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Bio::Phylo::PhyloWS(3)User Contributed Perl DocumentatioBio::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>

perl v5.32.0			  2017-10-30		Bio::Phylo::PhyloWS(3)

NAME | SYNOPSIS | DESCRIPTION | METHODS | SEE ALSO | CITATION

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