DOKK / manpages / debian 12 / libbio-perl-perl / Bio::Matrix::Scoring.3pm.en
Bio::Matrix::Scoring(3pm) User Contributed Perl Documentation Bio::Matrix::Scoring(3pm)

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

  use Bio::Matrix::Scoring;

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

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

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.

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/issues

Email jason-at-bioperl-dot-org

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

 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    :


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


 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)


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


 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)


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


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


 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)


 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)


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


 Title   : H
 Usage   : $obj->H($newval)
 Function: 
 Example : 
 Returns : value of H (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
2021-08-15 perl v5.32.1