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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CONTACT

            

              
              
Please email comments or questions to the public Ensembl
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Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.
            
          

NAME

Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor - Abstract Base class for AlignFeatureAdaptors

SYNOPSIS

Abstract class, should not be instantiated. Implementation of abstract methods must be performed by subclasses.

DESCRIPTION

This is a base adaptor for the align feature adaptors DnaAlignFeatureAdaptor and ProteinAlignFeatureAdaptor.

METHODS

fetch_all_by_Slice_and_hcoverage

            

              
              
Arg [1]    : Bio::EnsEMBL::Slice $slice
             The slice from which to obtain align features.
Arg [2]    : (optional) float $hcoverage 
             A lower bound for the hcoverage of feats to obtain.
Arg [3]    : (optional) string $logic_name
             The logic name of the type of features to obtain.
Example    : @feats = @{
              $adaptor->fetch_all_by_Slice_and_hcoverage( $slice,
                50.0 ) };
Description: Returns a listref of features created from the
             database which are on the Slice $slice and with a
             hcoverage greater than $hcoverage.  If logic name
             is defined, only features with an analysis of type
             $logic_name will be returned.
Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
             in Slice coordinates
Exceptions : none
Caller     : general
Status     : At Risk
            
          

fetch_all_by_Slice_and_external_db

            

              
              
Arg [1]    : Bio::EnsEMBL::Slice $slice
             The slice from which to obtain align features.
Arg [2]    : String $external_db_name
             Name of the external DB to which the align features
             should be restricted.
Arg [3]    : (optional) string $logic_name
             The logic name of the type of features to obtain.
Example    : @feats = @{
                $adaptor->fetch_all_by_Slice_and_external_db( $slice,
                  'EMBL' ) };
Description: Returns a listref of features created from the
             database which are on the Slice $slice and associated
             with external DB $external_db_name.  If logic name
             is defined, only features with an analysis of type
             $logic_name will be returned.
Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
             in Slice coordinates
Exceptions : thrown if $external_db_name is not defined or if
             the subclass does not return a table alias for the
             external_db table from _tables()
Caller     : general
Status     : At Risk
            
          

fetch_all_by_Slice_and_pid

            

              
              
Arg [1]    : Bio::EnsEMBL::Slice $slice
             The slice from which to obtain align features.
Arg [2]    : (optional) float $pid 
             A lower bound for the percentage identity of features
             to obtain.
Arg [3]    : (optional) string $logic_name
             The logic name of the type of features to obtain.
Example    : @feats =
               @{ $adaptor->fetch_all_by_Slice_and_pid( $slice, 50.0 ) };
Description: Returns a listref of features created from the
             database which are on the Slice $slice and with a
             percentage identity greater than $pid.  If logic name
             is defined, only features with an analysis of type
             $logic_name will be returned.
Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
             in Slice coordinates
Exceptions : none
Caller     : general
Status     : Stable
            
          

fetch_all_by_hit_name

            

              
              
Arg [1]    : string $hit_name
             The hit_name of the features to obtain
Arg [2]    : (optional) string $logic_name
             The analysis logic name of the type of features to
             obtain.
Example    : @feats =
               @{ $adaptor->fetch_all_by_hit_name( 'AK078491.1',
                 'vertrna' ); }
Description: Returns a listref of features created from the
             database which correspond to the given hit_name.  If
             logic name is defined, only features with an analysis
             of type $logic_name will be returned.
Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
Exceptions : thrown if hit_name is not defined
Caller     : general
Status     : Stable
            
          

fetch_all_by_hit_name_unversioned

            

              
              
Arg [1]    : string $hit_name
             The beginning of the hit_name of the features to
             obtain, e.g. AA768786 would retrieve AA768786.1,
             AA768786.2 etc.
Arg [2]    : (optional) string $logic_name
             The analysis logic name of the type of features to
             obtain.
Example    : @feats =
                @{ $adaptor->fetch_all_by_hit_name( $name,
                  $logic_name ) };
Description: Returns a listref of features created from the
             database which start with the given hit_name.  If
             logic name is defined, only features with an analysis
             of type $logic_name will be returned.
Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
Exceptions : thrown if hit_name is not defined
Caller     : general
Status     : At risk