BaseFeatureAdaptor.pm 30.9 KB
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#
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# EnsEMBL module for Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor
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#
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# Copyright (c) 2003 Ensembl
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#
# You may distribute this module under the same terms as perl itself

=head1 NAME

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Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor - An Abstract Base class for all
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FeatureAdaptors
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=head1 SYNOPSIS

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

=head1 DESCRIPTION

This is a base adaptor for feature adaptors. This base class is simply a way
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of eliminating code duplication through the implementation of methods
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common to all feature adaptors.

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=head1 CONTACT

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Contact Ensembl development list for info: <ensembl-dev@ebi.ac.uk>
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=head1 METHODS

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=cut

package Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
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use vars qw(@ISA);
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use strict;

use Bio::EnsEMBL::DBSQL::BaseAdaptor;
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use Bio::EnsEMBL::Utils::Cache;
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use Bio::EnsEMBL::Utils::Exception qw(warning throw deprecate);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);

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my $SLICE_FEATURE_CACHE_SIZE = 4;
my $MAX_SPLIT_QUERY_SEQ_REGIONS = 3;
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=head2 new

  Arg [1]    : list of args @args
               Superclass constructor arguments
  Example    : none
  Description: Constructor which just initializes internal cache structures
  Returntype : Bio::EnsEMBL::BaseFeatureAdaptor
  Exceptions : none
  Caller     : implementing subclass constructors

=cut

sub new {
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  my $caller = shift;
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  my $class = ref($caller) || $caller;
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  my $self = $class->SUPER::new(@_);
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  #initialize an LRU cache
  my %cache;
  tie(%cache, 'Bio::EnsEMBL::Utils::Cache', $SLICE_FEATURE_CACHE_SIZE);
  $self->{'_slice_feature_cache'} = \%cache;
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  return $self;
}
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=head2 generic_fetch

  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
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  Arg [2]    : (optional) Bio::EnsEMBL::AssemblyMapper $mapper
               A mapper object used to remap features
               as they are retrieved from the database
  Arg [3]    : (optional) Bio::EnsEMBL::Slice $slice
               A slice that features should be remapped to
  Arg [4]    : (optional) boolean $keep_all
               Set to 1 if all features, even ones entirely off slice,
               should be kept
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  Example    : $fts = $a->generic_fetch('contig_id in (1234, 1235)', 'Swall');
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  Description: Performs a database fetch and returns feature objects in
               contig coordinates.
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  Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
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  Exceptions : none
  Caller     : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::generic_fetch

=cut
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sub generic_fetch {
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  my ($self, $constraint, $mapper, $slice, $keep_all) = @_;

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  my @tabs = $self->_tables;
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  my $columns = join(', ', $self->_columns());
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  my $db = $self->db();
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  #
  # Construct a left join statement if one was defined, and remove the
  # left-joined table from the table list
  #
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  my @left_join_list = $self->_left_join();
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  my $left_join = '';
  my @tables;
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  if(@left_join_list) {
    my %left_join_hash = map { $_->[0] => $_->[1] } @left_join_list;
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    while(my $t = shift @tabs) {
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      if( exists $left_join_hash{ $t->[0] } ) {
        my $condition = $left_join_hash{ $t->[0] };
        my $syn = $t->[1];
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        $left_join .=  "LEFT JOIN\n       ".$t->[0]." $syn ON $condition ";
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      } else {
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        push @tables, $t;
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      }
    }
  } else {
    @tables = @tabs;
  }
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  #construct a nice table string like 'table1 t1, table2 t2'
  my $tablenames = join(', ', map({ join(' ', @$_) } @tables));

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  my $sql = "SELECT $columns\n  FROM $tablenames $left_join";
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  my $default_where = $self->_default_where_clause;
  my $final_clause = $self->_final_clause;

  #append a where clause if it was defined
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  if($constraint) {
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    $sql .= "\n WHERE $constraint ";
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    if($default_where) {
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      $sql .= " AND\n       $default_where ";
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    }
  } elsif($default_where) {
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    $sql .= "\n WHERE $default_where ";
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  }

