Inheritance diagram for Bio::EnsEMBL::DBSQL::CoordSystemAdaptor:

Public Member Functions
public Bio::EnsEMBL::DBSQL::CoordSystemAdaptor	new ()

protected	_cache_seq_region_mapping ()

protected	_cache_mapping_paths ()

public Listref	fetch_all ()

public Bio::EnsEMBL::CoordSystem	fetch_by_rank ()

public Bio::EnsEMBL::CoordSystem	fetch_by_name ()

public Listref	fetch_all_by_name ()

public ArrayRef	fetch_all_by_version ()

public Bio::EnsEMBL::CoordSystem	fetch_by_dbID ()

public Bio::EnsEMBL::CoordSystem	fetch_top_level ()

public Bio::EnsEMBL::CoordSystem	fetch_sequence_level ()

public String	get_default_version ()

public Listref	get_all_versions ()


public Reference	get_mapping_path ()

public Reference	store_mapping_path ()

public Reference	store_multiple_mapping_path ()

public Bio::EnsEMBL::CoordSystem	fetch_by_attrib ()

public Reference	fetch_all_by_attrib ()

public void	store ()

public void	remove ()

Public Member Functions inherited from Bio::EnsEMBL::DBSQL::BaseAdaptor
public Bio::EnsEMBL::DBSQL::BaseAdaptor	new ()

public DBI::StatementHandle	prepare ()

public Bio::EnsEMBL::DBSQL::DBAdaptor	db ()

public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()

public Boolean	is_multispecies ()

public Int	species_id ()

protected	_list_dbIDs ()

protected	_straight_join ()

protected	_can_straight_join ()

public Listref	bind_param_generic_fetch ()

protected	_bind_param_generic_fetch ()

public String	generate_in_constraint ()

public Listref	generic_fetch ()

public Int	generic_count ()

protected	_generate_sql ()

public Bio::EnsEMBL::Feature	fetch_by_dbID ()

protected	_uncached_fetch_by_dbID ()

public Listref	fetch_all_by_dbID_list ()

protected	_uncached_fetch_all_by_dbID_list ()

protected ArrayRef	_uncached_fetch_all_by_id_list ()

public	fetch_all ()

public Scalar	last_insert_id ()

public	insert_ignore_clause ()

protected Bio::EnsEMBL::DBSQL::Support::BaseCache	_id_cache ()

protected Boolean	_no_id_cache ()

public Boolean	ignore_cache_override ()

public Int	schema_version ()

protected	_tables ()

protected	_columns ()

protected	_default_where_clause ()

protected	_left_join ()

protected	_final_clause ()

protected	_objs_from_sth ()

protected	_build_id_cache ()

protected	_logic_name_to_constraint ()

Detailed Description

Synopsis

use Bio::EnsEMBL::Registry;
 
Bio::EnsEMBL::Registry->load_registry_from_db(
  -host => 'ensembldb.ensembl.org',
  -user => 'anonymous'
);
 
$csa = Bio::EnsEMBL::Registry->get_adaptor( "human", "core",
  "coordsystem" );
 
#
# Get all coord systems in the database:
#
foreach my $cs ( @{ $csa->fetch_all() } ) {
  print $cs->name, ' ', $cs->version, "\n";
}
 
#
# Fetching by name:
#
 
# use the default version of coord_system 'chromosome' (e.g. NCBI33):
$cs = $csa->fetch_by_name('chromosome');
 
# get an explicit version of coord_system 'chromosome':
$cs = $csa->fetch_by_name( 'chromsome', 'NCBI34' );
 
# get all coord_systems of name 'chromosome':
foreach $cs ( @{ $csa->fetch_all_by_name('chromosome') } ) {
  print $cs->name, ' ', $cs->version, "\n";
}
 
#
# Fetching by rank:
#
$cs = $csa->fetch_by_rank(2);
 
#
# Fetching the pseudo coord system 'toplevel'
#
 
# Get the default top_level coord system:
$cs = $csa->fetch_top_level();
 
# can also use an alias in fetch_by_name:
$cs = $csa->fetch_by_name('toplevel');
 
# can also request toplevel using rank=0
$cs = $csa->fetch_by_rank(0);
 
#
# Fetching by sequence level:
#
 
# Get the coord system which is used to store sequence:
$cs = $csa->fetch_sequence_level();
 
# can also use an alias in fetch_by_name:
$cs = $csa->fetch_by_name('seqlevel');
 
#
# Fetching by id
#
$cs = $csa->fetch_by_dbID(1);

Description

This adaptor allows the querying of information from the coordinate
system adaptor.

