Raw content of Bio::EnsEMBL::DensityPlot::BinValueSet =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::DensityPlot::BinValueSet =head1 SYNOPSIS =head1 DESCRIPTION =head1 METHODS =cut package Bio::EnsEMBL::DensityPlot::BinValueSet; use vars qw($AUTOLOAD @ISA); use strict; use Bio::EnsEMBL::DensityPlot::BinValue; # Object preamble - inheriets from Bio::Root::Object use Bio::EnsEMBL::Root; @ISA = qw(Bio::EnsEMBL::Root Exporter); #@EXPORT_OK = qw(); # new() is inherited from Bio::Root::Object # _initialize is where the heavy stuff will happen when new is called sub new { my ($class,@args) = @_; my $self = {}; bless $self,$class; $self->{'_bin_array'} = []; return $self; } =head2 add_binvalue Title : add_binValue Usage : Function: Example : Returns : Args : =cut sub add_binvalue{ my ($self,$value) = @_; defined ($value->chromosomestart) || $self->throw( "Bin Value object does not contain a ChromosomeStart method" ); defined ($value->chromosomeend) || $self->throw( "Bin Value object does not contain a ChromosomeEnd method" ); defined ($value->value) || $self->throw( "Bin Value object does not contain a Value method" ); $self->_store_biggest($value->value); $self->_store_smallest($value->value); push(@{$self->{'_bin_array'}},$value); } =head2 get_binvalues Title : get_binvalues Usage : my @binvalue_objects = $BVSet->get_binvalues Function: scales all the binvalues by the scale_factor and returns them. Example : Returns : array of BinValue objects Args : none =cut sub get_binvalues{ my $self = shift; my $biggest_value = $self->{'_biggest_value'} || 0; my $smallest_value = $self->{'_smallest_value'} || 0; if (!defined ($biggest_value)||!defined($smallest_value)){ $self->throw("Cannot scale - no values to scale against"); } my $width = $self->scale_to_fit(); if ($self->stretch && ($biggest_value-$smallest_value) ){ foreach my $bv (@{ $self->{'_bin_array'}}){ my $scaledval = (($bv->value - $smallest_value) / ($biggest_value-$smallest_value) )* $width; $bv->scaledvalue($scaledval); } } elsif($biggest_value) { foreach my $bv (@{ $self->{'_bin_array'}}){ my $scaledval = ($bv->value / $biggest_value) * $width; $bv->scaledvalue($scaledval); } } else { foreach my $bv (@{ $self->{'_bin_array'}}){ $bv->scaledvalue(0); } } return ( @{ $self->{'_bin_array'}} ); } sub size { my $self = shift; return scalar @{$self->{'_bin_array'}}; } =head2 position Title : position Usage : $obj->position($newval) Function: Returns : value of position Args : newvalue (optional) =cut sub position{ my $self = shift; if( @_ ) { my $value = shift; $self->{'position'} = $value; } return $self->{'position'}; } =head2 label Title : label Usage : $obj->label($newval) Function: Returns : value of label Args : newvalue (optional) =cut sub label{ my $self = shift; if( @_ ) { my $value = shift; $self->{'label'} = $value; } return $self->{'label'}; } =head2 label2 Title : label2 Usage : $obj->label2($newval) Function: Returns : value of label2 Args : newvalue (optional) =cut sub label2{ my $self = shift; if( @_ ) { my $value = shift; $self->{'label2'} = $value; } return $self->{'label2'}; } =head2 color Title : color Usage : $obj->color($newval) Function: Returns : value of color Args : newvalue (optional) =cut sub color{ my $self = shift; if( @_ ) { my $value = shift; $self->{'color'} = $value; } return $self->{'color'}; } =head2 shape Title : shape Usage : $obj->shape($newval) Function: Returns : value of shape Args : newvalue (optional) =cut sub shape{ my $self = shift; if( @_ ) { my $value = shift; $self->{'shape'} = $value; } return $self->{'shape'}; } =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) =cut sub stretch{ my ($self,$value) = @_; if( defined $value ) { $self->{'_stretch'} = $value; } 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) =cut sub scale_to_fit{ my $self = shift; if( @_ ) { my $value = shift; $self->{'_scale_to_fit'} = $value; } return $self->{'_scale_to_fit'}; } =head2 _store_biggest Title : _store_biggest Usage : $self->_store_biggest($newval) Function: internal method for storing the largest BinValue->value in this set. Returns : biggest value seen so far Args : value =cut sub _store_biggest { my ($self,$val) = @_; if (!defined $self->{'_biggest_value'} || $val > $self->{'_biggest_value'}){ $self->{'_biggest_value'}=$val; } return $self->{'_biggest_value'}; } =head2 _store_smallest Title : _store_smallest Usage : $self->_store_smallest($newval) Function: internal method for storing the smallest BinValue->value in this set. Returns : smallest value seen so far Args : value =cut sub _store_smallest { my ($self,$val) = @_; if (!defined($self->{'_smallest_value'})){ $self->{'_smallest_value'}=$val; } if (!defined($self->{'_smallest_value'}) || $val < $self->{'_smallest_value'}){ $self->{'_smallest_value'}=$val; } return $self->{'_smallest_value'}; } 1;