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Bio::NEXUS::NHXCmd(3) User Contributed Perl DocumentationBio::NEXUS::NHXCmd(3)

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

perl v5.32.0			  2007-09-21		 Bio::NEXUS::NHXCmd(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHORS | CONTRIBUTORS | METHODS

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