Raw content of Bio::EnsEMBL::DensityFeatureSet =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;