Christopher Fields
and 1 contributors


Bio::DB::SoapEUtilities::FetchAdaptor - Conversion of Entrez SOAP messages to BioPerl objects


 $fac = Bio::DB::SoapEUtilities->new();
 $soap_result = $fac->efetch( -db => 'protein', -id => 2597988 );
 $adp = Bio::DB::SoapEUtilities::FetchAdaptor(
         -result => $soap_result,
         -type => 'seq'
 while ( $gb_seq = $adp->next_obj ) {
    # do stuff


FetchAdaptor is the base class of a system, modeled after Bio::SeqIO, to parse SOAP responses from the NCBI Entrez efetch utility into germane BioPerl objects.

The user will rarely need to instantiate a FetchAdaptor with Bio::DB::SoapEUtilities::Result object as in the "SYNOPSIS". It usually suffices to use the -auto_adapt parameter in the factory run() method:

 my $fac = Bio::DB::SoapEUtilities->new();
 my $taxio = $fac->efetch(-db => 'taxonomy', -id => 1394)->run(-auto_adapt=>1);
 my $sp = $taxio->next_species; # Bio::Species objects
 my $seqio = $fac->efetch(-db => 'protein', -id => 730439)->run(-auto_adapt=>1);
 my $seq = $seqio->next_seq; # Bio::Seq::RichSeq objects


Bio::DB::SoapEUtilities, FetchAdaptor subclasses


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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : new
 Usage   : my $obj = new Bio::DB::SoapEUtilities::FetchAdaptor();
 Function: Builds a new Bio::DB::SoapEUtilities::FetchAdaptor object
 Returns : an instance of Bio::DB::SoapEUtilities::FetchAdaptor
 Args    : named arguments
           -som => $soap_som_object (soap message)
           -type => $type ( optional, forces loading of $type adaptor )


 Title   : _initialize
 Usage   : 
 Returns : 
 Args    : 


 Title   : _load_adaptor
 Usage   : 
 Function: loads a FetchAdaptor subclass
 Returns : 
 Args    : adaptor type (subclass name)


 Title   : obj_class
 Usage   : $adaptor->obj_class
 Function: Returns the fully qualified BioPerl classname
           of the objects returned by next_obj()
 Returns : scalar string (class name)
 Args    : none


 Title   : next_obj
 Usage   : $obj = $adaptor->next_obj
 Function: Returns the next parsed BioPerl object from the 
 Returns : object of class obj_class()
 Args    : none


 Title   : rewind
 Usage   : 
 Function: Rewind the adaptor's iterator
 Returns : 
 Args    : none


 Title   : result
 Usage   : 
 Function: contains the SoapEUtilities::Result object
 Returns : Bio::DB::SoapEUtilities::Result object
 Args    : none


 Title   : type
 Usage   : 
 Function: contains the fetch type of this adaptor
 Returns : 
 Args    :