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Man Pages


Manual Reference Pages  -  BIO::PHYLO::PHYLOWS (3)

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NAME

Bio::Phylo::PhyloWS - Base class for phylogenetic web services

CONTENTS

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 objects 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 objects 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 objects 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 objects 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 objects 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 objects 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:

<B>Rutger A VosB>, <B>Jason CaravasB>, <B>Klaas HartmannB>, <B>Mark A JensenB> and <B>Chase MillerB>, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics <B>12B>:63. <http://dx.doi.org/10.1186/1471-2105-12-63>

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perl v5.20.3 BIO::PHYLO::PHYLOWS (3) 2014-02-08

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