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>