  #append additional clauses which may have been defined
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  $sql .= "\n$final_clause";
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  ###print STDERR "\n\n$sql\n\n";

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  warn "JS5 misc set queries======================\n$sql\n ";
  
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  my $sth = $db->prepare($sql);

  $sth->execute;

  my $res = $self->_objs_from_sth($sth, $mapper, $slice, $keep_all);
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  return $res;
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}


=head2 fetch_by_dbID
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  Arg [1]    : int $id
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               The unique database identifier for the feature to be obtained
  Example    : $feat = $adaptor->fetch_by_dbID(1234));
               $feat = $feat->transform('contig');
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  Description: Returns the feature created from the database defined by the
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               the id $id.  The feature will be returned in its native
               coordinate system.  That is, the coordinate system in which it
               is stored in the database.  In order to convert it to a
               particular coordinate system use the transfer() or transform()
               method.  If the feature is not found in the database then
               undef is returned instead
  Returntype : Bio::EnsEMBL::Feature or undef
  Exceptions : thrown if $id arg is not provided
               does not exist
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  Caller     : general
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=cut

sub fetch_by_dbID{
  my ($self,$id) = @_;

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  throw("id argument is required") if(!defined $id);
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  #construct a constraint like 't1.table1_id = 123'
  my @tabs = $self->_tables;
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  my ($name, $syn) = @{$tabs[0]};
  my $constraint = "${syn}.${name}_id = $id";
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  #Should only be one
  my ($feat) = @{$self->generic_fetch($constraint)};

  return undef if(!$feat);

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  return $feat;
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}


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=head2 fetch_all_by_dbID_list

  Arg [1]    : listref of ints $id_list
               The unique database identifiers for the features to be obtained
  Example    : @feats = @{$adaptor->fetch_by_dbID_list([1234, 2131, 982]))};
  Description: Returns the features created from the database defined by the
               the ids in contained in the id list $id_list.  The features 
               will be returned in their native coordinate system. That is, 
               the coordinate system in which they are stored in the database.
               In order to convert the features to a particular coordinate 
               system use the transfer() or transform() method.  If none of the
               features are found in the database a reference to an empty 
               list is returned.
  Returntype : listref of Bio::EnsEMBL::Features
  Exceptions : thrown if $id arg is not provided
               does not exist
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  Caller     : general
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=cut

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sub fetch_all_by_dbID_list {
  my ($self,$id_list) = @_;
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  if(!defined($id_list) || ref($id_list) ne 'ARRAY') {
    throw("id_list list reference argument is required") if(!defined $id_list);
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  }

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  return [] if(!@$id_list);
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  my @out;
  #construct a constraint like 't1.table1_id = 123'
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  my @tabs = $self->_tables;
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  my ($name, $syn) = @{$tabs[0]};
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  #mysql is faster and we ensure that we do not exceed the max query size by
  #splitting large queries into smaller queries of 200 ids
  my $max_size = 200;
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  while(@$id_list) {
    my @ids;
    if(@$id_list > $max_size) {
      @ids = splice(@$id_list, 0, $max_size);
    } else {
      @ids = splice(@$id_list, 0);
    }
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    my $id_str;
    if(@ids > 1)  {
      $id_str = " IN (" . join(',', @ids). ")";
    } else {
      $id_str = " = " . $ids[0];
    }
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    my $constraint = "${syn}.${name}_id $id_str";
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    push @out, @{$self->generic_fetch($constraint)};
  }
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  return \@out;
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}



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=head2 fetch_all_by_Slice
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  Arg [1]    : Bio::EnsEMBL::Slice $slice
               the slice from which to obtain features
  Arg [2]    : (optional) string $logic_name
               the logic name of the type of features to obtain
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  Example    : $fts = $a->fetch_all_by_Slice($slice, 'Swall');
  Description: Returns a listref of features created from the database 
               which are on the Slice defined by $slice. If $logic_name is 
               defined only features with an analysis of type $logic_name 
               will be returned. 
  Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates
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  Exceptions : none
  Caller     : Bio::EnsEMBL::Slice

=cut

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sub fetch_all_by_Slice {
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  my ($self, $slice, $logic_name) = @_;
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  #fetch by constraint with empty constraint
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  return $self->fetch_all_by_Slice_constraint($slice, '', $logic_name);
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}


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=head2 fetch_all_by_Slice_and_score
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  Arg [1]    : Bio::EnsEMBL::Slice $slice
               the slice from which to obtain features
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  Arg [2]    : (optional) float $score
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               lower bound of the the score of the features retrieved
  Arg [3]    : (optional) string $logic_name
               the logic name of the type of features to obtain
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  Example    : $fts = $a->fetch_all_by_Slice($slice, 'Swall');
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  Description: Returns a list of features created from the database which are 
               are on the Slice defined by $slice and which have a score 
               greated than $score. If $logic_name is defined, 
               only features with an analysis of type $logic_name will be 
               returned. 
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  Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates
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  Exceptions : none
  Caller     : Bio::EnsEMBL::Slice

=cut

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sub fetch_all_by_Slice_and_score {
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  my ($self, $slice, $score, $logic_name) = @_;
  my $constraint;

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  if(defined $score) {
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    #get the synonym of the primary_table
    my @tabs = $self->_tables;
    my $syn = $tabs[0]->[1];
    $constraint = "${syn}.score > $score";
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  }

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  return $self->fetch_all_by_Slice_constraint($slice, $constraint, 
					      $logic_name);
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}
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=head2 fetch_all_by_Slice_constraint
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  Arg [1]    : Bio::EnsEMBL::Slice $slice
               the slice from which to obtain features
  Arg [2]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [3]    : (optional) string $logic_name
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               the logic name of the type of features to obtain
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  Example    : $fs = $a->fetch_all_by_Slice_constraint($slc, 'perc_ident > 5');
  Description: Returns a listref of features created from the database which 
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               are on the Slice defined by $slice and fulfill the SQL 
               constraint defined by $constraint. If logic name is defined, 
               only features with an analysis of type $logic_name will be 
               returned. 
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  Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates
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  Exceptions : thrown if $slice is not defined
  Caller     : Bio::EnsEMBL::Slice
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=cut

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sub fetch_all_by_Slice_constraint {
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  my($self, $orig_slice, $original_constraint, $logic_name) = @_;
  my @result_features;
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  if(!ref($orig_slice) || !$orig_slice->isa("Bio::EnsEMBL::Slice")) {
    throw("Slice arg must be a Bio::EnsEMBL::Slice not a [$orig_slice]\n");
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  }

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  $original_constraint ||= '';
  $original_constraint = $self->_logic_name_to_constraint($original_constraint,
                                                          $logic_name);

  #if the logic name was invalid, undef was returned
  return [] if(!defined($original_constraint));
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  #check the cache and return if we have already done this query
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  my $key = uc(join(':', $orig_slice->name, $original_constraint));

  if(exists($self->{'_slice_feature_cache'}->{$key})) {
    return $self->{'_slice_feature_cache'}->{$key};
  }

  my $slice_adaptor = $orig_slice->adaptor();

  #retrieve normalized 'non-symlinked' slices
  #this allows us to support haplotypes and PARs
  my @projection =
    @{$slice_adaptor->fetch_normalized_slice_projection($orig_slice)};

  if(@projection == 0) {
    throw('Could not retrieve normalized Slices. Database contains ' .
          'incorrect assembly_exception information.');
  }

  #we want to retrieve all features calculated on the FULL original slice 
  #as well as any symlinked slices.  

