Rutger Vos > Bio-Phylo-0.56 > Bio::Phylo::PhyloWS

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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

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