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.\" ========================================================================
.\"
.IX Title "Bio::Annotation::AnnotationFactory 3pm"
.TH Bio::Annotation::AnnotationFactory 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::Annotation::AnnotationFactory \- Instantiates a new 
Bio::AnnotationI (or derived class) through a factory
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 6
\&    use Bio::Annotation::AnnotationFactory;
\&    # 
\&    my $factory = Bio::Annotation::AnnotationFactory\->new(
\&                    \-type => \*(AqBio::Annotation::SimpleValue\*(Aq);
\&    my $ann = $factory\->create_object(\-value => \*(Aqperoxisome\*(Aq,
\&                                      \-tagname => \*(Aqcellular component\*(Aq);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object will build Bio::AnnotationI 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 5
\& Title   : new
\& Usage   : my $obj = Bio::Annotation::AnnotationFactory\->new();
\& Function: Builds a new Bio::Annotation::AnnotationFactory object 
\& Returns : Bio::Annotation::AnnotationFactory
\& Args    : \-type => string, name of a L<Bio::AnnotationI> derived class.
.Ve
.PP
If type is not set the module guesses it based on arguments passed to
method create_object.
.SS "create_object"
.IX Subsection "create_object"
.Vb 3
\& Title   : create_object
\& Usage   : my $seq = $factory\->create_object(<named parameters>);
\& Function: Instantiates new Bio::AnnotationI (or one of its child classes)
\&
\&           This object allows us to genericize the instantiation of
\&           cluster objects.
\&
\& Returns : L<Bio::AnnotationI> compliant object
\&           The return type is configurable using new(\-type =>"...").
\& Args    : initialization parameters specific to the type of annotation
\&           object we want.
.Ve
.SS "type"
.IX Subsection "type"
.Vb 3
\& Title   : type
\& Usage   : $obj\->type($newval)
\& Function: Get/set the type of L<Bio::AnnotationI> object to be created.
\&
\&           This may be changed at any time during the lifetime of this
\&           factory.
\&
\& Returns : value of type
\& Args    : newvalue (optional)
.Ve
.SS "_guess_type"
.IX Subsection "_guess_type"
.Vb 9
\& Title   : _guess_type
\& Usage   :
\& Function: Guesses the right type of L<Bio::AnnotationI> implementation
\&           based on initialization parameters for the prospective
\&           object.
\& Example :
\& Returns : the type (a string, the module name)
\& Args    : initialization parameters to be passed to the prospective
\&           cluster object
.Ve