SliceAdaptor.pm 67.5 KB
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=head1 LICENSE
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  Copyright (c) 1999-2011 The European Bioinformatics Institute and
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  Genome Research Limited.  All rights reserved.
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  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
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  developers list at <dev@ensembl.org>.
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  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.

=cut
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=head1 NAME

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Bio::EnsEMBL::DBSQL::SliceAdaptor - A database aware adaptor responsible for
the creation of Slice objects.
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=head1 SYNOPSIS

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  use Bio::EnsEMBL::Utils::Slice qw(split_Slices);
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  use Bio::EnsEMBL::Registry;

  Bio::EnsEMBL::Registry->load_registry_from_db(
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    -host => 'ensembldb.ensembl.org',
    -user => 'anonymous'
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  );

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  $slice_adaptor =
    Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "slice" );
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  # get a slice on the entire chromosome X
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  $chr_slice = $slice_adaptor->fetch_by_region( 'chromosome', 'X' );
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  # get a slice for each clone in the database
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  foreach $cln_slice ( @{ $slice_adaptor->fetch_all('clone') } ) {
    # do something with clone
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  }

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  # get a slice which is part of NT_004321
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  $spctg_slice =
    $slice_adaptor->fetch_by_region( 'supercontig', 'NT_004321',
    200_000, 600_000 );
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  # get all non-redundant slices from the highest possible coordinate
  # systems
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  $slices = $slice_adaptor->fetch_all('toplevel');

  # include non-reference regions
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  $slices = $slice_adaptor->fetch_all( 'toplevel', undef, 1 );
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  # include non-duplicate regions
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  $slices = $slice_adaptor->fetch_all( 'toplevel', undef, 0, 1 );
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  # split up a list of slices into smaller slices
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  $overlap    = 1000;
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  $max_length = 1e6;
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  $slices     = split_Slices( $slices, $max_length, $overlap );
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  # store a list of slice names in a file
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  open( FILE, ">$filename" ) or die("Could not open file $filename");
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  foreach my $slice (@$slices) {
    print FILE $slice->name(), "\n";
  }
  close FILE;

  # retreive a list of slices from a file
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  open( FILE, $filename ) or die("Could not open file $filename");
  while ( $name = <FILE> ) {
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    chomp($name);
    $slice = $slice_adaptor->fetch_by_name($name);
    # do something with slice
  }

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=head1 DESCRIPTION

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This module is responsible for fetching Slices representing genomic
regions from a database.  A Details on how slices can be used are in the
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Bio::EnsEMBL::Slice module.
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=head1 METHODS
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=cut


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

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use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Slice;
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use Bio::EnsEMBL::CircularSlice;
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use Bio::EnsEMBL::Mapper;
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use Bio::EnsEMBL::LRGSlice;
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use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning stack_trace_dump);
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@ISA = ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
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sub new {
  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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  # use a cache which is shared and also used by the assembly
  # mapper adaptor
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  my $seq_region_cache = $self->db->get_SeqRegionCache();

  $self->{'sr_name_cache'} = $seq_region_cache->{'name_cache'};
  $self->{'sr_id_cache'}   = $seq_region_cache->{'id_cache'};
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  $self->{'lrg_region_test'} = undef;
  my $meta_container = $self->db->get_MetaContainer();
  my @values = $meta_container->list_value_by_key("LRG");
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  if(scalar(@values) and $values[0]->[0]){
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    $self->{'lrg_region_test'} = $values[0]->[0];
  }
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  return $self;
}


