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

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CONTACT

  Please email comments or questions to the public Ensembl
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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

cpanm Bio::EnsEMBL

perl -MCPAN -e shell
install Bio::EnsEMBL