TFBS::PatternGen::Motif

Matrix

Methods description

Methods code

    my ($self, %args) = @_;
    return TFBS::Matrix::PFM->new (-name => "unknown",
				   -ID   => "unknown",
				   -class=> "unknown",
				   -tags => { %{$self->{'tags'} } },
				   %args,
				   -matrix => $self->_calculate_PFM()
				   );

 ## simplest case: matrix already IS PFM    my $self = shift;
    return [@{$self->{'matrix'}}];

    return @{$_[0]->{'sites'}};

    my ($caller, %args) = @_;
    ##my $matrix = TFBS::Matrix->new(%args, -matrixtype=>"PFM");
    ##my $self = bless $matrix, ref($caller) || $caller;
    my $self = $caller->SUPER::new(%args, -matrixtype=>"PFM");
    $self->{'length'} = $args{'-length'} || scalar @{$self->{'matrix'}->[0]};
    $self->{'nr_hits'} = ($args{'-nr_hits'} || undef);
    ##           || $self->throw("No -nr_hits provided.");
    ## Why was nr_hits required ?? (Boris)
    $self->{'sites'}=$args{'-sites'};
    ## $self->{'tags'} = ($args{'-tags'} || {});
    return $self;

    my ($self, %args ) = @_;
    $self->PFM(%args);

General documentation