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.

  [email protected]                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list: [email protected] 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    :