=head2 fetch_by_region

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  Arg [1]    : string $coord_system_name (optional)
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               The name of the coordinate system of the slice to be created
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               This may be a name of an actual coordinate system or an alias
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               to a coordinate system.  Valid aliases are 'seqlevel' or
               'toplevel'.
  Arg [2]    : string $seq_region_name
               The name of the sequence region that the slice will be
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               created on.
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  Arg [3]    : int $start (optional, default = 1)
               The start of the slice on the sequence region
  Arg [4]    : int $end (optional, default = seq_region length)
               The end of the slice on the sequence region
  Arg [5]    : int $strand (optional, default = 1)
               The orientation of the slice on the sequence region
  Arg [6]    : string $version (optional, default = default version)
               The version of the coordinate system to use (e.g. NCBI33)
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  Arg [7]    : boolean $no_fuzz (optional, default = undef (false))
               If true (non-zero), do not use "fuzzy matching" (see below).
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  Example    : $slice = $slice_adaptor->fetch_by_region('chromosome', 'X');
               $slice = $slice_adaptor->fetch_by_region('clone', 'AC008066.4');
  Description: Retrieves a slice on the requested region.  At a minimum the
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               name the name of the seq_region to fetch must be provided.

               If no coordinate system name is provided than a slice on the
               highest ranked coordinate system with a matching
               seq_region_name will be returned.  If a version but no
               coordinate system name is provided, the same behaviour will
               apply, but only coordinate systems of the appropriate version
               are considered.  The same applies if the 'toplevel' coordinate
               system is specified, however in this case the version is
               ignored.  The coordinate system should always be specified if
               it is known, since this is unambiguous and faster.
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               Some fuzzy matching is performed if no exact match for
               the provided name is found.  This allows clones to be
               fetched even when their version is not known.  For
               example fetch_by_region('clone', 'AC008066') will
               retrieve the sequence_region with name 'AC008066.4'.

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               The fuzzy matching can be turned off by setting the
               $no_fuzz argument to a true value.

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               If the requested seq_region is not found in the database undef
               is returned.

  Returntype : Bio::EnsEMBL::Slice or undef
  Exceptions : throw if no seq_region_name is provided
               throw if invalid coord_system_name is provided
               throw if start > end is provided
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  Caller     : general
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  Status     : Stable
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=cut

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#
# ARNE: This subroutine needs simplification!! 
#
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sub fetch_by_region {
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  my ( $self, $coord_system_name, $seq_region_name, $start, $end,
       $strand, $version, $no_fuzz )
    = @_;
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  if ( !defined($start) )  { $start  = 1 }
  if ( !defined($strand) ) { $strand = 1 }
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  if ( !defined($seq_region_name) ) {
    throw('seq_region_name argument is required');
  }
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  my $cs;
  my $csa = $self->db->get_CoordSystemAdaptor();
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  if ( defined($coord_system_name) ) {
    $cs = $csa->fetch_by_name( $coord_system_name, $version );
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    ## REMOVE THESE THREE LINES WHEN STICKLEBACK DB IS FIXED!
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    ## Anne/ap5 (2007-10-09):
    # The problem was that the stickleback genebuild called the
    # chromosomes 'groups', which meant they weren't being picked out by
    # the karyotype drawing code.  Apparently they are usually called
    # 'groups' in the stickleback community, even though they really are
    # chromosomes!

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    if ( !defined($cs) && $coord_system_name eq 'chromosome' ) {
      $cs = $csa->fetch_by_name( 'group', $version );
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    }

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    if ( !defined($cs) ) {
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      throw( sprintf( "Unknown coordinate system:\n"
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                        . "name='%s' version='%s'\n",
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                      $coord_system_name, $version ) );
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    }
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    # fetching by toplevel is same as fetching w/o name or version
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    if ( $cs->is_top_level() ) {
      $cs      = undef;
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      $version = undef;
    }
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  } ## end if ( defined($coord_system_name...))
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  my $constraint;
  my $sql;
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  my @bind_params;
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  my $key;

