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Summary

Bio::SeqIO::game::featureHandler - GAME helper via PerlSAX helper.

Package variables

Included modules

Inherit

XML::Handler::Subs

Synopsis

GAME helper for parsing new Feature objects from GAME XML. Do not use directly.

Description

No description!

Methods

Methods description

 Title   : AUTOLOAD
 Usage   : do not use directly
 Function: autoload handling of missing DESTROY method
 Returns : nothing
 Args    : text

 Title   : characters
 Usage   : $obj->end_element
 Function: PerlSAX method called when text between XML tags is reached
 Returns : nothing
 Args    : text

 Title   : end_document
 Usage   : $obj->end_document
 Function: PerlSAX method called when a document is finished for cleaning up
 Returns : list of features seen
 Args    : document name

 Title   : end_element
 Usage   : $obj->end_element
 Function: PerlSAX method called when an element is finished
 Returns : nothing
 Args    : element object

 Title   : in_element
 Usage   : $obj->in_element
 Function: PerlSAX method called to test if state is in a specific element
 Returns : boolean
 Args    : name of element

 Title   : start_document
 Usage   : $obj->start_document
 Function: PerlSAX method called when a new document is initialized
 Returns : nothing
 Args    : document name

 Title   : start_element
 Usage   : $obj->start_element
 Function: PerlSAX method called when a new element is reached
 Returns : nothing
 Args    : element object

 Title   : within_element
 Usage   : $obj->within_element
 Function: PerlSAX method called to list depth within specific element
 Returns : boolean
 Args    : name of element

Methods code

sub AUTOLOAD {

    my $self = shift;

    my $method = $AUTOLOAD;
    $method =~ s/.*:://;
    return if $method eq 'DESTROY';

    print "UNRECOGNIZED $method\n";
}

1;

__END__

}

sub characters {

    my ($self, $text) = @_;
    $self->{'string'} .= $text->{'Data'};

}

sub end_document {

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

    delete $self->{'Names'};
    return $self->{'feats'};

}

sub end_element {

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

    if ($self->in_element('bx-computation:program')) {
	$self->{'string'} =~ s/^\s+//g;
	$self->{'string'} =~ s/\s+$//;
	$self->{'string'} =~ s/\n//g;
	$self->{'feat'}->{'source_tag'} = $self->{'string'};
    }

    if ($self->in_element('bx-annotation:author')) {
	$self->{'string'} =~ s/^\s+//g;
	$self->{'string'} =~ s/\s+$//;
	$self->{'string'} =~ s/\n//g;
	$self->{'feat'}->{'source_tag'} = "Annotated by $self->{'string'}.";
    }

    if ($self->in_element('bx-feature:type')) {
	$self->{'string'} =~ s/^\s+//g;
	$self->{'string'} =~ s/\s+$//;
	$self->{'string'} =~ s/\n//g;
	$self->{'feat'}->{'primary_tag'} = $self->{'string'};
    }

    if ($self->in_element('bx-feature:start')) {
	$self->{'string'} =~ s/^\s+//g;
	$self->{'string'} =~ s/\s+$//;
	$self->{'string'} =~ s/\n//g;
	$self->{'feat'}->{'start'} = $self->{'string'};
    }

    if ($self->in_element('bx-feature:end')) {
	$self->{'string'} =~ s/^\s+//g;
	$self->{'string'} =~ s/\s+$//;
	$self->{'string'} =~ s/\n//g;
	$self->{'feat'}->{'end'} = $self->{'string'};
    }

    if ($self->in_element('bx-computation:score')) {
	$self->{'string'} =~ s/^\s+//g;
	$self->{'string'} =~ s/\s+$//;
	$self->{'string'} =~ s/\n//g;
	$self->{'feat'}->{'score'} = $self->{'string'};
    }

