update for sets

modules/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm

@@ -42,6 +42,7 @@ use strict;
 use POSIX;
 use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
 use Bio::EnsEMBL::DensityFeature;
+use Bio::EnsEMBL::DensityFeatureSet;
 use Bio::EnsEMBL::DensityType;
 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
 
@@ -499,5 +500,13 @@ sub store{
 }
 
 
+sub fetch_Featureset_by_Slice {
+  my $self = shift;  
+  my $dfeats = $self->fetch_all_by_Slice(@_);
+  my $dfeatSet = new Bio::EnsEMBL::DensityFeatureSet($dfeats);
+  
+  return ($dfeatSet);
+}
+
 
 1;

modules/Bio/EnsEMBL/DensityFeature.pm

@@ -100,8 +100,9 @@ sub new {
   $self->{'density_value'} = $dv;
 
   $self->{'slice'}    = $seq_region;
-  $self->{'seq_region_start'} = $start;
-  $self->{'seq_region_end'}   = $end;
+  $self->{'start'} = $start;
+  $self->{'end'}   = $end;
+  
 
   return $self;
 }
@@ -217,6 +218,97 @@ sub density_type{
   return $self->{'density_type'};
 }
 
+
+###BG########
+
+=head2 start
+
+ Title   : start
+ Usage   : $obj->start($newval)
+ Function: 
+ Returns : value of start
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub start{
+   my $obj = shift;
+   if( @_ ) {
+      my $value = shift;
+      $obj->{'start'} = $value;
+    }
+    return $obj->{'start'};
+
+}
+
+=head2 end
+
+ Title   : end
+ Usage   : $obj->end($newval)
+ Function: 
+ Returns : value of end
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub end{
+   my $obj = shift;
+   if( @_ ) {
+      my $value = shift;
+      $obj->{'end'} = $value;
+    }
+    return $obj->{'end'};
+
+}
+
+
+=head2 scaledvalue
+
+ Title   : scaledvalue
+ Usage   : $obj->scaledvalue($newval)
+ Function: 
+ Returns : this object's scaled value
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub scaledvalue{
+   my $obj = shift;
+   if( @_ ) {
+      my $scaledvalue = shift;
+      $obj->{'scaledvalue'} = $scaledvalue;
+    }
+    return $obj->{'scaledvalue'};
+
+}
+
+
+
+=head2 url
+
+ Title   : url
+ Usage   : $obj->url($newval)
+ Function: 
+ Returns : this object's url
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub url{
+   my $obj = shift;
+   if( @_ ) {
+      my $url = shift;
+      $obj->{'url'} = $url;
+    }
+    return $obj->{'url'};
+
+}
+
+
 1;
 
 

modules/Bio/EnsEMBL/DensityFeatureSet.pm

+#
+# Ensembl module for Bio::EnsEMBL::DensityFeatureSet
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=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,
+		  -max_value = $max_value,
+		  -min_value = $min_value,
+		
+		);
+
+=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 CONTACT
+
+Post comments/questions to the ensembl development list: ensembl-dev@ebi.ac.uk
+
+=head1 METHODS
+
+=cut
+
+
+use strict;
+use warnings;
+
+package Bio::EnsEMBL::DensityFeatureSet;
+
+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
+
+=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)
+
+
+=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)
+
+
+=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)
+
+
+=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)
+
+
+=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)
+
+
+=cut
+
+sub label2{
+    my $self = shift;
+   $self->{'label2'} = shift if (@_);
+   return $self->{'label2'};
+}
+
+
+=head2 get_all_binvalues
+
+ Title   : get_all_binvalues
+ Usage   : my @binvalue_objects = @{$BVSet->get_all_binvalues};
+ Function: scales all the binvalues by the scale_factor and returns them.
+ Example :
+ Returns : array of BinValue objects 
+ Args    : none
+
+
+=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() || $self->throw("Cannot scale values - scale_to_fit has not been set");  
+
+    if ($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'};  
+
+}
+
+sub max_value{ $_[0]->{'max_value'};}
+
+sub min_value{ $_[0]->{'min_value'};}
+ 
+
+1;
+sub size {
+    my $self = shift;
+    return scalar @{$self->{'bin_array'}};
+}
+
+1;
+
+
+