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

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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

SYNOPSIS

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  use Bio::Matrix::Scoring;

DESCRIPTION

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

FEEDBACK

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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:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich

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Email jason-at-bioperl-dot-org

APPENDIX

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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)
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::Matrix::Scoring
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Jason Stajich <jason-at-bioperl-dot-org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code



# Let the code begin...


package Bio::Matrix::Scoring;
use strict;


use base qw(Bio::Matrix::Generic);



sub new { 
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    
    my ($entropy,$expected,$scale,$scaleval,$database,
		  $lowestscore,$highestscore,$lambda,$H) = 
			 $self->_rearrange([qw(
        ENTROPY EXPECTED SCALE SCALE_VALUE DATABASE
		  LOWEST_SCORE HIGHEST_SCORE LAMBDA H)], @args);

    $self->entropy  ($entropy);
    $self->expected_score($expected);
    $self->scale    ($scale);
    $self->scale_value($scaleval);
    $self->database ($database);
    $self->lowest_score($lowestscore);
    $self->highest_score($highestscore);
    $self->lambda($lambda);
    $self->H($H);
				    
    return $self;
}


sub entropy{
    my $self = shift;

    return $self->{'entropy'} = shift if @_;
    return $self->{'entropy'};
}


sub expected_score{
    my $self = shift;

    return $self->{'expected'} = shift if @_;
    return $self->{'expected'};
}


sub scale{
    my $self = shift;

    return $self->{'scale'} = shift if @_;
    return $self->{'scale'};
}


sub scale_value{
    my $self = shift;

    return $self->{'scale_value'} = shift if @_;
    return $self->{'scale_value'};
}


sub description{
    my $self = shift;

    return $self->{'description'} = shift if @_;
    return $self->{'description'};
}


sub database{
    my $self = shift;

    return $self->{'database'} = shift if @_;
    return $self->{'database'};
}


sub lowest_score{
    my $self = shift;

    return $self->{'lowest_score'} = shift if @_;
    return $self->{'lowest_score'};
}


sub highest_score{
    my $self = shift;

    return $self->{'highest_score'} = shift if @_;
    return $self->{'highest_score'};
}


sub lambda{
    my $self = shift;

    return $self->{'lambda'} = shift if @_;
    return $self->{'lambda'};
}


sub H{
    my $self = shift;
    return $self->{'H'} = shift if @_;
    return $self->{'H'};
}

1;