view variant_effect_predictor/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

=head1 LICENSE

  Copyright (c) 1999-2012 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <[e-mail]>.

  Questions may also be sent to the Ensembl help desk at
  <[e-mail]>.

=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( $name,
                   $logic_name ); }
  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);
}



=head2 fetch_all_by_RawContig_and_pid

  Description: DEPRECATED use fetch_all_by_Slice_and_pid instead

=cut

sub fetch_all_by_RawContig_and_pid {
  my($self, $contig, $pid, $logic_name) = @_;

  my $constraint;

  #get the primary table alias
  my @tabs = $self->_tables;
  my $alias = $tabs[0]->[1];

  if(defined $pid) {
    $constraint = "${alias}.perc_ident > $pid";
  }

  return $self->fetch_all_by_RawContig_constraint($contig, 
						  $constraint, 
						  $logic_name);
}




##implemented by subclasses:
# store
# _tables
# _columns
# _obj_from_hashref



1;