Bio::EnsEMBL::RepeatFeature Class Reference

Inheritance diagram for Bio::EnsEMBL::RepeatFeature:

Public Member Functions
public Bio::EnsEMBL::RepeatFeature	new ()
public Bio::EnsEMBL::RepeatConsensus	repeat_consensus ()
public Int	hstart ()
public Int	score ()
public Int	hend ()
public Int	hstrand ()
public String	display_id ()
public Hashref	summary_as_hash ()
Public Member Functions inherited from Bio::EnsEMBL::Feature
public Bio::EnsEMBL::Feature	new ()
public Int	start ()
public Int	end ()
public Int	strand ()
public void	move ()
public Int	length ()
public Bio::EnsEMBL::Analysis	analysis ()
public Bio::EnsEMBL::Slice	slice ()
public Boolean Or Undef	equals ()
public Bio::EnsEMBL::Feature	transform ()
public Bio::EnsEMBL::Feature	transfer ()
public Listref	project_to_slice ()
public Listref	project ()
public String	seqname ()
public String	display_id ()
public String	version ()
public Bio::EnsEMBL::Slice	feature_Slice ()
public String	seq_region_name ()
public Int	seq_region_length ()
public Boolean	seq_region_strand ()
public Int	seq_region_start ()
public Int	seq_region_end ()
public String	coord_system_name ()
public String	seq ()
public Listref	get_all_alt_locations ()
public Boolean	overlaps ()
public Boolean	overlaps_local ()
public List	get_overlapping_Genes ()
public Bio::EnsEMBL::Gene	get_nearest_Gene ()
public String	feature_so_acc ()
public String	feature_so_term ()
public Hashref	summary_as_hash ()
public String	species ()
public	sub_SeqFeature ()
public	add_sub_SeqFeature ()
public	flush_sub_SeqFeature ()
Public Member Functions inherited from Bio::EnsEMBL::Storable
public Bio::EnsEMBL::Storable	new ()
public Instance	new_fast ()
public Int	dbID ()
public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()
public Boolean	is_stored ()
public	get_all_DAS_Features ()

Detailed Description

Synopsis

my $rf = new Bio::EnsEMBL::Feature(
  -start            => 100,
  -end              => 220,
  -strand           => -1,
  -slice            => $slice,
  -analysis         => $analysis,
  -repeat_consensus => $rc,
  -hstart           => 10,
  -hend             => 100,
  -hstrand          => 1,
  -score            => 83.2
);
 
my $hstart = $feat->hstart;
my $hend   = $feat->hend;
 
# move the feature to the chromosomal coordinate system
$feature = $feature->transform('chromosome');
 
# move the feature to a different slice
# (possibly on another coord system)
$feature = $feature->transfer($new_slice);
 
# project the feature onto another coordinate system possibly across
# boundaries:
@projection = @{ $feature->project('contig') };
 
# change the start, end, and strand of the feature in place
$feature->move( $new_start, $new_end, $new_strand );

Description

This a feature representing a repeat region on a sequence

Definition at line 45 of file RepeatFeature.pm.

Member Function Documentation

display_id()

public String Bio::EnsEMBL::RepeatFeature::display_id

(

)

  Arg [1]    : none
  Example    :

print $rf->display_id();

  Description: This method returns a string that is considered to be
               the 'display' identifier.  For repeat_features this is the 
               name of the repeat consensus if it is available otherwise it is
               an empty string.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

Code:

hend()

public Int Bio::EnsEMBL::RepeatFeature::hend

(

)

  Arg [1]    : (optional) int $hend
  Example    :

$hit_end = $repeat->hend;

  Description: Getter/Setter for the end bp of this repeat match on the 
               consensus sequence.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

hstart()

public Int Bio::EnsEMBL::RepeatFeature::hstart

(

)

  Arg [1]    : (optional) int $hstart
  Example    :

$hit_start = $repeat->hstart;

  Description: Getter/Setter for the start bp of this repeat match on the 
               consensus sequence.
  Returntype : int
  Exceptions : none 
  Caller     : general
  Status     : Stable

Code:

hstrand()

public Int Bio::EnsEMBL::RepeatFeature::hstrand

(

)

  Arg [1]    : none
  Example    :

none

  Description: always returns 1. method exists for consistancy with other 
               features.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

new()

public Bio::EnsEMBL::RepeatFeature Bio::EnsEMBL::RepeatFeature::new

(

)

  Arg [REPEAT_CONSENSUS] : Bio::EnsEMBL::RepeatConsensus (optional)
                           The repeat consensus for this repeat feature
  Arg [HSTART] : int (optional)
                 The hit start on the consensus sequence
  Arg [HEND]   : int (optional)
                 The hit end on the consensus sequence
  Arg [SCORE]  : float (optional)
                 The score
  Arg [...]    : Named arguments to superclass constructor
                 (see Bio::EnsEMBL::Feaure)
  Example    :

$rf = Bio::EnsEMBL::RepeatFeature->new(-REPEAT_CONSENSUS => $rc,
                                                     -HSTART => 10,
                                                     -HEND   => 100,
                                                     -SCORE  => 58.0,
                                                     -START  => 1_000_100,
                                                     -END    => 1_000_190,
                                                     -STRAND => 1,
                                                     -ANALYSIS => $an,
                                                     -SLICE  => $chr_slice);

  Description: Creates a new Bio::EnsEMBL::RepeatFeature object
  Returntype : Bio::EnsEMBL::RepeatFeature
  Exceptions : none
  Caller     : RepeatFeatureAdaptors
  Status     : Stable

Code:

repeat_consensus()

public Bio::EnsEMBL::RepeatConsensus Bio::EnsEMBL::RepeatFeature::repeat_consensus

(

)

  Arg [1]    : (optional) Bio::EnsEMBL::RepeatConsensus
  Example    :

$repeat_consensus = $repeat->repeat_consensus;

  Description: Getter/Setter for the repeat consensus of this repeat
  Returntype : Bio::EnsEMBL::RepeatConsensus
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

score()

public Int Bio::EnsEMBL::RepeatFeature::score

(

)

  Arg [1]    : (optional) float $score
  Example    :

$score = $repeat->score();

  Description: Getter/Setter for the score of this repeat feature
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

summary_as_hash()

public Hashref Bio::EnsEMBL::RepeatFeature::summary_as_hash

(

)

  Example       :

$repeat_feature_summary = $protein_feature->summary_as_hash();

  Description   : Retrieves a textual summary of this Repeat feature.
                  Not inherited from Feature.
  Returns       : hashref of arrays of descriptive strings
  Status        : Intended for internal use
 

Code:

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

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