The London Perl and Raku Workshop takes place on 26th Oct 2024. If your company depends on Perl, please consider sponsoring and/or attending.

NAME

Bio::DB::Query::DBQueryResult - DESCRIPTION of Object

SYNOPSIS

Give standard usage here

DESCRIPTION

This modules provides an implementation of Bio::DB::Query::QueryResultI for database queries through DBI.

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 - Hilmar Lapp

Email hlapp at gmx.net

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

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 = Bio::DB::Query::DBQueryResult->new();
 Function: Builds a new Bio::DB::Query::DBQueryResult object 
 Returns : an instance of Bio::DB::Query::DBQueryResult
 Args    : named parameters

           -sth        the statement handle (this object will not
                       execute it)

           -adaptor    the persistence adaptor (basically needs to 
                       implement instantiate_from_row($row, $factory)

           -factory    optionally, the object factory to pass to the
                       adaptor

	   -num_fks    the number of foreign key object columns in
                       the rows

           -flat_only  whether to retrieve and attach children when
                       building objects (default: false)

           If none of these are given at instantiation, at least sth() and
           persistence_adaptor() must be set prior to calling next_object().

next_object

Title   : next_object
Usage   :
Function: Obtain the next object from the result stream and return it.
Example :
Returns : A Bioperl object (implementing at least Bio::Root::RootI)
Args    : none

each_Object

Title   : each_Object
Usage   :
Function: This is primarily a convenience method and in most implementations
          will just loop over next_object() and return an array of all
          objects.
Example :
Returns : A reference to an array of objects.
Args    : Optionally, an anonymous function for filtering objects. If given,
          the function is passed one argument, the object to evaluate.
          The object will be included in the returned array if the function
          returns TRUE, and rejected otherwise.

finish

Title   : finish
Usage   :
Function: Indicate being finished with this result so that possibly used
          system resources can be released.
Example :
Returns : none
Args    : none

sth

Title   : sth
Usage   : $obj->sth($newval)
Function: Get/set statement handle from which to fetch the next row.

          This can be changed at any time. If changed, it means the next
          call to next_object() will fetch from the new handle. Also, the
          caller needs to finish() the previous handle if necessary (i.e.,
          if not exhausted).

          Note that this object will not execute the statement handle. The
          caller needs to ensure that has been happened until next_object()
          is called.
Example : 
Returns : value of sth (a DBI statement handle)
Args    : new value (a DBI statement handle, optional)

persistence_adaptor

Title   : persistence_adaptor
Usage   : $obj->persistence_adaptor($newval)
Function: Get/set the instantiation adaptor to which to delegate object
          instantiation from an array of row values.

          The adaptor can be any object that implements instantiate_from_row()
          with two arguments, a reference to an array of column values, and
          optionally an object factory.

          This can be changed at any time with no adverse side effect other
          than the kind of object built possibly changing.
Example : 
Returns : value of persistence_adaptor (an object)
Args    : new value (an object, optional)

object_factory

Title   : object_factory
Usage   : $obj->object_factory($newval)
Function: Get/set the object factory to pass to the instantiation adaptor.

          Setting this is optional because providing it to the instantiation
          adaptor is optional.
Example : 
Returns : value of object_factory (a Bio::Factory::ObjectFactoryI compliant
          instance)
Args    : new value (a Bio::Factory::ObjectFactoryI compliant
          instance, optional)

num_fks

Title   : num_fks
Usage   : $obj->num_fks($newval)
Function: Get/set the number of foreign key columns in a given result row.

          Setting this correctly is only important for query results for which
          the resulting objects must have the foreign key objects attached.
Example : 
Returns : value of num_fks (a scalar)
Args    : new value (a scalar, optional)

flat_retrieval

Title   : flat_retrieval
Usage   : $obj->flat_retrieval($newval)
Function: Get/set whether objects should be retrieved and built flat
          or with all their dependent objects fetched and attached.

          The default is to build full objects with all children
          attached which provides for no bad surprises when
          inspecting the results. However, building flat objects by
          disregarding children is potentially a lot faster, so this
          option is useful if, for instance, for a sequence you don't
          need any annotation or features.

Example : 
Returns : value of flat_retrieval (a scalar evaluating to true or false)
Args    : on set, new value (a scalar or undef, optional)