Bio::NEXUS::NHXCmd - Provides functions for manipulating nodes in trees
new Bio::NEXUS::NHXCmd;
Provides a few useful functions for nodes.
All feedback (bugs, feature enhancements, etc.) are all greatly appreciated. There are no mailing lists at this time for the Bio::NEXUS::Node module, so send all relevant contributions to Dr. Weigang Qiu (weigang@genectr.hunter.cuny.edu).
Mikhail Bezruchko (bezruchk@umbi.umd.edu), Vivek Gopalan
Title : new Usage : $nhx_cmd = new Bio::NEXUS::NHXCmd($comment_string); Function: Creates a new Bio::NEXUS::NHXCmd object Returns : Bio::NEXUS::NHXCmd object Args : $comment_string - a string representation of the comment (w/o brackets)
Title : to_string Usage : $comment_str = $nhx_obj->to_string Function: Returns a string representation of the NHX command Returns : String Args : None
Title : equals Usage : $nhx_one->equals($nhx_two); Function: compares two NHX objects for equality Returns : 1 if the two objects contain the same date; 0 if they don't Args : $nhx_two - a Bio::NEXUS::NHXCmd object
Title : clone Usage : $new_obj = $original->clone(); Function: Creates a "deep copy" of a Bio::NEXUS::NHXCmd Returns : A "deep copy" of a Bio::NEXUS::NHXCmd Args : None
Title : contains_tag Usage : $nhx_obj->_contains_tag($tag_name) Function: Checks if a given tag exists Returns : 1 if the tax exists, 0 if it doesn't Args : $tag_name - a string representation of a tag
Title : get_tags Usage : $nhx_obj->get_tags(); Function: Reads and returns an array of tags Returns : An array of tags Args : None
Title : get_values Usage : $nhx_obj->get_values($tag_name); Function: Returns the list of values associated with the given tag ($tag_name) Returns : Array of values Args : $tag_name - a string representation of the tag
Title : set_tag Usage : nhx_obj->set_tag($tag_name, $tag_reference); Function: Updates the list of values associated with a given tag Returns : Nothing Args : $tag_name - a string, $tag_reference - an array-reference
Title : check_tag_value Usage : $boolean = nhx_obj->check_tag_value($tag_name, $value); Function: check whether a particular value is present in a tag Returns : 0 or 1 [ true or false] Args : $tag_name - a string, $value - scalar (string or number)
Title : add_tag_value Usage : $nhx_obj->add_tag_value($tag_name, $tag_value); Function: Adds a new tag/value set to the $nhx_obj; Returns : 0 if not added or 1 if added [false or true] Args : $tag_name - a string, $tag_value - a string
Title : delete_tag Usage : $nhx_obj->delete_tag($tag_name); Function: Removes a given tag (and the associated valus) from the $nhx_obj Returns : Nothing Args : $tag_name - a string representation of the tag
Title : delete_all_tags Usage : $nhx_obj->delete_all_tags(); Function: Removes all tags from $nhx_obj Returns : Nothing Args : None
To install Bio::NEXUS, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::NEXUS
CPAN shell
perl -MCPAN -e shell install Bio::NEXUS
For more information on module installation, please visit the detailed CPAN module installation guide.