  #Filter out any partial slices from the normalized projection that are on 
  #the same seq region as the original slice
  my @new_projection = 
    grep { $_->[2]->seq_region_name() ne $orig_slice->seq_region_name() } 
    @projection;

  push( @new_projection, [ 1, $orig_slice->length(), $orig_slice ] );

  #fetch features for the primary slice AND all symlinked slices
  foreach my $segment (@new_projection) {
    my ($offset, $slice);
    ($offset, undef, $slice) = @$segment;

    my $slice_start  = $slice->start();
    my $slice_end    = $slice->end();
    my $slice_strand = $slice->strand();
    my $slice_cs     = $slice->coord_system();
    my $slice_seq_region = $slice->seq_region_name();

    #get the synonym and name of the primary_table
    my @tabs = $self->_tables;
    my ($tab_name, $tab_syn) = @{$tabs[0]};

    #find out what coordinate systems the features are in
    my $csa = $self->db->get_CoordSystemAdaptor();
    my @feat_css = @{$csa->fetch_all_by_feature_table($tab_name)};

    my $asma = $self->db->get_AssemblyMapperAdaptor();
    my @features;

    # fetch the features from each coordinate system they are stored in
  COORD_SYSTEM: foreach my $feat_cs (@feat_css) {
      my $mapper;
      my @coords;
      my @ids;
      
      if($feat_cs->equals($slice_cs)) {
        #no mapping is required if this is the same coord system
        my $constraint = $original_constraint;
        
        # obtain seq_region_id of this slice from db
        my $seq_region_id = 
          $self->db->get_SliceAdaptor->get_seq_region_id($slice);
        $constraint .= " AND " if($constraint);
        $constraint .=
          "${tab_syn}.seq_region_id = $seq_region_id AND " .
          "${tab_syn}.seq_region_start <= $slice_end AND " .
          "${tab_syn}.seq_region_end >= $slice_start";
        my $fs = $self->generic_fetch($constraint,undef,$slice);

        #features may still have to have coordinates made relative to slice 
        #start
        $fs = $self->_remap($fs, $mapper, $slice);

        push @features, @$fs;
      } else {
        $mapper = $asma->fetch_by_CoordSystems($slice_cs, $feat_cs);
        
        # Get a list of coordinates and corresponding internal ids for the
        # regions we are interested in
        @coords = $mapper->map($slice_seq_region, $slice_start, $slice_end,
                               $slice_strand, $slice_cs);

        @coords = grep {!$_->isa('Bio::EnsEMBL::Mapper::Gap')} @coords;

        next COORD_SYSTEM if(!@coords);

        @ids = map {$_->id()} @coords;
        @ids = @{$asma->seq_regions_to_ids($feat_cs, \@ids)};

        #if the regions are large and only partially spanned
        #it is faster to to limit the query with start and end constraints
        #however, it is difficult to tell if a region is large and only 
        #partially wanted. The easy approach is just to limit the queries if 
        #there are less than a certain number of regions. As well seperate 
        #queries are needed otherwise the indices will not be useful
        if(@coords > $MAX_SPLIT_QUERY_SEQ_REGIONS) {
          #do one query, and do not limit with start / end constraints
          my $constraint = $original_constraint;
          my $id_str = join(',', @ids);
          $constraint .= " AND " if($constraint);
          $constraint .= "${tab_syn}.seq_region_id IN ($id_str)";
          
          my $fs = 
            $self->generic_fetch($constraint, $mapper, $slice);
          
          $fs = $self->_remap($fs, $mapper, $slice);

          push @features, @$fs;

        } else {
          #do multiple split queries using start / end constraints
          my $len = @coords;
          for(my $i = 0; $i < $len; $i++) {
            my $constraint = $original_constraint;
            $constraint .= " AND " if($constraint);
            $constraint .=
              "${tab_syn}.seq_region_id = "     . $ids[$i] . " AND " .
              "${tab_syn}.seq_region_start <= " . $coords[$i]->end() . " AND ".
              "${tab_syn}.seq_region_end >= "   . $coords[$i]->start();
            my $fs = $self->generic_fetch($constraint,$mapper,$slice);

