Bio::EnsEMBL::DensityFeatureSet Class Reference

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

Detailed Description

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.

Member Function Documentation

colour()

public Value Bio::EnsEMBL::DensityFeatureSet::colour

(

)

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

Code:

get_all_binvalues()

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:

label()

public String Bio::EnsEMBL::DensityFeatureSet::label

(

)

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

Code:

label2()

public String Bio::EnsEMBL::DensityFeatureSet::label2

(

)

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

Code:

max_value()

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:

min_value()

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:

new()

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:

scale_to_fit()

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:

size()

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:

stretch()

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:

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

• ensembl/modules/Bio/EnsEMBL/DensityFeatureSet.pm