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Summary

Bio::SeqIO::game::gameHandler -- PerlSAX handler for game-XML

Package variables

Included modules

Inherit

Bio::SeqIO::game::gameSubs

Synopsis

This modules is not used directly

Description

Bio::SeqIO::game::gameHandler is the top-level XML handler invoked by PerlSAX

Methods

Methods description

 Title   : start_document
 Function: begin parsing the document

 Title   : end_document
 Function: finish parsing the document

 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)

 Title   : s_game
 Function: begin parsing game element

 Title   : e_game
 Function: process the game element

 Title   : e_seq
 Function: process the sequence element

 Title   : e_map_position
 Function: process the map_position element

 Title   : e_annotation
 Function: process the annotation

Methods code

sub start_document {

    my ($self, $document) = @_;

    $self->SUPER::start_document($document);
    
    $self->{sequences}    = {};
    $self->{annotations}  = {};
    $self->{computations} = {};
    $self->{map_position} = {};
    $self->{focus}        = {};

}

sub end_document {

    my ($self, $document) = @_;
    
    $self->SUPER::end_document($document);
    
    return $self;

}

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;

}

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");
    }

}

sub e_game {

    my ($self, $el) = @_;
    $self->flush( $el );

}

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;

}

sub e_map_position {

    my ($self, $e) = @_;
    my $el = $self->curr_element;
    $self->{map_position}->{$self->{game}} = $el;

}

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;

}

General documentation

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

Please direct usage questions or support issues to the mailing list:
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.

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:

  https://redmine.open-bio.org/projects/bioperl/

Email mckays@cshl.edu

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _