceI seq : sequences)
{
contents.append(MessageManager.formatMessage(
seq,
true,
true,
- false,
(ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr
.getMinMax() : null);
contents.append("</p>");
void addPDB()
{
- if (seq.getAllPDBEntries() != null)
+ Vector<PDBEntry> pdbs = seq.getAllPDBEntries();
+ if (pdbs != null&& !pdbs.isEmpty())
{
- PDBEntry entry = seq.getAllPDBEntries().firstElement();
+ PDBEntry entry = pdbs.firstElement();
if (ap.av.applet.jmolAvailable)
{
if (conservationMenuItem.getState())
{
-
- sg.cs.setConservation(Conservation.calculateConservation("Group", 3,
- sg.getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
- .getAlignment().getWidth(), false, ap.av
- .getConsPercGaps(), false));
+ sg.cs.setConservation(Conservation.calculateConservation("Group", sg
+ .getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
+ .getAlignment().getWidth(), false, ap.av.getConsPercGaps(),
+ false));
SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
SliderPanel.showConservationSlider();
}