DEVELOPMENT TO-DO LIST

      to-do-asap: INTERFACE CHANGE - Dna_to_Rna(),
                  Rna_to_Dna() and translate() need to
                  be modified so that they return
                  Bio::Seq objects

      to-do-soon: Configure procedure that keeps users
                  from having to edit the .pm (or t/*.t) files

      to-do: more alphabet support
      to-do: write sequence() method to replace use of _seq()
      to-do: get rid of dump()

      to-do-later: SeqFileHandle
      to-do-later: use SplitLine for Fasta Output
      to-do-later: parse_fasta(), etc should first check data, then assign
      to-do-later: consistency-check/invariants-check
      to-do-later: handle arbitrary numbering schemes
      to-do-later: use benchmark module to find best parsing/output code
      to-do-later: Method for reading/parsing 3-letter protein
  

     Steve's observations that have yet to be implemented
     ------------------------------------------------

General Observations:
=====================
- Users should not be expected to edit .pm files
  (we need a configuration process)

- Perhaps we need another option for sequence type
  that deals with alphabet stringency levels
  1 Strict    1 Gap
  2 Ambig     2 No-Gap   (2,1) Set as default?
  (and another option for completly "OFF")

- Does layout() need an option that would specify
  output to a file?

- translate() should be able to use different
  translation tables

Specific To-Do's:
=================

1. Need a validity marker that is set to 'false'
   when the program Carps() out

2. Constructor default ID field should be changed
   from "No_Id_Given" to "No_Id" plus a unique number

3. Constructor should attempt to guess alphabet (and origin?)
   before setting a default "not_given" setting

4. _file_read() is not efficient, just slurp file in with 
   a giant READ

5. type() should verify that the given type is valid for
   the sequence (in addition to being a supported type)

6. revcom() needs to check that the sequence is really
   nucleotide before applying the regular expression

*7. DNA_to_RNA() should return a Bio::Seq object, not a
      string or array

*8. translate() should return a Bio::Seq object, not a
      string or array

9. translate() treats ambiguity inconsistantly.