Bio::Annotation AnnotationFactory
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Summary
Bio::Annotation::AnnotationFactory - Instantiates a new
Bio::AnnotationI (or derived class) through a factory
Package variables
No package variables defined.
Inherit
Bio::Factory::ObjectFactoryI Bio::Root::Root
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.
Methods
newDescriptionCode
create_objectDescriptionCode
typeDescriptionCode
_guess_typeDescriptionCode
Methods description
newcode    nextTop
 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 Bio::AnnotationI derived class.
If type is not set the module guesses it based on arguments passed to
method create_object.
create_objectcodeprevnextTop
 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 : Bio::AnnotationI compliant object
The return type is configurable using new(-type =>"...").
Args : initialization parameters specific to the type of annotation
object we want.
typecodeprevnextTop
 Title   : type
Usage : $obj->type($newval)
Function: Get/set the type of 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_typecodeprevnextTop
 Title   : _guess_type
Usage :
Function: Guesses the right type of 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
Methods code
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;

    my $self = $class->SUPER::new(@args);
  
    my ($type) = $self->_rearrange([qw(TYPE)], @args);

    $self->{'_loaded_types'} = {};
    $self->type($type) if $type;

    return $self;
}
create_objectdescriptionprevnextTop
sub create_object {
   my ($self,@args) = @_;

   my $type = $self->type; 
   if(! $type) {
       # we need to guess this
$type = $self->_guess_type(@args); if(! $type) { $self->throw("No annotation type set and unable to guess."); } # load dynamically if it hasn't been loaded yet
if(! $self->{'_loaded_types'}->{$type}) { eval { $self->_load_module($type); $self->{'_loaded_types'}->{$type} = 1; }; if($@) { $self->throw("Bio::AnnotationI implementation $type ". "failed to load: ".$@); } } } return $type->new(-verbose => $self->verbose, @args);
}
typedescriptionprevnextTop
sub type {
    my $self = shift;

    if(@_) {
    my $type = shift;
    if($type && (! $self->{'_loaded_types'}->{$type})) {
        eval {
        $self->_load_module($type);
        };
        if( $@ ) {
        $self->throw("Annotation class '$type' failed to load: ".
                 $@);
        }
        my $a = bless {},$type;
        if( ! $a->isa('Bio::AnnotationI') ) {
        $self->throw("'$type' does not implement Bio::AnnotationI. ".
                 "Too bad.");
        }
        $self->{'_loaded_types'}->{$type} = 1;
    }
    return $self->{'type'} = $type;
    }
    return $self->{'type'};
}
_guess_typedescriptionprevnextTop
sub _guess_type {
    my ($self,@args) = @_;
    my $type;

    # we can only guess from a certain number of arguments
my ($val, $db, $text, $name, $authors, $start, $tree, $node) = $self->_rearrange([qw(VALUE DATABASE TEXT NAME AUTHORS START TREE_OBJ NODE )], @args); SWITCH: { $val && do { $type = ref($val) ? "TagTree" : "SimpleValue"; last SWITCH; }; $authors && do { $type = "Reference"; last SWITCH; }; $db && do { $type = "DBLink"; last SWITCH; }; $text && do { $type = "Comment"; last SWITCH; }; $name && do { $type = "OntologyTerm"; last SWITCH; }; $start && do { $type = "Target"; last SWITCH; }; $tree && do { $type = "Tree"; last SWITCH; }; $node && do { $type = "TagTree"; last SWITCH; }; # what else could we look for?
} $type = "Bio::Annotation::".$type; return $type; } #####################################################################
# aliases for naming consistency or other reasons #
#####################################################################
*create =\& create_object; 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar LappTop
Email hlapp at gmx.net
CONTRIBUTORSTop
This is mostly copy-and-paste with subsequent adaptation from
Bio::Seq::SeqFactory by Jason Stajich. Most credits should in fact go
to him.
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _