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Summary

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

Package variables

Included modules

Inherit

Bio::Root::Root XML::Handler::Subs

Synopsis

GAME helper for parsing new Sequence 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 sequences 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   : sequence_factory
 Usage   : $seqio->sequence_factory($builder)
 Function: Get/Set the Bio::Factory::SequenceFactoryI
 Returns : Bio::Factory::SequenceFactoryI
 Args    : [optional] Bio::Factory::SequenceFactoryI

 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->sequence_factory->create
	( -seq => $self->{'residues'},
	  -alphabet => $self->{'alphabet'},
	  -id => $self->{'seq'},
	  -accession => $self->{'accession'},
	  -desc => $self->{'desc'},
	  -length => $self->{'length'},
	  );

}

sub end_element {

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

    if ($self->{'in_current_seq'} eq 'true') {      
	if ($self->in_element('bx-seq:residues')) {
	    while ($self->{'string'} =~ s/\s+//) {};
	    $self->{'residues'} = $self->{'string'};
	}


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


	if ($self->in_element('bx-link:id')  && $self->within_element('bx-link:dbxref')) {
	    $self->{'string'} =~ s/^\s+//g;
	    $self->{'string'} =~ s/\s+$//;
	    $self->{'string'} =~ s/\n//g;
	    $self->{'accession'} = $self->{'string'};
	}

	if ($self->in_element('bx-seq:description')) {
	    $self->{'desc'} = $self->{'string'};
	}

	if ($self->in_element('bx-seq:seq')) {
	    $self->{'in_current_seq'} = 'false';
	}
    }

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

}

sub in_element {

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

    return ($self->{'Names'}[-1] eq $name);

}

sub new {

    my ($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
    my ($seq,$sb) = $self->_rearrange([qw(SEQ SEQBUILDER)], @args);
    $self->{'string'} = '';
    $self->{'seq'} = $seq;
    $self->sequence_factory($sb || new Bio::Seq::SeqFactory(-type => 'Bio::Seq'));
    return $self;

}

sub sequence_factory {

   my ($self,$obj) = @_;   
   if( defined $obj ) {
       if( ! ref($obj) || ! $obj->isa('Bio::Factory::SequenceFactoryI') ) {
	   $self->throw("Must provide a valid Bio::Factory::SequenceFactoryI object to ".ref($self)." sequence_factory()");
       }
       $self->{'_seqio_seqfactory'} = $obj;
   }
   if( ! defined $self->{'_seqio_seqfactory'} ) {
       $self->throw("No SequenceBuilder defined for SeqIO::game::seqHandler object");
   }

   return $self->{'_seqio_seqfactory'};

}

sub start_document {

    my ($self, $document) = @_;
    $self->{'in_current_seq'} = 'false';    
    $self->{'Names'} = [];
    $self->{'string'} = '';

}

sub start_element {

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

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

    if ($element->{'Name'} eq 'bx-seq:seq') {
	if ($element->{'Attributes'}->{'bx-seq:id'} eq $self->{'seq'}) {
	    $self->{'in_current_seq'} = 'true';
	    $self->{'alphabet'} = $element->{'Attributes'}->{'bx-seq:type'};
	    $self->{'length'} =  $element->{'Attributes'}->{'bx-seq:length'};
	} else {
	    #This is not the sequence we want to import, but that's ok
	}
    }
    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
  bioxml-dev@bioxml.org        - Technical discussion - Moderate volume
  bioxml-announce@bioxml.org   - General Announcements - Pretty dead
  http://www.bioxml.org/MailingLists/         - About the mailing lists

Email: bradmars@yahoo.com

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