LICENSE

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

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

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NAME

Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor

SYNOPSIS

DESCRIPTION

This object is responisble for all database interaction involving marker features including the fetching and storing of marker features.

The bulk of this objects' methods are inherited from Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor

METHODS

fetch_all_by_Marker

  Arg [1]    : Bio::EnsEMBL::Map::Marker
  Example    : @ms = @{$marker_feature_adaptor->fetch_by_Marker($mrkr)};
  Description: Retrieves a list of MarkerFeatures for a given marker
  Returntype : listref of Bio::EnsEMBL::MarkerFeatures
  Exceptions : none
  Caller     : general
  Status     : stable

fetch_all_by_Slice_and_MarkerName

  Arg [1]    : Bio::EnsEMBL::Slice $slice
  Arg [2]    : string marker name
  Example    : @ms = @{$marker_feature_adaptor->fetch_all_by_Slice_and_MarkerName($slice, $name)};
  Description: Retrieves a list of MarkerFeatures for a given marker name
  Returntype : listref of Bio::EnsEMBL::Map::MarkerFeatures
  Exceptions : none
  Caller     : general
  Status     : stable

fetch_all_by_Slice_and_priority

  Arg [1]    : Bio::EnsEMBL::Slice $slice
  Arg [2]    : (optional) int $priority
  Arg [3]    : (optional) int $map_weight
  Arg [3]    : (optional) string $logic_name
  Example    : @feats = @{$mfa->fetch_all_by_Slice_and_priority($slice,80,2)};
  Description: Retrieves all marker features above a specified threshold 
               priority which overlap the provided slice, below a 
               a specified map_weight.
  Returntype : listref of Bio::EnsEMBL::Map::MarkerFeatures in slice coords
  Exceptions : none
  Caller     : general
  Status     : stable

store

  Arg [1]    : Bio::EnsEMBL::Map::MarkerFeature
  Example    : $marker_feature_adaptor->store(@marker_features);
  Description: Stores a list of marker features in this database.
               The dbID and adaptor of each marker will be set on successful 
               storing.
  Returntype : none
  Exceptions : thrown if not all data needed for storing is populated in the
               marker features
  Caller     : general
  Status     : stable