/ 
bioperl-1.5.2_004-RCd
/ Bio::Matrix::Scoring

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

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 = new Bio::Matrix::Scoring();
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)