Bio::Phylo::PhyloWS::Service::Timetree - PhyloWS service wrapper for Timetree
# inside a CGI script: use CGI; use Bio::Phylo::PhyloWS::Service::Timetree; my $cgi = CGI->new; my $service = Bio::Phylo::PhyloWS::Service::Timetree->new( '-url' => $url ); $service->handle_request($cgi);
This is an example implementation of a PhyloWS service. The service wraps around the timetree web site (using screen scraping) and returns project objects that include a tree for every search result.
Gets a phylows cql query result
Type : Accessor Title : get_query_result Usage : my $result = $obj->get_query_result( $query ); Function: Gets a query result Returns : Bio::Phylo::Project Args : Required: $query
Gets an array ref of supported formats
Type : Accessor Title : get_supported_formats Usage : my @formats = @{ $obj->get_supported_formats }; Function: Gets an array ref of supported formats Returns : [ qw(nexml nexus newick html) ] Args : NONE
Gets a redirect URL if relevant
Type : Accessor Title : get_redirect Usage : my $url = $obj->get_redirect; Function: Gets a redirect URL if relevant Returns : String Args : $cgi Comments: This method is called by handle_request so that services can 303 redirect a record lookup to another URL. By default, this method returns undef (i.e. no redirect), but if this implementation is called to handle a request that specifies 'format=html' the request is forwarded to the appropriate page on the http://timetree.org website
There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com
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
To install Bio::Phylo, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Phylo
CPAN shell
perl -MCPAN -e shell install Bio::Phylo
For more information on module installation, please visit the detailed CPAN module installation guide.