DensityFeature.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::DensityFeature - A feature representing a density, or
precentage coverage etc. in a given region.
 
=head1 SYNOPSIS
 
  use Bio::EnsEMBL::DensityFeature;
 
  $feature = Bio::EnsEMBL::DensityFeature->new(
    -seq_region    => $region,
    -start         => 1,
    -end           => 1e6,
    -density_type  => $dt,
    -density_value => 98.5
  );
 
=head1 DESCRIPTION
 
A density feature represents a count, density, or percentage coverage,
etc. for a given region.
 
This module is part of the Ensembl project http://www.ensembl.org
 
=head1 METHODS
 
=cut
 
 
use strict;
use warnings;
 
package Bio::EnsEMBL::DensityFeature;
 
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw);
use Bio::EnsEMBL::DensityType;
 
use vars qw(@ISA);
 
@ISA = qw(Bio::EnsEMBL::Feature);
 
 
=head2 new
 
  Arg [SEQ_REGION] : the sequence over which the density was calculated.
 
  Arg [START] : start point on the seq at which density was calulated.
 
  Arg [END] : end point on the seq at which density was calulated.
 
  Arg [DENSITY_TYPE] : the type of density calculated.
 
  Arg [DENSITY_VALUE] : the density.
 
  Arg [...]  : Named arguments passed to superclass
  Example    : $feature = Bio::EnsEMBL::DensityFeature->new
                            (-seq_region    => $region,
                 -start         => 1,
                             -end           => 1e6,
                             -density_type  => $dt,
                 -density_value => 98.5)
 
  Description: Creates a new density feature.
  Returntype : Bio::EnsEMBL::DensityFeature
  Exceptions : throw if invalid density value type is provided
  Caller     : general
  Status     : Stable
 
=cut
 
sub new {
  my $caller = shift;
 
  #allow constructor to be called as class or object method
  my $class = ref($caller) || $caller;
 
  my $self = $class->SUPER::new(@_);
 
  my($seq_region, $start, $end, $dt, $dv) =
    rearrange(['SEQ_REGION', 'START', 'END', 'DENSITY_TYPE', 'DENSITY_VALUE'],
              @_);
 
  throw("Density value must be >= 0.") if($dv < 0);
 
  if(!defined($dt)){
    throw("Density Type is NOT optional.");
  }
 
  $self->{'density_type'} = $dt;
  $self->{'density_value'} = $dv;
 
  $self->{'slice'}    = $seq_region;
  $self->{'start'} = $start;
  $self->{'end'}   = $end;
  
 
  return $self;
}
 
 
 
=head2 strand
 
  Arg [1]    : none
  Example    : $strand = $df->strand();
  Description: Getter fot the strand attribute. Density features always have
               strand 0 and this attribute is not settable.
  Returntype : int (always 0)
  Exceptions : warning if an attempt is made to set the strand
  Caller     : general
  Status     : Stable
 
=cut
 
sub strand {
  my $self = shift;
  warning("DensityFeature strand is not settable") if(@_);
  return 0;
}
 
 
 
=head2 density_value
 
  Arg [1]    : (optional) float $density_value
  Example    : $dv = $density_feature->density_value();
  Description: Getter/Setter for the density value of this DensityFeature.
               The density value may be a count, a percentage, or a coverage
               of a feature type in the area defined by this feature.
  Returntype : float
  Exceptions : throw if a negative density value is provided
  Caller     : general
  Status     : Stable
 
=cut
 
sub density_value {
  my $self = shift;
 
  if(@_) {
    my $density_value = shift;
    throw("Density value must be >= 0.") if($density_value < 0);
    $self->{'density_value'} = $density_value;
  }
 
  return $self->{'density_value'};
}
 
 
 
=head2 analysis
 
  Arg [1]    : (optional) Bio::EnsEMBL::Analysis $analysis
               New value for the analysis of the attached DensityType
  Example    : print $df->analysis()->logic_name();
  Description: Overridden superclass analysis method, to chain to analysis
               method on attached DensityType.
  Returntype : Bio::EnsEMBL::Analysis
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub analysis {
  my $self = shift;
 
  my $dt = $self->density_type();
 
  return undef if(!$dt);
 
  return $dt->analysis(@_);
}
 
 
 
=head2 density_type
 
  Arg [1]    : string $newval (optional) 
               The new value to set the density_value_type attribute to
  Example    : $density_value_type = $obj->density_value_type()
  Description: Getter/Setter for the density_value_type attribute
  Returntype : Bio::EnsEMBL::DensityType
  Exceptions : if object passed is not of type DensityType
  Caller     : general
  Status     : Stable
 
=cut
 
sub density_type{
  my $self = shift;
  if(@_) {
    my $type = shift;
    if( !ref $type || !$type->isa("Bio::EnsEMBL::DensityType")){
      throw("object passed must be an ensembl DensityType ". 
        "not a [".ref($type)."]");
    }
    else{
      $self->{'density_type'}=$type;
    }
  }
  return $self->{'density_type'};
}
 
 
###BG########
 
=head2 scaledvalue
 
 Title   : scaledvalue
 Usage   : $obj->scaledvalue($newval)
 Function:
 Returns : scalar - object's scaled value
 Args    : newvalue (optional)
 Status  : Stable
 
=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 : String containing this object's url
 Args    : newvalue (optional)
 Status  : Stable
 
 
=cut
 
sub url{
   my $obj = shift;
   if( @_ ) {
      my $url = shift;
      $obj->{'url'} = $url;
    }
    return $obj->{'url'};
 
}
 
 
1;