Bio::Factory::SequenceFactoryI.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Factory::SequenceFactoryI - This interface allows for generic building of sequences in factories which create sequences (like SeqIO)

SYNOPSIS

# do not use this object directly it is an interface # get a Bio::Factory::SequenceFactoryI object like
     use Bio::Seq::SeqFactory;
     my $seqbuilder = Bio::Seq::SeqFactory->new('-type' => 'Bio::PrimarySeq');
 
     my $seq = $seqbuilder->create(-seq => 'ACTGAT',
                                   -display_id => 'exampleseq');
 
     print "seq is a ", ref($seq), "\n";
 
 

DESCRIPTION

A generic way to build Sequence objects via a pluggable factory. This reduces the amount of code that looks like
   if( $type  eq 'Bio::PrimarySeq' ) { ... } 
   elsif( $type eq 'Bio::Seq::RichSeq' ) { ... }
 
 

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.
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

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 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:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason-at-bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

create

  Title   : create
  Usage   : my $seq = $seqbuilder->create(-seq => 'CAGT', 
                                          -id => 'name');
  Function: Instantiates new Bio::PrimarySeqI (or one of its child classes)
            This object allows us to genericize the instantiation of sequence
            objects.
  Returns : Bio::PrimarySeqI
  Args    : initialization parameters specific to the type of sequence
            object we want.  Typically 
            -seq        => $str,
            -display_id => $name