NAME

Bio::Tools::Analysis::SimpleAnalysisBase - abstact superclass for SimpleAnalysis implementations

SYNOPSIS

  # no to be run directly

DESCRIPTION

This class is a generic implementation of SimpleAnalysisI and should be used as a base class for specific implementations.

SimpleAnalysis implementing modules just need to provide a specific _run() result() and _init() methods, plus any get/set methods for parameter to the analysis program.

SEE ALSO

Bio::SimpleAnalysisI, Bio::WebAgent

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 one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                       - General discussion
  http://bio.perl.org/MailList.html           - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

AUTHORS

Richard Adams, Richard.Adams@ed.ac.uk, Heikki Lehvaslaiho, heikki@ebi.ac.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Usage   : $job->new(...)
 Returns : a new analysis object, 
 Args    : none (but an implementation may choose
           to add arguments representing parameters for the analysis
           program. Each key value of must have a method implemented
           for it in a subclass. A seq () method is provided here as
           this will probably be needed by all sequence analysis programs

seq

 Usage   : $job->seq()
 Returns : a Bio::PrimarySeqI implementing sequence object, or void
 Args    : None, or a Bio::PrimarySeqI implementing object 

analysis_name

    Useage   :  $analysis->analysis_name();
    Returns  :  The analysis name
    Arguments:  none

analysis_spec

    Useage   :  $analysis->analysis_spec();
    Returns  :  a hash reference to  a hash of analysis parameters. See
                Bio::SimpleAnalysisI for a list of recommended key values.
    Arguments:  none

clear

    Usage     :$analysis->clear();
    Returns   :true value on success
    Arguments :none
    Purpose   :to remove raw results from a previous analysis so that
               an analysis can be repeated with different parameters.

input_spec

    Useage   :  $analysis->input_spec();
    Returns  :  a  reference to  an array of  hashes of analysis parameters. See
                Bio::SimpleAnalysisI for a list of recommended key values.
    Arguments:  none

result_spec

    Useage   :  $analysis->result_spec();
    Returns  :  a  reference to  a   hashes of resultformats. See
                Bio::SimpleAnalysisI for a list of recommended key values. The key
                values can be used as parameters to the result() method, the values
                provide descriptions.
    Arguments:  none

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq