NAME¶
Bio::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://redmine.open-bio.org/projects/bioperl/
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¶
- •
- 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;