Bio::Seq SeqFactory
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Summary
Bio::Seq::SeqFactory - Instantiation of generic Bio::PrimarySeqI (or derived) objects through a factory
Package variables
No package variables defined.
Inherit
Bio::Factory::SequenceFactoryI Bio::Root::Root
Synopsis
    use Bio::Seq::SeqFactory;
my $factory = Bio::Seq::SeqFactory->new();
my $primaryseq = $factory->create( -seq => 'WYRAVLC',
-id => 'name' );
# Create Bio::Seq instead of Bio::PrimarySeq objects: my $factory = Bio::Seq::SeqFactory->new( -type => 'Bio::Seq' );
Description
This object will build Bio::PrimarySeqI and Bio::SeqI objects
generically.
Methods
newDescriptionCode
createDescriptionCode
typeDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Seq::SeqFactory->new();
Function: Builds a new Bio::Seq::SeqFactory object
Returns : Bio::Seq::SeqFactory
Args : -type => string, name of a PrimarySeqI derived class
This is optional. Default=Bio::PrimarySeq.
createcodeprevnextTop
 Title   : create
Usage : my $seq = $seqbuilder->create(-seq => 'CAGT', -id => 'name');
Function: Instantiates new Bio::SeqI (or one of its child classes)
This object allows us to genericize the instantiation of sequence
objects.
Returns : Bio::PrimarySeq object (default)
The return type is configurable using new(-type =>"...").
Args : initialization parameters specific to the type of sequence
object we want. Typically
-seq => $str,
-display_id => $name
typecodeprevnextTop
 Title   : type
Usage : $obj->type($newval)
Function:
Returns : value of type
Args : newvalue (optional)
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  my ($type) = $self->_rearrange([qw(TYPE)], @args);
  if( ! defined $type ) { 
      $type = 'Bio::PrimarySeq';
  }
  $self->type($type);
  return $self;
}
createdescriptionprevnextTop
sub create {
   my ($self,@args) = @_;
   return $self->type->new(-verbose => $self->verbose, @args);
}
typedescriptionprevnextTop
sub type {
   my ($self, $value) = @_;
   if (defined $value) {
       eval "require $value";
       if( $@ ) { $self->throw("$@: Unrecognized Sequence type for SeqFactory '$value'");}
       
       my $a = bless {},$value;
       unless( $a->isa('Bio::PrimarySeqI') ||
               $a->isa('Bio::Seq::QualI' ) ) {
           $self->throw("Must provide a valid Bio::PrimarySeqI or Bio::Seq::QualI or child class to SeqFactory Not $value");
       }
       $self->{'type'} = $value;
    }
    return $self->{'type'};
}

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 - Jason StajichTop
Email jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _