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::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