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Bio-Phylo-0.48
River stage two • 9 direct dependents • 18 total dependents
/ Bio::Phylo::NeXML::DOM::Document::Twig

NAME

Bio::Phylo::NeXML::DOM::Document::Twig - XML DOM document mappings to the XML::Twig package

SYNOPSIS

Don't use directly; use Bio::Phylo::NeXML::DOM->new( -format => 'twig' ) instead.

DESCRIPTION

This module provides mappings the methods specified in the Bio::Phylo::NeXML::DOM::Document abstract class to the XML::Twig package.

AUTHOR

Mark A. Jensen ( maj -at- fortinbras -dot- us )

Constructor

new()
Type    : Constructor
Title   : new
Usage   : $doc = Bio::Phylo::NeXML::DOM::Document->new(@args)
Function: Create a Document object using the underlying package
Returns : Document object or undef on fail
Args    : Package-specific arguments
parse_document()
Type    : Factory method
Title   : parse_document
Usage   : $doc = $dom->parse_document($text)
Function: Create a new XML DOM document from XML text
Returns : DOM document
Args    : An XML String

Document property accessors/mutators

set_encoding()
Type    : Mutator
Title   : set_encoding
Usage   : $doc->set_encoding($enc)
Function: Set encoding for document
Returns : True on success
Args    : Encoding descriptor as string
get_encoding()
Type    : Accessor
Title   : get_encoding
Usage   : $doc->get_encoding()
Function: Get encoding for document
Returns : Encoding descriptor as string
Args    : none
set_root()
Type    : Mutator
Title   : set_root
Usage   : $doc->set_root($elt)
Function: Set the document's root element
Returns : True on success
Args    : Element object
get_root()
Type    : Accessor
Title   : get_root
Usage   : $doc->get_root()
Function: Get the document's root element
Returns : Element object or undef if DNE
Args    : none

Document element accessors

get_element_by_id()
Type    : Accessor
Title   : get_element_by_id
Usage   : $doc->get_element_by_id($id)
Function: Get element having id $id
Returns : Element object or undef if DNE
Args    : id designator as string
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 
Returns : Array of elements or undef if no match
Args    : tag name as string

Output methods

to_xml()
Type    : Serializer
Title   : to_xml
Usage   : $doc->to_xml
Function: Create XML string from document
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