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Summary

Bio::SeqIO::tinyseq::tinyseqHandler - XML event handlers to support NCBI TinySeq XML parsing

Package variables

Inherit

Bio::Root::Root

Synopsis

Do not use this module directly; use the SeqIO handler system:

  $stream = Bio::SeqIO->new( -file => $filename, -format => 'tinyseq' );

  while ( my $seq = $stream->next_seq ) {
    ....
  }

Description

This object provides event handler methods for parsing sequence files
in the NCBI TinySeq XML format. A TinySeq is a lightweight XML file
of sequence information on one or more sequences, analgous to FASTA
format.
See http://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.mod.dtd for the DTD.

Methods

Methods description

  Title		: new
  Usage		: $handler = Bio::SeqIO::tinyseq::tinyseqHandler->new()
  Function	: instantiates a tinyseqHandler for use by
                  XML::Parser::PerlSAX
  Returns	: Bio::SeqIO::tinyseq::tinyseqHandler object
  Args		: NONE

  Title		: start_document
  Usage		: NONE
  Function	: start_document handler for use by XML::Parser::PerlSAX
  Returns	: NONE
  Args		: NONE

  Title		: end_document
  Usage		: NONE
  Function	: end_document handler for use by XML::Parser::PerlSAX
  Returns	: NONE
  Args		: NONE

  Title		: start_element
  Usage		: NONE
  Function	: start_element handler for use by XML::Parser::PerlSAX
  Returns	: NONE
  Args		: NONE

  Title		: end_element
  Usage		: NONE
  Function	: end_element handler for use by XML::Parser::PerlSAX
  Returns	: NONE
  Args		: NONE

  Title		: characters
  Usage		: NONE
  Function	: characters handler for use by XML::Parser::PerlSAX
  Returns	: NONE
  Args		: NONE

  Title		: TSeq
  Usage		: NONE
  Function	: event handler for END of a TSeq element
  Returns	: loh of parsed sequence atts for Bio::SeqIO::tinyseq
  Args		: NONE

  Title		: _current_element
  Usage		: Internal method
  Function	: Utility method to return current element info
  Returns	: XML::Parser::PerlSAX hash for current element
  Args		: NONE

Methods code

sub new {

    my ($proto, @args) = @_;
    my $class = ref($proto) || $proto;

    my $self =  bless({}, $class);

    return $self;
}

#######################################
# Event hadling methods for PerlSax   #
#######################################

}

sub doctype_decl {

    my ($self, $doctype) = @_;
    # make sure we have a tinyseq
    unless ($doctype->{'SystemId'} eq 'http://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.dtd') {
	$self->throw("This document doesn't use the NCBI TinySeq dtd; it's a ", $doctype->{'SystemId'} );
    }

}

sub start_document {

    my ($self) = @_;

    $self->{'_seqatts'} = [];
    $self->{'_elements'} = [];

}

sub end_document {

    my ($self) = @_;
    return $self->{'_seqatts'};

}

sub start_element {

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

    push(@{$self->{'_elements'}}, $starting);

}

sub end_element {

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

    # do I have a handler for this element?
    my $ename = $ending->{'Name'};
    $self->$ename if ($self->can($ename));

}

sub characters {

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

    my $data = $characters->{'Data'};

    return unless (defined($data) and $data =~ /\S/);

    my $current = $self->_current_element;
    $current->{'Data'} = $data;
}


###########################################
# Element-specific handlers
# called at END of element name
##########################################

}

sub TSeq {

    my ($self) = @_;

    my %seqatts;

    # map elements onto PrimarySeq keys
    while (my $element = pop @{ $self->{'_elements'} }) {
	my $element_name = $element->{'Name'};
	last if ($element_name eq 'TSeq');

	my $conversion = $ATTMAP{$element_name} or next;

	while(my($element_att, $pseq_att) = each %$conversion) {
	    $seqatts{$pseq_att} = $element->{$element_att};
	}
    }

    push(@{ $self->{'_seqatts'} },\% seqatts);

}

#############################################
# Utility method to return current element info
##############################################

}

sub _current_element {

    my ($self) = @_;
    return $self->{'_elements'}->[-1];
}




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
the Bioperl mailing list. 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/

Bio::SeqIO, Bio::Seq.

Donald Jackson, <donald.jackson@bms.com>

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