Provided by: libbio-perl-perl_1.6.924-3_all bug

NAME

       Bio::SearchDist - A perl wrapper around Sean Eddy's histogram object

SYNOPSIS

         $dis = Bio::SearchDist->new();
         foreach $score ( @scores ) {
            $dis->add_score($score);
         }

         if( $dis->fit_evd() ) {
           foreach $score ( @scores ) {
             $evalue = $dis->evalue($score);
             print "Score $score had an evalue of $evalue\n";
           }
         } else {
           warn("Could not fit histogram to an EVD!");
         }

DESCRIPTION

       The Bio::SearchDist object is a wrapper around Sean Eddy's excellent histogram object. The
       histogram object can bascially take in a number of scores which are sensibly distributed
       somewhere around 0 that come from a supposed Extreme Value Distribution. Having add all
       the scores from a database search via the add_score method you can then fit a extreme
       value distribution using fit_evd(). Once fitted you can then get out the evalue for each
       score (or a new score) using evalue($score).

       The fitting procedure is better described in Sean Eddy's own code (available from
       http://hmmer.janelia.org/, or in the histogram.h header file in Compile/SW). Bascially it
       fits a EVD via a maximum likelhood method with pruning of the top end of the distribution
       so that real positives are discarded in the fitting procedure. This comes from an
       orginally idea of Richard Mott's and the likelhood fitting is from a book by Lawless
       [should ref here].

       The object relies on the fact that the scores are sensibly distributed around about 0 and
       that integer bins are sensible for the histogram. Scores based on bits are often ideal for
       this (bits based scoring mechanisms is what this histogram object was originally designed
       for).

CONTACT

       The original code this was based on comes from the histogram module as part of the HMMer2
       package. Look at http://hmmer.janelia.org/

       Its use in Bioperl is via the Compiled XS extension which is cared for by Ewan Birney
       (birney@ebi.ac.uk). Please contact Ewan first about the use of this module

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://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 the bugs and their
       resolution.  Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

APPENDIX

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

   add_score
        Title   : add_score
        Usage   : $dis->add_score(300);
        Function: Adds a single score to the distribution
        Returns : nothing
        Args    :

   fit_evd
        Title   : fit_evd
        Usage   : $dis->fit_evd();
        Function: fits an evd to the current distribution
        Returns : 1 if it fits successfully, 0 if not
        Args    :

   fit_Gaussian
        Title   : fit_Gaussian
        Usage   :
        Function:
        Example :
        Returns :
        Args    :

   evalue
        Title   : evalue
        Usage   : $eval = $dis->evalue($score)
        Function: Returns the evalue of this score
        Returns : float
        Args    :

   _engine
        Title   : _engine
        Usage   : $obj->_engine($newval)
        Function: underlyine bp_sw:: histogram engine
        Returns : value of _engine
        Args    : newvalue (optional)