NAME

Bio::Phylo::PhyloWS - Base class for phylogenetic web services

SYNOPSIS

            

              
              
# no direct usage, used by child classes
            
          

DESCRIPTION

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.

METHODS

MUTATORS

set_format()

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.
            
          

set_section()

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.
            
          

set_query()

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.
            
          

set_authority()

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:
            
          

ACCESSORS

get_url()

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    :
            
          

get_action()

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).

            

              
              
Type    : Accessor
Title   : get_action
Usage   : my $action = $obj->get_action;
Function: Returns the object's url action.
Returns : A string
Args    :
            
          

get_query_keyword()

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).

            

              
              
Type    : Accessor
Title   : get_query_keyword
Usage   : my $keyword = $obj->get_query_keyword;
Function: Returns the object's query keyword
Returns : A string
Args    :
            
          

get_url_prefix()

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    :
            
          

get_format()

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
            
          

get_authority()

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:
            
          

get_section()

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
            
          

get_query()

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
            
          

SEE ALSO

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

CITATION

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