Bio::Phylo::PhyloWS - Base class for phylogenetic web services
# no direct usage, used by child classes
This is the base class for clients and service that implement the PhyloWS (http://evoinfo.nescent.org/PhyloWS) recommendations. This base class isn't used directly, it contains useful methods that are inherited by its children.
Sets invocant's preferred serialization format.
Type : Mutator Title : set_format Usage : $obj->set_format($format); Function: Assigns an object's serialization format. Returns : Modified object. Args : Argument must be a string.
Sets invocant's section ("table") to operate on, e.g. 'taxon', 'tree', etc.
Type : Mutator Title : set_section Usage : $obj->set_section($section); Function: Sets section Returns : Modified object. Args : Argument must be a string.
Sets invocant's query parameter
Type : Mutator Title : set_query Usage : $obj->set_query($query); Function: Assigns an object's query. Returns : Modified object. Args : Argument must be a string.
Sets the authority prefix (e.g. TB2) for the implementing service
Type : Mutator Title : set_authority Usage : $obj->set_authority('TB2'); Function: Sets authority prefix Returns : $self Args : String Comments:
Gets invocant's url. This constructs the full url including section, authority prefix, uid and query string.
Type : Accessor Title : get_url Usage : my $url = $obj->get_url; Function: Returns the object's url. Returns : A string Args :
Constructs a url prefix to which an ID can be appended in order to resolve to some resource. Combined with get_authority these form the moving parts for how PhyloWS services could be plugged into the http://lsrn.org system.
Type : Accessor Title : get_url_prefix Usage : my $prefix = $obj->get_url_prefix; Function: Returns the object's url prefix. Returns : A string Args :
Gets invocant's preferred serialization format
Type : Accessor Title : get_format Usage : my $format = $obj->get_format; Function: Returns the object's preferred serialization format Returns : A string Args : None
Gets the authority prefix (e.g. TB2) for the implementing service
Type : Accessor Title : get_authority Usage : my $auth = $obj->get_authority; Function: Gets authority prefix Returns : String Args : None Comments:
Gets invocant's section ("table") to operate on, e.g. 'taxon', 'tree', etc.
Type : Accessor Title : get_section Usage : my $section = $obj->get_section; Function: Gets section Returns : String Args : None
Gets invocant's query parameter
Type : Accessor Title : get_query Usage : my $query = $obj->get_query; Function: Retrieves an object's query. Returns : Query Args : None
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.