Raw content of Bio::SeqIO::MultiFile
<![CDATA[# $Id: MultiFile.pm,v 1.8 2002/10/22 07:38:42 lapp Exp $
#
# BioPerl module for Bio::SeqIO::MultiFile
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqIO::MultiFile - Treating a set of files as a single input stream
=head1 SYNOPSIS
$seqin = Bio::SeqIO::MultiFile( '-format' => 'Fasta',
'-files' => ['file1','file2'] );
while((my $seq = $seqin->next_seq)) {
# do something with $seq
}
=head1 DESCRIPTION
Bio::SeqIO::MultiFile provides a simple way of bundling a whole
set of identically formatted sequence input files as a single stream.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://www.bioperl.org/MailList.shtml - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Ewan Birney
Email birney@ebi.ac.uk
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::SeqIO::MultiFile;
use strict;
use vars qw(@ISA);
use Bio::SeqIO;
@ISA = qw(Bio::SeqIO);
# _initialize is where the heavy stuff will happen when new is called
sub _initialize {
my($self,@args) = @_;
$self->SUPER::_initialize(@args);
my ($file_array,$format) = $self->_rearrange([qw(
FILES
FORMAT
)],
@args,
);
if( !defined $file_array || ! ref $file_array ) {
$self->throw("Must have an array files for MultiFile");
}
if( !defined $format ) {
$self->throw("Must have a format for MultiFile");
}
$self->{'_file_array'} = [];
$self->_set_file(@$file_array);
$self->_format($format);
if( $self->_load_file() == 0 ) {
$self->throw("Unable even to initialise the first file");
}
}
=head2 next_seq
Title : next_seq
Usage :
Function:
Example :
Returns :
Args :
=cut
sub next_seq{
my ($self,@args) = @_;
my $seq = $self->_current_seqio->next_seq();
if( !defined $seq ) {
if( $self->_load_file() == 0) {
return undef;
} else {
return $self->next_seq();
}
} else {
return $seq;
}
}
=head2 next_primary_seq
Title : next_primary_seq
Usage :
Function:
Example :
Returns :
Args :
=cut
sub next_primary_seq{
my ($self,@args) = @_;
my $seq = $self->_current_seqio->next_primary_seq();
if( !defined $seq ) {
if( $self->_load_file() == 0) {
return undef;
} else {
return $self->next_primary_seq();
}
} else {
return $seq;
}
}
=head2 _load_file
Title : _load_file
Usage :
Function:
Example :
Returns :
Args :
=cut
sub _load_file{
my ($self,@args) = @_;
my $file = shift(@{$self->{'_file_array'}});
if( !defined $file ) {
return 0;
}
my $seqio = Bio::SeqIO->new( '-format' => $self->_format(), -file => $file);
# should throw an exception - but if not...
if( !defined $seqio) {
$self->throw("no seqio built for $file!");
}
$self->_current_seqio($seqio);
return 1;
}
=head2 _set_file
Title : _set_file
Usage :
Function:
Example :
Returns :
Args :
=cut
sub _set_file{
my ($self,@files) = @_;
push(@{$self->{'_file_array'}},@files);
}
=head2 _current_seqio
Title : _current_seqio
Usage : $obj->_current_seqio($newval)
Function:
Example :
Returns : value of _current_seqio
Args : newvalue (optional)
=cut
sub _current_seqio{
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'_current_seqio'} = $value;
}
return $obj->{'_current_seqio'};
}
=head2 _format
Title : _format
Usage : $obj->_format($newval)
Function:
Example :
Returns : value of _format
Args : newvalue (optional)
=cut
sub _format{
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'_format'} = $value;
}
return $obj->{'_format'};
}
1;
]]>