@Override
public void focusGained(FocusEvent e)
{
- Desktop.setCurrentAlignFrame(AlignFrame.this);
+ Jalview.setCurrentAlignFrame(AlignFrame.this);
}
});
final boolean dna = viewport.getAlignment().isNucleotide();
List<String> ptypes = (seqs == null || seqs.length == 0) ? null
: new CrossRef(seqs, dataset)
- .findXrefSourcesForSequences();
+ .findXrefSourcesForSequences(dna);
for (final String source : ptypes)
{
* @param source
* the database to show cross-references for
*/
- protected void showProductsFor(final SequenceI[] sel, final boolean dna,
+ protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
final String source)
{
Runnable foo = new Runnable()
.getAlignment();
AlignmentI dataset = alignment.getDataset() == null ? alignment
: alignment.getDataset();
- AlignmentI xrefs = new CrossRef(sel, alignment)
- .findXrefSequences(source);
+ boolean dna = alignment.isNucleotide();
+ if (_odna!=dna)
+ {
+ System.err
+ .println("Conflict: showProducts for alignment originally "
+ + "thought to be "
+ + (_odna ? "DNA" : "Protein")
+ + " now searching for "
+ + (dna ? "DNA" : "Protein") + " Context.");
+ }
+ AlignmentI xrefs = new CrossRef(sel, dataset)
+ .findXrefSequences(source, dna);
if (xrefs == null)
{
return;
sprods[s].updatePDBIds();
}
Alignment al = new Alignment(sprods);
- al.setDataset((Alignment) dataset);
+ al.setDataset(dataset);
return al;
}
@Override
protected void runGroovy_actionPerformed()
{
- Desktop.setCurrentAlignFrame(this);
+ Jalview.setCurrentAlignFrame(this);
groovy.ui.Console console = Desktop.getGroovyConsole();
if (console != null)
{