int mappedEndResidue = 0;
for (AlignedCodonFrame acf : codonFrames)
{
+ // rather than use acf.getCoveringMapping() we iterate through all
+ // mappings to make sure all CDS are selected for a protein
for (SequenceToSequenceMapping map: acf.getMappings())
{
if (map.covers(selected) && map.covers(seq))
{
for (AlignedCodonFrame acf : mappings)
{
- SequenceI mappedSeq = mappingToNucleotide ? acf.getDnaForAaSeq(seq)
- : acf.getAaForDnaSeq(seq);
- if (mappedSeq != null)
- {
for (SequenceI seq2 : mapTo.getSequences())
{
- if (seq2.getDatasetSequence() == mappedSeq)
+ /*
+ * the corresponding peptide / CDS is the one for which there is
+ * a complete ('covering') mapping to 'seq'
+ */
+ SequenceI peptide = mappingToNucleotide ? seq2 : seq;
+ SequenceI cds = mappingToNucleotide ? seq : seq2;
+ SequenceToSequenceMapping s2s = acf.getCoveringMapping(cds,
+ peptide);
+ if (s2s != null)
{
mappedOrder.add(seq2);
j++;
break;
}
}
- }
}
}
if (colsel == null)
{
- return; // mappedColumns;
+ return;
}
char fromGapChar = mapFrom.getAlignment().getGapCharacter();
mapHiddenColumns(regions.next(), codonFrames, newHidden,
fromSequences, toSequences, fromGapChar);
}
- return; // mappedColumns;
+ return;
}
/**
*/
for (SequenceI toSeq : toSequences)
{
- if (toSeq.getDatasetSequence() == mappedSeq)
+ if (toSeq.getDatasetSequence() == mappedSeq
+ && mappedStartResidue >= toSeq.getStart()
+ && mappedEndResidue <= toSeq.getEnd())
{
int mappedStartCol = toSeq.findIndex(mappedStartResidue);
int mappedEndCol = toSeq.findIndex(mappedEndResidue);