Bio::Phylo::NeXML::DOM::Document(3)

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

SYNOPSIS
Not used directly.

DESCRIPTION
This module describes an abstract implementation of a DOM document 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 DocumentI 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   : $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>