Steve's notes on

Steven E. Brenner
Fri, 7 Mar 1997 22:27:44 +0900 (JST)

Thanks for writing up all the notes!

> Perhaps we can kick
> these notes around and come up with a "MUST DO NOW" list of essentials that
> need to be fixed prior to the next version?

The essentials are things which either:

 1) Are seriously broken (very very few)
 2) Alter the interface (some)

> Personally, I feel that moving all ReadSeq stuff into a would be
> worth the effort at this point.

Until we figure out how parsing and IO is going to be done, I would say
the interface isn't fixed.  So, yes, this is very important.

> o 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?
A third option would be "on" or "off"

> 3. Settle the "_nofile" or "undef" question
>    in the constructor method
Georg agreed to _undef for Bio::UnivAln, so I think that makes sense here.

> 6. _file_read() is innefficient, just slurp file in with
>    a giant READ
Inefficiency like this is ok for now, I think.  But it should be fixed
very soon.

> 7. Resolve this conflict: names() currently will ADD the values
>    of a passed in hash referance to the existing %names hash.
>    However, the POD docs state that the method SETS (overwrites)
>    the hash values. Which should it do?
Let's make it 'set'

> **13. DNA_to_RNA() should return a Bio::Seq object, not a
>       string or array
> **14. translate() should return a Bio::Seq object, not a
>       string or array

** Yes. :)  (Why the **?)

> 17. rename seq_length() to seq_len()

> 18. rename ary() and str() to seq_ary() and seq_str()
Actually, I've changed my mind about this, and think it might be better to
leave it as-is.  I can give my rationale if people care.