[Bioperl-l] How to get the full methods of a bioperl object?

Nathan Haigh n.haigh at sheffield.ac.uk
Fri Aug 17 10:27:43 UTC 2007

De-Jian,ZHAO wrote:
> Dear list members,
> I have a question about the methods of bioperl objects.It is how and
> where we can get the whole methods of a bioperl object.
> Take Bio::Tools::Run::RemoteBlast for example. In the synopsis of
> this object, some sample codes are given.The following five clauses
> are excerpted from the synopsis.
> (1)my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
> (2)while ( my @rids = $factory->each_rid ) {
> (3)$factory->remove_rid($rid);
> (4)my $rc = $factory->retrieve_blast($rid);
> (5)my $r = $factory->submit_blast($input);
> The five clauses use five methods of the RemoteBlast object,i.e.
> (1)new, (2)each_rid, (3)remove_rid,(4)retrieve_blast,and
> (5)submit_blast. However,I only find part of them(45) are listed in
> the appendix while others(123) are absent. Are there some more
> methods not explictly declared? I don't know.This will lead to the
> partial understanding and utilization of the module.Therefore I come
> here for the way to get the full methods of a bioperl object.
> Thanks!

You should check out the Deobfuscator at:

Search and choose the object of choice. e.g. Bio::Tools::Run::RemoteBlast

You will be provided a list of methods available to that object,
including all the methods up the inheritance hierarchy. Unfortunately,
some bioperl modules are documented more thoroughly than others.


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