Bio::Tools::Run::AnalyUseraContributed PerlBio::Tools::Run::AnalysisFactory(3)NAMEBio::Tools::Run::AnalysisFactory - A directory of analysis tools
SYNOPSIS
# list all available analyses from the default location,
# using a default (SOAP) access method
use Bio::Tools::Run::AnalysisFactory;
my $list = Bio::Tools::Run::AnalysisFactory->new();
->available_analyses;
use Data::Dumper; print Dumper ($list);
# ditto, but from a different location
use Bio::Tools::Run::AnalysisFactory;
my $list =
Bio::Tools::Run::AnalysisFactory->new(-location => 'http://somewhere/something')
->available_analyses;
# ...and using a different access method
# (this example is not yet impelmented)
use Bio::Tools::Run::AnalysisFactory;
my $list =
Bio::Tools::Run::AnalysisFactory->new(-location => 'http://somewhere/something',
-access => 'novella')
->available_analyses;
# list available categories of analyses
use Bio::Tools::Run::AnalysisFactory;
my $categories =
Bio::Tools::Run::AnalysisFactory->new();
->available_categories;
use Data::Dumper; print Dumper ($categories);
# show all analyses group by categories
use Bio::Tools::Run::AnalysisFactory;
my $factory = Bio::Tools::Run::AnalysisFactory->new();
foreach $cat ( @{ $factory->available_categories } ) {
my @sublist = @{ $factory->available_analyses ($cat) };
print "$cat:\n\t",
join ("\n\t", @{ $factory->available_analyses ($cat) }),
"\n";
}
# create an analysis object
use Bio::Tools::Run::AnalysisFactory;
$service = Bio::Tools::Run::AnalysisFactory->new();
->create_analysis ('edit.seqret');
$service->run (
#...
)->results;
DESCRIPTION
The module represents a list of available analysis tools from a given
location using a given access method. Additionally, for any of the
available analyses, it can create an object of type
"Bio::Tools::Run::Analysis".
The module is a higher-level abstraction whose main job is to load a
'real-work-doing' implementation. Which one is used, it depends on the
"-access" parameter. The same design is used here as for
"Bio::Tools::Run::Analysis" module.
There is available a SOAP access to almost all EMBOSS applications,
running at European Bioinformatics Institute.
The documentation of all "public" methods are to be found in
"Bio::Factory::AnalysisI".
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and
data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of
the bugs and their resolution. Bug reports can be submitted via the
web:
http://bugzilla.open-bio.org/
AUTHOR
Martin Senger (martin.senger@gmail.com)
COPYRIGHT
Copyright (c) 2003, Martin Senger and EMBL-EBI. All Rights Reserved.
This module is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.
DISCLAIMER
This software is provided "as is" without warranty of any kind.
SEE ALSO
ยท http://www.ebi.ac.uk/soaplab/Perl_Client.html
APPENDIX
Here is the rest of the object methods. Internal methods are preceded
with an underscore _.
new
Usage : my $factory =
Bio::Tools::Run::AnalysisFactory->new(-access => 'soap',
-location => 'http://...');
Returns : a new Bio::Tools::Run::AnalysisFactory object representing a list
of available analyses
Args : There may be additional arguments which are specific
to the access method (see methods 'new' or '_initialize'
of the access-specific implementations (such as module
Bio::Tools::Run::AnalysisFactory::soap for a SOAP-based access).
The recognised and used arguments are:
-access
-location
-httpproxy
-timeout
It builds, populates and returns a new
"Bio::Tools::Run::AnalysisFactory" object. This is how it is seen from
the outside. But in fact, it builds, populates and returns a more
specific lower-level object, for example
"Bio::Tools::Run::AnalysisFactory::soap" object - which one it is it
depends on the "-access" parameter.
-access
It indicates what lower-level module to load. Default is 'soap'.
Other (but future) possibilities are:
-access => 'novella'
-access => 'local'
-location
A location of the service. The contents is access-specific (see
details in the lower-level implementation modules).
Default is "http://www.ebi.ac.uk/soaplab/services" (there are
services running at European Bioinformatics Institute on top of
most of EMBOSS analyses, and on some others).
-httpproxy
In addition to the location parameter, you may need to specify also
a location/URL of an HTTP proxy server (if your site requires one).
The expected format is "http://server:port". There is no default
value. It is also an access-specific parameter which may not be
used by all access methods.
-timeout
For long(er) running jobs the HTTP connection may be time-outed. In
order to avoid it (or, vice-versa, to call timeout sooner) you may
specify "timeout" with the number of seconds the connection will be
kept alive. Zero means to keep it alive forever. The default value
is two minutes.
_load_access_module
Usage : $class->_load_access_module ($access)
Returns : 1 on success, undef on failure
Args : 'access' should contain the last part of the
name of a module who does the real implementation
It does (in the run-time) a similar thing as
require Bio::Tools::Run::AnalysisFactory::$access
It prints an error on STDERR if it fails to find and load the module
(for example, because of the compilation errors in the module).
_guess_access
Usage : $class->_guess_access ($rh_params)
Returns : string with a guessed access protocol (e.g. 'soap'),
or undef if the guessing failed
Args : 'rh_params' is a hash reference containing parameters given
to the 'new' method.
It makes an expert guess what kind of access/transport protocol should
be used to access the underlying analysis. The guess is based on the
parameters in rh_params. Rememeber that this method is called only if
there was no -access parameter which could tell directly what access
method to use.
VERSION and Revision
Usage : print $Bio::Tools::Run::AnalysisFactory::VERSION;
print $Bio::Tools::Run::AnalysisFactory::Revision;
perl v5.14.12011-07-2Bio::Tools::Run::AnalysisFactory(3)