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Bio::Phylo::NeXML::DOMUsereContributed Perl Bio::Phylo::NeXML::DOM::Element(3)

NAME
       Bio::Phylo::NeXML::DOM::Element - XML DOM Abstract class	for flexible
       document	object model implementation

SYNOPSIS
       Not used	directly.

DESCRIPTION
       This module describes an	abstract implementation	of a DOM object	as
       expected	by Bio::Phylo. The methods here	must be	overridden in any
       concrete	implementation.	The idea is that different implementations use
       a particular XML	DOM package, binding the methods here to analogous
       package methods.

       This set	of methods is intentionally minimal. The concrete instances of
       this class should inherit both from ElementI and	the underlying XML DOM
       object class, so	that package-specific methods can be directly accessed
       from the	instantiated object.

AUTHOR
       Mark A. Jensen -	maj -at- fortinbras -dot- us

   Constructor
       new()
	    Type    : Constructor
	    Title   : new
	    Usage   : $elt = Bio::Phylo::NeXML::DOM::Element->new($tag,	$attr)
	    Function: Create a new XML DOM element
	    Returns : DOM element object
	    Args    : Optional:
		      '-tag' =>	$tag  -	tag name as string
		      '-attr'	 => $attr - hashref of attributes/values

       parse_element()
	    Type    : Factory method
	    Title   : parse_element
	    Usage   : $elt = $dom->parse_element($text)
	    Function: Create a new XML DOM element from	XML text
	    Returns : DOM element
	    Args    : An XML String

   Namespace accessors/mutators
       o

	    Type    :
	    Title   :
	    Usage   :
	    Function:
	    Returns :
	    Args    :

   Tagname mutators/accessors
       get_tag()
	    Type    : Accessor
	    Title   : get_tag
	    Usage   : $elt->get_tag()
	    Function: Get tag name
	    Returns : Tag name as scalar string
	    Args    : none

       set_tag()
	    Type    : Mutator
	    Title   : set_tag
	    Usage   : $elt->set_tag( $tagname )
	    Function: Set tagname
	    Returns : True on success
	    Args    : Tag name as scalar string

   Attribute mutators/accessors
       get_attributes()
	    Type    : Accessor
	    Title   : get_attributes
	    Usage   : $elt->get_attributes( @attribute_names )
	    Function: Get attribute values
	    Returns : A	hash ref of key/value pairs
	    Args    : Optional,	[a list	of] attribute name[s] as string[s]

       set_attributes()
	    Type    : Mutator
	    Title   : set_attributes
	    Usage   : $elt->set_attributes( @attribute_assoc_array )
	    Function: Set attribute values
	    Returns : True on success
	    Args    : An associative array of form ( $name => $value, ... )

       clear_attributes()
	    Type    : Mutator
	    Title   : clear_attributes
	    Usage   : $elt->clear_attributes( @attribute_names )
	    Function: Remove attributes	from element
	    Returns : Hash of removed attributes/values
	    Args    : Array of attribute names

   Content mutators/accessors
       set_text()
	    Type    : Mutator
	    Title   : set_text
	    Usage   : $elt->set_text($text_content)
	    Function: Add a #TEXT node to the element
	    Returns : True on success
	    Args    : scalar string

       get_text()
	    Type    : Accessor
	    Title   : get_text
	    Usage   : $elt->get_text()
	    Function: Retrieve direct #TEXT descendants	as (concatenated) string
	    Returns : scalar string (the text content)
	    Args    : none

       clear_text()
	    Type    : Mutator
	    Title   : clear_text
	    Usage   : $elt->clear_text()
	    Function: Remove direct #TEXT descendant nodes from	element
	    Returns : True on success; false if	no #TEXT nodes removed
	    Args    : none

   Traversal methods
       get_parent()
	    Type    : Accessor
	    Title   : get_parent
	    Usage   : $elt->get_parent()
	    Function: Get parent DOM node of invocant
	    Returns : Element object or	undef if invocant is root
	    Args    : none

       get_children()
	    Type    : Accessor
	    Title   : get_children
	    Usage   : $elt->get_children()
	    Function: Get child	nodes of invocant
	    Returns : Array ref	of Elements
	    Args    : none

       get_first_daughter()
	    Type    : Accessor
	    Title   : get_first_daughter
	    Usage   : $elt->get_first_daughter()
	    Function: Get first	child (as defined by underlying	package) of invocant
	    Returns : Element object or	undef if invocant is childless
	    Args    : none

       get_last_daughter()
	    Type    : Accessor
	    Title   : get_last_daughter
	    Usage   : $elt->get_last_daughter()
	    Function: Get last child (as defined by underlying package)	of invocant
	    Returns : Element object or	undef if invocant is childless
	    Args    : none

       get_next_sister()
	    Type    : Accessor
	    Title   : get_next_sister
	    Usage   : $elt->get_next_sister()
	    Function: Gets next	sibling	(as defined by underlying package) of invocant
	    Returns : Element object or	undef if invocant is the rightmost element
	    Args    : none

       get_previous_sister()
	    Type    : Accessor
	    Title   : get_previous_sister
	    Usage   : $elt->get_previous_sister()
	    Function: Get previous sibling (as defined by underlying package) of invocant
	    Returns : Element object or	undef if invocant is leftmost element
	    Args    : none

       get_elements_by_tagname()
	    Type    : Accessor
	    Title   : get_elements_by_tagname
	    Usage   : $elt->get_elements_by_tagname($tagname)
	    Function: Get array	of elements having given tag name from invocant's
		      descendants
	    Returns : Array of elements	or undef if no match
	    Args    : tag name as string

   Prune and graft methods
       set_child()
	    Type    : Mutator
	    Title   : set_child
	    Usage   : $elt->set_child($child)
	    Function: Add child	element	object to invocant's descendants
	    Returns : the element object added
	    Args    : Element object

       prune_child()
	    Type    : Mutator
	    Title   : prune_child
	    Usage   : $elt->prune_child($child)
	    Function: Remove the subtree rooted	by $child from among the invocant's
		      descendants
	    Returns : $child or	undef if $child	is not among the children of invocant
	    Args    : Element object

   Output methods
       to_xml()
	    Type    : Serializer
	    Title   : to_xml
	    Usage   : $elt->to_xml
	    Function: Create XML string	from subtree rooted by invocant
	    Returns : XML string
	    Args    : Formatting arguments as allowed by underlying package

CITATION
       If you use Bio::Phylo in	published research, please cite	it:

       Rutger A	Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase
       Miller, 2011. Bio::Phylo	- phyloinformatic analysis using Perl.	BMC
       Bioinformatics 12:63.  <http://dx.doi.org/10.1186/1471-2105-12-63>

perl v5.32.0			  2017-10-30Bio::Phylo::NeXML::DOM::Element(3)

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