Bio::Tools::Run AnalysisFactory
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::Tools::Run::AnalysisFactory - A directory of analysis tools
Package variables
No package variables defined.
Included modules
Bio::Factory::AnalysisI Bio::Root::Root
  # list all available analyses from the default location,
# using a default (SOAP) access method
use Bio::Tools::Run::AnalysisFactory;
my $list = Bio::Tools::Run::AnalysisFactory->new();
use Data::Dumper; print Dumper ($list);
# ditto, but from a different location use Bio::Tools::Run::AnalysisFactory; my $list = Bio::Tools::Run::AnalysisFactory->new(-location => 'http://somewhere/something')
# ...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')
# 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;
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.
Methods description
newcode    nextTop
 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
    It indicates what lower-level module to load. Default is 'soap'.
Other (but future) possibilities are:
   -access => 'novella'
-access => 'local'
    A location of the service. The contents is access-specific (see
details in the lower-level implementation modules).
    Default is (there are
services running at European Bioinformatics Institute on top of most
of EMBOSS analyses, and on some others).
    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.
    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.
 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).
 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.
Methods code
    $Revision = q$$Id: 15558 2009-02-21 22:07:57Z maj $;
sub new {
    my ($caller,@args) = @_;
    my $class = ref($caller) || $caller;
    if ($class eq 'Bio::Tools::Run::AnalysisFactory') {

	# this is called only the first time when somebody calls: 'new
# Bio::Tools::Run::AnalysisFactory (...)', and it actually loads a
# 'real-work-doing' module and call this new() method again
# (unless the loaded module has its own new() method)
my %param = @args; @param { map { lc $_ } keys %param } = values %param; # lowercase keys
my $access = $param {'-access'} || # use -access parameter
$class->_guess_access (\% param ) || # or guess from other parameters
'soap'; # or use a default access method
$access = "\L$access"; # normalize capitalization to lower case
# remember the access method (putting it into @args means that the
# object - when created - will remember it)
push (@args, (-access => $access)) unless $param {'-access'}; # load module with the real implementation - as defined in $access
return undef unless (&_load_access_module ($access)); # this calls this same method new() - but now its object part
# (see the upper branche above) is called
return "Bio::Tools::Run::AnalysisFactory::$access"->new (@args); } else { # if $caller is an object, or if it is an underlying
# 'real-work-doing' class (e.g. Bio::Tools::Run::AnalysisFactory::soap)
# then we want to call SUPER to create and bless a new object
my ($self) = $class->SUPER::new (@args); # now the $self is an empty object - we will populate it from
# the $caller - if $caller is an object (so we do cloning here)
if (ref ($caller)) { %{ $self } = %{ $caller }; } # and finally add values from '@args' into the newly created
# object (the values will overwrite the values copied above);
# this is done by calling '_initialize' of the 'real-work-doing'
# class (if there is no one there, there is always an empty one
# in Bio::Root::Root)
$self->_initialize (@args); return $self; } } # -----------------------------------------------------------------------------
sub _load_access_module {
  my ($access) = @_;

  my $load = "Bio/Tools/Run/AnalysisFactory/$";
  eval {
    require $load;

  if ( $@ ) {
    Bio::Root::Root->throw (<<END);
$load: $access cannot be found or loaded
Exception $@
For more information about the Analysis system please see the Bio::Tools::Run::AnalysisFactory docs.
  return 1;

# -----------------------------------------------------------------------------
sub _guess_access {
   my ($class, $rh_params) = @_;
   return undef;

# -----------------------------------------------------------------------------
General documentation
Mailing ListsTop
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Support Top
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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 BugsTop
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
Martin Senger (
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.
This software is provided "as is" without warranty of any kind.
Here is the rest of the object methods. Internal methods are preceded
with an underscore _.
VERSION and RevisionTop
 Usage   : print $Bio::Tools::Run::AnalysisFactory::VERSION;
print $Bio::Tools::Run::AnalysisFactory::Revision;