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Bio-EnsEMBL-112.0.0_57
River stage zero No dependents
/ Bio::EnsEMBL::MiscFeature

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

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NAME

Bio::EnsEMBL::MiscFeature - A miscelaneous feature with arbitrary features and associations.

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.

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

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

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

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

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

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

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

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

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