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

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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