// Translate the SeqCoord c from the frame of coord[0] to coord[1]
SeqCoord Match::translate(const SeqCoord& c) const
{
// In overlap with indelsm the coord[] are not the same length
// assert(coord[0].length() == coord[1].length()); // ensure translation is valid
SeqCoord out;
out.seqlen = coord[1].seqlen;
//The offset of start and end should be adjusted according to the indels.
out.interval.start = c.interval.start + calculateTranslation();
out.interval.end = c.interval.end + calculateTranslationEnd();
if(isRC())
out.flip();
// the offset t is not accurate under indels overlap
// if(out.interval.end >= out.seqlen)
// out.interval.end = out.seqlen-1;
// if(out.interval.start <0)
// out.interval.start = 0;
// assert(out.interval.start>=0 && out.interval.start<out.interval.end);
return out;
}
// Calculation the translation offset to shift
// a coord[1] position to a coord[0]. This must be calculated
// using canonical coordinates
int Match::calculateInverseTranslation() const
{
if(!isRC())
return coord[0].interval.start - coord[1].interval.start;
else
{
SeqCoord f = coord[0];
f.flip();
return f.interval.start - coord[1].interval.start;
}
}
int Match::calculateTranslationEnd() const
{
if(!isRC())
return coord[1].interval.end - coord[0].interval.end;
else
{
SeqCoord f = coord[1];
f.flip();
return f.interval.end - coord[0].interval.end;
}
}
// Translate the SeqCoord c from the frame of coord[1] to coord[0]
SeqCoord Match::inverseTranslate(const SeqCoord& c) const
{
// assert(c.isExtreme());
SeqCoord out;
out.seqlen = coord[0].seqlen; //seqlen was extended
out.interval.start = c.interval.start + calculateInverseTranslation();
out.interval.end = c.interval.end + calculateInverseTranslationEnd();
if(isRC())
out.flip();
// if((int)c.length() !=(int)out.length())
// std::cout << c.length() << "\t"<< out.length() <<"\n";
// assert(out.interval.start>=0 && out.interval.start<out.interval.end);
return out;
}
