[Bioperl-l] SeqIO parsing

[Hilmar Lapp]

I fixed the ones in Bio/Annotation/*. -hilmar

On Wednesday, September 25, 2002, at 01:49 AM, Heikki Lehvaslaiho wrote:

> On Tue, 2002-09-24 at 17:01, Ewan Birney wrote:
>>
>>   this scheme in my mind has one *SERIOUS* gotcha. People *have* 
>> to write
>> their @ISA's with their implementation tree *first* and their 
>> interface
>> inheritance second. Is this ok with people?
>
> That is how it should be. I checked the bioperl-live an found only the
> following cases:
>
> ./Bio/Annotation/Comment.pm:51:
> 	@ISA = qw(Bio::AnnotationI Bio::Root::Root);
> ./Bio/Annotation/Reference.pm:60:
> 	@ISA = qw(Bio::AnnotationI Bio::Annotation::DBLink);
> ./Bio/DB/Universal.pm:114:
> 	@ISA = qw(Bio::DB::RandomAccessI Bio::Root::Root);
> ./Bio/DB/Fasta.pm:397: @ISA = qw(Bio::DB::SeqI Bio::Root::Root);
> ./Bio/DB/BioFetch.pm:97: @ISA = qw(Bio::DB::WebDBSeqI Bio::Root::Root);
>
> in all other cases the interfaces are after implementing classes.
> Most of these are "inteface" classes are these "decorated inteface"
> which actually implement methods.
>
>
> is it time  we get rid of them?
>
> 	-heikki
>
>
>
>
>> The nice thing about (a) is that it should give speed ups across the
>> entire system, not just SeqIO.
>>
>>
>> Jason/Hilmar - is there a hidden gotcha here somewhere?
>>
>>
>>
>>
>>   (b) Making a new Bio::Seq::SeqFactory with privledged access to
>> functions in Bio::Seq and Bio::PrimarySeq to make fast access 
>> objects, eg,
>> not going through a second alphabet on setting seq.
>>
>>
>>
>> (b) is SeqIO specific so I want to do this second.
>>
>>
>>
>>
>>
>> BTW - I think I can cut the object creation time by a factor of 6 
>> in my
>> tests if I get this written right ;)
>>
>>
>>
>>
>>
>>
>>
>> -----------------------------------------------------------------
>> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
>> <birney@ebi.ac.uk>.
>> -----------------------------------------------------------------
>>
>>
>>
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> --
> ______ _/      _/_____________________________________________________
>       _/      _/                      http://www.ebi.ac.uk/mutations/
>      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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--
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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