NAME

Bio::Phylo::NeXML::DOM - XML DOM support for Bio::Phylo

SYNOPSIS

 use Bio::Phylo::NeXML::DOM;
 use Bio::Phylo::IO qw( parse );
 Bio::Phylo::NeXML::DOM->new(-format => 'twig');
 my $project = parse( -file=>'my.nex', -format=>'nexus' );
 my $nex_twig = $project->doc();

DESCRIPTION

This module adds to_dom methods to Bio::Phylo::NeXML::Writable classes, which provide NeXML-valid objects for document object model manipulation. DOM formats currently available are XML::Twig and XML::LibXML. For any XMLWritable object, use to_dom in place of to_xml to create DOM nodes.

The doc() method is also added to the Bio::Phylo::Project class. It returns a NeXML document as a DOM object populated by the current contents of the Bio::Phylo::Project object.

MOTIVATION

The NeXML parsing/writing capability of Bio::Phylo goes a long way towards wider adoption of this useful standard.

However, while Bio::Phylo can write NeXML-valid XML, the way in which it does this natively is somewhat hard-coded and therefore restricted, and is essentially oriented toward text file output. As such, there is a mismatch between the sophisticated Bio::Phylo data structure and its own ability to manipulate and serialize that structure in sophisticated but interoperable ways. Finer manipulations of XML-represented data are possible via through a variety of Perl packages that can store and control XML according to a document object model (DOM). Many of these packages allow extremely flexible computation over large datasets stored in XML format, and admit the use of XML-related facilities such as XPath and XSLT programmatically.

The purpose of Bio::Phylo::NeXML::DOM is to introduce integrated DOM object creation and manipulation to Bio::Phylo, both to make DOM computation in Bio::Phylo more convenient, and also to provide a platform for potentially more sophisticated Bio::Phylo modules to come.

DESIGN

Besides the notion that DOM capability should be optional for the user, there are two main design ideas. First, for each Bio::Phylo object that can be parsed/written as NeXML (i.e., for each Bio::Phylo::NeXML::Writable object), we provide analogous method for creating a representative DOM object, or element. These elements are aggregatable in a DOM document object, whose native stringifying method can be used to generate valid NeXML.

Second, we allow flexibility and extensibility in the choice of the underlying DOM package, while maintaining a consistent DOM interface that is similar in semantic and syntactic style to the accessors and mutators that act on the Bio::Phylo objects themselves. This is achieved through the DOM::DocumentI and DOM::ElementI interfaces, which define a minimal subset of DOM accessors and mutators, their inputs and outputs. Concrete instances of these interface classes provide the bindings between the abstract methods and their counterparts in the desired DOM implementation. Currently, there are bindings for two popular packages, XML::Twig and XML::LibXML.

Another priority was simplicity of use; most of the details remain under the hood in practice. The Bio/Phylo/Util/DOM.pm file defines the to_dom() method for each XMLWritable package, as well as the Bio::Phylo::NeXML::DOM package proper. The DOM object is a factory that is used to create Element and Document objects; it is an inside-out object that subclasses Bio::Phylo. To curb the proliferation of method arguments, a DOM factory instance (set by the latest invocation of Bio::Phylo::NeXML::DOM->new()) is maintained in a package global. This is used by default for object creation with DOM methods if a DOM factory object is not explicitly provided in the argument list.

The underlying DOM implementation is set with the DOM factory constructor's single argument, -format. Even this can be left out; the default implementation is XML::Twig, which is already required by Bio::Phylo. Thus, for example, one can use the DOM to convert a Nexus file to a DOM representation as follows:

 use Bio::Phylo::NeXML::DOM;
 use Bio::Phylo::IO qw( parse );
 Bio::Phylo::NeXML::DOM->new();
 my $project = parse( -file=>'my.nex', -format=>'nexus' );
 my $nex_twig =  $project->doc();
 # The end.

Underlying DOM packages are loaded at runtime as specified by the -format argument. Packages for unused formats do not need to be installed.

INTERFACE METHODS

The minimal DOM interface specifies the following methods. Details can be obtained from the Element and Document POD.

Bio::Phylo::NeXML::DOM::Element - DOM Element abstract class

 get_tagname()
 set_tagname()
 get_attributes()
 set_attributes()
 clear_attributes()
 get_text()
 set_text()
 clear_text()

 get_parent()
 get_children()
 get_first_child()
 get_last_child()
 get_next_sibling()
 get_prev_sibling()
 get_elements_by_tagname()

 set_child()
 prune_child()

 to_xml_string()

Bio::Phylo::NeXML::DOM::Document - DOM Document

 get_encoding()
 set_encoding()

 get_root()
 set_root()

 get_element_by_id()
 get_elements_by_tagname()

 to_xml_string()
 to_xml_file()

METHODS

CONSTRUCTOR

new()

 Type    : Constructor
 Title   : new
 Usage   : $dom = Bio::Phylo::NeXML::DOM->new(-format=>$format)
 Function: Create a new DOM factory
 Returns : DOM object
 Args    : optional: -format => DOM format (defaults to 'twig')

FACTORY METHODS

create_element()

 Type    : Factory method
 Title   : create_element
 Usage   : $elt = $dom->create_element()
 Function: Create a new XML DOM element
 Returns : DOM element
 Args    : Optional:
           -tag => $tag_name
           -attr => \%attr_hash

parse_element()

 Type    : Factory method
 Title   : parse_element
 Usage   : $elt = $dom->parse_element($text)
 Function: Create a new XML DOM element from XML text
 Returns : DOM element
 Args    : An XML String

create_document()

 Type    : Creator
 Title   : create_document
 Usage   : $doc = $dom->create_document()
 Function: Create a new XML DOM document
 Returns : DOM document
 Args    : Package-specific args

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

MUTATORS

set_format()

 Type    : Mutator
 Title   : set_format
 Usage   : $dom->set_format($format)
 Function: Set the format (underlying DOM package bindings) for this object
 Returns : format designator as string
 Args    : format designator as string

ACCESSORS

get_format()

 Type    : Accessor
 Title   : get_format
 Usage   : $dom->get_format()
 Function: Get the format designator for this object
 Returns : format designator as string
 Args    : none

get_dom()

 Type    : Static accessor
 Title   : get_dom
 Usage   : __PACKAGE__->get_dom()
 Function: Get the singleton DOM object
 Returns : instance of this __PACKAGE__
 Args    : none

SEE ALSO

There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.

The DOM creator abstract classes: Bio::Phylo::NeXML::DOM::Element, Bio::Phylo::NeXML::DOM::Document

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

AUTHOR

Mark A. Jensen (maj -at- fortinbras -dot- us), refactored by Rutger Vos

TODO

The Bio::Phylo::Annotation class is not yet DOMized.

cpanm Bio::Phylo

perl -MCPAN -e shell
install Bio::Phylo