BaseAlignFeatureAdaptor.pm

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=head1 LICENSE
 
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regarding copyright ownership.
 
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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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
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=cut
 
 
=head1 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>.
 
=cut
 
=head1 NAME
 
Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor - Abstract Base class for
AlignFeatureAdaptors
 
=head1 SYNOPSIS
 
Abstract class, should not be instantiated.  Implementation of abstract
methods must be performed by subclasses.
 
=head1 DESCRIPTION
 
This is a base adaptor for the align feature adaptors
DnaAlignFeatureAdaptor and ProteinAlignFeatureAdaptor.
 
=head1 METHODS
 
=cut
 
package Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor;
use vars qw(@ISA @EXPORT);
use strict;
 
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
 
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);
 
@EXPORT = (@{$DBI::EXPORT_TAGS{'sql_types'}});
 
=head2 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
 
=cut
 
sub fetch_all_by_Slice_and_hcoverage {
  my ( $self, $slice, $hcoverage, $logic_name ) = @_;
 
  my $constraint;
  if ( defined($hcoverage) ) {
    $constraint = "hcoverage > $hcoverage";
  }
 
  return
    $self->fetch_all_by_Slice_constraint( $slice, $constraint,
                                          $logic_name );
}
 
=head2 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
 
=cut
 
sub fetch_all_by_Slice_and_external_db {
  my ( $self, $slice, $external_db_name, $logic_name ) = @_;
 
  if ( !defined($external_db_name) ) {
    throw("Need name of external DB to restrict to");
  }
 
  my @join_tables = $self->_tables();
 
  my $edb_alias;
  foreach my $join_table (@join_tables) {
    my ( $table, $table_alias ) = @{$join_table};
    if ( $table eq 'external_db' ) {
      $edb_alias = $table_alias;
      last;
    }
  }
 
  if ( !defined($edb_alias) ) {
    throw("Can not find alias for external_db table");
  }
 
  my $constraint = sprintf( "%s.db_name = %s",
                            $edb_alias,
                            $self->dbc()->db_handle()
                              ->quote( $external_db_name, SQL_VARCHAR )
  );
 
  return
    $self->fetch_all_by_Slice_constraint( $slice, $constraint,
                                          $logic_name );
} ## end sub fetch_all_by_Slice_and_external_db
 
=head2 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
 
=cut
 
sub fetch_all_by_Slice_and_pid {
  my ( $self, $slice, $pid, $logic_name ) = @_;
 
  #  #get the primary table alias
  #  my @tabs = $self->_tables;
  #  my $alias = $tabs[0]->[1];
 
  #  if(defined $pid) {
  #    $constraint = "${alias}.perc_ident > $pid";
  #  }
 
  my $constraint;
  if ( defined($pid) ) {
    $constraint = sprintf( "perc_ident > %s",
                           $self->dbc()->db_handle()
                             ->quote( $pid, SQL_FLOAT ) );
  }
 
  return
    $self->fetch_all_by_Slice_constraint( $slice, $constraint,
                                          $logic_name );
}
 
 
=head2 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
 
=cut
 
sub fetch_all_by_hit_name {
  my ( $self, $hit_name, $logic_name ) = @_;
 
  if ( !defined($hit_name) ) {
    throw("hit_name argument is required");
  }
 
  # Construct a constraint like 't1.hit_name = "123"'
  my @tabs = $self->_tables();
  my ( $name, $syn ) = @{ $tabs[0] };
 
  my $constraint = sprintf( "%s.hit_name = %s",
           $syn,
           $self->dbc()->db_handle()->quote( $hit_name, SQL_VARCHAR ) );
 
  if ( defined($logic_name) ) {
    # Add the $logic_name constraint
    $constraint =
      $self->_logic_name_to_constraint( $constraint, $logic_name );
  }
 
  return $self->generic_fetch($constraint);
}
 
 
=head2 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
 
=cut
 
sub fetch_all_by_hit_name_unversioned {
  my ( $self, $hit_name, $logic_name ) = @_;
 
  if ( !defined($hit_name) ) {
    throw("hit_name argument is required");
  }
  $hit_name =~ s/_/\\_/;
 
  #construct a constraint like 't1.hit_name = "123"'
  my @tabs = $self->_tables;
  my ( $name, $syn ) = @{ $tabs[0] };
 
  my $constraint = sprintf( "%s.hit_name LIKE %s",
    $syn,
    $self->dbc()->db_handle()->quote( $hit_name . '.%', SQL_VARCHAR ) );
 
  if ( defined($logic_name) ) {
    # Add the $logic_name constraint
    $constraint =
      $self->_logic_name_to_constraint( $constraint, $logic_name );
  }
 
  return $self->generic_fetch($constraint);
}
 
 
##implemented by subclasses:
# store
# _tables
# _columns
# _obj_from_hashref
 
 
 
1;