Method: Bio::Nexus::DataBlock#to_nexus

Defined in:
lib/bio/db/nexus.rb

#to_nexus ⇒ Object

Returns a String describing this block as nexus formatted data.

Returns

String



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# File 'lib/bio/db/nexus.rb', line 1241

def to_nexus
  line_1 = String.new
  line_1 << DIMENSIONS  
  if ( Nexus::Util::larger_than_zero( get_number_of_taxa ) )
    line_1 << " " <<  NTAX << "=" << get_number_of_taxa
  end
  if ( Nexus::Util::larger_than_zero( get_number_of_characters ) )
    line_1 << " " <<  NCHAR << "=" << get_number_of_characters
  end
  line_1 << DELIMITER
  
  line_2 = String.new
  line_2 << FORMAT  
  if ( Nexus::Util::longer_than_zero( get_datatype ) )
    line_2 << " " <<  DATATYPE << "=" << get_datatype
  end
  if ( Nexus::Util::longer_than_zero( get_missing ) )
    line_2 << " " <<  MISSING << "=" << get_missing
  end
  if ( Nexus::Util::longer_than_zero( get_gap_character ) )
    line_2 << " " <<  GAP << "=" << get_gap_character
  end
  if ( Nexus::Util::longer_than_zero( get_match_character ) )
    line_2 << " " <<  MATCHCHAR << "=" << get_match_character
  end
  line_2 << DELIMITER
  
  line_3 = String.new
  line_3 << TAXLABELS << " " << Nexus::Util::array_to_string( get_taxa )
  line_3 << DELIMITER
  
  line_4 = String.new
  line_4 << MATRIX 
  Nexus::Util::to_nexus_helper( DATA_BLOCK, [ line_1, line_2, line_3, line_4 ] +
                                get_matrix.to_nexus_row_array  )
end