[BioC] pairwiseAlignment and issue mapping

[James Bullard]

Hi All,

this should be an easy question and answer, it is mostly about the  
best way to do this with the Bioconductor S4 classes. I have a  
pairwise alignment: A and I want a function which maps from a position  
in the original sequence (either subject: s, or pattern: p) to the  
position in the aignment. Essentially, I want a function that looks  
like:

subject  alignment
1		1
2		2
3		4
4		5

alignmentPosition(i, which = c("subject", "pattern")), i in  
1:length(s) => j in 1:length(alignment)

If I had just characters, it would be easy, but since I have objects  
of type: PairwiseAlignedFixedSubject, I am slightly overwhelmed by the  
class hierarchy, and the best way to do this.

thanks, jim