Replace the using of enum arrays (State2Phase, State2Frame, State2Status) by the calling to methods from State class.

Code reindentation

Add reading of gff3 file in AltEst class, now AltEst builder need sequence data to check if strand correpond to position.

Compatibility between an alternative EST nad the prediction works even if there is NO gene predicted in the region of the alternative EST

Possible source of the AltEst problem: when several EST matches have the same sequence name, all of them were put together, even if this was two unrelated matches.