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

De-Jian,ZHAO zhaodj at ioz.ac.cn
Sat Aug 18 11:06:41 EDT 2007


Thank you,Nathan.
The Deobfuscator is very helpful.

On Fri, Aug 17, 2007 18:27, Nathan Haigh wrote:
> 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:
> http://bioperl.org/cgi-bin/deob_interface.cgi
>
> 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.
>
> Nath
>


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