diff variant_effect_predictor/Bio/EnsEMBL/DensityFeatureSet.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/DensityFeatureSet.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,287 @@
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 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
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=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 http://www.ensembl.org
+
+=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);
+
+=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 : String containing 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 : String containing 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;
+
+
+