Bio::EnsEMBL MappedSlice
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Summary
Bio::EnsEMBL::MappedSlice - an object representing a mapped slice
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Mapper
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Bio::EnsEMBL::Utils::Exception qw ( throw warning )
Scalar::Util qw ( weaken )
Synopsis
  # get a reference slice
  my $slice =
    $slice_adaptor->fetch_by_region( 'chromosome', 14, 900000, 950000 );

  # create MappedSliceContainer based on the reference slice
  my $msc = Bio::EnsEMBL::MappedSliceContainer->new( -SLICE => $slice );

  # set the adaptor for fetching AssemblySlices
  my $asa = $slice->adaptor->db->get_AssemblySliceAdaptor;
  $msc->set_AssemblySliceAdaptor($asa);

  # add an AssemblySlice to your MappedSliceContainer
  $msc->attach_AssemblySlice('NCBIM36');

  foreach my $mapped_slice ( @{ $msc->get_all_MappedSlices } ) {
    print $mapped_slice->name, "\n";

    foreach my $sf ( @{ $mapped_slice->get_all_SimpleFeatures } ) {
      print "  ", &to_string($sf), "\n";
    }
  }
Description
NOTE: this code is under development and not fully functional nor tested
yet. Use only for development.
This object represents a mapped slice, i.e. a slice that's attached
to a reference slice and a mapper to convert coordinates to/from the
reference. The attachment is done via a MappedSliceContainer which
has the reference slice and the "container slice" defining the common
coordinate system for all MappedSlices.
A MappedSlice is supposed to behave as close to a Bio::EnsEMBL::Slice
as possible. Most Slice methods are implemented in MappedSlice and will
return an equivalent value to what Slice does. There are some exceptions
of unimplemented methods, either because there is no useful equivalent
for a MappedSlice to do, or they are too complicated.
Not supported Bio::EnsEMBL::Slice methods:
  All deprecated methods
  All Bio::PrimarySeqI compliance methods
  expand
  get_generic_features
  get_seq_region_id
  seq_region_Slice
Not currently supported but maybe should/could:
  calculate_pi
  calculate_theta
  get_base_count
  get_by_Individual
  get_by_strain
  invert
Internally, a MappedSlice is a collection of Bio::EnsEMBL::Slices and
associated Bio::EnsEMBL::Mappers which map the slices to the common
container coordinate system.
MappedSlices are usually created and attached to a MappedSliceContainer
by an adaptor/factory.
Methods
AUTOLOADDescriptionCode
adaptorDescriptionCode
add_Slice_Mapper_pairDescriptionCode
centrepointDescriptionCode
containerDescriptionCode
coord_systemDescriptionCode
coord_system_nameDescriptionCode
endDescriptionCode
get_all_Slice_Mapper_pairsDescriptionCode
get_repeatmasked_seq
No description
Code
is_toplevelDescriptionCode
lengthDescriptionCode
nameDescriptionCode
newDescriptionCode
project
No description
Code
seq
No description
Code
seq_region_lengthDescriptionCode
seq_region_nameDescriptionCode
startDescriptionCode
strandDescriptionCode
sub_MappedSlice
No description
Code
subseq
No description
Code
Methods description
AUTOLOADcode    nextTop
  Arg[1..N]   : Arguments passed on to the calls on the underlying slices.
  Example     : my @simple_features = @{ $mapped_slice->get_all_SimpleFeatures };
  Description : Aggregate data gathered from composing Slices.
                This will call Slice->get_all_* and combine the results.
                Coordinates will be transformed to be on the container slice
                coordinate system.

                Calls involving DAS features are skipped since the DAS adaptor
                handles coordinate conversions natively.
  Return type : listref of features (same type as corresponding Slice method)
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
adaptorcodeprevnextTop
  Arg[1]      : (optional) Adaptor $adaptor - the adaptor/factory for this
                object
  Example     : $mapped_slice->adaptor($assembly_slice_adaptor);
  Description : Getter/setter for the adaptor/factory for this object.
  Return type : Adaptor of appropriate type
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
add_Slice_Mapper_pair codeprevnextTop
  Arg[1]      : Bio::EnsEMBL::Slice $slice - slice to add
  Arg[2]      : Bio::EnsEMBL::Mapper $mapper - the mapper for this slice
  Example     : $mapped_slice->add_Slice_Mapper_pair($slice, $mapper);
  Description : Adds a native slice and a corresponding mapper to map to/from
                the artificial container coord system.
  Return type : listref of Bio::EnsEMBL::MappedSlice
  Exceptions  : thrown on wrong or missing arguments
  Caller      : general, MappedSlice adaptors
  Status      : At Risk
              : under development
centrepointcodeprevnextTop
  Example     : my $centrepoint = $mapped_slice->centrepoint;
  Description : Returns the centrepoint of the container slice.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
containercodeprevnextTop
  Arg[1]      : (optional) Bio::EnsEMBL::MappedSliceContainer - the container
                this object is attached to
  Example     : my $container = $mapped_slice->container;
                print $container->ref_slice->name, "\n";
  Description : Getter/setter for the container this object is attached to. The
                container will give you access to the reference slice, a common
                artificial container slice, and a mapper to map to it from the
                container coord system.

