a couple of fixes typos etc

removed hard coded values

clean up, removed cruft etc

emptyied options of specific settings cleaned up a bit

changes so no longer relies on bioperl swisprot parser but using one inside the script

Bio::SeqFeature::Gene::GeneStructure -> Bio::EnsEMBL::Gene
Bio::SeqFeature::Gene::Transcript -> Bio::EnsEMBL::Transcript
Bio::SeqFeature::Gene::Exon -> Bio::EnsEMBL::Exon

make the flexible way to accept database information as well as analysis and contig, during the conversion of seqfeature a sort from bioperl to ensembl.

to the existing "isa", and added a friendly throw to
AUTOLOAD if the method does not exist on the object.

external_db db_name enum