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#
# 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
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=head1 NAME
Bio::Matrix::Scoring - Object which can hold scoring matrix information
=head1 SYNOPSIS
  use Bio::Matrix::Scoring;
=head1 DESCRIPTION
An object which can handle AA or NT scoring matrix information.  Some
transformation properties are available too.
=head1 FEEDBACK
=head2 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
=head2 Support 
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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/issues
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Matrix::Scoring;
$Bio::Matrix::Scoring::VERSION = '1.7.8';
use strict;
use base qw(Bio::Matrix::Generic);
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=head2 new
 Title   : new
 Usage   : my $obj = Bio::Matrix::Scoring->new();
 Function: Builds a new Bio::Matrix::Scoring object 
 Returns : an instance of Bio::Matrix::Scoring
 Args    :
=cut
sub new { 
    my ($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;
}
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=head2 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)
=cut
sub entropy{
    my $self = shift;
    return $self->{'entropy'} = shift if @_;
    return $self->{'entropy'};
}
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=head2 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)
=cut
sub expected_score{
    my $self = shift;
    return $self->{'expected'} = shift if @_;
    return $self->{'expected'};
}
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=head2 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)
=cut
sub scale{
    my $self = shift;
    return $self->{'scale'} = shift if @_;
    return $self->{'scale'};
}
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=head2 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)
=cut
sub scale_value{
    my $self = shift;
    return $self->{'scale_value'} = shift if @_;
    return $self->{'scale_value'};
}
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=head2 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)
=cut
sub description{
    my $self = shift;
    return $self->{'description'} = shift if @_;
    return $self->{'description'};
}
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=head2 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)
=cut
sub database{
    my $self = shift;
    return $self->{'database'} = shift if @_;
    return $self->{'database'};
}
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=head2 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)
=cut
sub lowest_score{
    my $self = shift;
    return $self->{'lowest_score'} = shift if @_;
    return $self->{'lowest_score'};
}
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=head2 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)
=cut
sub highest_score{
    my $self = shift;
    return $self->{'highest_score'} = shift if @_;
    return $self->{'highest_score'};
}
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=head2 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)
=cut
sub lambda{
    my $self = shift;
    return $self->{'lambda'} = shift if @_;
    return $self->{'lambda'};
}
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=head2 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)
=cut
sub H{
    my $self = shift;
    return $self->{'H'} = shift if @_;
    return $self->{'H'};
}
1;