registerPDBFile(pdb.getId().trim(), pdbFile);
}
// if PDBId is unavailable then skip SIFTS mapping execution path
- isMapUsingSIFTs = pdb.isPPDBIdAvailable();
+ isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable();
} catch (Exception ex)
{
return;
}
- SearchResultsI results = new SearchResults();
+ SearchResultsI results = findAlignmentPositionsForStructurePositions(atoms);
+ for (Object li : listeners)
+ {
+ if (li instanceof SequenceListener)
+ {
+ ((SequenceListener) li).highlightSequence(results);
+ }
+ }
+ }
+
+ /**
+ * Constructs a SearchResults object holding regions (if any) in the Jalview
+ * alignment which have a mapping to the structure viewer positions in the
+ * supplied list
+ *
+ * @param atoms
+ * @return
+ */
+ public SearchResults findAlignmentPositionsForStructurePositions(
+ List<AtomSpec> atoms)
+ {
+ SearchResults results = new SearchResults();
for (AtomSpec atom : atoms)
{
SequenceI lastseq = null;
}
}
}
- for (Object li : listeners)
- {
- if (li instanceof SequenceListener)
- {
- ((SequenceListener) li).highlightSequence(results);
- }
- }
+ return results;
}
/**