Note that many coordinate systems do not have a concept of a version
for the entire coordinate system (though they may have a per-sequence
version).  The 'chromosome' coordinate system usually has a version
(i.e. the assembly version) but the clonal coordinate system does not
(despite having individual sequence versions).  In the case where a
coordinate system does not have a version an empty string ('') is used
instead.

Definition at line 91 of file CoordSystemAdaptor.pm.

Member Function Documentation

◆ _cache_mapping_paths()

protected Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::_cache_mapping_paths ( )

Undocumented method

Code:

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sub _cache_mapping_paths {
  # Retrieve a list of available mappings from the meta table.  This
  # may eventually be moved a table of its own if this proves too
  # cumbersome.
 
  my ($self) = @_;
 
  my %mapping_paths;
  my $mc = $self->db()->get_MetaContainer();
 
MAP_PATH:
  foreach
    my $map_path ( @{ $mc->list_value_by_key('assembly.mapping') } )
  {
    my @cs_strings = split( /[|#]/, $map_path );
 
    if ( scalar(@cs_strings) < 2 ) {
      warning(   "Incorrectly formatted assembly.mapping value in meta "
               . "table: $map_path" );
      next MAP_PATH;
    }
 
    my @coord_systems;
    foreach my $cs_string (@cs_strings) {
      my ( $name, $version ) = split( /:/, $cs_string );
 
      my $cs = $self->fetch_by_name( $name, $version );
 
      if ( !defined($cs) ) {
        warning(   "Unknown coordinate system specified in meta table "
                 . " assembly.mapping:\n  $name:$version" );
        next MAP_PATH;
      }
 
      push( @coord_systems, $cs );
    }
 
    # If the delimiter is a '#' we want a special case, multiple parts
    # of the same component map to the same assembly part.  As this
    # looks like the "long" mapping, we just make the path a bit longer
    # :-)
 
    if ( index( $map_path, '#' ) != -1 && scalar(@coord_systems) == 2 )
    {
      splice( @coord_systems, 1, 0, (undef) );
    }
 
    my $cs1 = $coord_systems[0];
    my $cs2 = $coord_systems[$#coord_systems];
 
    my $key1 = $cs1->name();
    $key1 .= ':' . $cs1->version() if $cs1->version();
    my $key2 = $cs2->name();
    $key2 .= ':' . $cs2->version() if $cs2->version();
 
    if ( exists( $mapping_paths{"$key1|$key2"} ) ) {
      warning(   "Meta table specifies multiple mapping paths between "
               . "coord systems $key1 and $key2.\n"
               . "Choosing shorter path arbitrarily." );
 
      if ( scalar( @{ $mapping_paths{"$key1|$key2"} } ) <
           scalar(@coord_systems) )
      {
        next MAP_PATH;
      }
    }
 
    $mapping_paths{"$key1|$key2"} = \@coord_systems;
  } ## end foreach my $map_path ( @{ $mc...
 
  # Create the pseudo coord system 'toplevel' and cache it so that only
  # one of these is created for each database.
 
  my $toplevel =
    Bio::EnsEMBL::CoordSystem->new( -TOP_LEVEL => 1,
                                    -NAME      => 'toplevel',
                                    -ADAPTOR   => $self );
 
  $self->{'_top_level'}     = $toplevel;
  $self->{'_mapping_paths'} = \%mapping_paths;
 
  return 1;
} ## end sub _cache_mapping_paths

◆ _cache_seq_region_mapping()

protected Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::_cache_seq_region_mapping ( )

Undocumented method

Code:

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◆ fetch_all()

public Listref Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::fetch_all ( )

  Arg [1]    : none
  Example    :

foreach my $cs (@{$csa->fetch_all()}) {
                print $cs->name(), ' ', $cs->version(), "\n";
              }

  Description: Retrieves every coordinate system defined in the DB.
               These will be returned in ascending order of rank. I.e.
               The highest coordinate system with rank=1 would be first in the
               array.
  Returntype : listref of Bio::EnsEMBL::CoordSystems
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_all_by_attrib()

public Reference Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::fetch_all_by_attrib ( )

  Arg [1]    : string attrib
  Example    :

$csa->fetch_all_by_attrib('default_version');

  Description: Retrieves all CoordSystem object from the database that have the specified
               attrib.
  Returntype : reference to a list of Bio::EnsEMBL::CoordSystem objects
  Exceptions : throw when attrib not present
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_all_by_name()

public Listref Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::fetch_all_by_name ( )

  Arg [1]    : string $name
               The name of the coordinate system to retrieve.  This can be
               the name of an actual coordinate system or an alias for a
               coordinate system.  Valid aliases are 'toplevel' and 'seqlevel'.
  Example    :

foreach my $cs (@{$csa->fetch_all_by_name('chromosome')}){
                print $cs->name(), ' ', $cs->version();
              }

  Description: Retrieves all coordinate systems of a particular name
  Returntype : listref of Bio::EnsEMBL::CoordSystem objects
  Exceptions : throw if no name argument provided
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_all_by_version()

public ArrayRef Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::fetch_all_by_version ( )

  Arg [1]    : string $version
               The version of the coordinate systems to retrieve.
  Example    :

foreach my $cs (@{$csa->fetch_all_by_version('GRCh37')}){
                print $cs->name(), ' ', $cs->version();
              }

  Description: Retrieves all coordinate systems of a particular version
  Returntype : ArrayRef of Bio::EnsEMBL::CoordSystem objects
  Exceptions : throw if no name argument provided
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_by_attrib()

public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::fetch_by_attrib ( )

  Arg [1]    : string attrib
  Arg [2]    : (optional) string version
  Example    :

$csa->fetch_by_attrib('default_version','NCBIM37');

  Description: Retrieves a CoordSystem object from the database that have the specified
               attrib and version, if no version is specified, returns the default version
  Returntype : Bio::EnsEMBL::CoordSystem object
  Exceptions : throw when attrib not present
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_by_dbID()

public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::fetch_by_dbID ( )

  Arg [1]    : int dbID
  Example    :

$cs = $csa->fetch_by_dbID(4);

  Description: Retrieves a coord_system via its internal
               identifier, or undef if no coordinate system with the provided
               id exists.
  Returntype : Bio::EnsEMBL::CoordSystem or undef
  Exceptions : thrown if no coord_system exists for specified dbID
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_by_name()

public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::fetch_by_name ( )

  Arg [1]    : string $name
               The name of the coordinate system to retrieve.  Alternatively
               this may be an alias for a real coordinate system.  Valid
               aliases are 'toplevel' and 'seqlevel'.
  Arg [2]    : string $version (optional)
               The version of the coordinate system to retrieve.  If not
               specified the default version will be used.
  Example    :

 $coord_sys = $csa->fetch_by_name('clone');
               $coord_sys = $csa->fetch_by_name('chromosome', 'NCBI33');
@section autotoc_md4 toplevel is an pseudo coord system representing the highest
@section autotoc_md5 coord system in a given region
@section autotoc_md6 such as the chromosome coordinate system
               $coord_sys = $csa->fetch_by_name('toplevel');
               #seqlevel is an alias for the sequence level coordinate system
               #such as the clone or contig coordinate system
               $coord_sys = $csa->fetch_by_name('seqlevel');

  Description: Retrieves a coordinate system by its name
  Returntype : Bio::EnsEMBL::CoordSystem
  Exceptions : throw if no name argument provided
               warning if no version provided and default does not exist
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_by_rank()

public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::fetch_by_rank ( )

  Arg [1]    : int $rank
  Example    :

my $cs = $coord_sys_adaptor->fetch_by_rank(1);

  Description: Retrieves a CoordinateSystem via its rank. 0 is a special
               rank reserved for the pseudo coordinate system 'toplevel'.
               undef is returned if no coordinate system of the specified rank
               exists.
  Returntype : Bio::EnsEMBL::CoordSystem
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_sequence_level()

public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::fetch_sequence_level ( )

  Arg [1]    : none
  Example    :

($id, $name, $version) = $csa->fetch_sequence_level();

  Description: Retrieves the coordinate system at which sequence
               is stored at.
  Returntype : Bio::EnsEMBL::CoordSystem
  Exceptions : throw if no sequence_level coord system exists at all
               throw if multiple sequence_level coord systems exists
  Caller     : general
  Status     : Stable

