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Bio-EnsEMBL-112.0_52
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
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Questions may also be sent to the Ensembl help desk at
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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