Bio::EnsEMBL::MiscFeature Class Reference

Inheritance diagram for Bio::EnsEMBL::MiscFeature:

Public Member Functions
public Bio::EnsEMBL::MiscFeature	new ()
public void	add_Attribute ()
public void	add_MiscSet ()
public Listref	get_all_MiscSets ()
public Listref	get_all_Attributes ()
public Listref	get_all_attribute_values ()
public Scalar	get_scalar_attribute ()
public	get_first_scalar_attribute ()
public String	display_id ()
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::MiscFeature;
use Bio::EnsEMBL::MiscSet;
use Bio::EnsEMBL::Attribute;
 
my $mfeat = Bio::EnsEMBL::MiscFeature->new(
  -START  => 1200,
  -END    => 100_000,
  -STRAND => 1,
  -SLICE  => $slice
);
 
# Can add attributes to the misc feature and associate with various
# sets
my $clone_set = Bio::EnsEMBL::MiscSet->new(
  -CODE        => 'clone',
  -NAME        => '1MB clone set',
  -DESCRIPTION => '1MB CloneSet'
);
 
my $tiling_path_set = Bio::EnsEMBL::MiscSet->new(
  -CODE => 'tilingpath',
  -NAME => 'tiling path set'
);
 
my $attrib1 = Bio::EnsEMBL::Attribute->new(
  -VALUE => 'RLX12451',
  -CODE  => 'name',
  -NAME  => 'name'
);
 
my $attrib2 = Bio::EnsEMBL::Attribute->new(
  -VALUE => '4',
  -CODE  => 'version',
  -NAME  => 'version'
);
 
my $attrib3 = Bio::EnsEMBL::Attribute->new(
  -VALUE => 'AL42131.4',
  -CODE  => 'synonym',
  -NAME  => 'synonym'
);
 
# can associate a misc feature with any number of sets
 
$mfeat->add_MiscSet($clone_set);
$mfeat->add_MiscSet($tiling_path_set);
 
# can add arbitrary attributes to a misc feature
 
$mfeat->add_Attribute($attrib1);
$mfeat->add_Attribute($attrib2);
$mfeat->add_Attribute($attrib3);
 
my ($name_attrib) = @{ $mfeat->get_all_Attributes('name') };
my @all_attribs = @{ $mfeat->get_all_Attributes() };
 
my @all_sets = @{ $mfeat->get_all_MiscSets() };
my ($clone_set) = @{ $mfeat->get_all_CloneSets('clone') };
 
 
# Can do normal feature operations as well
$mfeat = $mfeat->transform('supercontig');
print $mfeat->slice->seq_region_name, ' ', $mfeat->start, '-',
  $mfeat->end;

Description

MiscFeatures are extremely general features with a location, and an
arbitrary group of attributes.  They are grouped with other features of
the same 'type' through the use of MiscSets (see Bio::EnsEMBL::MiscSet).
Attributes are attached in the fom of Bio::EnsEMBL::Attribute objects.
See Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor for ways to fetch or store
MiscFeatures.

Definition at line 86 of file MiscFeature.pm.

Member Function Documentation

add_Attribute()

public void Bio::EnsEMBL::MiscFeature::add_Attribute

(

)

  Arg [1]    : Bio::EnsEMBL::Attribute $attribute
  Example    :

$misc_feature->add_attribute($attribute);

  Description: Adds an attribute to this misc. feature
  Returntype : none
  Exceptions : throw on wrong argument type
  Caller     : general
  Status     : Stable

Code:

add_MiscSet()

public void Bio::EnsEMBL::MiscFeature::add_MiscSet

(

)

  Arg [1]    : Bio::EnsEMBL::MiscSet $set
               The set to add
  Example    :

$misc_feature->add_MiscSet(Bio::EnsEMBL::MiscSet->new(...));

  Description: Associates this MiscFeature with a given Set.
  Returntype : none
  Exceptions : throw if the set arg is not provided,
               throw if the set to be added does not have a code
  Caller     : general
  Status     : Stable

