Bio::Phylo::PhyloWS(3)

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>