Code:

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◆ fetch_top_level()

public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::fetch_top_level ( )

  Arg [1]    : none
  Example    :

$cs = $csa->fetch_top_level();

  Description: Retrieves the toplevel pseudo coordinate system.
  Returntype : Bio::EnsEMBL::CoordSystem object
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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◆ get_all_versions()

public Listref Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::get_all_versions ( )

  Arg [1]    : none
  Example    :

@versions = $csa->get_all_versions();

  Description: Retrieves all the available versions of assemblies
  Returntype : Listref of versions (strings)
  Exceptions : throw if no version is defined
  Caller     : general
  Status     : Stable

Code:

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◆ get_default_version()

public String Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::get_default_version ( )

  Arg [1]    : none
  Example    :

$version = $csa->get_default_version();

  Description: Retrieves the default version of the assembly
  Returntype : String
  Exceptions : throw if no default version is defined
  Caller     : general
  Status     : Stable

Code:

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◆ get_mapping_path()

public Reference Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::get_mapping_path ( )

  Arg [1]    : Bio::EnsEMBL::CoordSystem $cs1
  Arg [2]    : Bio::EnsEMBL::CoordSystem $cs2
  Example    :

foreach my $cs @{$csa->get_mapping_path($cs1,$cs2);

  Description: Given two coordinate systems this will return a mapping path
               between them if one has been defined.  Allowed Mapping paths are
               explicitly defined in the meta table.  The following is an
               example:

          mysql> select * from meta where meta_key = 'assembly.mapping';
          +---------+------------------+--------------------------------------+
          | meta_id | meta_key         | meta_value                           |
          +---------+------------------+--------------------------------------+
          |      20 | assembly.mapping | chromosome:NCBI34|contig             |
          |      21 | assembly.mapping | clone|contig                         |
          |      22 | assembly.mapping | supercontig|contig                   |
          |      23 | assembly.mapping | chromosome:NCBI34|contig|clone       |
          |      24 | assembly.mapping | chromosome:NCBI34|contig|supercontig |
          |      25 | assembly.mapping | supercontig|contig|clone             |
          +---------+------------------+--------------------------------------+

               For a one-step mapping path to be valid there needs to be
               a relationship between the two coordinate systems defined in
               the assembly table.  Two step mapping paths work by building
               on the one-step mapping paths which are already defined.

               The first coordinate system in a one step mapping path must
               be the assembled coordinate system and the second must be
               the component.

               Example of use:
               my $cs1 = $cs_adaptor->fetch_by_name('contig');
               my $cs2 = $cs_adaptor->fetch_by_name('chromosome');

               my @path =$cs_adaptor->get_mapping_path($cs1,$cs2)};

               if(!@path) {
                 print "No mapping path.";
               }
               elsif(@path == 2) {
                 print "2 step mapping path.";
                 print "Assembled = " . $path[0]->name() . "\n";
                 print "Component = " . $path[1]->name() . "\n";
               } else {
                 print "Multi step mapping path\n";
               }

  Returntype : reference to a list of Bio::EnsEMBL::CoordSystem objects

  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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sub get_mapping_path {
  my $self = shift;
  my $cs1 = shift;
  my $cs2 = shift;
 
  if(!ref($cs1) || !ref($cs2) ||
     !$cs1->isa('Bio::EnsEMBL::CoordSystem') ||
     !$cs2->isa('Bio::EnsEMBL::CoordSystem')) {
    throw('Two Bio::EnsEMBL::CoordSystem arguments expected.');
  }
 
  my $key1 = $cs1->name();
  $key1 .= ':' . $cs1->version() if ($cs1->version());
  my $key2 = $cs2->name();
  $key2 .= ':' . $cs2->version() if ($cs2->version());
 
  my $path = $self->{'_mapping_paths'}->{"$key1|$key2"};
 
  return $path if($path);
 
  $path = $self->{'_mapping_paths'}->{"$key2|$key1"};
 
  if(!$path) {
    # No path was explicitly defined, but we might be able to guess a
    # suitable path.  We only guess for missing 2 step paths.
 
