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