Bio::BioVeL::Service::NeXMLExtractor - extracts and converts data from a NeXML document
use Bio::BioVeL::Service::NeXMLExtractor; # arguments can either be passed in from the command line argument array or as # HTTP request parameters, e.g. from $QUERY_STRING @ARGV = ( '-nexml' => $nexml, '-object' => 'Trees', '-treeformat' => 'newick', '-dataformat' => 'nexus' ); my $extractor = Bio::BioVeL::Service::NeXMLExtractor->new; my $data = $extractor->response_body;
This package extracts phylogenetic data from 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.
The constructor typically receives no arguments.
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.
Generates the requested response. It does this by reading a NeXML document and collecting objects of the type specified by the object() property (i.e. 'Matrices', 'Trees' or 'Taxa'). It then serializes these to the requested format.