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Bio::OntologyIO::Handlers::BaseSAXHandler - base class for SAX Handlers


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.

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.

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;


Mailing Lists

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.                  - General discussion  - About the mailing lists


Please direct usage questions or support issues to the mailing list:

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 Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:


Juguang Xiao,


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


  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]