Bio::SeqIO::game gameHandler
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Summary
Bio::SeqIO::game::gameHandler -- PerlSAX handler for game-XML
Package variables
No package variables defined.
Included modules
Bio::SeqIO::game::seqHandler
strict
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
start_documentDescriptionCode
end_documentDescriptionCode
loadDescriptionCode
s_gameDescriptionCode
e_gameDescriptionCode
e_seqDescriptionCode
e_map_positionDescriptionCode
e_annotationDescriptionCode
Methods description
start_documentcode    nextTop
 Title   : start_document
Function: begin parsing the document
end_documentcodeprevnextTop
 Title   : end_document
Function: finish parsing the document
loadcodeprevnextTop
 Title   : load
Usage : $seqs = $handler->load
Function: start parsing
Returns : a ref to a list of sequence objects
Args : an optional flag to supress <computation_analysis> elements (not used yet)
s_gamecodeprevnextTop
 Title   : s_game
Function: begin parsing game element
e_gamecodeprevnextTop
 Title   : e_game
Function: process the game element
e_seqcodeprevnextTop
 Title   : e_seq
Function: process the sequence element
e_map_positioncodeprevnextTop
 Title   : e_map_position
Function: process the map_position element
e_annotationcodeprevnextTop
 Title   : e_annotation
Function: process the annotation
Methods code
start_documentdescriptionprevnextTop
sub start_document {
    my ($self, $document) = @_;

    $self->SUPER::start_document($document);
    
    $self->{sequences}    = {};
    $self->{annotations}  = {};
    $self->{computations} = {};
    $self->{map_position} = {};
    $self->{focus}        = {};
}
end_documentdescriptionprevnextTop
sub end_document {
    my ($self, $document) = @_;
    
    $self->SUPER::end_document($document);
    
    return $self;
}
loaddescriptionprevnextTop
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;
}
s_gamedescriptionprevnextTop
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 $version is not supported\n",
		        "I'll try anyway but I may fail!\n");
    }
}
e_gamedescriptionprevnextTop
sub e_game {
    my ($self, $el) = @_;
    $self->flush( $el );
}
e_seqdescriptionprevnextTop
sub e_seq {
    my ($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;
    
    $self->flush;
}
e_map_positiondescriptionprevnextTop
sub e_map_position {
    my ($self, $e) = @_;
    my $el = $self->curr_element;
    $self->{map_position}->{$self->{game}} = $el;
}
e_annotationdescriptionprevnextTop
sub e_annotation {
    my ($self, $e) = shift;
    my $el = $self->curr_element;
    $self->{annotations}->{$self->{game}} ||= [];
    my $anns = $self->{annotations}->{$self->{game}};
    push @{$anns}, $el;
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
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.
Reporting BugsTop
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/
AUTHOR - Sheldon McKayTop
Email mckays@cshl.edu
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _