BaseFeatureAdaptor.pm 23.5 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 @EXPORT);
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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 stack_trace_dump);
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use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);

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@EXPORT = (@{$DBI::EXPORT_TAGS{'sql_types'}});

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our $SLICE_FEATURE_CACHE_SIZE = 4;
our $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
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  Status     : Stable
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=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 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
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  Status     : Stable
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=cut

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sub fetch_all_by_Slice {
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  my ($self, $slice, $logic_name) = @_;
  #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 = $a->fetch_all_by_Slice_and_score($slice,90,'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 
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               greater than $score. If $logic_name is defined, 
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               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
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  Status     : Stable
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=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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  Status     : Stable
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=cut

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

  my @result;
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  if(!ref($slice) || !$slice->isa("Bio::EnsEMBL::Slice")) {
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    throw("Bio::EnsEMBL::Slice argument expected.");
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  }

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  $constraint ||= '';
  $constraint = $self->_logic_name_to_constraint($constraint, $logic_name);
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  #if the logic name was invalid, undef was returned
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  return [] if(!defined($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(':', $slice->name, $constraint));
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  if(exists($self->{'_slice_feature_cache'}->{$key})) {
    return $self->{'_slice_feature_cache'}->{$key};
  }

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  my $sa = $slice->adaptor();
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  # Hap/PAR support: retrieve normalized 'non-symlinked' slices
  my @proj = @{$sa->fetch_normalized_slice_projection($slice)};
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  if(@proj == 0) {
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    throw('Could not retrieve normalized Slices. Database contains ' .
          'incorrect assembly_exception information.');
  }
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  # Want to get features on the FULL original slice
  # as well as any symlinked slices
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  # Filter out partial slices from projection that are on
  # same seq_region as original slice
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  my $sr_id = $slice->get_seq_region_id();
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  @proj = grep { $_->to_Slice->get_seq_region_id() != $sr_id } @proj;
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  my $segment = bless([1,$slice->length(),$slice ],
                      'Bio::EnsEMBL::ProjectionSegment');
  push( @proj, $segment );
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  # construct list of Hap/PAR boundaries for entire seq region
  my @bounds;
  my $ent_slice = $sa->fetch_by_seq_region_id($sr_id);
  $ent_slice    = $ent_slice->invert() if($slice->strand == -1);
  my @ent_proj  = @{$sa->fetch_normalized_slice_projection($ent_slice)};

  shift @ent_proj; # skip first
  @bounds = map {$_->from_start - $slice->start() + 1} @ent_proj;


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  # fetch features for the primary slice AND all symlinked slices
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  foreach my $seg (@proj) {
    my $offset = $seg->from_start();
    my $seg_slice  = $seg->to_Slice();
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    my $features = $self->_slice_fetch($seg_slice, $constraint); ## NO RESULTS
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    # if this was a symlinked slice offset the feature coordinates as needed
    if($seg_slice->name() ne $slice->name()) {
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    FEATURE:
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      foreach my $f (@$features) {
        if($offset != 1) {
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          $f->{'start'} += $offset-1;
          $f->{'end'}   += $offset-1;
        }
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        # discard boundary crossing features from symlinked regions
        foreach my $bound (@bounds) {
          if($f->{'start'} < $bound && $f->{'end'} >= $bound) {
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	    print STDERR "BOUNDRY CROSSED\n";
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            next FEATURE;
          }
        }

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        $f->{'slice'} = $slice;
        push @result, $f;
      }
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    }
    else {
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      push @result, @$features;
    }
  }

  $self->{'_slice_feature_cache'}->{$key} = \@result;
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  return \@result;
}
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=head2 fetch_all_by_logic_name

  Arg [3]    : string $logic_name
               the logic name of the type of features to obtain
  Example    : $fs = $a->fetch_all_by_logic_name('foobar');
  Description: Returns a listref of features created from the database. 
               only features with an analysis of type $logic_name will be 
               returned. 
  Returntype : listref of Bio::EnsEMBL::SeqFeatures
  Exceptions : thrown if $logic_name
  Caller     : General
  Status     : Experimental

=cut

sub fetch_all_by_logic_name {
  my $self = shift;
  my $logic_name = shift || throw( "Need a logic_name" );
  my $constraint = $self->_logic_name_to_constraint( '',$logic_name );
  return $self->fetch_all( $constraint )
}

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#
# helper function used by fetch_all_by_Slice_constraint method
#
sub _slice_fetch {
  my $self = shift;
  my $slice = shift;
  my $orig_constraint = shift;

  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();
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  my $slice_seq_region_id = $slice->get_seq_region_id();
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  #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 $mcc = $self->db->get_MetaCoordContainer();
  my @feat_css = @{$mcc->fetch_all_CoordSystems_by_feature_type($tab_name)};

  my $asma = $self->db->get_AssemblyMapperAdaptor();
  my @features;
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  # 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
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      my $max_len = $self->_max_feature_length() ||
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        $mcc->fetch_max_length_by_CoordSystem_feature_type($feat_cs,$tab_name);

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      my $constraint = $orig_constraint;

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      my $sr_id;
      if( $slice->adaptor() ) {
	$sr_id = $slice->adaptor()->get_seq_region_id($slice);
      } else {
	$sr_id = $self->db()->get_SliceAdaptor()->get_seq_region_id($slice);
      }

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      $constraint .= " AND " if($constraint);
      $constraint .=
          "${tab_syn}.seq_region_id = $sr_id AND " .
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          "${tab_syn}.seq_region_start <= $slice_end AND " .
          "${tab_syn}.seq_region_end >= $slice_start";
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      if($max_len) {
        my $min_start = $slice_start - $max_len;
        $constraint .=
          " AND ${tab_syn}.seq_region_start >= $min_start";
      }

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      my $fs = $self->generic_fetch($constraint,undef,$slice);
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      # features may still have to have coordinates made relative to slice
      # start
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      $fs = _remap($fs, $mapper, $slice);
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      push @features, @$fs;
    } else {
      $mapper = $asma->fetch_by_CoordSystems($slice_cs, $feat_cs);
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      next unless defined $mapper;

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      # Get list of coordinates and corresponding internal ids for
      # regions the slice spans
      @coords = $mapper->map($slice_seq_region, $slice_start, $slice_end,
                             $slice_strand, $slice_cs);
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      @coords = grep {!$_->isa('Bio::EnsEMBL::Mapper::Gap')} @coords;
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      next COORD_SYSTEM if(!@coords);

      @ids = map {$_->id()} @coords;
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#coords are now id rather than name
#      @ids = @{$asma->seq_regions_to_ids($feat_cs, \@ids)};
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      # When regions are large and only partially spanned by slice
      # it is faster to to limit the query with start and end constraints.
      # Take simple approach: use regional constraints if there are less
      # than a specific number of regions covered.

      if(@coords > $MAX_SPLIT_QUERY_SEQ_REGIONS) {
        my $constraint = $orig_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);
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        $fs = _remap($fs, $mapper, $slice);
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        push @features, @$fs;

      } else {
        # do multiple split queries using start / end constraints
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        my $max_len = $self->_max_feature_length() ||
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          $mcc->fetch_max_length_by_CoordSystem_feature_type($feat_cs,
                                                             $tab_name);
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        my $len = @coords;
        for(my $i = 0; $i < $len; $i++) {
          my $constraint = $orig_constraint;
          $constraint .= " AND " if($constraint);
          $constraint .=
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              "${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();
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          if($max_len) {
            my $min_start = $coords[$i]->start() - $max_len;
            $constraint .=
              " AND ${tab_syn}.seq_region_start >= $min_start";
          }

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          my $fs = $self->generic_fetch($constraint,$mapper,$slice);
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          $fs = _remap($fs, $mapper, $slice);
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          push @features, @$fs;
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        }
      }
    }
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  } #COORD system loop
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  return \@features;
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}
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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.');
  }

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  # make sure feature coords are relative to start of entire seq_region
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  if($slice->start != 1 || $slice->strand != 1) {
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    #move feature onto a slice of the entire seq_region
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    $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');
    }
  }

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

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

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  my $mcc = $db->get_MetaCoordContainer();

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  $mcc->add_feature_type($cs, $tabname, $feature->length);
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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 {
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  my ($features, $mapper, $slice) = @_;
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  #check if any remapping is actually needed
  if(@$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_id = $slice->get_seq_region_id();
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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();
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    my $fseq_region_id = $fslice->get_seq_region_id();
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    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) =
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        $mapper->fastmap($fseq_region_id,$f->start(),$f->end(),$f->strand(),$fcs);
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      # 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
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    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) {
    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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  Status     : At Risk
             : throws if called.
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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
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  Status     : Stable
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=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 = ?");
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  $sth->bind_param(1,$feature->dbID,SQL_INTEGER);
  $sth->execute();
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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
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  Example    : $feature_adaptor->remove_by_Slice($slice);
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  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
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  Status     : Stable
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=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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  $sth->bind_param(1,$seq_region_id,SQL_INTEGER);
  $sth->bind_param(2,$start,SQL_INTEGER);
  $sth->bind_param(3,$end,SQL_INTEGER);
  $sth->execute();
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  $sth->finish();
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}


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#
# Internal function. Allows the max feature length which is normally
# retrieved from the meta_coord table to be overridden.  This allows
# for some significant optimizations to be put in when it is known
# that requested features will not be over a certain size.
#
sub _max_feature_length {
  my $self = shift;
  return $self->{'_max_feature_length'} = shift if(@_);
  return $self->{'_max_feature_length'};
}



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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;