ensembl-hive
2.6
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Public Member Functions | |
public Bio::EnsEMBL::MappedSlice | new () |
public Listref | add_Slice_Mapper_pair () |
public Listref | get_all_Slice_Mapper_pairs () |
public Adaptor | adaptor () |
public Bio::EnsEMBL::MappedSliceContainer | container () |
public String | name () |
public String | seq_region_name () |
public Int | start () |
public Int | end () |
public Int | strand () |
public Int | length () |
public Int | seq_region_length () |
public Int | centrepoint () |
public Bio::EnsEMBL::CoordSystem | coord_system () |
public Int | coord_system_name () |
public Int | is_toplevel () |
public String | seq () |
public | subseq () |
public | get_repeatmasked_seq () |
public | sub_MappedSlice () |
public | project () |
public Listref | AUTOLOAD () |
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 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.
Definition at line 75 of file MappedSlice.pm.
public Adaptor Bio::EnsEMBL::MappedSlice::adaptor | ( | ) |
Arg[1] : (optional) Adaptor $adaptor - the adaptor/factory for this object Example :
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
public Listref Bio::EnsEMBL::MappedSlice::add_Slice_Mapper_pair | ( | ) |
Arg[1] : Bio::EnsEMBL::Slice $slice - slice to add Arg[2] : Bio::EnsEMBL::Mapper $mapper - the mapper for this slice Example :
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
public Listref Bio::EnsEMBL::MappedSlice::AUTOLOAD | ( | ) |
Arg[1..N] : Arguments passed on to the calls on the underlying slices. Example :
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
public Int Bio::EnsEMBL::MappedSlice::centrepoint | ( | ) |
Example :
Description : Returns the centrepoint of the container slice. Return type : Int Exceptions : none Caller : general Status : At Risk : under development
public Bio::EnsEMBL::MappedSliceContainer Bio::EnsEMBL::MappedSlice::container | ( | ) |
Arg[1] : (optional) Bio::EnsEMBL::MappedSliceContainer - the container this object is attached to Example :
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
public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::MappedSlice::coord_system | ( | ) |
Example :
Description : Returns the coord system of the container slice. Return type : Bio::EnsEMBL::CoordSystem Exceptions : none Caller : general Status : At Risk : under development
public Int Bio::EnsEMBL::MappedSlice::coord_system_name | ( | ) |
Example :
Description : Returns the coord system name of the container slice. Return type : Int Exceptions : none Caller : general Status : At Risk : under development
public Int Bio::EnsEMBL::MappedSlice::end | ( | ) |
Example :
Description : Returns the end of the container slice. Return type : Int Exceptions : none Caller : general Status : At Risk : under development
public Listref Bio::EnsEMBL::MappedSlice::get_all_Slice_Mapper_pairs | ( | ) |
Example :
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
public Bio::EnsEMBL::MappedSlice::get_repeatmasked_seq | ( | ) |
Undocumented method
public Int Bio::EnsEMBL::MappedSlice::is_toplevel | ( | ) |
Example :
Description : Returns weather the container slice is toplevel. Return type : Int Exceptions : none Caller : general Status : At Risk : under development
public Int Bio::EnsEMBL::MappedSlice::length | ( | ) |
Example :
Description : Returns the length of the container slice Return type : Int Exceptions : none Caller : general Status : At Risk : under development
public String Bio::EnsEMBL::MappedSlice::name | ( | ) |
Arg[1] : String - the name of this object Example :
Description : Getter/setter for this object's name Return type : String Exceptions : none Caller : general Status : At Risk : under development
public Bio::EnsEMBL::MappedSlice Bio::EnsEMBL::MappedSlice::new | ( | ) |
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 :
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
public Bio::EnsEMBL::MappedSlice::project | ( | ) |
Undocumented method
public String Bio::EnsEMBL::MappedSlice::seq | ( | ) |
Example :
Description : Retrieves the expanded sequence of this mapped slice, including "-" characters where there are inserts in any other mapped slices. This will align with the sequence returned by the container's seq() method. Return type : String Exceptions : none Caller : general Status : At Risk : under development
public Int Bio::EnsEMBL::MappedSlice::seq_region_length | ( | ) |
Example :
Description : Returns the seq_region length of the reference slice. Return type : Int Exceptions : none Caller : general Status : At Risk : under development
public String Bio::EnsEMBL::MappedSlice::seq_region_name | ( | ) |
Example :
Description : Returns the seq_region name of the reference slice. Return type : String Exceptions : none Caller : general Status : At Risk : under development
public Int Bio::EnsEMBL::MappedSlice::start | ( | ) |
Example :
Description : Returns the start of the container slice. Return type : Int Exceptions : none Caller : general Status : At Risk : under development
public Int Bio::EnsEMBL::MappedSlice::strand | ( | ) |
Example :
Description : Returns the strand of the container slice. Return type : Int Exceptions : none Caller : general Status : At Risk : under development
public Bio::EnsEMBL::MappedSlice::sub_MappedSlice | ( | ) |
Undocumented method
public Bio::EnsEMBL::MappedSlice::subseq | ( | ) |
Undocumented method