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.
-
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
-
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