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  if ( defined($cs) ) {
    $sql = sprintf( "SELECT sr.name, sr.seq_region_id, sr.length, %d "
                      . "FROM seq_region sr ",
                    $cs->dbID() );
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    $constraint = "AND sr.coord_system_id = ?";
    push( @bind_params, [ $cs->dbID(), SQL_INTEGER ] );
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    $key = "$seq_region_name:" . $cs->dbID();
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  } else {
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    $sql =
      "SELECT sr.name, sr.seq_region_id, sr.length, cs.coord_system_id "
      . "FROM seq_region sr, coord_system cs ";
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    $constraint = "AND sr.coord_system_id = cs.coord_system_id "
      . "AND cs.species_id = ? ";
    push( @bind_params, [ $self->species_id(), SQL_INTEGER ] );

    if ( defined($version) ) {
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      $constraint .= "AND cs.version = ? ";
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      push( @bind_params, [ $version, SQL_VARCHAR ] );
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    }
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    $constraint .= "ORDER BY cs.rank ASC";
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  }

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  # check the cache so we only go to the db if necessary
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  my $length;
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  my $arr;
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  if ( defined($key) ) { $arr = $self->{'sr_name_cache'}->{$key} }

  if ( defined($arr) ) {
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    $length = $arr->[3];
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  } else {
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    my $sth =
      $self->prepare( $sql . "WHERE sr.name = ? " . $constraint );

    unshift( @bind_params, [ $seq_region_name, SQL_VARCHAR ] );

    my $pos = 0;
    foreach my $param (@bind_params) {
      $sth->bind_param( ++$pos, $param->[0], $param->[1] );
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    }
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    $sth->execute();
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    if ( $sth->rows() == 0 ) {
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      $sth->finish();
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      # try synonyms
      my $syn_sql_sth = $self->prepare("select s.name from seq_region s, seq_region_synonym ss where s.seq_region_id = ss.seq_region_id and ss.synonym = ?");
      $syn_sql_sth->bind_param(1, $seq_region_name, SQL_VARCHAR);
      $syn_sql_sth->execute();
      my $new_name;
      $syn_sql_sth->bind_columns( \$new_name);
      if($syn_sql_sth->fetch){
	$syn_sql_sth->finish;
	return $self->fetch_by_region($coord_system_name, $new_name, $start, $end, $strand, $version, $no_fuzz);
      }
      $syn_sql_sth->finish;


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      if ($no_fuzz) { return undef }

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      # Do fuzzy matching, assuming that we are just missing a version
      # on the end of the seq_region name.
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      $sth =
        $self->prepare( $sql . " WHERE sr.name LIKE ? " . $constraint );
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      $bind_params[0] =
        [ sprintf( '%s.%%', $seq_region_name ), SQL_VARCHAR ];

      $pos = 0;
      foreach my $param (@bind_params) {
        $sth->bind_param( ++$pos, $param->[0], $param->[1] );
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      }
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      $sth->execute();
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      my $prefix_len = length($seq_region_name) + 1;
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      my $high_ver   = undef;
      my $high_cs    = $cs;
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      # Find the fuzzy-matched seq_region with the highest postfix
      # (which ought to be a version).
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      my ( $tmp_name, $id, $tmp_length, $cs_id );
      $sth->bind_columns( \( $tmp_name, $id, $tmp_length, $cs_id ) );
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      my $i = 0;
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      while ( $sth->fetch ) {
        my $tmp_cs =
          ( defined($cs) ? $cs : $csa->fetch_by_dbID($cs_id) );
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        # cache values for future reference
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        my $arr = [ $id, $tmp_name, $cs_id, $tmp_length ];
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        $self->{'sr_name_cache'}->{"$tmp_name:$cs_id"} = $arr;
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        $self->{'sr_id_cache'}->{"$id"}                = $arr;

        my $tmp_ver = substr( $tmp_name, $prefix_len );

