I am not massively familiar with Bio::SimpleAlign, but a few things might help you work out what is going on: _seq is not a method, it is part of the structure of the object (a blessed hash), which from the looks of the source code, holds the sequence objects used in the multiple alignment.

So i would hazard a guess this code is doing first checking to see if a sequence of the given name already exists in the lookup hash ( ->{_seq} ) and then warns you conditional on the 'verbose' setting.

Usually 'verbose' setting control how much output a program gives, so this is probably a 'suppress warnings' construct. If the author used exists this would stop autovivification, and allow you to check for a sequence twice!

I couldn't find the verbose method, but the Bio::SimpleAlign inherits from :

use base qw(Bio::Root::Root Bio::Align::AlignI Bio::AnnotatableI 
        Bio::FeatureHolderI);

[download]
So I suspect that one of these will hold the answer on that...

So your error is probably coming from overwriting a named code... You should be able to check beforehand, to make sure you don't do this.

Hope this helps ( and if i am wrong, it will be pointed out pretty quickly... ), and if you have more questions, we'll need to see more code and examples.

Just a something something...

In reply to Re: [BioPerl] a warning I do not understand omits a sequence by BioLion
in thread [BioPerl] a warning I do not understand omits a sequence by Anonymous Monk

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