return filter == null ? true : filter.matches(sf);
}
- /**
- * Answers a bean containing a mapping, and a list of features in this
- * alignment at a position (or range) which is mappable from the given
- * sequence residue position in a mapped alignment. Features are returned in
- * render order of feature type (on top last), with order within feature type
- * undefined. If no features or mapping are found, answers null.
- *
- * @param sequence
- * @param pos
- * @return
- */
+ @Override
public MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence,
int pos)
{
.getCodonFrame(sequence);
/*
+ * fudge: if no mapping found, check the complementary alignment
+ * todo: only store in one place? StructureSelectionManager?
+ */
+ if (mappings.isEmpty())
+ {
+ mappings = this.av.getCodingComplement().getAlignment()
+ .getCodonFrame(sequence);
+ }
+
+ /*
* todo: direct lookup of CDS for peptide and vice-versa; for now,
* have to search through an unordered list of mappings for a candidate
*/
for (AlignedCodonFrame acf : mappings)
{
- mapping = acf.getMappingForSequence(sequence, true);
- if (mapping == null || mapping.getMap().getFromRatio() == mapping
- .getMap().getToRatio())
+ mapping = acf.getMappingForSequence(sequence);
+ if (mapping == null || !mapping.getMap().isTripletMap())
{
continue; // we are only looking for 3:1 or 1:3 mappings
}