Bio::OntologyIO::Handlers BaseSAXHandler
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::OntologyIO::Handlers::BaseSAXHandler base class for SAX Handlers
Package variables
No package variables defined.
See description.
This module is an abstract module, serving as the base of any SAX Handler
implementation. It tries to offer the framework that SAX handlers generally
need, such as tag_stack, char_store, etc.
In the implementation handler, you can take advantage of this based module by
the following suggestions.
1) In start_element,
 sub start_element {
my $self=shift;
my $tag=$_[0]->{Name};
my %args=%{$_[0]->{Attributes}};
# Your code here.
# Before you conclude the method, write these 2 line. $self->_visited_count_inc($tag); $self->_push_tag($tag); }
2) In end_element,
 sub end_element {
my $self=shift;
my $tag=shift->{Name};
# Your code here.
# Before you conclude the method, write these 2 lines. $self->_visited_count_dec($tag); $self->_pop_tag; }
3) In characters, or any other methods where you may use the tag
stack or count
 sub characters {
my $self=shift;
my $text=shift->{Data};
$self->_chars_hash->{$self->_top_tag} .= $text; } $count = $self->_visited_count('myTag'); $tag = $self->_top_tag;
No description
No description
Methods description
_tag_stackcode    nextTop
  Title   : _tag_stack
Usage : @tags = $self->_tag_stack;
Function: Get an array of tags that have been accessed but not enclosed.
Return :
Args :
  Title   : _top_tag
Usage : $top = $self->_top_tag;
Function: get the top tag in the tag stack.
Return : a tag name
Args : [none]
  Title   : _chars_hash
Usage : $hash= $self->_chars_hash;
Function: return the character cache for the specific tag
Return : a hash reference, which is intent for character storage for tags
Args : [none]
  Title   : _vistied_count_inc
Usage : $self->vistied_count_inc($tag); # the counter for the tag increase
Function: the counter for the tag increase
Return : the current count after this increment
Args : the tag name [scalar]
  Title   : _visited_count_dec
Usage : $self->_visited_count_dec($tag);
Function: the counter for the tag decreases by one
Return : the current count for the specific tag after the decrement
Args : the tag name [scalar]
  Title   : _visited_count
Usage : $count = $self->_visited_count
Function: return the counter for the tag
Return : the current counter for the specific tag
Args : the tag name [scalar]
Methods code
sub new {
    my ($class, @args) = @_;
    my $self=$class->SUPER::new(@args);
    return $self;
sub _initialize {
    my $self = shift;
    $self->{_tag_stack} = [];
    $self->{_visited_count} = {};
    $self->{_chars_hash} = {};
    $self->{_current_hash} = {};
sub _tag_stack {
    return @{shift->{_tag_stack}};
sub _push_tag {
    push @{$self->{_tag_stack}}, $tag;
sub _pop_tag {
    my $self=shift;
    return pop @{$self->{_tag_stack}};
sub _top_tag {
    my $self = shift;
    my @stack=@{$self->{_tag_stack}};
    return $stack[-1];
# get the last element in an array while remaining it in. There are few  ways
# 1) $stack[-1]
# 2) $stack[$#stack]
# 3) $stack[@stack-1]
sub _chars_hash {
    return shift->{_chars_hash};
sub _current_hash {
    return  shift->{_current_hash};
sub _visited_count_inc {
    my ($self, $tag) = @_;
    my $visited_count=$self->{_visited_count};
    if(exists $visited_count->{$tag}){
    return $visited_count->{$tag};
sub _visited_count_dec {
    my ($self, $tag) = @_;
    my $visited_count=$self->{_visited_count};
    if(exists $visited_count->{$tag}){
        $self->throw("'$tag' has not been visited yet. How to decrease it?!");
    return $visited_count->{$tag};
sub _visited_count {
    my ($self, $tag) = @_;
    return $self->{_visited_count}->{$tag};

General documentation
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with code and data examples if at all possible.
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Report bugs to the Bioperl bug tracking system to help us keep track
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The rest of the documentation details each of the object methods.
Interal methods are usually preceded with a _