Raw content of Bio::Seq::SeqFastaSpeedFactory # $Id: SeqFastaSpeedFactory.pm,v 1.3 2002/11/07 23:54:23 lapp Exp $ # # BioPerl module for Bio::Seq::SeqFactory # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::SeqFactory - Instantiates a new Bio::PrimarySeqI (or derived class) through a factory =head1 SYNOPSIS use Bio::Seq::SeqFactory; my $factory = new Bio::Seq::SeqFactory; my $seq = $factory->create(-seq => 'WYRAVLC', -id => 'name'); # If you want the factory to create Bio::Seq objects instead # of the default Bio::PrimarySeq objects, use the -type parameter: my $factory = new Bio::Seq::SeqFactory(-type => 'Bio::Seq'); =head1 DESCRIPTION This object will build Bio::Seq objects generically. =head1 FEEDBACK =head2 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/MailList.shtml - About the mailing lists =head2 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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Jason Stajich Email jason@bioperl.org Describe contact details here =head1 CONTRIBUTORS Additional contributors names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::SeqFastaSpeedFactory; use vars qw(@ISA); use strict; use Bio::Root::Root; use Bio::Factory::SequenceFactoryI; use Bio::Seq; use Bio::PrimarySeq; @ISA = qw(Bio::Root::Root Bio::Factory::SequenceFactoryI); =head2 new Title : new Usage : my $obj = new Bio::Seq::SeqFactory(); Function: Builds a new Bio::Seq::SeqFactory object Returns : Bio::Seq::SeqFactory Args : -type => string, name of a PrimarySeqI derived class This is optional. Default=Bio::PrimarySeq. =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); return $self; } =head2 create Title : create Usage : my $seq = $seqbuilder->create(-seq => 'CAGT', -id => 'name'); Function: Instantiates a new Bio::Seq object, correctly built but very fast, knowing stuff about Bio::PrimarySeq and Bio::Seq Returns : Bio::Seq Args : initialization parameters specific to the type of sequence object we want. Typically -seq => $str, -id => $name =cut sub create { my ($self,%param) = @_; my $sequence = $param{'-seq'} || $param{'-SEQ'}; my $fulldesc = $param{'-desc'} || $param{'-DESC'}; my $id = $param{'-id'} || $param{'-ID'} || $param{'-primary_id'} || $param{'-PRIMARY_ID'}; my $seq = bless {}, "Bio::Seq"; my $t_pseq = $seq->{'primary_seq'} = bless {}, "Bio::PrimarySeq"; $t_pseq->{'seq'} = $sequence; $t_pseq->{'desc'} = $fulldesc; $t_pseq->{'display_id'} = $id; $t_pseq->{'primary_id'} = $id; $seq->{'primary_id'} = $id; # currently Bio::Seq does not delegate this if( $sequence ) { $t_pseq->_guess_alphabet(); } return $seq; } 1;