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# $Id: 
#
# BioPerl module for Bio::SeqIO::game::gameHandler
#
# Cared for by Sheldon McKay <mckays@cshl.edu>
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
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=head1 NAME
Bio::SeqIO::game::gameHandler -- PerlSAX handler for game-XML
=head1 SYNOPSIS
This modules is not used directly
=head1 DESCRIPTION
Bio::SeqIO::game::gameHandler is the top-level XML handler invoked by PerlSAX
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
  http://bugzilla.open-bio.org/
=head1 AUTHOR - Sheldon McKay
Email mckays@cshl.edu
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::SeqIO::game::gameHandler;
use Bio::SeqIO::game::seqHandler;
use strict;
use vars qw {};
use base qw(Bio::SeqIO::game::gameSubs);
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=head2 start_document
 Title   : start_document
 Function: begin parsing the document
=cut
sub start_document {
    my ($self, $document) = @_;
    $self->SUPER::start_document($document);
     
    $self->{sequences}    = {};
    $self->{annotations}  = {};
    $self->{computations} = {};
    $self->{map_position} = {};
    $self->{focus}        = {};
}
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=head2 end_document
 Title   : end_document
 Function: finish parsing the document
=cut
sub end_document {
    my ($self, $document) = @_;
     
    $self->SUPER::end_document($document);
     
    return $self;    
}
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=head2 load
 Title   : load
 Usage   : $seqs = $handler->load
 Function: start parsing
 Returns : a ref to a list of sequence objects
 Args    : an optional flag to supress <computation_analysis> elements (not used yet)
=cut
sub load {
    my $self = shift;
    my $suppress_comps = shift;
    my @seqs = ();
     
    for ( 1..$self->{game} ) {
        my $seq  = $self->{sequences}->{$_} 
          or $self->throw("No sequences defined");
        my $ann  = $self->{annotations}->{$_};
        my $comp = $self->{computations}->{$_};
        my $map  = $self->{map_position}->{$_};
        my $foc  = $self->{focus}->{$_}
          or $self->throw("No main sequence defined");
        my $src  = $self->{has_source};
         
        my $bio = Bio::SeqIO::game::seqHandler->new( $seq, $ann, $comp, $map, $src );
        push @seqs, $bio->convert;
    }
     
    \@seqs;
}
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=head2 s_game
 Title   : s_game
 Function: begin parsing game element
=cut
sub s_game {
    my ($self, $e) = @_;
    my $el = $self->curr_element;
    $self->{game}++;
     
    my $version = $el->{Attributes}->{version};
     
    unless ( defined $version ) {
        $self->complain("No GAME-xml version specified -- guessing v1.2\n");
        $version = 1.2;
    }
    if ( defined($version) && $version == 1.2) {
        $self->{origin_offset} = 1;
    } else {
        $self->{origin_offset} = 0;
    }
    if (defined($version) && ($version != 1.2)) {
        $self->complain("GAME version $version is not supported\n",
                        "I'll try anyway but I may fail!\n");
    }
     
}
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=head2 e_game
 Title   : e_game
 Function: process the game element
=cut
sub e_game {
    my ($self, $el) = @_;
    $self->flush( $el );
}
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=head2 e_seq
 Title   : e_seq
 Function: process the sequence element
=cut
sub e_seq {
    my ($self, $e) = @_;
    my $el = $self->curr_element();
    $self->{sequences}->{$self->{game}} ||= [];
    my $seqs = $self->{sequences}->{$self->{game}};
     
    if ( defined $el->{Attributes}->{focus} ) {
        $self->{focus}->{$self->{game}} = $el;
    }
    push @{$seqs}, $el;
     
    $self->flush;
}
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=head2 e_map_position
 Title   : e_map_position
 Function: process the map_position element
=cut
sub e_map_position {
    my ($self, $e) = @_;
    my $el = $self->curr_element;
    $self->{map_position}->{$self->{game}} = $el;
}
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=head2 e_annotation
 Title   : e_annotation
 Function: process the annotation
=cut
sub e_annotation {
    my ($self, $e) = shift;
    my $el = $self->curr_element;
    $self->{annotations}->{$self->{game}} ||= [];
    my $anns = $self->{annotations}->{$self->{game}};
    push @{$anns}, $el;
}
1;