NAME

Bio::NEXUS::NHXCmd - Provides functions for manipulating nodes in trees

SYNOPSIS

new Bio::NEXUS::NHXCmd;

DESCRIPTION

Provides a few useful functions for nodes.

FEEDBACK

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).

AUTHORS

Mikhail Bezruchko (bezruchk@umbi.umd.edu), Vivek Gopalan

CONTRIBUTORS

METHODS

new

 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)

to_string

 Title   : to_string
 Usage   : $comment_str = $nhx_obj->to_string
 Function: Returns a string representation of the NHX command
 Returns : String
 Args    : None

equals

 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

clone

 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

contains_tag

 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

get_tags

 Title   : get_tags
 Usage   : $nhx_obj->get_tags(); 
 Function: Reads and returns an array of tags
 Returns : An array of tags
 Args    : None

get_values

 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

set_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

check_tag_value_present

 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)

add_tag_value

 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

delete_tag

 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

delete_all_tags

 Title   : delete_all_tags
 Usage   : $nhx_obj->delete_all_tags();
 Function: Removes all tags from $nhx_obj
 Returns : Nothing
 Args    : None