make Sequence a subclass of std::string

make Sequence a subclass of std::string
There were a lot of changes associated with making Sequence a subclass
of std::string. Hopefully that'll make it easier for me to use paircomp
at some point.

However the major useful new feature is subseq now returns a Sequence
instead of a string, and this sub-sequence has the header copied over
and the annotations copied (and their start/end locations adjusted).

Additionally this patch includes adding the coordianates copied with the
copySelectedSequenceAsFasta command to the header.

I'm getting closer to have the parts needed to do a sub-analysis.