Changes to sequence input

Changed how sequences are input so now the format of an input file is
infered from the filename extension i.e. after the "." alternativeley,
the user can force an extention or give the name of a compatible object
in place of a filename and if possible, HybRIDS will convert interpret
it and read it into a HybRIDSdna object.

This change is in preparation for more future support for more file
formats - we start with the FASTA file format support, and also support
for the DNAbin object.
Finished laying groundwork for multiple dna sequence input methods and storage options.

We do this by specifying the default HybRIDSseq object which just
stores everything as R normally does in active memory and then other
objects that inherit from HybRIDSseq provide the special storage
options.
Corrected a bug in switching the no DNA flag