Bio::EnsEMBL::SimpleFeature Class Reference

Inheritance diagram for Bio::EnsEMBL::SimpleFeature:

Public Member Functions
public Bio::EnsEMBL::Feature	new ()
public String	display_label ()
public String	display_id ()
public String	score ()
public Hash	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

use Bio::EnsEMBL::SimpleFeature;
 
$feature = Bio::EnsEMBL::SimpleFeature->new(
  -start         => 100,
  -end           => 220,
  -strand        => -1,
  -slice         => $slice,
  -analysis      => $analysis,
  -score         => 58,
  -display_label => 'EponineTSS',
  -dbID          => 1230,
  -adaptor       => $adaptor
);

Description

This is a simple feature which extends the Feature class to add
display_label and score attributes.

Definition at line 31 of file SimpleFeature.pm.

Member Function Documentation

display_id()

public String Bio::EnsEMBL::SimpleFeature::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 simple features this is the 
               display_label if it is available otherwise it is an empty 
               string.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

Code:

display_label()

public String Bio::EnsEMBL::SimpleFeature::display_label

(

)

  Arg [1]    : (optional) string $value
  Example    :

$label = $simple_feature->display_label();

  Description: Getter/Setter for the display label associated with this
               feature.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

new()

public Bio::EnsEMBL::Feature Bio::EnsEMBL::SimpleFeature::new

(

)

  Arg [DISPLAY_LABEL]: The label assigned to this simple feature
  Arg [...]  : Named arguments passed to superclass
  Example    :

$feature = Bio::EnsEMBL::SimpleFeature->new
                       (-start    => 1,
                        -end      => 100,
                        -strand   => 1,
                        -slice    => $slice,
                        -analysis => $analysis,
                        -adaptor => $adaptor,
                        -dbID    => 10,
                        -display_label => 'EponineTSS',
                        -score => 100);

  Description: Constructs a new Bio::EnsEMBL::Feature.  Generally subclasses
               of this method are instantiated, rather than this class itself.
  Returntype : Bio::EnsEMBL::Feature
  Exceptions : Thrown on invalid -SLICE, -ANALYSIS, -STRAND arguments
  Caller     : general, subclass constructors
  Status     : Stable

Code:

score()

public String Bio::EnsEMBL::SimpleFeature::score

(

)

  Arg [1]    : (optional) string $value
  Example    :

$score = $simple_feature->score();

  Description: Getter/Setter for the score associated with this
               feature.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

summary_as_hash()

public Hash Bio::EnsEMBL::SimpleFeature::summary_as_hash

(

)

  Example    :

my $hash = $simple_feature->summary_as_hash();

  Description: Generates a HashRef compatible with GFFSerializer. Adds
               score, external_name and logic_name to the basic Feature
               hash
  Returntype : Hash
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

---

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

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