        # skip versions which are non-numeric and apparently not
        # versions
        if ( $tmp_ver !~ /^\d+$/ ) { next }

        # take version with highest num, if two versions match take one
        # with highest ranked coord system (lowest num)
        if ( !defined($high_ver)
          || $tmp_ver > $high_ver
          || ( $tmp_ver == $high_ver && $tmp_cs->rank < $high_cs->rank )
          )
        {
          $seq_region_name = $tmp_name;
          $length          = $tmp_length;
          $high_ver        = $tmp_ver;
          $high_cs         = $tmp_cs;
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        }
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        $i++;
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      } ## end while ( $sth->fetch )
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      $sth->finish();

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      # warn if fuzzy matching found more than one result
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      if ( $i > 1 ) {
        warning(
          sprintf(
            "Fuzzy matching of seq_region_name "
              . "returned more than one result.\n"
              . "You might want to check whether the returned seq_region\n"
              . "(%s:%s) is the one you intended to fetch.\n",
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            $high_cs->name(), $seq_region_name ) );
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      }

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      $cs = $high_cs;

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      # return if we did not find any appropriate match:
      if ( !defined($high_ver) ) { return undef }
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    } else {

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      my ( $id, $cs_id );
      ( $seq_region_name, $id, $length, $cs_id ) =
        $sth->fetchrow_array();
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      $sth->finish();
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      # cache to speed up for future queries
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      my $arr = [ $id, $seq_region_name, $cs_id, $length ];
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      $self->{'sr_name_cache'}->{"$seq_region_name:$cs_id"} = $arr;
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      $self->{'sr_id_cache'}->{"$id"}                       = $arr;
      $cs = $csa->fetch_by_dbID($cs_id);
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    }
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  } ## end else [ if ( defined($arr) ) ]
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  if ( !defined($end) ) { $end = $length }
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  if ( $end + 1 < $start ) {
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    my $new_sl =
      Bio::EnsEMBL::CircularSlice->new(
                                   -COORD_SYSTEM    => $cs,
                                   -SEQ_REGION_NAME => $seq_region_name,
                                   -SEQ_REGION_LENGTH => $length,
                                   -START             => $start,
                                   -END               => $end,
                                   -STRAND            => 1,
                                   -ADAPTOR           => $self );

    return $new_sl;
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  }

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  if ( defined( $self->{'lrg_region_test'} )
       and substr( $cs->name, 0, 3 ) eq $self->{'lrg_region_test'} )
  {
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    return
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      Bio::EnsEMBL::LRGSlice->new( -COORD_SYSTEM    => $cs,
                                   -SEQ_REGION_NAME => $seq_region_name,
                                   -SEQ_REGION_LENGTH => $length,
                                   -START             => $start,
                                   -END               => $end,
                                   -STRAND            => $strand,
                                   -ADAPTOR           => $self );
  } else {
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    return
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      Bio::EnsEMBL::Slice->new_fast( {
                                  'coord_system'    => $cs,
                                  'seq_region_name' => $seq_region_name,
                                  'seq_region_length' => $length,
                                  'start'             => $start,
                                  'end'               => $end,
                                  'strand'            => $strand,
                                  'adaptor'           => $self } );
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  }
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} ## end sub fetch_by_region
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=head2 fetch_by_toplevel_location

  Arg [1]     : string $location
  Example     : my $slice = $sa->fetch_by_toplevel_location('X:1-10000')
  Description : Converts an Ensembl location/region into the sequence region
                name, start and end and passes them onto C<fetch_by_region()>. 
                The code assumes that the required slice is on the top level
                coordinate system.
  Returntype  : Bio::EnsEMBL::Slice
  Exceptions  : If $location is false otherwise see C<fetch_by_region()>
  Caller      : General
  Status      : Beta

=cut

sub fetch_by_toplevel_location {
  my ($self, $location) = @_;
  throw 'You must specify a location' if ! $location;
  my $regex = qr/^(\w+) :? (\d+)? (?:-|[.]{2})? (\d+)?/xms;
  my ($seq_region_name, $start, $end) = $location =~ $regex;
  my $coord_system_name = 'toplevel';
  return $self->fetch_by_region($coord_system_name, $seq_region_name, $start, $end, undef, undef, 0);
}

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=head2 fetch_by_region_unique
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  Arg [1]    : string $coord_system_name (optional)
               The name of the coordinate system of the slice to be created
               This may be a name of an actual coordinate system or an alias
               to a coordinate system.  Valid aliases are 'seqlevel' or
               'toplevel'.
  Arg [2]    : string $seq_region_name
               The name of the sequence region that the slice will be
               created on.
  Arg [3]    : int $start (optional, default = 1)
               The start of the slice on the sequence region
  Arg [4]    : int $end (optional, default = seq_region length)
               The end of the slice on the sequence region
  Arg [5]    : int $strand (optional, default = 1)
               The orientation of the slice on the sequence region
  Arg [6]    : string $version (optional, default = default version)
               The version of the coordinate system to use (e.g. NCBI33)
  Arg [7]    : boolean $no_fuzz (optional, default = undef (false))
               If true (non-zero), do not use "fuzzy matching" (see below).
  Example    : $slice = $slice_adaptor->fetch_by_region_unique('chromosome', 'HSCHR6_MHC_COX');
  Description: Retrieves a slice on the requested region but returns only the unique
               parts of the slice.  At a minimum the
               name the name of the seq_region to fetch must be provided.
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               If no coordinate system name is provided than a slice on the
               highest ranked coordinate system with a matching
               seq_region_name will be returned.  If a version but no
               coordinate system name is provided, the same behaviour will
               apply, but only coordinate systems of the appropriate version
               are considered.  The same applies if the 'toplevel' coordinate
               system is specified, however in this case the version is
               ignored.  The coordinate system should always be specified if
               it is known, since this is unambiguous and faster.

               Some fuzzy matching is performed if no exact match for
               the provided name is found.  This allows clones to be
               fetched even when their version is not known.  For
               example fetch_by_region('clone', 'AC008066') will
               retrieve the sequence_region with name 'AC008066.4'.

               The fuzzy matching can be turned off by setting the
               $no_fuzz argument to a true value.

               If the requested seq_region is not found in the database undef
               is returned.

  Returntype : listref Bio::EnsEMBL::Slice
  Exceptions : throw if no seq_region_name is provided
               throw if invalid coord_system_name is provided
               throw if start > end is provided
  Caller     : general
  Status     : Stable

=cut

sub fetch_by_region_unique {
  my $self = shift;

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  my @out   = ();
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  my $slice = $self->fetch_by_region(@_);
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  if ( !exists( $self->{'asm_exc_cache'} ) ) {
    $self->_build_exception_cache();
  }

  if ( exists(
          $self->{'asm_exc_cache'}->{ $self->get_seq_region_id($slice) }
       ) )
  {
    # Dereference symlinked assembly regions.  Take out any regions
    # which are symlinked because these are duplicates.
    my @projection =
      @{ $self->fetch_normalized_slice_projection($slice) };

    foreach my $segment (@projection) {
      if ( $segment->[2]->seq_region_name() eq $slice->seq_region_name()
        && $segment->[2]->coord_system->equals( $slice->coord_system ) )
      {
        push( @out, $segment->[2] );
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      }
    }
  }
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  return \@out;
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} ## end sub fetch_by_region_unique
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=head2 fetch_by_name
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  Arg [1]    : string $name
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  Example    : $name  = 'chromosome:NCBI34:X:1000000:2000000:1';
               $slice = $slice_adaptor->fetch_by_name($name);
               $slice2 = $slice_adaptor->fetch_by_name($slice3->name());
  Description: Fetches a slice using a slice name (i.e. the value returned by
               the Slice::name method).  This is useful if you wish to 
               store a unique identifier for a slice in a file or database or
               pass a slice over a network.
               Slice::name allows you to serialise/marshall a slice and this
               method allows you to deserialise/unmarshal it.
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               Returns undef if no seq_region with the provided name exists in
               the database.

  Returntype : Bio::EnsEMBL::Slice or undef
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  Exceptions : throw if incorrent arg provided
  Caller     : Pipeline
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  Status     : Stable
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=cut

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sub fetch_by_name {
  my $self = shift;
  my $name = shift;
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  if(!$name) {
    throw("name argument is required");
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  }
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  my @array = split(/:/,$name);

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  if(scalar(@array) < 3 || scalar(@array) > 6) {
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    throw("Malformed slice name [$name].  Format is " .
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        "coord_system:version:name:start:end:strand");
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  }

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  # Rearrange arguments to suit fetch_by_region
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  my @targetarray;

  $targetarray[0]=$array[0];
  $targetarray[5]=(($array[1]&&$array[1] ne "")?$array[1]:undef);
  $targetarray[1]=(($array[2]&&$array[2] ne "")?$array[2]:undef);
  $targetarray[2]=(($array[3]&&$array[3] ne "")?$array[3]:undef);
  $targetarray[3]=(($array[4]&&$array[4] ne "")?$array[4]:undef);
  $targetarray[4]=(($array[5]&&$array[5] ne "")?$array[5]:undef);
  return $self->fetch_by_region(@targetarray);
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}
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=head2 fetch_by_seq_region_id

  Arg [1]    : string $seq_region_id
               The internal identifier of the seq_region to create this slice
               on
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  Arg [2]    : optional start
  Arg [3]    : optional end
  Arg [4]    : optional strand
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  Example    : $slice = $slice_adaptor->fetch_by_seq_region_id(34413);
  Description: Creates a slice object of an entire seq_region using the
               seq_region internal identifier to resolve the seq_region.
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               Returns undef if no such slice exists.
  Returntype : Bio::EnsEMBL::Slice or undef
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  Exceptions : none
  Caller     : general
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  Status     : Stable
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=cut

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sub fetch_by_seq_region_id {
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  my ( $self, $seq_region_id, $start, $end, $strand ) = @_;
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  my $arr = $self->{'sr_id_cache'}->{$seq_region_id};
  my ( $name, $length, $cs, $cs_id );
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  if ( $arr && defined( $arr->[2] ) ) {
    ( $name, $cs_id, $length ) = ( $arr->[1], $arr->[2], $arr->[3] );
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    $cs = $self->db->get_CoordSystemAdaptor->fetch_by_dbID($cs_id);
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  } else {
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    my $sth =
      $self->prepare(   "SELECT sr.name, sr.coord_system_id, sr.length "
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                      . "FROM seq_region sr "
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                      . "WHERE sr.seq_region_id = ? " );
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    $sth->bind_param( 1, $seq_region_id, SQL_INTEGER );
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    $sth->execute();
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    if ( $sth->rows() == 0 ) { return undef }
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    ( $name, $cs_id, $length ) = $sth->fetchrow_array();
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    $sth->finish();

    $cs = $self->db->get_CoordSystemAdaptor->fetch_by_dbID($cs_id);

    #cache results to speed up repeated queries
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    my $arr = [ $seq_region_id, $name, $cs_id, $length ];
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    $self->{'sr_name_cache'}->{"$name:$cs_id"} = $arr;
    $self->{'sr_id_cache'}->{"$seq_region_id"} = $arr;
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  }