Code:

display_id()

public String Bio::EnsEMBL::MiscFeature::display_id

(

)

  Arg [1]    : none
  Example    :

print $kb->display_id();

  Description: This method returns a string that is considered to be
               the 'display' identifier.  For misc_features this is the first
               name or synonym attribute or '' if neither are defined.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

Code:

get_all_attribute_values()

public Listref Bio::EnsEMBL::MiscFeature::get_all_attribute_values

(

)

  Arg [1]    : string $code
               The code of the Attribute object values to retrieve
  Example    :

@attributes_vals = @{$misc_feature->get_all_attribute_values('name')};

  Description: Retrieves a list of Attribute object values for given code or all
               of the associated Attributes.
  Returntype : listref of values
  Exceptions : 
  Caller     : general
  Status     : Stable

Code:

get_all_Attributes()

public Listref Bio::EnsEMBL::MiscFeature::get_all_Attributes

(

)

  Arg [1]    : optional string $code
               The code of the Attribute objects to retrieve
  Example    :

@attributes = @{ $misc_feature->get_all_Attributes('name') };

  Description: Retrieves a list of Attribute objects for given code or all
               of the associated Attributes.
  Returntype : listref of Bio::EnsEMBL::Attribute
  Exceptions : 
  Caller     : general
  Status     : Stable

Code:

get_all_MiscSets()

public Listref Bio::EnsEMBL::MiscFeature::get_all_MiscSets

(

)

  Arg [1]    : optional string $code
               The code of the set to retrieve
  Example    :

$set = $misc_feature->get_all_MiscSets($code);

  Description: Retrieves a set that this feature is associated with via its
               code. Can return empty lists. Usually returns about one elements lists.
  Returntype : listref of Bio::EnsEMBL::MiscSet
  Exceptions : throw if the code arg is not provided
  Caller     : general
  Status     : Stable

Code:

get_first_scalar_attribute()

public Bio::EnsEMBL::MiscFeature::get_first_scalar_attribute

(

)

Undocumented method

Code:

get_scalar_attribute()

public Scalar Bio::EnsEMBL::MiscFeature::get_scalar_attribute

(

)

  Arg [1]    : string $code
               The code of the Attribute object values to retrieve
  Example    :

$vals = $misc_feature->get_scalar_attribute('name');

  Description: Retrieves a value for given code or all
               of the associated Attributes.
  Returntype : scalar value
  Exceptions : 
  Caller     : general
  Status     : Stable

Code:

new()

public Bio::EnsEMBL::MiscFeature Bio::EnsEMBL::MiscFeature::new

(

)

  Arg [-SLICE]: Bio::EnsEMBL::SLice - Represents the sequence that this
                feature is on. The coordinates of the created feature are
                relative to the start of the slice.
  Arg [-START]: The start coordinate of this feature relative to the start
                of the slice it is sitting on.  Coordinates start at 1 and
                are inclusive.
  Arg [-END]  : The end coordinate of this feature relative to the start of
                the slice it is sitting on.  Coordinates start at 1 and are
                inclusive.
  Arg [-STRAND]: The orientation of this feature.  Valid values are 1,-1,0.
  Arg [-SEQNAME] : A seqname to be used instead of the default name of the
                of the slice.  Useful for features that do not have an
                attached slice such as protein features.
  Arg [-dbID]   : (optional) internal database id
  Arg [-ADAPTOR]: (optional) Bio::EnsEMBL::DBSQL::BaseAdaptor
  Example    :

$feature = Bio::EnsEMBL::MiscFeature->new(-start    => 1,
                                                    -end      => 100,
                                                    -strand   => 1,
                                                    -slice    => $slice,
                                                    -analysis => $analysis);

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

Code:

summary_as_hash()

public Hash Bio::EnsEMBL::MiscFeature::summary_as_hash

(

)

  Example    :

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

  Description: Generates a HashRef compatible with GFFSerializer. Adds
               all attribute key value pairs plus MiscSet codes and names
  Returntype : Hash
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

---

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

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