import jalview.api.FeaturesDisplayedI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.MappedFeatures;
import jalview.datamodel.Mapping;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResults;
}
/**
- * Answers a (possibly empty) list of features in this alignment at a position
- * (or range) which is mappable from the given sequence residue position in a
- * mapped alignment.
+ * 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
*/
- public List<SequenceFeature> findComplementFeaturesAtResidue(SequenceI sequence, int pos)
+ public MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence,
+ int pos)
{
SequenceI ds = sequence.getDatasetSequence();
- List<SequenceFeature> result = new ArrayList<>();
+ if (ds == null)
+ {
+ ds = sequence;
+ }
+ final char residue = ds.getCharAt(pos - ds.getStart());
+
+ List<SequenceFeature> found = new ArrayList<>();
List<AlignedCodonFrame> mappings = this.av.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
*/
+ Mapping mapping = null;
+ SequenceI mapFrom = null;
+
for (AlignedCodonFrame acf : mappings)
{
- Mapping mapping = acf.getMappingForSequence(sequence, true);
+ mapping = acf.getMappingForSequence(sequence, true);
if (mapping == null || mapping.getMap().getFromRatio() == mapping
.getMap().getToRatio())
{
{
int fromRes = match.getStart();
int toRes = match.getEnd();
+ mapFrom = match.getSequence();
List<SequenceFeature> fs = findFeaturesAtResidue(
match.getSequence(), fromRes, toRes);
for (SequenceFeature sf : fs)
{
- if (!result.contains(sf))
+ if (!found.contains(sf))
+ {
+ found.add(sf);
+ }
+ }
+ }
+
+ /*
+ * just take the first mapped features we find
+ */
+ if (!found.isEmpty())
+ {
+ break;
+ }
+ }
+ if (found.isEmpty())
+ {
+ return null;
+ }
+
+ /*
+ * sort by renderorder, inefficiently
+ */
+ List<SequenceFeature> result = new ArrayList<>();
+ for (String type : renderOrder)
+ {
+ for (SequenceFeature sf : found)
+ {
+ if (type.equals(sf.getType()))
+ {
+ result.add(sf);
+ if (result.size() == found.size())
{
- result.add(sf);
+ return new MappedFeatures(mapping, mapFrom, pos, residue,
+ result);
}
}
}
}
- return result;
+ return new MappedFeatures(mapping, mapFrom, pos, residue, result);
}
}