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  return
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    Bio::EnsEMBL::Slice->new_fast({ 
	                      'coord_system'     => $cs,
                              'seq_region_name'  => $name,
                              'seq_region_length'=> $length,
                              'start'            => $start || 1,
                              'end'              => $end || $length,
                              'strand'           => $strand || 1,
                              'adaptor'           => $self} );
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} ## end sub fetch_by_seq_region_id
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=head2 get_seq_region_id
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  Arg [1]    : Bio::EnsEMBL::Slice $slice
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               The slice to fetch a seq_region_id for
  Example    : $srid = $slice_adaptor->get_seq_region_id($slice);
  Description: Retrieves the seq_region id (in this database) given a slice
               Seq region ids are not stored on the slices themselves
               because they are intended to be somewhat database independant
               and seq_region_ids vary accross databases.
  Returntype : int
  Exceptions : throw if the seq_region of the slice is not in the db
               throw if incorrect arg provided
  Caller     : BaseFeatureAdaptor
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  Status     : Stable
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=cut
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sub get_seq_region_id {
  my $self = shift;
  my $slice = shift;
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  if(!$slice || !ref($slice) || !($slice->isa('Bio::EnsEMBL::Slice') or $slice->isa('Bio::EnsEMBL::LRGSlice'))) {
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    throw('Slice argument is required');
  }
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  my $seq_region_name = $slice->seq_region_name();
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  my $key = $seq_region_name.":".$slice->coord_system->dbID();
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  my $arr = $self->{'sr_name_cache'}->{"$key"};
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  if( $arr ) {
    return $arr->[0];
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  }

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  my $cs_id = $slice->coord_system->dbID();
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  my $sth = $self->prepare("SELECT seq_region_id, length " .
                           "FROM seq_region " .
                           "WHERE name = ? AND coord_system_id = ?");

  #force seq_region_name cast to string so mysql cannot treat as int
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  $sth->bind_param(1,"$seq_region_name",SQL_VARCHAR);
  $sth->bind_param(2,$cs_id,SQL_INTEGER);
  $sth->execute();
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  if($sth->rows() != 1) {
    throw("Non existant or ambigous seq_region:\n" .
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          "  coord_system=[$cs_id],\n" .
          "  name=[$seq_region_name],\n");

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  }

  my($seq_region_id, $length) = $sth->fetchrow_array();
  $sth->finish();

  #cache information for future requests
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  $arr = [ $seq_region_id, $seq_region_name, $cs_id, $length ];
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  $self->{'sr_name_cache'}->{"$seq_region_name:$cs_id"} = $arr;
  $self->{'sr_id_cache'}->{"$seq_region_id"} = $arr;

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  return $seq_region_id;
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}
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=head2 fetch_all

  Arg [1]    : string $coord_system_name
               The name of the coordinate system to retrieve slices of.
               This may be a name of an acutal coordinate system or an alias
               to a coordinate system.  Valid aliases are 'seqlevel' or
               'toplevel'.
  Arg [2]    : string $coord_system_version (optional)
               The version of the coordinate system to retrieve slices of
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  Arg [3]    : bool $include_non_reference (optional)
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               If this argument is not provided then only reference slices
               will be returned. If set, both reference and non refeference
               slices will be rerurned.
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  Arg [4]    : int $include_duplicates (optional)
               If set duplicate regions will be returned.
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               NOTE: if you do not use this option and you have a PAR
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               (pseudo-autosomal region) at the beginning of your seq_region
               then your slice will not start at position 1, so coordinates
               retrieved from this slice might not be what you expected.
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  Arg[5]     : bool $include_lrg (optional)  (default 0)
               If set lrg regions will be returned aswell.


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  Example    : @chromos = @{$slice_adaptor->fetch_all('chromosome','NCBI33')};
               @contigs = @{$slice_adaptor->fetch_all('contig')};

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               # get even non-reference regions
               @slices = @{$slice_adaptor->fetch_all('toplevel',undef,1)};

               # include duplicate regions (such as pseudo autosomal regions)
               @slices = @{$slice_adaptor->fetch_all('toplevel', undef,0,1)};
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  Description: Retrieves slices of all seq_regions for a given coordinate
               system.  This is analagous to the methods fetch_all which were
               formerly on the ChromosomeAdaptor, RawContigAdaptor and
               CloneAdaptor classes.  Slices fetched span the entire
               seq_regions and are on the forward strand.
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               If the coordinate system with the provided name and version
               does not exist an empty list is returned.
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               If the coordinate system name provided is 'toplevel', all
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               non-redundant toplevel slices are returned (note that any
               coord_system_version argument is ignored in that case).
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               Retrieved slices can be broken into smaller slices using the
               Bio::EnsEMBL::Utils::Slice module.

