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 :
Returns any appropriate action verb that needs to be composed into the URL. By default this is find, but child classes can override this to something else (or nothing at all).
find
Type : Accessor Title : get_action Usage : my $action = $obj->get_action; Function: Returns the object's url action. Returns : A string Args :
Returns any appropriate action verb that needs to be composed into the query string as the keyword to identify the search string. By default this is query, but child classes can override this to something else (or nothing at all).
query
Type : Accessor Title : get_query_keyword Usage : my $keyword = $obj->get_query_keyword; Function: Returns the object's query keyword 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.