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