Bio::Matrix::Scoring.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Matrix::Scoring - Object which can hold scoring matrix information

SYNOPSIS

   use Bio::Matrix::Scoring;
 
 

DESCRIPTION

An object which can handle AA or NT scoring matrix information. Some transformation properties are available too.

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://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

APPENDIX

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

new

  Title   : new
  Usage   : my $obj = Bio::Matrix::Scoring->new();
  Function: Builds a new Bio::Matrix::Scoring object 
  Returns : an instance of Bio::Matrix::Scoring
  Args    :
 
 

entropy

  Title   : entropy
  Usage   : $obj->entropy($newval)
  Function: 
  Example : 
  Returns : value of entropy (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

expected_score

  Title   : expected_score
  Usage   : $obj->expected_score($newval)
  Function: 
  Example : 
  Returns : value of expected (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

scale

  Title   : scale
  Usage   : $obj->scale($newval)
  Function: 
  Example : 
  Returns : value of scale (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

scale_value

  Title   : scale_value
  Usage   : $obj->scale_value($newval)
  Function: 
  Example : 
  Returns : value of scale_value (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

description

  Title   : description
  Usage   : $obj->description($newval)
  Function: 
  Example : 
  Returns : value of description (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

database

  Title   : database
  Usage   : $obj->database($newval)
  Function: 
  Example : 
  Returns : value of database (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

lowest_score

  Title   : lowest_score
  Usage   : $obj->lowest_score($newval)
  Function: 
  Example : 
  Returns : value of lowest_score (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

highest_score

  Title   : highest_score
  Usage   : $obj->highest_score($newval)
  Function: 
  Example : 
  Returns : value of highest_score (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

lambda

  Title   : lambda
  Usage   : $obj->lambda($newval)
  Function: 
  Example : 
  Returns : value of lambda (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

H

  Title   : H
  Usage   : $obj->H($newval)
  Function: 
  Example : 
  Returns : value of H (a scalar)
  Args    : on set, new value (a scalar or undef, optional)