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#
# BioPerl module for Bio::SeqIO::MultiFile
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# 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
HideShow 58 lines of Pod
=head1 NAME
Bio::SeqIO::MultiFile - Treating a set of files as a single input stream
=head1 SYNOPSIS
   my $seqin = Bio::SeqIO::MultiFile->new( -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.
File format is automatically determined by C<Bio::SeqIO>.
=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/wiki/Mailing_lists  - About the mailing lists
=head2 Support 
Please direct usage questions or support issues to the mailing list:
I<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.
=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 the web:
  https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Ewan Birney
Email birney@ebi.ac.uk
=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;
$Bio::SeqIO::MultiFile::VERSION = '1.7.8';
use strict;
use base qw(Bio::SeqIO);
# _initialize is where the heavy stuff will happen when new is called
sub _initialize {
    my($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");
    }
    $self->{'_file_array'} = [];
    $self->_set_file(@$file_array);
    $self->format($format) if defined $format;
    if( $self->_load_file() == 0 ) {
        $self->throw("Unable to initialise the first file");
    }
}
HideShow 11 lines of Pod
=head2 next_seq
 Title   : next_seq
 Usage   :
 Function:
 Example :
 Returns :
 Args    :
=cut
sub next_seq{
    my ($self, @args) = @_;
    my $seq = $self->_current_seqio->next_seq();
    if( !defined $seq ) {
        if( $self->_load_file() == 0) {
            return;
        } else {
            return $self->next_seq();
        }
    } else {
        return $seq;
    }
}
HideShow 11 lines of Pod
=head2 next_primary_seq
 Title   : next_primary_seq
 Usage   :
 Function:
 Example :
 Returns :
 Args    :
=cut
sub next_primary_seq{
    my ($self, @args) = @_;
    my $seq = $self->_current_seqio->next_primary_seq();
    if( !defined $seq ) {
        if( $self->_load_file() == 0) {
            return;
        } else {
            return $self->next_primary_seq();
        }
    } else {
        return $seq;
    }
}
HideShow 11 lines of Pod
=head2 _load_file
 Title   : _load_file
 Usage   :
 Function:
 Example :
 Returns :
 Args    :
=cut
sub _load_file{
    my ($self, @args) = @_;
    my $file = shift @{$self->{'_file_array'}};
    if( !defined $file ) {
        return 0;
    }
    my $seqio;
    my $format = $self->format;
    if ($format) {
        $seqio = Bio::SeqIO->new( -file => $file, -format => $format );
    } else {
        $seqio = Bio::SeqIO->new( -file => $file );
        $self->format($seqio->format) if not $format;
    }
    # should throw an exception - but if not...
    if( !defined $seqio) {
        $self->throw("Could not build SeqIO object for $file!");
    }
    $self->_current_seqio($seqio);
    return 1;
}
HideShow 11 lines of Pod
=head2 _set_file
 Title   : _set_file
 Usage   :
 Function:
 Example :
 Returns :
 Args    :
=cut
sub _set_file{
    my ($self, @files) = @_;
    push @{$self->{'_file_array'}}, @files;
}
HideShow 11 lines of Pod
=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 $obj->{'_current_seqio'};
}
# We overload the format() method of Bio::Root::IO by a simple get/set
sub format{
    my ($obj, $value) = @_;
    if( defined $value) {
        $obj->{'_format'} = $value;
    }
    return $obj->{'_format'};
}
1;