Raw content of Bio::SeqIO::alf # $Id: alf.pm,v 1.7 2002/10/22 07:38:42 lapp Exp $ # BioPerl module for Bio::SeqIO::alf # # Cared for by Aaron Mackey <amackey@virginia.edu> # # Copyright Aaron Mackey # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::alf - alf trace sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. =head1 DESCRIPTION This object can transform Bio::Seq objects to and from alf trace files. =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 one of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ =head1 AUTHORS - Aaron Mackey Email: amackey@virginia.edu =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::SeqIO::alf; use vars qw(@ISA $READ_AVAIL); use strict; # Object preamble - inherits from Bio::Root::Object use Bio::SeqIO; use Bio::Seq::SeqFactory; push @ISA, qw( Bio::SeqIO ); sub BEGIN { eval { require Bio::SeqIO::staden::read; }; if ($@) { $READ_AVAIL = 0; } else { push @ISA, "Bio::SeqIO::staden::read"; $READ_AVAIL = 1; } } sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); if( ! defined $self->sequence_factory ) { $self->sequence_factory(new Bio::Seq::SeqFactory(-verbose => $self->verbose(), -type => 'Bio::Seq')); } unless ($READ_AVAIL) { Bio::Root::Root->throw( -class => 'Bio::Root::SystemException', -text => "Bio::SeqIO::staden::read is not available; make sure the bioperl-ext package has been installed successfully!" ); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::SeqWithQuality object Args : NONE =cut sub next_seq { my ($self) = @_; my ($seq, $id, $desc, $qual) = $self->read_trace($self->_fh, 'alf'); # create the seq object $seq = $self->sequence_factory->create(-seq => $seq, -id => $id, -primary_id => $id, -desc => $desc, -alphabet => 'DNA', -qual => $qual ); return $seq; } =head2 write_seq Title : write_seq Usage : $stream->write_seq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object =cut sub write_seq { my ($self,@seq) = @_; my $fh = $self->_fh; foreach my $seq (@seq) { $self->write_trace($fh, $seq, 'alf'); } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } 1;