            $fs = $self->_remap($fs, $mapper, $slice);
            
            push @features, @$fs;
          }
        }
      }
    } #COORD system loop
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    #if this was a symlinked slice offset the feature coordinates as needed
    if($slice != $orig_slice) {
      foreach my $f (@features) {
        #function calls are slow!
        if($offset != 1) {
          $f->{'start'} += $offset-1;
          $f->{'end'}   += $offset-1;
        }
        $f->{'slice'} = $orig_slice;
        push @result_features, $f;
      }
    } else {
      push @result_features, @features;
    }
    
  } #slice & symmlinked slice loop
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  $self->{'_slice_feature_cache'}->{$key} = \@result_features;
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  return \@result_features;
}
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#
# Helper function containing some common feature storing functionality
#
# Given a Feature this will return a copy (or the same feature if no changes 
# to the feature are needed) of the feature which is relative to the start
# of the seq_region it is on. The seq_region_id of the seq_region it is on
# is also returned.
#
# This method will also ensure that the database knows which coordinate
# systems that this feature is stored in.
#

sub _pre_store {
  my $self    = shift;
  my $feature = shift;

  if(!ref($feature) || !$feature->isa('Bio::EnsEMBL::Feature')) {
    throw('Expected Feature argument.');
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  }
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  $self->_check_start_end_strand($feature->start(),$feature->end(),
                                 $feature->strand());

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  my $db = $self->db();

  my $slice_adaptor = $db->get_SliceAdaptor();
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  my $slice = $feature->slice();

  if(!ref($slice) || !$slice->isa('Bio::EnsEMBL::Slice')) {
    throw('Feature must be attached to Slice to be stored.');
  }

  # make sure that the feature coordinates are relative to
  # the start of the entire seq_region
  if($slice->start != 1 || $slice->strand != 1) {
    #move the feature onto a slice of the entire seq_region
    $slice = $slice_adaptor->fetch_by_region($slice->coord_system->name(),
                                             $slice->seq_region_name(),
                                             undef, #start
                                             undef, #end
                                             undef, #strand
                                             $slice->coord_system->version());

    $feature = $feature->transfer($slice);

    if(!$feature) {
      throw('Could not transfer Feature to slice of ' .
            'entire seq_region prior to storing');
    }
  }

  #
  # Ensure that this type of feature is known to be stored in this coord
  # system.
  #
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  my $csa = $db->get_CoordSystemAdaptor();
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  my $cs = $slice->coord_system;

  my ($tab) = $self->_tables();
  my $tabname = $tab->[0];

  $csa->add_feature_table($cs, $tabname);

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  # we have to update the meta coord table in both the dna db and the feature
  # db so that the feature db can be used independently later

  if($db->dnadb() != $db) {
    my $dnadb = $db->dnadb();
    $db->dnadb(undef); # unset the dnadb temporarily

    #get a coord system adaptor from the feature database
    $csa = $db->get_CoordSystemAdaptor();
    $csa->add_feature_table($cs, $tabname);

    $db->dnadb($dnadb); # reinstate the dnadb
  }

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  my $seq_region_id = $slice_adaptor->get_seq_region_id($slice);

  if(!$seq_region_id) {
    throw('Feature is associated with seq_region which is not in this DB.');
  }

  return ($feature, $seq_region_id);
}


#
# helper function used to validate start/end/strand and 
# hstart/hend/hstrand etc.
#
sub _check_start_end_strand {
  my $self = shift;
  my $start = shift;
  my $end   = shift;
  my $strand = shift;

  #
  # Make sure that the start, end, strand are valid
  #
  if(int($start) != $start) {
    throw("Invalid Feature start [$start].  Must be integer.");
  }
  if(int($end) != $end) {
    throw("Invalid Feature end [$end]. Must be integer.");
  }
  if(int($strand) != $strand || $strand < -1 || $strand > 1) {
    throw("Invalid Feature strand [$strand]. Must be -1, 0 or 1.");
  }
  if($end < $start) {
    throw("Invalid Feature start/end [$start/$end]. Start must be less " .
          "than or equal to end.");
  }

  return 1;
}


#
# Given a list of features checks if they are in the correct coord system
# by looking at the first features slice.  If they are not then they are
# converted and placed on the slice.
#
sub _remap {
  my ($self, $features, $mapper, $slice) = @_;

