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::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