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.\" ========================================================================
.\"
.IX Title "Bio::Factory::ObjectFactory 3pm"
.TH Bio::Factory::ObjectFactory 3pm "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Bio::Factory::ObjectFactory \- Instantiates a new Bio::Root::RootI (or derived class) through a factory
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&    use Bio::Factory::ObjectFactory;
\&
\&    my $factory = Bio::Factory::ObjectFactory\->new(\-type => \*(AqBio::Ontology::GOterm\*(Aq);
\&    my $term = $factory\->create_object(\-name => \*(Aqperoxisome\*(Aq,
\&                                       \-ontology => \*(AqGene Factory\*(Aq,
\&                                       \-identifier => \*(AqGO:0005777\*(Aq);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object will build Bio::Root::RootI objects generically.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Hilmar Lapp"
.IX Header "AUTHOR - Hilmar Lapp"
Email hlapp at gmx.net
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
This is mostly copy-and-paste with subsequent adaptation from
Bio::Seq::SeqFactory by Jason Stajich. Most credits should in fact go
to him.
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 9
\& Title   : new
\& Usage   : my $obj = Bio::Factory::ObjectFactory\->new();
\& Function: Builds a new Bio::Factory::ObjectFactory object 
\& Returns : Bio::Factory::ObjectFactory
\& Args    : \-type      => string, name of a L<Bio::Root::RootI> derived class.
\&                         There is no default.
\&           \-interface => string, name of the interface or class any type
\&                         specified needs to at least implement.
\&                         The default is Bio::Root::RootI.
.Ve
.SS "create_object"
.IX Subsection "create_object"
.Vb 3
\& Title   : create_object
\& Usage   : my $seq = $factory\->create_object(<named parameters>);
\& Function: Instantiates a new object of the previously set type.
\&
\&           This object allows us to genericize the instantiation of
\&           objects.
\&
\&           You must have provided \-type at instantiation, or have
\&           called type($mytype) before you can call this method.
\&
\& Returns : an object of the type returned by type()
\&
\&           The return type is configurable using new(\-type =>"..."),
\&           or by calling $self\->type("My::Fancy::Class").
\& Args    : Initialization parameters specific to the type of
\&           object we want. Check the POD of the class you set as type.
.Ve
.SS "type"
.IX Subsection "type"
.Vb 3
\& Title   : type
\& Usage   : $obj\->type($newval)
\& Function: Get/set the type of object to be created.
\&
\&           This may be changed at any time during the lifetime of this
\&           factory.
\&
\& Returns : value of type (a string)
\& Args    : newvalue (optional, a string)
.Ve
.SS "interface"
.IX Subsection "interface"
.Vb 7
\& Title   : interface
\& Usage   : $obj\->interface($newval)
\& Function: Get/set the interface or base class that supplied types
\&           must at least implement (inherit from).
\& Example : 
\& Returns : value of interface (a scalar)
\& Args    : on set, new value (a scalar or undef, optional)
.Ve
.SS "_validate_type"
.IX Subsection "_validate_type"
.Vb 4
\& Title   : _validate_type
\& Usage   : $factory\->_validate_type($object)
\& Function: Called to let derived factories validate the type set
\&           via type().
\&
\&           The default implementation here checks whether the supplied
\&           object skeleton implements the interface set via \-interface
\&           upon factory instantiation.
\&
\& Example :
\& Returns : TRUE if the type is to be considered valid, and FALSE otherwise.
\&           Instead of returning FALSE this method may also just throw
\&           an informative exception.
\&
\&           The default implementation here will throw an exception
\&           if the supplied object does not inherit from the interface
\&           provided by the interface() method.
\&
\& Args    : A hash reference blessed into the specified type, allowing
\&           queries like isa().
.Ve