Bio::Annotation::AnnotationFactory

NAME

Bio::Annotation::AnnotationFactory - Instantiates a new Bio::AnnotationI (or derived class) through a factory

SYNOPSIS

    use Bio::Annotation::AnnotationFactory;
    # 
    my $factory = Bio::Annotation::AnnotationFactory->new(
                    -type => 'Bio::Annotation::SimpleValue');
    my $ann = $factory->create_object(-value => 'peroxisome',
                                      -tagname => 'cellular component');

DESCRIPTION

This object will build Bio::AnnotationI objects generically.

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:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Hilmar Lapp

Email hlapp at gmx.net

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.

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::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.

If type is not set the module guesses it based on arguments passed to method create_object.

create_object

 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.

type

 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)

_guess_type

 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