Raw content of Bio::EnsEMBL::DensityType
<![CDATA[=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::DensityType - A type representing a density, or percentage
coverage etc. in a given region.
=head1 SYNOPSIS
use Bio::EnsEMBL::DensityType;
$type = Bio::EnsEMBL::DensityType->new(
-analysis => $analysis,
-blocksize => 1000000,
-value_type => $type
);
=head1 DESCRIPTION
A density type represents a density, or percentage coverage etc. in a
given region.
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::DensityType;
use Bio::EnsEMBL::Storable;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Storable);
=head2 new
Arg [..] : Takes a set of named arguments
Example : $dt = new Bio::EnsEMBL::DensityType::DensityType(
-analysis => $analysis,
-blocksize => 1e6,
-value_type => 'sum')
Description: Creates a new Density Type object
Returntype : Bio::EnsEMBL::DensityType
Exceptions : blocksize > 0,
valuetype must be 'sum' or 'ratio',
valid analysis object must be passed
Caller : general
Status : Stable
=cut
sub new {
my $class = shift;
my $self = $class->SUPER::new(@_);
my ($analysis, $block_size, $value_type, $region_features) =
rearrange(['ANALYSIS','BLOCK_SIZE','VALUE_TYPE','REGION_FEATURES'],@_);
if($analysis) {
if(!ref($analysis) || !$analysis->isa('Bio::EnsEMBL::Analysis')) {
throw('-ANALYSIS argument must be a Bio::EnsEMBL::Analysis not '.
$analysis);
}
}
if($value_type ne "sum" and $value_type ne "ratio"){
throw('-VALUE_TYPE argument must be "ratio" or "sum" not *'.
$value_type."*");
}
$block_size |= 0;
$region_features |= 0;
if(! ($block_size xor $region_features )){
throw('Set either -BLOCK_SIZE or -REGION_FEATURES, not both');
}
if( $block_size <0 or $region_features < 0 ) {
throw( 'No negative values for -BLOCK_SIZE or -REGION_FEATURES' );
}
$self->{'analysis'} = $analysis;
$self->{'block_size'} = $block_size;
$self->{'value_type'} = $value_type;
$self->{'region_features'} = $region_features;
return $self;
}
=head2 analysis
Arg [1] : Bio::EnsEMBL::Analysi
Example : none
Description: get/set for attribute analysis
Returntype : Bio::EnsEMBL::Analysis
Exceptions : none
Caller : general
Status : Stable
=cut
sub analysis{
my $self = shift;
if(@_) {
my $a = shift;
if(defined($a) && (!ref($a) || !$a->isa('Bio::EnsEMBL::Analysis'))) {
throw("Argument must be undef or a Bio::EnsEMBL::Analysis object.");
}
$self->{'analysis'} = $a;
}
return $self->{'analysis'};
}
=head2 value_type
Arg [1] : string $value_type
Example : none
Description: gettter/setter for the
Returntype : float
Exceptions : none
Caller : general
Status : Stable
=cut
sub value_type{
my $self = shift;
$self->{'value_type'} = shift if(@_);
return $self->{'value_type'};
}
=head2 block_size
Arg [1] : int
Example : none
Description: getter/setter for attribute block_size
Returntype : int
Exceptions : none
Caller : general
Status : Stable
=cut
sub block_size{
my $self = shift;
$self->{'block_size'} = shift if(@_);
return $self->{'block_size'};
}
=head2 region_features
Arg [1] : int $region_features
Example : The number of features per seq_region inside this density_type..
Description: get/set for attribute region_features
Returntype : string
Exceptions : none
Caller : general
=cut
sub region_features {
my $self = shift;
$self->{'region_features'} = shift if( @_ );
return $self->{'region_features'};
}
1;
]]>