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