| Bio::Phylo::Util::DOM::DocumentI - Abstract interface class for |
Bio::Phylo::Util::DOM::DocumentI - Abstract interface class for flexible XML document object model implementation
Not used directly.
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.
Mark A. Jensen - maj -at- fortinbras -dot- us
new()
Type : Constructor Title : new Usage : $doc = Bio::Phylo::Util::Dom::Document->new(@args) Function: Create a Document object using the underlying package Returns : Document object or undef on fail Args : Package-specific arguments
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
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
to_xml_string()
Type : Serializer Title : to_xml_string Usage : $doc->to_xml_string Function: Create XML string from document Returns : XML string Args : Formatting arguments as allowed by underlying package
to_xml_file()
Type : Serializer Title : to_xml_file Usage : $doc->to_xml_file() Function: Create XML file from document Returns : True on success Args : filename, formatting arguments as allowed by underlying package
throw_not_implemented()
Type : Exception
Title : throw_not_implemented
Usage : $elt->throw_not_implemented
Function: Throw exception to indicate a method is not overridden in an
instance class
Returns : Bio::Phylo::Util::Exceptions object
Args : none
_rearrange()
Type : Title : _rearrange Usage : my ($arg1, $arg2, ...) = _rearrange( [qw( arg1 arg2 ... )], @input_args Function: Assign a named argument list to subroutine-local variables Returns : rearranged argument values Args : arrayref to argument names, copy of argument array Note : Ripped from BioPerl RootI.pm
| Bio::Phylo::Util::DOM::DocumentI - Abstract interface class for |