Bio::Matrix Scoring
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Matrix::Scoring - Object which can hold scoring matrix information
Package variables
No package variables defined.
Included modules
Bio::Matrix::Generic
Inherit
Bio::Matrix::Generic
Synopsis
  use Bio::Matrix::Scoring;
Description
An object which can handle AA or NT scoring matrix information. Some
transformation properties are available too.
Methods
newDescriptionCode
entropyDescriptionCode
expected_scoreDescriptionCode
scaleDescriptionCode
scale_valueDescriptionCode
descriptionDescriptionCode
databaseDescriptionCode
lowest_scoreDescriptionCode
highest_scoreDescriptionCode
lambdaDescriptionCode
HDescriptionCode
Methods description
newcode    nextTop
 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    :
entropycodeprevnextTop
 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_scorecodeprevnextTop
 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)
scalecodeprevnextTop
 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_valuecodeprevnextTop
 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)
descriptioncodeprevnextTop
 Title   : description
 Usage   : $obj->description($newval)
 Function: 
 Example : 
 Returns : value of description (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
databasecodeprevnextTop
 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_scorecodeprevnextTop
 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_scorecodeprevnextTop
 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)
lambdacodeprevnextTop
 Title   : lambda
 Usage   : $obj->lambda($newval)
 Function: 
 Example : 
 Returns : value of lambda (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
HcodeprevnextTop
 Title   : H
 Usage   : $obj->H($newval)
 Function: 
 Example : 
 Returns : value of H (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
Methods code
newdescriptionprevnextTop
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;
}
entropydescriptionprevnextTop
sub entropy {
    my $self = shift;

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

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

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

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

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

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

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

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

    return $self->{'lambda'} = shift if @_;
    return $self->{'lambda'};
}
HdescriptionprevnextTop
sub H {
    my $self = shift;
    return $self->{'H'} = shift if @_;
    return $self->{'H'};
}
General documentation
FEEDBACKTop
Mailing ListsTop
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/MailList.shtml  - About the mailing lists
Reporting BugsTop
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.bioperl.org/
AUTHOR - Jason StajichTop
Email jason-at-bioperl-dot-org
Describe contact details here
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _