Summary

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

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

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

Description

No description!

Methods

Methods description

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

 Title   : end_document
 Usage   : $obj->end_document
 Function: PerlSAX method called when a document is finished for cleaning up
 Returns : list of ids seen
 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   : end_element
 Usage   : $obj->end_element
 Function: PerlSAX method called when an element is finished
 Returns : nothing
 Args    : element object

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

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

Methods code

sub new {

    my ($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
    
    # initialize ids
    $self->{'ids'} = [];

    return $self;

}

sub start_document {

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

}

sub end_document {

    my ($self, $document) = @_;
    return $self->{'ids'};

}

sub start_element {

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

    if ($element->{'Name'} eq 'bx-seq:seq') {
	if ($element->{'Attributes'}->{'bx-seq:id'}) {
	    push @{$self->{'ids'}}, $element->{'Attributes'}->{'bx-seq:id'};
	} else {
	    if ($self->can('warn')) {
		$self->warn('WARNING: Attribute bx-seq:id is required on bx-seq:seq. Sequence will not be parsed.');
	    } else {
		warn('WARNING: Attribute bx-seq:id is required on bx-seq:seq. Sequence will not be parsed.');
	    }
	}
    }
    return 0;

}

sub end_element {

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

}

sub characters {

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

}

sub AUTOLOAD {

    my $self = shift;

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

    print "UNRECOGNIZED $method\n";

}

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 _