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

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NAME

Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor

SYNOPSIS

$mfa = $database_adaptor->get_MiscFeatureAdaptor();

# retrieve a misc feature by its dbID
my $misc_feat = $mfa->fetch_by_dbID(1234);

# retrieve all misc features in a given region
my @misc_feats = @{ $mfa->fetch_all_by_Slice($slice) };

# retrieve all misc features in a given region with a given set code
my @misc_clones =
  @{ $mfa->fetch_all_by_Slice_and_set_code('cloneset') };

# store some misc features in the database
$mfa->store(@misc_features);

DESCRIPTION

This is an adaptor for the retrieval and storage of MiscFeatures. Misc Features are extremely generic features that can be added with minimal effort to the database. Currently misc features are used to describe the locations of clone sets and tiling path information, but arbitrary features can be stored. Misc features are grouped into sets and can be fetched according to their grouping using the fetch_all_by_Slice_and_set_code and fetch_all_by_set_code methods. MiscFeatures may belong to more than one set.

METHODS

fetch_all_by_Slice_and_set_code

Arg [1]    : Bio::EnsEMBL::Slice $slice
             A slice representing the region to fetch from
Arg [2...] : string $set_code
             The code of the set to retrieve features from
Example    : @feats = @{$mfa->fetch_all_by_Slice_and_set_code('cloneset')};
Description: Retrieves a set of MiscFeatures which have a particular set code
             and which lie in a particular region.  All features with the
             provide set code and which overlap the given slice are returned.
Returntype : listref of Bio::EnsEMBL::MiscFeatures
Exceptions : throw if set_code is not provided
             warning if no set for provided set code exists
Caller     : general
Status     : Stable

fetch_all_by_attribute_type_value

Arg [1]    : string $attrib_type_code
             The code of the attribute type to fetch features for
Arg [2]    : (optional) string $attrib_value
             The value of the attribute to fetch features for
Example    : 
       #get all misc features that have an embl accession
       @feats = @{$mfa->fetch_all_by_attrib_type_value('embl_acc')};
       #get the misc feature with synonym 'AL014121'
       ($feat)=@{$mfa->fetch_all_by_attrib_type_value('synonym','AL014121');
Description: Retrieves MiscFeatures which have a particular attribute.
             If the attribute value argument is also provided only
             features which have the attribute AND a particular value
             are returned.  The features are returned in their native
             coordinate system (i.e. the coordinate system that they
             are stored in).
Returntype : listref of Bio::EnsEMBL::MiscFeatures
Exceptions : throw if attrib_type code arg is not provided
Caller     : general
Status     : Stable

fetch_by_attribute_set_value

Arg [1]    : string $attrib_type_code
             The code of the attribute type to fetch features for
Arg [2]    : (optional) string $attrib_value
             The value of the attribute to fetch features for
Arg [3]    : (optional) string $misc_set
             The name of the set to which the feature belongs
Example    :
       $feat = $mfa->fetch_by_attribute_set_value('clone', 'RP11-411G9', 'tilepath');
       # Get the clone belonging to the tilepath
Description: Retrieves MiscFeatures which have a particular attribute.
             If the attribute value argument is also provided only
             features which have the attribute AND a particular value
             are returned.  The features are returned in their native
             coordinate system (i.e. the coordinate system that they
             are stored in).
Returntype : listref of Bio::EnsEMBL::MiscFeatures
Exceptions : throw if attrib_type code arg is not provided
Caller     : general
Status     : Stable

list_dbIDs

Arg [1]    : none
Example    : @feature_ids = @{$misc_feature_adaptor->list_dbIDs()};
Description: Gets an array of internal ids for all misc_features in the 
             current db
Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
Returntype : list of ints
Exceptions : none
Caller     : ?
Status     : Stable

store

Arg [1]    : list of Bio::EnsEMBL::MiscFeatures @misc_features
Example    : $misc_feature_adaptor->store(@misc_features);
Description: Stores a list of MiscFeatures in this database.  The stored
             features will have their 
Returntype : none
Exceptions : throw on invalid arguments
             warning if misc feature is already stored in this database
             throw if start/end/strand attribs are not valid
Caller     : general
Status     : Stable