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  Returntype : listref of Bio::EnsEMBL::Slices
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  Exceptions : none
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  Caller     : general
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  Status     : Stable
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=cut

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sub fetch_all {
  my $self = shift;
  my $cs_name = shift;
  my $cs_version = shift || '';

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  my ($include_non_reference, $include_duplicates, $include_lrg) = @_;
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  #
  # verify existance of requested coord system and get its id
  #
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  my $csa       = $self->db->get_CoordSystemAdaptor();
  my $orig_cs   = $csa->fetch_by_name($cs_name, $cs_version);

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  return [] if ( !$orig_cs );
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  my %bad_vals=();
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  #
  # Get a hash of non reference seq regions
  #
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  if ( !$include_non_reference ) {
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    my $sth =
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      $self->prepare(   'SELECT sr.seq_region_id '
                      . 'FROM seq_region sr, seq_region_attrib sra, '
                      . 'attrib_type at, coord_system cs '
                      . 'WHERE at.code = "non_ref" '
                      . 'AND sra.seq_region_id = sr.seq_region_id '
                      . 'AND at.attrib_type_id = sra.attrib_type_id '
                      . 'AND sr.coord_system_id = cs.coord_system_id '
                      . 'AND cs.species_id = ?' );

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    $sth->bind_param( 1, $self->species_id(), SQL_INTEGER );
    $sth->execute();
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    my ($seq_region_id);
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    $sth->bind_columns( \$seq_region_id );
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    while ( $sth->fetch() ) {
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      $bad_vals{$seq_region_id} = 1;
    }
  }
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  #
  # if we do not want lrg's then add them to the bad list;
  #
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  if ( !$include_lrg ) {
    my $sth =
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      $self->prepare(   'SELECT sr.seq_region_id '
                      . 'FROM seq_region sr, seq_region_attrib sra, '
                      . 'attrib_type at, coord_system cs '
                      . 'WHERE at.code = "LRG" '
                      . 'AND sra.seq_region_id = sr.seq_region_id '
                      . 'AND at.attrib_type_id = sra.attrib_type_id '
                      . 'AND sr.coord_system_id = cs.coord_system_id '
                      . 'AND cs.species_id = ?' );

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    $sth->bind_param( 1, $self->species_id(), SQL_INTEGER );
    $sth->execute();
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    my ($seq_region_id);
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    $sth->bind_columns( \$seq_region_id );
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    while ( $sth->fetch() ) {
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      $bad_vals{$seq_region_id} = 1;
    }
  }

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  #
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  # Retrieve the seq_regions from the database
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  #
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  my $sth;
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  if ( $orig_cs->is_top_level() ) {
    $sth =
      $self->prepare(   'SELECT sr.seq_region_id, sr.name, '
                      . 'sr.length, sr.coord_system_id '
                      . 'FROM seq_region sr, seq_region_attrib sra, '
                      . 'attrib_type at, coord_system cs '
                      . 'WHERE at.code = "toplevel" '
                      . 'AND at.attrib_type_id = sra.attrib_type_id '
                      . 'AND sra.seq_region_id = sr.seq_region_id '
                      . 'AND sr.coord_system_id = cs.coord_system_id '
                      . 'AND cs.species_id = ?' );

    $sth->bind_param( 1, $self->species_id(), SQL_INTEGER );
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    $sth->execute();
  } else {
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    $sth =
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      $self->prepare(   'SELECT sr.seq_region_id, sr.name, '
                      . 'sr.length, sr.coord_system_id '
                      . 'FROM seq_region sr '
                      . 'WHERE sr.coord_system_id = ?' );
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    $sth->bind_param( 1, $orig_cs->dbID, SQL_INTEGER );
    $sth->execute();
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  }
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