{
return AlignmentUtils.alignCdsAsProtein(this, al);
}
- return AlignmentUtils.alignAs(this, al);
+ else if (thatIsProtein && !thisIsNucleotide)
+ {
+ // honour sense we were called - align this according to al
+ return AlignmentUtils.alignAs(this, al);
+ }
+ // otherwise doing a DNA to DNA alignment - so use legacy obverse sense
+ return AlignmentUtils.alignAs(this,al);
}
/**