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Bio::EnsEMBL::DensityFeatureSet Class Reference

List of all members.


Class Summary

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
 

Definition at line 25 of file DensityFeatureSet.pm.

Available Methods

public Value colour ()
public Reference get_all_binvalues ()
public Value label ()
public Value label2 ()
public Int max_value ()
public Int min_value ()
public
Bio::EnsEMBL::DensityFeatureSet 
new ()
public Scale_to_fit scale_to_fit ()
public Int size ()
public Value stretch ()

Method Documentation

public Value Bio::EnsEMBL::DensityFeatureSet::colour ( )
 Title   : colour
 Usage   : $obj->colour($newval)
 Function: 
 Returns : value of colour
 Args    : newvalue (optional)
 Status  : Stable
 
Code:
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public Reference Bio::EnsEMBL::DensityFeatureSet::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
 
Code:
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public Value Bio::EnsEMBL::DensityFeatureSet::label ( )
 Title   : label
 Usage   : $obj->label($newval)
 Function: 
 Returns : value of label
 Args    : newvalue (optional)
 Status  : Stable
 
Code:
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public Value Bio::EnsEMBL::DensityFeatureSet::label2 ( )
 Title   : label2
 Usage   : $obj->label2($newval)
 Function: 
 Returns : value of label2
 Args    : newvalue (optional)
 Status  : Stable
 
Code:
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public Int Bio::EnsEMBL::DensityFeatureSet::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
 
Code:
click to view
public Int Bio::EnsEMBL::DensityFeatureSet::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
 
Code:
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public Bio::EnsEMBL::DensityFeatureSet Bio::EnsEMBL::DensityFeatureSet::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
 
Code:
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public Scale_to_fit Bio::EnsEMBL::DensityFeatureSet::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
 
Code:
click to view
public Int Bio::EnsEMBL::DensityFeatureSet::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
 
Code:
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public Value Bio::EnsEMBL::DensityFeatureSet::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
 
Code:
click to view

The documentation for this class was generated from the following file: