Bio::SeqIO::tinyseq tinyseqHandler
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Summary
Bio::SeqIO::tinyseq::tinyseqHandler - XML event handlers to support NCBI TinySeq XML parsing
Package variables
No package variables defined.
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
newDescriptionCode
doctype_decl
No description
Code
start_documentDescriptionCode
end_documentDescriptionCode
start_elementDescriptionCode
end_elementDescriptionCode
charactersDescriptionCode
TSeqDescriptionCode
_current_elementDescriptionCode
Methods description
newcode    nextTop
  Title		: new
Usage : $handler = Bio::SeqIO::tinyseq::tinyseqHandler->new()
Function : instantiates a tinyseqHandler for use by
XML::Parser::PerlSAX
Returns : Bio::SeqIO::tinyseq::tinyseqHandler object
Args : NONE
start_documentcodeprevnextTop
  Title		: start_document
Usage : NONE
Function : start_document handler for use by XML::Parser::PerlSAX
Returns : NONE
Args : NONE
end_documentcodeprevnextTop
  Title		: end_document
Usage : NONE
Function : end_document handler for use by XML::Parser::PerlSAX
Returns : NONE
Args : NONE
start_elementcodeprevnextTop
  Title		: start_element
Usage : NONE
Function : start_element handler for use by XML::Parser::PerlSAX
Returns : NONE
Args : NONE
end_elementcodeprevnextTop
  Title		: end_element
Usage : NONE
Function : end_element handler for use by XML::Parser::PerlSAX
Returns : NONE
Args : NONE
characterscodeprevnextTop
  Title		: characters
Usage : NONE
Function : characters handler for use by XML::Parser::PerlSAX
Returns : NONE
Args : NONE
TSeqcodeprevnextTop
  Title		: TSeq
Usage : NONE
Function : event handler for END of a TSeq element
Returns : loh of parsed sequence atts for Bio::SeqIO::tinyseq
Args : NONE
_current_elementcodeprevnextTop
  Title		: _current_element
Usage : Internal method
Function : Utility method to return current element info
Returns : XML::Parser::PerlSAX hash for current element
Args : NONE
Methods code
newdescriptionprevnextTop
sub new {
    my ($proto, @args) = @_;
    my $class = ref($proto) || $proto;

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

    return $self;
}

#######################################
# Event hadling methods for PerlSax #
#######################################
}
doctype_decldescriptionprevnextTop
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 ", $doctype->{'SystemId'} ); }
}
start_documentdescriptionprevnextTop
sub start_document {
    my ($self) = @_;

    $self->{'_seqatts'} = [];
    $self->{'_elements'} = [];
}
end_documentdescriptionprevnextTop
sub end_document {
    my ($self) = @_;
    return $self->{'_seqatts'};
}
start_elementdescriptionprevnextTop
sub start_element {
    my ($self, $starting) = @_;

    push(@{$self->{'_elements'}}, $starting);
}
end_elementdescriptionprevnextTop
sub end_element {
    my ($self, $ending) = @_;

    # do I have a handler for this element?
my $ename = $ending->{'Name'}; $self->$ename if ($self->can($ename));
}
charactersdescriptionprevnextTop
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
##########################################
}
TSeqdescriptionprevnextTop
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(@{ $self->{'_seqatts'} },\% seqatts); } #############################################
# Utility method to return current element info
##############################################
}
_current_elementdescriptionprevnextTop
sub _current_element {
    my ($self) = @_;
    return $self->{'_elements'}->[-1];
}




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
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
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/
SEE ALSOTop
Bio::SeqIO, Bio::Seq.
AUTHORTop
Donald Jackson, <donald.jackson@bms.com>
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _