Bio SimpleAnalysisI
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Summary
Bio::SimpleAnalysisI - A simple interface to any (local or remote) analysis tool
Package variables
No package variables defined.
Inherit
Bio::Root::RootI
Synopsis
This is an interface module - you do not instantiate it.
Use other modules instead (those that implement this interface).
Description
This interface contains public methods for accessing and controlling
local and remote analysis tools. It is meant to be used on the client
side. The interface consists only of a necessary set of methods for
synchronous invocation of analysis tools. For more complex set,
including an asynchronous access, see interface Bio::AnalysisI
(which inherits from this one, by the way).
Methods
analysis_nameDescriptionCode
analysis_specDescriptionCode
input_specDescriptionCode
result_specDescriptionCode
runDescriptionCode
wait_forDescriptionCode
statusDescriptionCode
resultDescriptionCode
Methods description
analysis_namecode    nextTop
 Usage   : $tool->analysis_name;
Returns : a name of this analysis
Args : none
analysis_speccodeprevnextTop
 Usage   : $tool->analysis_spec;
Returns : a hash reference describing this analysis
Args : none
The returned hash reference uses the following keys (not all of them always
present, perhaps others present as well): name, type, version,
supplier, installation, description.
input_speccodeprevnextTop
 Usage   : $tool->input_spec;
Returns : an array reference with hashes as elements
Args : none
The analysis input data are named, and can be also associated with a
default value, with allowed values and with few other attributes. The
names are important for feeding the analysis with the input data (the
inputs are given to methods run and wait_for as name/value
pairs).
result_speccodeprevnextTop
 Usage   : $tool->result_spec;
Returns : a hash reference with result names as keys
and result types as values
Args : none
An analysis can produce several results, or the same result in several
different formats. All such results are named and can be retrieved
using their names by metod result.
Here is an example of the result specification:
  $result_spec = {
'outseq' => 'String',
'report' => 'String',
'detailed_status' => 'String'
};
runcodeprevnextTop
 Usage   : $tool->run ( ['sequence=@my.seq', 'osformat=embl'] )
Returns : $self
Args : data and parameters for this execution
(in various formats)
Create a job, start it, and wait for its completion. The method is
identical to the method wait_for. Why there are two methods doing
the same? Because it is expected that the sub-classes may implement
them differently (an example is an interface Bio::AnalysisI which
uses method run for an asynchronous execution and method
wait_for for a synchronous one.
Usually, after this call, you ask for results of the finished job:
    $analysis->run (...)->result;
The input data and prameters for this execution can be specified in
various ways:
    array reference
    The array has scalar elements of the form
   name = [[@]value]
    where name is the name of an input data or input parameter (see
method input_spec for finding what names are recognized by this
analysis) and value is a value for this data/parameter. If value
is missing a 1 is assumed (which is convenient for the boolean
options). If value starts with @ it is treated as a local
filename, and its contents is used as the data/parameter value.
    hash reference
    The same as with the array reference but now there is no need to use
an equal sign. The hash keys are input names and hash values their
data. The values can again start with a @ sign indicating a local
filename.
wait_forcodeprevnextTop
 Usage   : $tool->wait_for ( { 'sequence' => '@my,file' } )
Returns : $self
Args : the same as for method 'run'
Create a job, start it and wait for its completion. The method is
identical to the method run. See details in the run method.
statuscodeprevnextTop
 Usage   : $tool->status
Returns : string describing a status of the execution
Args : none
It returns one of the following strings (and perhaps more if a server
implementation extended possible job states):
   CREATED              (not run yet)
COMPLETED (run and finished normally)
TERMINATED_BY_ERROR (run and finished with an error or a signal)
resultcodeprevnextTop
 Usage   : $job->result (...)
Returns : a result created by running an analysis
Args : none (but an implementation may choose
to add arguments for instructions how to process
the raw result)
The method returns a scalar representing a result of an executed
job. If the job was terminated by an error the result may contain an
error message instead of the real data (or both, depending on the
implementation).
Methods code
analysis_namedescriptionprevnextTop
sub analysis_name {
 shift->throw_not_implemented();
}
analysis_specdescriptionprevnextTop
sub analysis_spec {
 shift->throw_not_implemented();
}
input_specdescriptionprevnextTop
sub input_spec {
 shift->throw_not_implemented();
}
result_specdescriptionprevnextTop
sub result_spec {
 shift->throw_not_implemented();
}
rundescriptionprevnextTop
sub run {
 shift->throw_not_implemented();
}
wait_fordescriptionprevnextTop
sub wait_for {
 shift->throw_not_implemented();
}
statusdescriptionprevnextTop
sub status {
 shift->throw_not_implemented();
}
resultdescriptionprevnextTop
sub result {
 shift->throw_not_implemented();
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 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
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHORTop
Martin Senger (martin.senger@gmail.com)
COPYRIGHTTop
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.
DISCLAIMERTop
This software is provided "as is" without warranty of any kind.
SEE ALSOTop
    *
http://www.ebi.ac.uk/Tools/webservices/soaplab/guide
APPENDIXTop
This is actually the main documentation...
If you try to call any of these methods directly on this
Bio::SimpleAnalysisI object you will get a not implemented error
message.