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Rutger Vos > Bio-Phylo > 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_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

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