    my %mid1;
    my %mid2;
 
    foreach my $path (values(%{$self->{'_mapping_paths'}})) {
      next if(@$path != 2);
 
      my $match = undef;
 
      if($path->[0]->equals($cs1)) {
        $match = 1;
      } elsif($path->[1]->equals($cs1)) {
        $match = 0;
      }
 
      if(defined($match)) {
        my $mid = $path->[$match];
        my $midkey = $mid->name() . ':' . $mid->version();
 
        # is the same cs mapped to by other cs?
        if($mid2{$midkey}) {
          my $path = [$cs1,$mid,$cs2];
          $self->{'_mapping_paths'}->{"$key1|$key2"} = $path;
          $key1 =~ s/\:$//;
          $key2 =~ s/\:$//;
          $midkey =~ s/\:$//;
          warning("Using implicit mapping path between '$key1' and '$key2' " .
                  "coord systems.\n" .
                  "An explicit 'assembly.mapping' entry should be added " .
                  "to the meta table.\nExample: " .
                  "'$key1|$midkey|$key2'\n");
          return $path;
        } else {
          $mid1{$midkey} = $mid;
        }
      }
 
      $match = undef;
 
      if($path->[0]->equals($cs2)) {
        $match = 1;
      } elsif($path->[1]->equals($cs2)) {
        $match = 0;
      }
 
 
      if(defined($match)) {
        my $mid = $path->[$match];
        my $midkey = $mid->name() . ':' . $mid->version();
 
        # is the same cs mapped to by other cs?
        if($mid1{$midkey}) {
          my $path = [$cs2,$mid,$cs1];
          $self->{'_mapping_paths'}->{"$key2|$key1"} = $path;
 
          $key1 =~ s/\:$//;
          $key2 =~ s/\:$//;
          $midkey =~ s/\:$//;
          warning("Using implicit mapping path between '$key1' and '$key2' " .
                  "coord systems.\n" .
                  "An explicit 'assembly.mapping' entry should be added " .
                  "to the meta table.\nExample: " .
                  "'$key1|$midkey|$key2'\n");
 
          return $path;
        } else {
          $mid2{$midkey} = $mid;
        }
      }
    }
  }
 
  return $path || [];
}

◆ new()

public Bio::EnsEMBL::DBSQL::CoordSystemAdaptor Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::new ( )

  Arg [1]    : See BaseAdaptor for arguments (none specific to this
               subclass)
  Example    :

$cs = $db->get_CoordSystemAdaptor(); #better than new()

  Description: Creates a new CoordSystem adaptor and caches the contents
               of the coord_system table in memory.
  Returntype : Bio::EnsEMBL::DBSQL::CoordSystemAdaptor
  Exceptions : none
  Caller     :
  Status     : Stable

Code:

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sub new {
  my ( $proto, @args ) = @_;
 
  my $class = ref($proto) || $proto;
  my $self = $class->SUPER::new(@args);
 
  #
  # Cache the entire contents of the coord_system table cross-referenced
  # by dbID and name.
  #
 
  # keyed on name, list of coord_system value
  $self->{'_name_cache'} = {};
 
  # keyed on id, coord_system value
  $self->{'_dbID_cache'} = {};
 
  # keyed on rank
  $self->{'_rank_cache'} = {};
 
  # keyed on id, 1/undef values
  $self->{'_is_sequence_level'}  = {};
  $self->{'_is_default_version'} = {};
 
  #cache to store the seq_region_mapping information
  #from internal->external
  $self->{'_internal_seq_region_mapping'} = {};
  #from external->internal
  $self->{'_external_seq_region_mapping'} = {};
 
  my $sth = $self->prepare(
                  'SELECT `coord_system_id`, `name`, `rank`, `version`, `attrib` '
                    . 'FROM coord_system '
                    . 'WHERE species_id = ?' );
 
  $sth->bind_param( 1, $self->species_id(), SQL_INTEGER );
  $sth->execute();
 
  my ( $dbID, $name, $rank, $version, $attrib );
  $sth->bind_columns( \( $dbID, $name, $rank, $version, $attrib ) );
 
  while ( $sth->fetch() ) {
    my $seq_lvl = 0;
    my $default = 0;
 
    if ( defined($attrib) ) {
      foreach my $attrib ( split( ',', $attrib ) ) {
        $self->{"_is_$attrib"}->{$dbID} = 1;
        if ( $attrib eq 'sequence_level' ) {
          $seq_lvl = 1;
        } elsif ( $attrib eq 'default_version' ) {
          $default = 1;
        }
      }
    }
 
    my $cs =
      Bio::EnsEMBL::CoordSystem->new( -DBID           => $dbID,
                                      -ADAPTOR        => $self,
                                      -NAME           => $name,
                                      -VERSION        => $version,
                                      -RANK           => $rank,
                                      -SEQUENCE_LEVEL => $seq_lvl,
                                      -DEFAULT        => $default );
 
    $self->{'_dbID_cache'}->{$dbID} = $cs;
 
    $self->{'_name_cache'}->{ lc($name) } ||= [];
    $self->{'_rank_cache'}->{$rank} = $cs;
 
    push @{ $self->{'_name_cache'}->{ lc($name) } }, $cs;
 
  } ## end while ( $sth->fetch() )
  $sth->finish();
 
  $self->_cache_mapping_paths();
 
  $self->_cache_seq_region_mapping();
 
  return $self;
} ## end sub new

◆ remove()

public void Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::remove ( )

  Arg [1]    : Bio::EnsEMBL::CoordSystem
  Example    :

$csa->remove($coord_system);

  Description: Removes a CoordSystem object from the database.
  Returntype : none
  Exceptions : Warning if CoordSystem is not stored in this database.
  Caller     : none
  Status     : Stable

Code:

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◆ store()

public void Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::store ( )

  Arg [1]    : Bio::EnsEMBL::CoordSystem
  Example    :

$csa->store($coord_system);

  Description: Stores a CoordSystem object in the database.
  Returntype : none
  Exceptions : Warning if CoordSystem is already stored in this database.
  Caller     : none
  Status     : Stable

Code:

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sub store {
  my $self = shift;
  my $cs = shift;
 
  if(!$cs || !ref($cs) || !$cs->isa('Bio::EnsEMBL::CoordSystem')) {
    throw('CoordSystem argument expected.');
  }
 
  my $db = $self->db();
  my $name = $cs->name();
  my $version = $cs->version();
  my $rank    = $cs->rank();
 
  my $seqlevel = $cs->is_sequence_level();
  my $default  = $cs->is_default();
 
  my $toplevel = $cs->is_top_level();
 
  if($toplevel) {
    throw("The toplevel CoordSystem cannot be stored");
  }
 
  #
  # Do lots of sanity checking to prevent bad data from being entered
  #
 
  if($cs->is_stored($db)) {
    warning("CoordSystem $name $version is already in db.\n");
    return;
  }
 
  if($name eq 'toplevel' || $name eq 'seqlevel' || !$name) {
    throw("[$name] is not a valid name for a CoordSystem.");
  }
 
  if($seqlevel && keys(%{$self->{'_is_sequence_level'}})) {
    throw("There can only be one sequence level CoordSystem.");
  }
 
  if(exists $self->{'_name_cache'}->{lc($name)}) {
    my @coord_systems = @{$self->{'_name_cache'}->{lc($name)}};
    foreach my $c (@coord_systems) {
      if(lc($c->version()) eq lc($version)) {
        warning("CoordSystem $name $version is already in db.\n");
        return;
      }
      if($default && $self->{'_is_default_version'}->{$c->dbID()}) {
        throw("There can only be one default version of CoordSystem $name");
      }
    }
  }
 
  if($rank !~ /^\d+$/) {
    throw("Rank attribute must be a positive integer not [$rank]");
  }
  if($rank == 0) {
    throw("Only toplevel CoordSystem may have rank of 0.");
  }
 
  if(defined($self->{'_rank_cache'}->{$rank})) {
    throw("CoordSystem with rank [$rank] already exists.");
  }
 
  my @attrib;
 
  push @attrib, 'default_version' if($default);
  push @attrib, 'sequence_level' if($seqlevel);
 
  my $attrib_str = (@attrib) ? join(',', @attrib) : undef;
 
  #
  # store the coordinate system in the database
  #
 
  my $sth =
    $db->dbc->prepare(   'INSERT INTO coord_system '
                       . '( `name`, `version`, `attrib`, `rank`, `species_id` ) '
                         . 'VALUES ( ?, ?, ?, ?, ? )' );
 
