[Bioperl-l] Re: SeqFactory diff

[Michal Kurowski]

Hilmar Lapp [hlapp at gmx.net] wrote:

> could you post a test case please along with the error that it produces.

MSG: Can't locate MySeq.pm in @INC (@INC contains: CODE(0x84d79b8) 
/usr/lib/perl5/i386-linux /usr/lib/perl5 /usr/lib/perl5/site_perl/i386-linux 
/usr/lib/perl5/site_perl /usr/lib/perl5/site_perl .) at (eval 8) line 3.
: Unrecognized Sequence type for SeqFactory 'MySeq'
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/Bio/Root/Root.pm:342
STACK: Bio::Seq::SeqFactory::type /usr/lib/perl5/site_perl/Bio/Seq/SeqFactory.pm:144
STACK: Bio::Seq::SeqFactory::new /usr/lib/perl5/site_perl/Bio/Seq/SeqFactory.pm:103
STACK: /home/michal/bin/uploader2.pl:49

> The lines you're commenting out are there for a conscious reason, and 
> just removing them is unlikely to be accepted into the code base without 
> further grounds that that would be the sole way to let you do what you 
> wanted to do.

You're right. The change breaks a lot of code and I reverted it.
Sorry, a long working hours case ;-).

The problem remains though. require/use will not do if you have 
a PrimarySeq derived class and a client  code in the same file.


-- 
Michal Kurowski
<mkur at poczta.gazeta.pl>