  #check if any remapping is actually needed
  if(@$features && (!$features->[0]->isa('Bio::EnsEMBL::Feature') ||
                    $features->[0]->slice == $slice)) {
    return $features;
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  }
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  #remapping has not been done, we have to do our own conversion from
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  #to slice coords

  my @out;

  my $slice_start = $slice->start();
  my $slice_end   = $slice->end();
  my $slice_strand = $slice->strand();
  my $slice_cs    = $slice->coord_system();

  my ($seq_region, $start, $end, $strand);
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  my $slice_seq_region = $slice->seq_region_name();
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  foreach my $f (@$features) {
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    #since feats were obtained in contig coords, attached seq is a contig
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    my $fslice = $f->slice();
    if(!$fslice) {
      throw("Feature does not have attached slice.\n");
    }
    my $fseq_region = $fslice->seq_region_name();
    my $fcs = $fslice->coord_system();
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    if(!$slice_cs->equals($fcs)) {
      #slice of feature in different coord system, mapping required
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      ($seq_region, $start, $end, $strand) =
        $mapper->fastmap($fseq_region,$f->start(),$f->end(),$f->strand(),$fcs);

      # undefined start means gap
      next if(!defined $start);
    } else {
      $start      = $f->start();
      $end        = $f->end();
      $strand     = $f->strand();
      $seq_region = $f->slice->seq_region_name();
    }

    # maps to region outside desired area
    next if ($start > $slice_end) || ($end < $slice_start) || ($slice_seq_region ne $seq_region);
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    #shift the feature start, end and strand in one call
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    if($slice_strand == -1) {
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      $f->move( $slice_end - $end + 1, $slice_end - $start + 1, $strand * -1 );
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    } else {
      $f->move( $start - $slice_start + 1, $end - $slice_start + 1, $strand );
    }
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    $f->slice($slice);

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    push @out,$f;
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  }
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  return \@out;
}


#
# Given a logic name and an existing constraint this will
# add an analysis table constraint to the feature.  Note that if no
# analysis_id exists in the columns of the primary table then no
# constraint is added at all
#
sub _logic_name_to_constraint {
  my $self = shift;
  my $constraint = shift;
  my $logic_name = shift;

  return $constraint if(!$logic_name);

  #make sure that an analysis_id exists in the primary table
  my ($prim_tab) = $self->_tables();
  my $prim_synonym = $prim_tab->[1];

  my $found_analysis=0;
  foreach my $col ($self->_columns) {
    my ($syn,$col_name) = split(/\./,$col);
    next if($syn ne $prim_synonym);
    if($col_name eq 'analysis_id') {
      $found_analysis = 1;
      last;
    }
  }

  if(!$found_analysis) {
    warning("This feature is not associated with an analysis.\n" .
            "Ignoring logic_name argument = [$logic_name].\n");
    return $constraint;
  }

  my $aa = $self->db->get_AnalysisAdaptor();
  my $an = $aa->fetch_by_logic_name($logic_name);

  if(!$an) {
    warning("No analysis exists with logic_name = [$logic_name].\n" .
            "Returning empty list.\n");
    return undef;
  }

  my $an_id = $an->dbID();

  $constraint .= ' AND' if($constraint);
  $constraint .= " ${prim_synonym}.analysis_id = $an_id";
  return $constraint;
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}


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=head2 store
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  Arg [1]    : list of Bio::EnsEMBL::SeqFeature
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  Example    : $adaptor->store(@feats);
  Description: ABSTRACT  Subclasses are responsible for implementing this 
               method.  It should take a list of features and store them in 
               the database.
  Returntype : none
  Exceptions : thrown method is not implemented by subclass
  Caller     : general
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=cut

sub store{
  my $self = @_;

