ensembl-hive
2.6
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Public Member Functions | |
public Bio::EnsEMBL::DBSQL::TopLevelAssemblyMapper | new () |
public | adaptor () |
public List | map () |
public void | flush () |
public List | fastmap () |
public Bio::EnsEMBL::CoordSystem | assembled_CoordSystem () |
public Bio::EnsEMBL::CoordSystem | component_CoordSystem () |
protected | _list () |
public List | list_seq_regions () |
public List | list_ids () |
The TopLevelAssemblyMapper performs mapping between a provided coordinate system and the toplevel pseudo cooordinate system. The toplevel coordinate system is not a real coordinate system, but represents the highest coordinate system that can be mapped to in a given region. It is only possible to perform unidirectional mapping using this mapper, because it does not make sense to map from the toplevel coordinate system to another coordinate system.
Definition at line 40 of file TopLevelAssemblyMapper.pm.
protected Bio::EnsEMBL::TopLevelAssemblyMapper::_list | ( | ) |
Undocumented method
public Bio::EnsEMBL::TopLevelAssemblyMapper::adaptor | ( | ) |
Undocumented method
public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::TopLevelAssemblyMapper::assembled_CoordSystem | ( | ) |
Arg [1] : none Example :
Description: Retrieves the assembled CoordSystem from this mapper Returntype : Bio::EnsEMBL::CoordSystem Exceptions : none Caller : internal, AssemblyMapperAdaptor Status : Stable
public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::TopLevelAssemblyMapper::component_CoordSystem | ( | ) |
Arg [1] : none Example :
Description: Retrieves the component CoordSystem from this mapper Returntype : Bio::EnsEMBL::CoordSystem Exceptions : none Caller : internal, AssemblyMapperAdaptor Status : Stable
public List Bio::EnsEMBL::TopLevelAssemblyMapper::fastmap | ( | ) |
Arg [1] : string $frm_seq_region The name of the sequence region to transform FROM Arg [2] : int $frm_start The start of the region to transform FROM Arg [3] : int $frm_end The end of the region to transform FROM Arg [4] : int $strand The strand of the region to transform FROM Arg [5] : Bio::EnsEMBL::CoordSystem The coordinate system to transform FROM Example :
Description: Transforms coordinates from one coordinate system to another. Returntype : List of Bio::EnsEMBL::Mapper::Coordinate and/or Bio::EnsEMBL::Mapper:Gap objects Exceptions : thrown if if the specified TO coordinate system is not one of the coordinate systems associated with this mapper Caller : general Status : Stable
public void Bio::EnsEMBL::TopLevelAssemblyMapper::flush | ( | ) |
Args : none Example :
Description: polymorphism with AssemblyMapper, does nothing Returntype : none Exceptions : none Status : Stable
public List Bio::EnsEMBL::TopLevelAssemblyMapper::list_ids | ( | ) |
Arg [1] : string $frm_seq_region The name of the sequence region of interest. Arg [2] : int $frm_start The start of the region of interest Arg [3] : int $frm_end The end of the region to transform of interest Arg [5] : Bio::EnsEMBL::CoordSystem $frm_cs The coordinate system to obtain overlapping ids of Example :
Description: Retrieves a list of overlapping seq_region internal identifiers of another coordinate system. This is the same as the list_seq_regions method but uses internal identfiers rather than seq_region strings Returntype : List of ints Exceptions : thrown if the from CoordSystem is the toplevel coord system thrown if the from CoordSystem is not the one used in the mapper Caller : general Status : Stable
public List Bio::EnsEMBL::TopLevelAssemblyMapper::list_seq_regions | ( | ) |
Arg [1] : string $frm_seq_region The name of the sequence region of interest Arg [2] : int $frm_start The start of the region of interest Arg [3] : int $frm_end The end of the region to transform of interest Arg [5] : Bio::EnsEMBL::CoordSystem $frm_cs The coordinate system to obtain overlapping ids of Example :
Description: Retrieves a list of overlapping seq_region names of another coordinate system. This is the same as the list_ids method but uses seq_region names rather internal ids Returntype : List of strings Exceptions : none Caller : general Status : Stable
public List Bio::EnsEMBL::TopLevelAssemblyMapper::map | ( | ) |
Arg [1] : string $frm_seq_region The name of the sequence region to transform FROM Arg [2] : int $frm_start The start of the region to transform FROM Arg [3] : int $frm_end The end of the region to transform FROM Arg [4] : int $strand The strand of the region to transform FROM Arg [5] : Bio::EnsEMBL::CoordSystem The coordinate system to transform FROM Arg [6] : if set will do a fastmap Arg [7] : (optional) dummy placeholder to keep the interface consistent across different mappers Arg [8] : (optional) boolean Whether or not to include the original coordinates Example :
Description: Transforms coordinates from one coordinate system to another. Returntype : List of Bio::EnsEMBL::Mapper::Coordinate and/or Bio::EnsEMBL::Mapper:Gap objects Exceptions : thrown if if the specified TO coordinate system is not one of the coordinate systems associated with this mapper Caller : general Status : Stable
public Bio::EnsEMBL::DBSQL::TopLevelAssemblyMapper Bio::EnsEMBL::TopLevelAssemblyMapper::new | ( | ) |
Arg [1] : Bio::EnsEMBL::DBAdaptor $dbadaptor the adaptor for the database this mapper is using. Arg [2] : Toplevel CoordSystem Arg [3] : Other CoordSystem Description: Creates a new TopLevelAssemblyMapper object Returntype : Bio::EnsEMBL::DBSQL::TopLevelAssemblyMapper Exceptions : throws if any of the 3 arguments are missing/ not : of the correct type. Caller : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor Status : Stable