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 listsSupport
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:
https://github.com/bioperl/bioperl-live/issuesAUTHOR - 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)