    if ($self->in_element('bx-feature:seq_relationship')) {
	
	if ($self->{'feat'}->{'start'} > $self->{'feat'}->{'end'}) {
	    my $new_start = $self->{'feat'}->{'end'};
	    $self->{'feat'}->{'end'} = $self->{'feat'}->{'start'};
	    $self->{'feat'}->{'start'} = $new_start;
	    $self->{'feat'}->{'strand'} = -1;
	} else {
	    $self->{'feat'}->{'strand'} = 1;
	}
	my $new_feat = new Bio::SeqFeature::Generic
	    (
	     -start   => $self->{'feat'}->{'start'},
	     -end     => $self->{'feat'}->{'end'},
	     -strand  => $self->{'feat'}->{'strand'},
	     -source  => $self->{'feat'}->{'source_tag'},
	     -primary => $self->{'feat'}->{'primary_tag'},
	     -score   => $self->{'feat'}->{'score'},
	     );
	
	if (defined $self->{'feat'}->{'computation_id'}) {
	    $new_feat->add_tag_value('computation_id', 
				     $self->{'feat'}->{'computation_id'} );
	} elsif (defined $self->{'feat'}->{'annotation_id'}) {
	    $new_feat->add_tag_value('annotation_id', 
				     $self->{'feat'}->{'annotation_id'} );
	}
	if (defined $self->{'feat'}->{'id'}) {
	    $new_feat->add_tag_value('id', $self->{'feat'}->{'id'} );
	}

	push @{$self->{'feats'}}, $new_feat;
	$self->{'feat'} = { 
	    seqid => $self->{'feat'}->{'curr_seqid'},
	    primary_tag => $self->{'feat'}->{'primary_tag'},
	    source_tag => $self->{'feat'}->{'source_tag'},
	    computation_id => $self->{'feat'}->{'computation_id'},
	    annotation_id => $self->{'feat'}->{'annotation_id'}
	}
    }


    pop @{$self->{'Names'}};
    pop @{$self->{'Nodes'}};

}

sub in_element {

    my ($self, $name) = @_;
    
    return (defined $self->{'Names'}[-1] && 
	    $self->{'Names'}[-1] eq $name);

}

sub new {

    my ($caller,$seq,$length,$type) = @_;
    my $class = ref($caller) || $caller;
    my $self = bless ({
	seq      => $seq,
	type     => $type,
	length   => $length,
	string   => '',
	feat     => {},
	feats    => [],
	comp_id  => 1,
    }, $class);
    return $self;

}

sub start_document {

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

    $self->{'Names'} = [];
    $self->{'Nodes'} = [];
    $self->{'feats'} = [];

}

sub start_element {

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

    push @{$self->{'Names'}}, $element->{'Name'};
    $self->{'string'} = '';

    if ($self->in_element('bx-feature:seq_relationship')) {
	if (defined $element->{'Attributes'}->{'bx-feature:seq'} && 
	    defined $self->{'seq'} &&
	    $element->{'Attributes'}->{'bx-feature:seq'} eq $self->{'seq'}) {
	    $self->{'in_current_seq'} = 'true';
	} 
    }


    if ($self->in_element('bx-computation:computation')) {
	$self->{'feat'} = {};
	if (defined $element->{'Attributes'}->{'bx-computation:id'}) {
	    $self->{'feat'}->{'computation_id'} = $element->{'Attributes'}->{'bx-computation:id'};
	}  else {
	    $self->{'feat'}->{'computation_id'} = $self->{'comp_id'};
	    $self->{'comp_id'}++;
	}
    }

    if ($self->in_element('bx-feature:feature')) {
	if (defined $element->{'Attributes'}->{'bx-feature:id'}) {
	    $self->{'feat'}->{'id'} = $element->{'Attributes'}->{'bx-feature:id'};
	}
    }

    if ($self->in_element('bx-annotation:annotation')) {
	$self->{'feat'} = {};
	$self->{'feat'}->{'annotation_id'} = $element->{'Attributes'}->{'bx-annotation:id'};
	$self->{'feat'}->{'annotation_name'} = $element->{'Attributes'}->{'bx-annotation:name'};
    }

    return 0;

}

sub within_element {

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

    my $count = 0;
    foreach my $el_name (@{$self->{'Names'}}) {
	$count ++ if ($el_name eq $name);
    }

    return $count;

}

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        - Bioperl list
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  bioxml-announce@bioxml.org   - General Announcements - Pretty dead
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Email: bradmars@yahoo.com

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