ensembl-hive
2.6
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Public Member Functions | |
public Bio::EnsEMBL::MappedSliceContainer | new () |
protected | _create_container_slice () |
public Same | set_adaptor () |
public An | get_adaptor () |
public Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor | set_AssemblySliceAdaptor () |
public Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor | get_AssemblySliceAdaptor () |
public | set_AlignSliceAdaptor () |
public | get_AlignSliceAdaptor () |
public | set_StrainSliceAdaptor () |
public | get_StrainSliceAdaptor () |
public void | attach_AssemblySlice () |
public void | attach_StrainSlice () |
public Listref | get_all_MappedSlices () |
public | sub_MappedSliceContainer () |
public Bio::EnsEMBL::Slice | ref_slice () |
public Bio::EnsEMBL::Slice | container_slice () |
public Bio::EnsEMBL::Mapper | mapper () |
public Boolean | expanded () |
public String | seq () |
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.
Definition at line 62 of file MappedSliceContainer.pm.
protected Bio::EnsEMBL::MappedSliceContainer::_create_container_slice | ( | ) |
Undocumented method
public void Bio::EnsEMBL::MappedSliceContainer::attach_AssemblySlice | ( | ) |
Arg[1] : String $version - assembly version to attach Example :
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
public void Bio::EnsEMBL::MappedSliceContainer::attach_StrainSlice | ( | ) |
Arg[1] : String $strain - name of strain to attach Example :
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
public Bio::EnsEMBL::Slice Bio::EnsEMBL::MappedSliceContainer::container_slice | ( | ) |
Arg[1] : (optional) Bio::EnsEMBL::Slice - the container slice to set Example :
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
public Boolean Bio::EnsEMBL::MappedSliceContainer::expanded | ( | ) |
Arg[1] : (optional) Boolean - expanded mode to set Example :
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
public An Bio::EnsEMBL::MappedSliceContainer::get_adaptor | ( | ) |
Arg[1] : String $type - the type of adaptor to get Example :
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
public Bio::EnsEMBL::MappedSliceContainer::get_AlignSliceAdaptor | ( | ) |
Undocumented method
public Listref Bio::EnsEMBL::MappedSliceContainer::get_all_MappedSlices | ( | ) |
Example :
Description : Returns all MappedSlices attached to this container. Return type : listref of Bio::EnsEMBL::MappedSlice Exceptions : none Caller : general Status : At Risk : under development
public Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor Bio::EnsEMBL::MappedSliceContainer::get_AssemblySliceAdaptor | ( | ) |
Example :
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
public Bio::EnsEMBL::MappedSliceContainer::get_StrainSliceAdaptor | ( | ) |
Undocumented method
public Bio::EnsEMBL::Mapper Bio::EnsEMBL::MappedSliceContainer::mapper | ( | ) |
Arg[1] : (optional) Bio::EnsEMBL::Mapper - the mapper to set Example :
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
public Bio::EnsEMBL::MappedSliceContainer Bio::EnsEMBL::MappedSliceContainer::new | ( | ) |
Arg [SLICE] : Bio::EnsEMBL::Slice $slice - the reference slice for this container Arg [EXPANDED] : (optional) Boolean $expanded - set expanded mode (default: collapsed) Example :
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
public Bio::EnsEMBL::Slice Bio::EnsEMBL::MappedSliceContainer::ref_slice | ( | ) |
Arg[1] : (optional) Bio::EnsEMBL::Slice - the reference slice to set Example :
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
public String Bio::EnsEMBL::MappedSliceContainer::seq | ( | ) |
Example :
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
public Same Bio::EnsEMBL::MappedSliceContainer::set_adaptor | ( | ) |
Arg[1] : String $type - the type of adaptor to set Arg[2] : Adaptor $adaptor - the adaptor to set Example :
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
public Bio::EnsEMBL::MappedSliceContainer::set_AlignSliceAdaptor | ( | ) |
Undocumented method
public Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor Bio::EnsEMBL::MappedSliceContainer::set_AssemblySliceAdaptor | ( | ) |
Arg[1] : Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor - the adaptor to set Example :
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
public Bio::EnsEMBL::MappedSliceContainer::set_StrainSliceAdaptor | ( | ) |
Undocumented method
public Bio::EnsEMBL::MappedSliceContainer::sub_MappedSliceContainer | ( | ) |
Undocumented method