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  throw("Abstract method store not defined by implementing subclass\n");
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}


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=head2 remove

  Arg [1]    : A feature $feature 
  Example    : $feature_adaptor->remove($feature);
  Description: This removes a feature from the database.  The table the
               feature is removed from is defined by the abstract method
               _tablename, and the primary key of the table is assumed
               to be _tablename() . '_id'.  The feature argument must 
               be an object implementing the dbID method, and for the
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               feature to be removed from the database a dbID value must
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               be returned.
  Returntype : none
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  Exceptions : thrown if $feature arg does not implement dbID(), or if
               $feature->dbID is not a true value
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  Caller     : general

=cut

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sub remove {
  my ($self, $feature) = @_;

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  if(!$feature || !ref($feature) || !$feature->isa('Bio::EnsEMBL::Feature')) {
    throw('Feature argument is required');
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  }

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  if(!$feature->is_stored($self->db)) {
    throw("This feature is not stored in this database");
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  }

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  my @tabs = $self->_tables;
  my ($table) = @{$tabs[0]};
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  my $sth = $self->prepare("DELETE FROM $table WHERE ${table}_id = ?");
  $sth->execute($feature->dbID());

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  #unset the feature dbID ad adaptor
  $feature->dbID(undef);
  $feature->adaptor(undef);

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  return;
}


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=head2 remove_by_Slice
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  Arg [1]    : Bio::Ensembl::Slice $slice
  Example    : $feature_adaptor->remove_by_RawContig($slice);
  Description: This removes features from the database which lie on a region
               represented by the passed in slice.  Only features which are
               fully contained by the slice are deleted; features which overlap
               the edge of the slice are not removed.
               The table the features are removed from is defined by
               the abstract method_tablename.
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  Returntype : none
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  Exceptions : thrown if no slice is supplied
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  Caller     : general

=cut

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sub remove_by_Slice {
  my ($self, $slice) = @_;
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  if(!$slice || !ref($slice) || !$slice->isa('Bio::EnsEMBL::Slice')) {
    throw("Slice argument is required");
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  }

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  my @tabs = $self->_tables;
  my ($table_name) = @{$tabs[0]};
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  my $seq_region_id = $self->db->get_SliceAdaptor->get_seq_region_id($slice);
  my $start = $slice->start();
  my $end   = $slice->end();
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  #
  # Delete only features fully on the slice, not overlapping ones
  #
  my $sth = $self->prepare("DELETE FROM $table_name " .
                           "WHERE seq_region_id = ? " .
                           "AND   seq_region_start >= ? " .
                           "AND   seq_region_end <= ?");
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  $sth->execute($seq_region_id, $start, $end);
  $sth->finish();
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}



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#_tables
#
#  Args       : none
#  Example    : $tablename = $self->_table_name()
#  Description: ABSTRACT PROTECTED Subclasses are responsible for implementing
#               this method.  It should list of [tablename, alias] pairs.  
#               Additionally the primary table (with the dbID, analysis_id, and
#               score) should be the first table in the list.
#               e.g:
#               ( ['repeat_feature',   'rf'],
#                 ['repeat_consensus', 'rc']);
#               used to obtain features.  
#  Returntype : list of [tablename, alias] pairs
#  Exceptions : thrown if not implemented by subclass
#  Caller     : BaseFeatureAdaptor::generic_fetch
#
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sub _tables {
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  my $self = shift;

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  throw("abstract method _tables not defined by implementing" .
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               " subclass of BaseFeatureAdaptor");
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  return undef;
}

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#_columns
#
#  Args       : none
#  Example    : $tablename = $self->_columns()
#  Description: ABSTRACT PROTECTED Subclasses are responsible for implementing
#               this method.  It should return a list of columns to be used
#               for feature creation
#  Returntype : list of strings
#  Exceptions : thrown if not implemented by subclass
#  Caller     : BaseFeatureAdaptor::generic_fetch
#
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sub _columns {
  my $self = shift;