                The implementation uses a weak reference to attach the container
                since the container holds a list of MappedSlices itself.
  Return type : Bio::EnsEMBL::MappedSliceContainer
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
coord_systemcodeprevnextTop
  Example     : my $cs = $mapped_slice->coord_system;
  Description : Returns the coord system of the container slice.
  Return type : Bio::EnsEMBL::CoordSystem
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
coord_system_namecodeprevnextTop
  Example     : my $cs_name = $mapped_slice->coord_system_name;
  Description : Returns the coord system name of the container slice.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
endcodeprevnextTop
  Example     : my $end = $mapped_slice->end;
  Description : Returns the end of the container slice.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
get_all_Slice_Mapper_pairs codeprevnextTop
  Example     : foreach my $pair (@{ $self->get_all_Slice_Mapper_pairs }) {
                  my ($slice, $mapper) = @$pair;

                  # get container coordinates
                  my @coords = $mapper->map_coordinates(
                    $slice->seq_region_name,
                    $slice->start,
                    $slice->end,
                    $slice->strand,
                    'mapped_slice'
                  );

                  # ....
                }
  Description : Gets all Slice/Mapper pairs this MappedSlice is composed of.
                Each slice (and features on it) can be mapped onto the
                artificial container coord system using the mapper.
  Return type : listref of listref of a Bio::EnsEMBL::Slice and
                Bio::EnsEMBL::Mapper pair
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
is_toplevelcodeprevnextTop
  Example     : my $toplevel_flag = $mapped_slice->is_toplevel;
  Description : Returns weather the container slice is toplevel.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
lengthcodeprevnextTop
  Example     : my $length = $mapped_slice->length;
  Description : Returns the length of the container slice
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
namecodeprevnextTop
  Arg[1]      : String - the name of this object
  Example     : my $name = $mapped_slice->container->ref_slice->name .
                  ":mapped_" . $ident_string;
                $mapped_slice->name($name);
  Description : Getter/setter for this object's name
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
newcodeprevnextTop
  Arg [ADAPTOR]   : Adaptor $adaptor - an adaptor of the appropriate type
  Arg [CONTAINER] : Bio::EnsEMBL::MappedSliceContainer $container - the
                    container this MappedSlice is attached to
  Arg [NAME]      : String $name - name
  Example     : my $mapped_slice = Bio::EnsEMBL::MappedSlice->new(
                  -ADAPTOR   => $adaptor,
                  -CONTAINER => $container,
                  -NAME      => $name,
                );
  Description : Constructor. Usually you won't call this method manually, but
                the MappedSlice will be constructed by an adaptor/factory.
  Return type : Bio::EnsEMBL::MappedSlice
  Exceptions  : thrown on wrong or missing arguments
  Caller      : general, MappedSlice adaptors
  Status      : At Risk
              : under development
seq_region_lengthcodeprevnextTop
  Example     : my $sr_length = $mapped_slice->seq_region_length;
  Description : Returns the seq_region length of the reference slice.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
seq_region_namecodeprevnextTop
  Example     : my $sr_name = $mapped_slice->seq_region_name;
  Description : Returns the seq_region name of the reference slice.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
startcodeprevnextTop
  Example     : my $start = $mapped_slice->start;
  Description : Returns the start of the container slice.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
strandcodeprevnextTop
  Example     : my $strand = $mapped_slice->strand;
  Description : Returns the strand of the container slice.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
Methods code
AUTOLOADdescriptionprevnextTop
sub AUTOLOAD {
  my $self = shift;
  
  my $method = $AUTOLOAD;
  $method =~ s/.*:://;
  
  # AUTOLOAD should only deal with get_all_* methods
  return unless ($method =~ /^get_all_/);

  # skip DAS methods
  return if ($method =~ /DAS/);
  
  my @mapped_features = ();

  foreach my $pair (@{ $self->get_all_Slice_Mapper_pairs }) {
    my ($slice, $mapper) = @$pair;
    #warn $slice->name;

    # call $method on each native slice composing the MappedSlice
    my @features = @{ $slice->$method(@_) };
    
    # map features onto the artificial container coordinate system
    foreach my $f (@features) {
      
      my @coords = $mapper->map_coordinates(
          $f->slice->seq_region_name,
          $f->start,
          $f->end,
          $f->strand,
          'mapped_slice'
      );

      # sanity check
      if (scalar(@coords) > 1) {
        warning("Got more than one Coordinate returned, expected only one!\n");
      }

      $f->start($coords[0]->start);
      $f->end($coords[0]->end);
      $f->strand($coords[0]->strand);
      $f->slice($self->container->container_slice);

      push @mapped_features, $f;
    }

  }

  return\@ mapped_features;
}


1;
}
adaptordescriptionprevnextTop
sub adaptor {
  my $self = shift;
  $self->{'adaptor'} = shift if (@_);
  return $self->{'adaptor'};
}
add_Slice_Mapper_pairdescriptionprevnextTop
sub add_Slice_Mapper_pair {
  my $self = shift;
  my $slice = shift;
  my $mapper = shift;

  # argument check
  unless ($slice and ref($slice) and $slice->isa('Bio::EnsEMBL::Slice')) {
    throw("You must provide a slice.");
  }

  unless ($mapper and ref($mapper) and $mapper->isa('Bio::EnsEMBL::Mapper')) {
    throw("You must provide a mapper.");
  }

  push @{ $self->{'slice_mapper_pairs'} }, [ $slice, $mapper ];
  
  return $self->{'slice_mapper_pairs'};
}
centrepointdescriptionprevnextTop
sub centrepoint {
  my $self = shift;
  return $self->container->container_slice->centrepoint;
}
containerdescriptionprevnextTop
sub container {
  my $self = shift;
  weaken($self->{'container'} = shift) if (@_);
  return $self->{'container'};
}
coord_systemdescriptionprevnextTop
sub coord_system {
  my $self = shift;
  return $self->container->container_slice->coord_system;
}
coord_system_namedescriptionprevnextTop
sub coord_system_name {
  my $self = shift;
  return $self->container->container_slice->coord_system_name;
}
enddescriptionprevnextTop
sub end {
  my $self = shift;
  return $self->container->container_slice->end;
}
get_all_Slice_Mapper_pairsdescriptionprevnextTop
sub get_all_Slice_Mapper_pairs {
  my $self = shift;
  return $self->{'slice_mapper_pairs'};
}
get_repeatmasked_seqdescriptionprevnextTop
sub get_repeatmasked_seq {}
is_topleveldescriptionprevnextTop
sub is_toplevel {
  my $self = shift;
  return $self->container->container_slice->is_toplevel;
}
lengthdescriptionprevnextTop
sub length {
  my $self = shift;
  return $self->container->container_slice->length;
}
namedescriptionprevnextTop
sub name {
  my $self = shift;
  $self->{'name'} = shift if (@_);
  return $self->{'name'};
}
newdescriptionprevnextTop
sub new {
  my $caller = shift;
  my $class = ref($caller) || $caller;

  my ($adaptor, $container, $name) =
    rearrange([qw(ADAPTOR CONTAINER NAME)], @_);

  # arguement check
  unless ($container and ref($container) and
          $container->isa('Bio::EnsEMBL::MappedSliceContainer')) {
    throw("Need a MappedSliceContainer.");
  }

  my $self = {};
  bless ($self, $class);

  #
  # initialise object
  #
  
  # need to weaken reference to prevent circular reference
  weaken($self->{'container'} = $container);

  $self->{'adaptor'} = $adaptor if (defined($adaptor));
  $self->{'name'} = $name if (defined($name));

  $self->{'slice_mapper_pairs'} = [];

  return $self;
}
projectdescriptionprevnextTop
sub project {}
seqdescriptionprevnextTop
sub seq {}
seq_region_lengthdescriptionprevnextTop
sub seq_region_length {
  my $self = shift;
  return $self->container->ref_slice->seq_region_length;
}
seq_region_namedescriptionprevnextTop
sub seq_region_name {
  my $self = shift;
  return $self->container->ref_slice->seq_region_name;
}
startdescriptionprevnextTop
sub start {
  my $self = shift;
  return $self->container->container_slice->start;
}
stranddescriptionprevnextTop
sub strand {
  my $self = shift;
  return $self->container->container_slice->strand;
}
sub_MappedSlicedescriptionprevnextTop
sub sub_MappedSlice {}
subseqdescriptionprevnextTop
sub subseq {}
General documentation
LICENSETop
  Copyright (c) 1999-2009 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

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

    /info/about/code_licence.html
CONTACTTop
  Please email comments or questions to the public Ensembl
  developers list at <ensembl-dev@ebi.ac.uk>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.
RELATED MODULESTop
  Bio::EnsEMBL::MappedSlice
  Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor
  Bio::EnsEMBL::Compara::AlignSlice
  Bio::EnsEMBL::Compara::AlignSlice::Slice
  Bio::EnsEMBL::AlignStrainSlice
  Bio::EnsEMBL::StrainSlice