Rutger Vos
and 1 contributors

NAME

Bio::BioVeL::Service::NeXMLMerger - merges phylogenetic data and metadata into NeXML

SYNOPSIS

 use Bio::BioVeL::Service::NeXMLMerger;

 # arguments can either be passed in from the command line argument array or as 
 # HTTP request parameters, e.g. from $QUERY_STRING
 @ARGV = (
        '-data'          => $data,  # a location, either local or as URL
        '-trees'         => $tree,  # a location, either local or as URL
        '-meta'          => $meta,  # a location, either local or as URL
        '-charsets'      => $sets,  # a location, either local or as URL
        '-dataformat'    => 'nexus',
        '-treeformat'    => 'newick',
        '-metaformat'    => 'json',
        '-charsetformat' => 'nexus',
 );

 my $merger = Bio::BioVeL::Service::NeXMLMerger->new;
 my $nexml = $merger->response_body;

DESCRIPTION

This package merges phylogenetic data and metadata to produce a NeXML document. Although it can be used inside scripts that receive command line arguments, it is intended to be used as a RESTful web service that clients can be written against, e.g. in http://taverna.org.uk for inclusion in http://biovel.eu workflows.

METHODS

new

The constructor typically receives no arguments.

response_header

Returns the MIME-type HTTP header. Note: at present this isn't really used, it needs refactoring to play nice with the way mod_perl constructs response headers. This would probably be done by only returning the MIME-type itself, which is then included in the header by the superclass.

response_body

Generates the NeXML response body by reading the input data and metadata objects and folding them into a single Bio::Phylo::Project object that is serialized to NeXML.