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Bio-EnsEMBL-113.0.0
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/ Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor

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::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