BinValueSet.pm

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=head1 LICENSE
 
See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
 
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
 
     http://www.apache.org/licenses/LICENSE-2.0
 
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
 
=cut
 
 
=head1 CONTACT
 
  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
 
  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.
 
=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
 
@ISA = qw(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'};
}
 
 
 
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