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Man Pages


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

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NAME

Bio::Phylo::PhyloWS::Client - Base class for phylogenetic web service clients

CONTENTS

SYNOPSIS



 #!/usr/bin/perl
 use strict;
 use warnings;
 use Bio::Phylo::Factory;

 my $fac = Bio::Phylo::Factory->new;
 my $client = $fac->create_client(
        -base_uri  => http://nexml-dev.nescent.org/nexml/phylows/tolweb/phylows/,
        -authority => uBioNB,
 );
 my $desc = $client->get_query_result(
        -query     => Homo sapiens,
        -section   => taxon,
 );
 for my $res ( @{ $desc->get_entities } ) {
        my $proj = $client->get_record( -guid => $res->get_guid );
        print $proj->to_nexus, "\n";
 }



DESCRIPTION

This is the base class for clients connecting to services that implement the PhyloWS (<http://evoinfo.nescent.org/PhyloWS>) recommendations.

METHODS

    CONSTRUCTOR

new()


 Type    : Constructor
 Title   : new
 Usage   : my $phylows = Bio::Phylo::PhyloWS::Client->new( -url => $url );
 Function: Instantiates Bio::Phylo::PhyloWS::Client object
 Returns : a Bio::Phylo::PhyloWS::Client object
 Args    : Required: -url => $url
           Optional: any number of setters. For example,
                   Bio::Phylo::PhyloWS->new( -name => $name )
                   will call set_name( $name ) internally



    MUTATORS

set_ua() Assigns a new LWP::UserAgent object that the client uses to communicate with the service. Typically you don’t have to use this unless you have to configure a user agent for things such as proxies. Normally a default user agent is instantiated when the client constructor is called.



 Type    : Mutator
 Title   : set_ua
 Usage   : $obj->set_ua( LWP::UserAgent->new );
 Function: Assigns another (non-default) user agent
 Returns : $self
 Args    : An LWP::UserAgent object (or child class)



    ACCESSORS

get_query_result() Gets search query result



 Type    : Accessor
 Title   : get_query_result
 Usage   : my $res = $obj->get_query_result( -query => $query );
 Function: Returns Bio::Phylo::PhyloWS::Description object
 Returns : A string
 Args    : Required: -query => $cql_query
           Optional: -section, -recordSchema



get_record() Gets a PhyloWS database record



 Type    : Accessor
 Title   : get_record
 Usage   : my $rec = $obj->get_record( -guid => $guid );
 Function: Gets a PhyloWS database record
 Returns : Bio::Phylo::Project object
 Args    : Required: -guid => $guid



get_ua() Gets the underlying LWP::UserAgent object that the client uses to communicate with the service



 Type    : Accessor
 Title   : get_ua
 Usage   : my $ua = $obj->get_ua;
 Function: Gets user agent
 Returns : LWP::UserAgent object
 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::CLIENT (3) 2014-02-08

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