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Bio-EnsEMBL-112.0.0_58
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/ Bio::EnsEMBL::DensityFeatureSet

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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.

CONTACT

Please email comments or questions to the public Ensembl
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Questions may also be sent to the Ensembl help desk at
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NAME

Bio::EnsEMBL::DensityFeatureSet - A feature representing a set of density features

SYNOPSIS

use Bio::EnsEMBL::DensityFeatureSet;

my $densitySet = Bio::EnsEMBL::DensityFeatureSet->new(
  -bin_array = \@out,
  -stretch   = 1,
);

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

METHODS

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

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

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

colour

Title   : colour
Usage   : $obj->colour($newval)
Function: 
Returns : value of colour
Args    : newvalue (optional)
Status  : Stable

label

Title   : label
Usage   : $obj->label($newval)
Function: 
Returns : String containing label
Args    : newvalue (optional)
Status  : Stable

label2

Title   : label2
Usage   : $obj->label2($newval)
Function: 
Returns : String containing label2
Args    : newvalue (optional)
Status  : Stable

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

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

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

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