NAME

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

SYNOPSIS

See description.

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;

FEEDBACK

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.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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 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:

https://github.com/bioperl/bioperl-live/issues

AUTHOR

Juguang Xiao, juguang@tll.org.sg

APPENDIX

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

_tag_stack

Title   : _tag_stack
Usage   : @tags = $self->_tag_stack;
Function: Get an array of tags that have been accessed but not enclosed.
Return  : 
Args    :    

_push_tag

_pop_tag

_top_tag

Title   : _top_tag
Usage   : $top = $self->_top_tag;
Function: get the top tag in the tag stack.
Return  : a tag name
Args    : [none]   

_chars_hash

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]

_current_hash

_visited_count_inc

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]

_visited_count_dec

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]

_visited_count

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]

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq