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Bio-EnsEMBL-112.0_54
River stage zero No dependents
/ Bio::EnsEMBL::MappedSliceContainer

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.

NAME

Bio::EnsEMBL::MappedSliceContainer - container for mapped slices

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.

A MappedSliceContainer holds a collection of one or more Bio::EnsEMBL::MappedSlices. It is based on a real reference slice and contains an artificial "container slice" which defines the common coordinate system used by all attached MappedSlices. There is also a mapper to convert coordinates between the reference and the container slice.

Attaching MappedSlices to the container is delegated to adaptors (which act more as object factories than as traditional Ensembl db adaptors). The adaptors will also modify the container slice and associated mapper if required. This design allows us to keep the MappedSliceContainer generic and encapsulate the data source specific code in the adaptor/factory module.

In the simplest use case, all required MappedSlices are attached to the MappedSliceContainer at once (by a single call to the adaptor). This object should also allow "hot-plugging" of MappedSlices (e.g. attach a MappedSlice representing a strain to a container that already contains a multi-species alignment). The methods for attaching new MappedSlice will be responsable to perform the necessary adjustments to coordinates and mapper on the existing MappedSlices.

METHODS

  new
  set_adaptor
  get_adaptor
  set_AssemblySliceAdaptor
  get_AssemblySliceAdaptor
  set_AlignSliceAdaptor (not implemented yet)
  get_AlignSliceAdaptor (not implemented yet)
  set_StrainSliceAdaptor (not implemented yet)
  get_StrainSliceAdaptor (not implemented yet)
  attach_AssemblySlice
  attach_AlignSlice (not implemented yet)
  attach_StrainSlice (not implemented yet)
  get_all_MappedSlices
  sub_MappedSliceContainer (not implemented yet)
  ref_slice
  container_slice
  mapper
  expanded

RELATED MODULES

  Bio::EnsEMBL::MappedSlice
  Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor
  Bio::EnsEMBL::Compara::AlignSlice
  Bio::EnsEMBL::Compara::AlignSlice::Slice
  Bio::EnsEMBL::StrainSlice

new

  Arg [SLICE]     : Bio::EnsEMBL::Slice $slice - the reference slice for this
                    container
  Arg [EXPANDED]  : (optional) Boolean $expanded - set expanded mode (default:
                    collapsed)
  Example     : my $slice = $slice_adaptor->fetch_by_region('chromosome', 1,
                  9000000, 9500000);
                my $msc = Bio::EnsEMBL::MappedSliceContainer->new(
                    -SLICE    => $slice,
                    -EXPANDED => 1,
                );
  Description : Constructor. See the general documentation of this module for 
                details about this object. Note that the constructor creates an
                empty container, so you'll have to attach MappedSlices to it to
                be useful (this is usually done by an adaptor/factory).
  Return type : Bio::EnsEMBL::MappedSliceContainer
  Exceptions  : thrown on wrong or missing argument
  Caller      : general
  Status      : At Risk
              : under development

set_adaptor

  Arg[1]      : String $type - the type of adaptor to set
  Arg[2]      : Adaptor $adaptor - the adaptor to set
  Example     : my $adaptor = Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor->new;
                $msc->set_adaptor('assembly', $adaptor);
  Description : Parameterisable wrapper for all methods that set adaptors (see
                below).
  Return type : same as Arg 2
  Exceptions  : thrown on missing type
  Caller      : general
  Status      : At Risk
              : under development

get_adaptor

  Arg[1]      : String $type - the type of adaptor to get
  Example     : my $assembly_slice_adaptor = $msc->get_adaptor('assembly');
  Description : Parameterisable wrapper for all methods that get adaptors (see
                below).
  Return type : An adaptor for the requested type of MappedSlice.
  Exceptions  : thrown on missing type
  Caller      : general
  Status      : At Risk
              : under development

set_AssemblySliceAdaptor

  Arg[1]      : Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor - the adaptor to set
  Example     : my $adaptor = Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor->new;
                $msc->set_AssemblySliceAdaptor($adaptor);
  Description : Sets an AssemblySliceAdaptor for this container. The adaptor can
                be used to attach MappedSlice for alternative assemblies.
  Return type : Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor
  Exceptions  : thrown on wrong or missing argument
  Caller      : general, $self->get_adaptor
  Status      : At Risk
              : under development

get_AssemblySliceAdaptor

  Example     : my $assembly_slice_adaptor = $msc->get_AssemblySliceAdaptor;
  Description : Gets a AssemblySliceAdaptor from this container. The adaptor can
                be used to attach MappedSlice for alternative assemblies.
  Return type : Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor
  Exceptions  : thrown on wrong or missing argument
  Caller      : general, $self->get_adaptor
  Status      : At Risk
              : under development

attach_AssemblySlice

  Arg[1]      : String $version - assembly version to attach
  Example     : $msc->attach_AssemblySlice('NCBIM36');
  Description : Attaches a MappedSlice for an alternative assembly to this
                container.
  Return type : none
  Exceptions  : thrown on missing argument
  Caller      : general, Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor
  Status      : At Risk
              : under development

attach_StrainSlice

  Arg[1]      : String $strain - name of strain to attach
  Example     : $msc->attach_StrainSlice('Watson');
  Description : Attaches a MappedSlice for an alternative strain to this
                container.
  Return type : none
  Exceptions  : thrown on missing argument
  Caller      : general, Bio::EnsEMBL::DBSQL::StrainSliceAdaptor
  Status      : At Risk
              : under development

get_all_MappedSlices

  Example     : foreach my $mapped_slice (@{ $msc->get_all_MappedSlices }) {
                  print $mapped_slice->name, "\n";
                }
  Description : Returns all MappedSlices attached to this container.
  Return type : listref of Bio::EnsEMBL::MappedSlice
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

ref_slice

  Arg[1]      : (optional) Bio::EnsEMBL::Slice - the reference slice to set
  Example     : my $ref_slice = $mapped_slice_container->ref_slice;
                print "This MappedSliceContainer is based on the reference
                  slice ", $ref_slice->name, "\n";
  Description : Getter/setter for the reference slice.
  Return type : Bio::EnsEMBL::Slice
  Exceptions  : thrown on wrong argument type
  Caller      : general
  Status      : At Risk
              : under development

container_slice

  Arg[1]      : (optional) Bio::EnsEMBL::Slice - the container slice to set
  Example     : my $container_slice = $mapped_slice_container->container_slice;
                print "The common slice used by this MappedSliceContainer is ",
                  $container_slice->name, "\n";
  Description : Getter/setter for the container slice. This is an artificial
                slice which defines the common coordinate system used by the
                MappedSlices attached to this container.
  Return type : Bio::EnsEMBL::Slice
  Exceptions  : thrown on wrong argument type
  Caller      : general
  Status      : At Risk
              : under development

mapper

  Arg[1]      : (optional) Bio::EnsEMBL::Mapper - the mapper to set
  Example     : my $mapper = Bio::EnsEMBL::Mapper->new('ref', 'mapped');
                $mapped_slice_container->mapper($mapper);
  Description : Getter/setter for the mapper to map between reference slice and
                the artificial container coord system.
  Return type : Bio::EnsEMBL::Mapper
  Exceptions  : thrown on wrong argument type
  Caller      : internal, Bio::EnsEMBL::MappedSlice->AUTOLOAD
  Status      : At Risk
              : under development

expanded

  Arg[1]      : (optional) Boolean - expanded mode to set
  Example     : if ($mapped_slice_container->expanded) {
                  # do more elaborate mapping than in collapsed mode
                  [...]
                }
  Description : Getter/setter for expanded mode.
                
                By default, MappedSliceContainer use collapsed mode, which
                means that no inserts in the reference sequence are allowed
                when constructing the MappedSlices. in this mode, the
                mapped_slice artificial coord system will be identical with the
                ref_slice coord system.
                
                By setting expanded mode, you allow inserts in the reference
                sequence.
  Return type : Boolean
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

seq

  Example     : my $seq = $container->seq()
  Description : Retrieves the expanded sequence of the artificial container
                slice, including "-" characters where there are inserts in any
                of the attached mapped slices.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development