/ 
BioPerl-Run-1.007001
River stage one • 2 direct dependents • 2 total dependents
/ Bio::DB::SoapEUtilities::FetchAdaptor

NAME

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

SYNOPSIS

$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
}

DESCRIPTION

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

SEE ALSO

Bio::DB::SoapEUtilities, FetchAdaptor subclasses

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Mark A. Jensen

Email maj -at- fortinbras -dot- us

APPENDIX

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

new

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 )

_initialize()

Title   : _initialize
Usage   : 
Function: 
Returns : 
Args    :

_load_adaptor()

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

obj_class()

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

next_obj()

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

rewind()

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

result()

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

type()

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