PhyloSoC:BioPerl integration of the NeXML exchange standard and Bio::Phylo toolkit/alignIO attribute mapping

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Below depicts preliminary mapping of the attributes between Bioperl and Bio::Phylo as represented. Classes are in bold, attributes are preceded by a "-" and two things are related by the '<=>' symbol.

 Bioperl                          <=>          Biophylo
   SimpleAlign                    <=>	           Matrices::Matrix
      -ID                         <=>	            -Biophylo label
      Bio::LocatableSeq           <=>               Matrices::Datum
           -display_ID            <=>                  -label.row_id+
           -seq                   <=>                  -chars
           -description           <=>                  -?
           -alphabet              <=>                  -mol_type++

+Since each row does not have an ID, the alignment ID (Biophylo label) will be used with the row number appended to it (e.g. if label = "DnaSeqs" the display_ID in bioperl for the first sequence in the matrix would be "DnaSeqs.row_1".

++as of now I'm only converting mol_types of 'dna', 'rna', or 'protein' into bioperl. I'm disregarding 'continuous', 'restriction, and 'standard' b\c I'm not sure if it makes sense for those to be converted into bioperl objects.