Raw content of Bio::EnsEMBL::DensityFeatureSet
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::DensityFeatureSet -
A feature representing a set of density features
=head1 SYNOPSIS
use Bio::EnsEMBL::DensityFeatureSet;
my $densitySet = Bio::EnsEMBL::DensityFeatureSet->new(
-bin_array = \@out,
-stretch = 1,
);
=head1 DESCRIPTION
A density feature set is a wrap around a array of density features with
additional information about the collective density feature set, such as
max_min_values and scale factors etc. a given region.
This module is part of the Ensembl project
=head1 METHODS
=cut
package Bio::EnsEMBL::DensityFeatureSet;
use strict;
use warnings;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw);
use Data::Dumper;
=head2 new
Description: Creates a new density feature set.
Returntype : Bio::EnsEMBL::DensityFeatureSet
Exceptions : throw if invalid density value type is provided
Caller : general
Status : Stable
=cut
sub new {
my $class = shift;
my $max_value = undef;
my $min_value = undef;
my($dfeats, $stretch, $scale_to_fit) =
rearrange(['FEATURES', 'STRETCH', 'SCALE_TO_FIT'], @_);
foreach (@$dfeats){
my $value = $_->density_value;
$max_value = $value if (!defined($max_value) || $value > $max_value);
$min_value = $value if (!defined($min_value) || $value < $min_value);
}
return bless {'bin_array' => $dfeats,
'stretch' => $stretch,
'scale_to_fit' => $scale_to_fit,
'min_value' => $min_value,
'max_value' => $max_value}, $class;
}
=head2 stretch
Title : stretch
Usage : $obj->stretch($newval)
Function: gets/sets a boolean for whether we should stretch the data over the
range (i.e. from min to max rather than absolute numbers).
Returns : value of _stretch
Args : newvalue (optional)
Status : Stable
=cut
sub stretch{
my $self = shift;
$self->{'stretch'} = shift if(@_);
return $self->{'stretch'};
}
=head2 scale_to_fit
Title : scale_to_fit
Usage : $obj->scale_to_fit($newval)
Function: gets/sets the number that the BinValues are to be scaled against -
i.e. the greatest BinValue->value will be scaled to this number, and the rest
scaled in proportion.
Returns : scale_to_fit value
Args : newvalue (optional)
Status : Stable
=cut
sub scale_to_fit{
my $self = shift;
$self->{'scale_to_fit'} = shift if (@_);
return $self->{'scale_to_fit'};
}
=head2 colour
Title : colour
Usage : $obj->colour($newval)
Function:
Returns : value of colour
Args : newvalue (optional)
Status : Stable
=cut
sub colour{
my $self = shift;
$self->{'color'} = shift if(@_);
return $self->{'color'};
}
=head2 label
Title : label
Usage : $obj->label($newval)
Function:
Returns : value of label
Args : newvalue (optional)
Status : Stable
=cut
sub label{
my $self = shift;
$self->{'label'} = shift if (@_);
return $self->{'label'};
}
=head2 label2
Title : label2
Usage : $obj->label2($newval)
Function:
Returns : value of label2
Args : newvalue (optional)
Status : Stable
=cut
sub label2{
my $self = shift;
$self->{'label2'} = shift if (@_);
return $self->{'label2'};
}
=head2 get_all_binvalues
Arg [1] : none
Example : @binvalues = @{$dfs->get_all_binvalues};
Description: Scales all of the contained DensityFeatures by $scalefactor
and returns them.
Returntype : reference to a list of DensityFeatures
Exceptions : none
Caller : general
Status : Stable
=cut
sub get_all_binvalues{
my $self = shift;
my $max_value = $self->max_value();
my $min_value = $self->min_value();
return [] if(!@{$self->{'bin_array'}});
my $width = $self->scale_to_fit();
return [] unless defined($width);
# throw("Cannot scale values - scale_to_fit has not been set");
if ($self->stretch && ($max_value-$min_value) ){
foreach my $bv (@{ $self->{'bin_array'}}){
my $scaledval = (($bv->density_value - $min_value) /
($max_value-$min_value) )* $width;
$bv->scaledvalue($scaledval);
}
} elsif($max_value) {
foreach my $bv (@{ $self->{'bin_array'}}){
my $scaledval = ($bv->density_value / $max_value) * $width;
$bv->scaledvalue($scaledval);
}
} else {
foreach my $bv (@{ $self->{'bin_array'}}){
$bv->scaledvalue(0);
}
}
return $self->{'bin_array'};
}
=head2 max_value
Arg [1] : none
Example : my $max = $dfs->max_value();
Description: Returns the maximum density feature value from the density
feature set
Returntype : int
Exceptions : none
Caller : general
Status : Stable
=cut
sub max_value{ $_[0]->{'max_value'};}
=head2 min_value
Arg [1] : none
Example : my $min = $dfs->min_value();
Description: Returns the minimum density feature value from the density
feature set.
Returntype : int
Exceptions : none
Caller : general
Status : Stable
=cut
sub min_value{ $_[0]->{'min_value'};}
=head2 size
Arg [1] : none
Example : my $num_features = $dfs->size();
Description: Returns the number of density features in this density feature
set.
Returntype : int
Exceptions : none
Caller : general
Status : Stable
=cut
sub size {
my $self = shift;
return scalar @{$self->{'bin_array'}};
}
1;
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