  $sth->bind_param( 1, $name,               SQL_VARCHAR );
  $sth->bind_param( 2, $version,            SQL_VARCHAR );
  $sth->bind_param( 3, $attrib_str,         SQL_VARCHAR );
  $sth->bind_param( 4, $rank,               SQL_INTEGER );
  $sth->bind_param( 5, $self->species_id(), SQL_INTEGER );
 
  $sth->execute();
  my $dbID = $self->last_insert_id('coord_system_id', undef, 'coord_system');
  $sth->finish();
 
  if(!$dbID) {
    throw("Did not get dbID from store of CoordSystem.");
  }
 
  $cs->dbID($dbID);
  $cs->adaptor($self);
 
  #
  # update the internal caches that are used for fetching
  #
  $self->{'_is_default_version'}->{$dbID} = 1 if($default);
  $self->{'_is_sequence_level'}->{$dbID} = 1 if($seqlevel);
 
  $self->{'_name_cache'}->{lc($name)} ||= [];
  push @{$self->{'_name_cache'}->{lc($name)}}, $cs;
 
  $self->{'_dbID_cache'}->{$dbID} = $cs;
  $self->{'_rank_cache'}->{$rank} = $cs;
 
  return $cs;
}

◆ store_mapping_path()

public Reference Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::store_mapping_path ( )

  Arg [1]    : Bio::EnsEMBL::CoordSystem $cs1
  Arg [2]    : Bio::EnsEMBL::CoordSystem $cs2
  Arg [3..n] : Bio::EnsEMBL::CoordSystem $cs3..$csN
  Example    :

my $pathref = $csa->store_mapping_path($cs1,$cs2);

  Description: Given two or more coordinate systems this will store 
               mapping paths between them in the database.

               For example, if $cs1 represents chrs of version
               V1, $cs2 represents contigs, and $cs3 clones then, unless
               they already exist, the following entries will be created 
               in the meta table;
               +------------------+---------------------+ 
               | meta_key         | meta_value          |
               +------------------+---------------------+ 
               | assembly.mapping | chr:V1|clone        |
               | assembly.mapping | clone|contig        |
               | assembly.mapping | chr:V1|clone|contig |
               +------------------+---------------------+

               For a one-step mapping path to be valid there needs to be
               a relationship between the two coordinate systems defined in
               the assembly table.  Two step mapping paths work by building
               on the one-step mapping paths which are already defined.

               The first coordinate system in a one step mapping path must
               be the assembled coordinate system and the second must be
               the component.

  Returntype : reference to a list of lists of new meta_value mapping strings
               created for assembly.mapping
  Exceptions : CoordSystems with no rank/duplicated rank
  Caller     : general
  Status     : Experimental

Code:

click to view

◆ store_multiple_mapping_path()

public Reference Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::store_multiple_mapping_path ( )

  Arg [1]    : Bio::EnsEMBL::CoordSystem $cs1
  Arg [2]    : Bio::EnsEMBL::CoordSystem $cs2
  Arg [3..n] : Bio::EnsEMBL::CoordSystem $cs3..$csN
  Example    :

my $pathref = $csa->store_multiple_mapping_path($cs1,$cs2);

  Description: Given two or more coordinate systems this will store 
               multiple mapping paths between them in the database.

               Works similarly to the store_mapping_path method
               But will presume every coord system can be mapped in multiple
               ways to the other coord systems
               This is represented by the use of '#' instead of '|'
               in the mapping key

  Returntype : reference to a list of lists of new meta_value mapping strings
               created for assembly.mapping
  Exceptions : CoordSystems with no rank/duplicated rank
  Caller     : general
  Status     : Experimental

Code:

click to view

The documentation for this class was generated from the following file:

ensembl/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ _cache_mapping_paths()

◆ _cache_seq_region_mapping()

◆ fetch_all()

◆ fetch_all_by_attrib()

◆ fetch_all_by_name()

◆ fetch_all_by_version()

◆ fetch_by_attrib()

◆ fetch_by_dbID()

◆ fetch_by_name()

◆ fetch_by_rank()

◆ fetch_sequence_level()

◆ fetch_top_level()

◆ get_all_versions()

◆ get_default_version()

◆ get_mapping_path()

◆ new()

◆ remove()

◆ store()

◆ store_mapping_path()

◆ store_multiple_mapping_path()