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  throw("abstract method _columns not defined by implementing" .
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               " subclass of BaseFeatureAdaptor");
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}


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# _default_where_clause
#
#  Arg [1]    : none
#  Example    : none
#  Description: May be overridden to provide an additional where constraint to 
#               the SQL query which is generated to fetch feature records.
#               This constraint is always appended to the end of the generated
#               where clause
#  Returntype : string
#  Exceptions : none
#  Caller     : generic_fetch
#
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sub _default_where_clause {
  my $self = shift;
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  return '';
}
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# _left_join
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#  Arg [1]    : none
#  Example    : none
#  Description: Can be overridden by a subclass to specify any left joins
#               which should occur. The table name specigfied in the join
#               must still be present in the return values of
#  Returntype : a {'tablename' => 'join condition'} pair
#  Exceptions : none
#  Caller     : general
#
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sub _left_join {
  my $self = shift;
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  return ();
}
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#_final_clause

#  Arg [1]    : none
#  Example    : none
#  Description: May be overriden to provide an additional clause to the end
#               of the SQL query used to fetch feature records.  
#               This is useful to add a required ORDER BY clause to the 
#               query for example.
#  Returntype : string
#  Exceptions : none
#  Caller     : generic_fetch

sub _final_clause {
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  my $self = shift;

  return '';
}


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#_objs_from_sth
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#  Arg [1]    : DBI::row_hashref $hashref containing key-value pairs 
#               for each of the columns specified by the _columns method
#  Example    : my @feats = $self->_obj_from_hashref
#  Description: ABSTRACT PROTECTED The subclass is responsible for implementing
#               this method.  It should take in a DBI row hash reference and
#               return a list of created features in contig coordinates.
#  Returntype : list of Bio::EnsEMBL::*Features in contig coordinates
#  Exceptions : thrown if not implemented by subclass
#  Caller     : BaseFeatureAdaptor::generic_fetch
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sub _objs_from_sth {
  my $self = shift;
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  throw("abstract method _obj_from_sth not defined by implementing"
             . " subclass of BaseFeatureAdaptor");
}
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# deleteObj
#
#  Arg [1]    : none
#  Example    : none
#  Description: Cleans up internal caches and references to other objects so
#               that correct garbage collection may occur.
#  Returntype : none
#  Exceptions : none
#  Caller     : Bio::EnsEMBL::DBConnection::deleteObj


sub deleteObj {
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  my $self = shift;

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  #flush feature cache
  %{$self->{'_slice_feature_cache'}} = ();
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}


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=head1 DEPRECATED METHODS
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=cut
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=head2 fetch_all_by_RawContig_constraint

  Description: DEPRECATED use fetch_all_by_RawContig_constraint instead
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=cut

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sub fetch_all_by_RawContig_constraint {
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  my $self = shift;
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  deprecate('Use fetch_all_by_Slice_constraint() instead.');
  return $self->fetch_all_by_slice_constraint(@_);
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}

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=head2 fetch_all_by_RawContig
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  Description: DEPRECATED use fetch_all_by_Slice instead
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=cut

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sub fetch_all_by_RawContig {
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  my $self = shift;
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  deprecate('Use fetch_all_by_Slice() instead.');
  return $self->fetch_all_by_Slice(@_);
}
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=head2 fetch_all_by_RawContig_and_score
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  Description: DEPRECATED use fetch_all_by_Slice_and_score instead
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=cut
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sub fetch_all_by_RawContig_and_score{
  my $self = shift;
  deprecate('Use fetch_all_by_Slice_and_score() instead.');
  return $self->fetch_all_by_Slice_and_score(@_);
}

=head2 remove_by_RawContig

  Description: DEPRECATED use remove_by_Slice instead
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=cut

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sub remove_by_RawContig {
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  my $self = shift;
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  deprecate("Use remove_by_Slice instead");
  return $self->remove_by_Slice(@_);
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}

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1;