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_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