/ 
Bio-EnsEMBL-113.0.0
River stage zero No dependents
/ Bio::EnsEMBL::DBSQL::MetaCoordContainer

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

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.

fetch_all_CoordSystems_by_feature_type

Arg [1]    : string $table - the name of the table to retrieve coord systems
             for.  E.g. 'gene', 'exon', 'dna_align_feature'
Example    : @css = @{$mcc->fetch_all_CoordSystems_by_feature_type('gene')};
Description: This retrieves the list of coordinate systems that features
             in a particular table are stored.  It is used internally by
             the API to perform queries to these tables and to ensure that
             features are only stored in appropriate coordinate systems.
Returntype : listref of Bio::EnsEMBL::CoordSystem objects
Exceptions : throw if name argument not provided
Caller     : BaseFeatureAdaptor
Status     : Stable

fetch_max_length_by_CoordSystem_feature_type

Arg [1]    : Bio::EnsEMBL::CoordSystem $cs
Arg [2]    : string $table
Example    : $max_len = $mcc->fetch_max_length_by_CoordSystem_feature_type($cs,'gene');
Description: Returns the maximum length of features of a given type in
             a given coordinate system.
Returntype : int or undef
Exceptions : throw on incorrect argument
Caller     : BaseFeatureAdaptor
Status     : Stable

add_feature_type

Arg [1]    : Bio::EnsEMBL::CoordSystem $cs
             The coordinate system to associate with a feature table
Arg [2]    : string $table - the name of the table in which features of
             a given coordinate system will be stored in
Arg [3]    : int $length
             This length is used to update the max_length in the database
             and the internal cache. 
Example    : $csa->add_feature_table($chr_coord_system, 'gene');
Description: This function tells the coordinate system adaptor that
             features from a specified table will be stored in a certain
             coordinate system.  If this information is not already stored
             in the database it will be added.
Returntype : none
Exceptions : none
Caller     : BaseFeatureAdaptor
Status     : Stable

remove_feature_type

Arg [1]    : Bio::EnsEMBL::CoordSystem $cs
             The coordinate system to associate with a feature table
Arg [2]    : string $table - the name of the table in which features of
             a given coordinate system are being removed
Example    : $csa->remove_feature_table($chr_coord_system, 'gene');
Description: This function tells the coordinate system adaptor that
             features have been fully removed from a certain coordinate system.
             Use with caution as it will cause issues if there are still features
             left.
Returntype : none
Exceptions : none
Caller     : BaseFeatureAdaptor
Status     : Stable