ensembl-hive
2.6
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Public Member Functions | |
public Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor | new () |
public Int | max_pair_count () |
public void | register_all () |
public List | map () |
public void | flush () |
public Int | size () |
public List | fastmap () |
public List | list_ids () |
public List | list_seq_regions () |
public Boolean | have_registered_component () |
public Boolean | have_registered_assembled () |
public void | register_component () |
public void | register_assembled () |
public Bio::EnsEMBL::Mapper | mapper () |
public Bio::EnsEMBL::CoordSystem | assembled_CoordSystem () |
public Bio::EnsEMBL::CoordSystem | component_CoordSystem () |
public Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor | adaptor () |
The AssemblyMapper is a database aware mapper which faciliates conversion of coordinates between any two coordinate systems with an relationship explicitly defined in the assembly table. In the future it may be possible to perform multiple step (implicit) mapping between coordinate systems. It is implemented using the Bio::EnsEMBL::Mapper object, which is a generic mapper object between disjoint coordinate systems.
Definition at line 49 of file AssemblyMapper.pm.
public Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor Bio::EnsEMBL::AssemblyMapper::adaptor | ( | ) |
Arg [1] : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor $adaptor Description: Getter/set terfor this object's database adaptor. Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor Exceptions : None Caller : General Status : Stable
public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::AssemblyMapper::assembled_CoordSystem | ( | ) |
Arg [1] : None Example :
Description: Retrieves the assembled CoordSystem from this assembly mapper. Return type: Bio::EnsEMBL::CoordSystem Exceptions : None Caller : Internal, AssemblyMapperAdaptor Status : Stable
public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::AssemblyMapper::component_CoordSystem | ( | ) |
Arg [1] : None Example :
Description: Retrieves the component CoordSystem from this assembly mapper. Return type: Bio::EnsEMBL::CoordSystem Exceptions : None Caller : Internal, AssemblyMapperAdaptor Status : Stable
public List Bio::EnsEMBL::AssemblyMapper::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. Return type: List of Bio::EnsEMBL::Mapper::Coordinate and/or Bio::EnsEMBL::Mapper:Gap objects. Exceptions : Throws if the specified TO coordinat system is not one of the coordinate systems associated with this assembly mapper. Caller : General Status : Stable
public void Bio::EnsEMBL::AssemblyMapper::flush | ( | ) |
Args : None Example :
Description: Remove all cached items from this AssemblyMapper. Return type: None Exceptions : None Caller : AssemblyMapperAdaptor Status : Stable
public Boolean Bio::EnsEMBL::AssemblyMapper::have_registered_assembled | ( | ) |
Arg [1] : string $asm_seq_region The name of the sequence region to check for registration. Arg [2] : int $chunk_id The chunk number of the provided seq_region to check for registration. Example :
Description: Returns true if a given assembled region chunk has been registered with this assembly mapper. This should only be called by this class or the AssemblyMapperAdaptor. In other words, do not use this method unless you really know what you are doing. Return type: Boolean (0 or 1) Exceptions : Throws on incorrect arguments Caller : Internal, AssemblyMapperAdaptor Status : Stable
public Boolean Bio::EnsEMBL::AssemblyMapper::have_registered_component | ( | ) |
Arg [1] : string $cmp_seq_region The name of the sequence region to check for registration. Example :
Description: Returns true if a given component region has been registered with this assembly mapper. This should only be called by this class or the AssemblyMapperAdaptor. In other words, do not use this method unless you really know what you are doing. Return type: Boolean (0 or 1) Exceptions : Throws on incorrect arguments. Caller : Internal, AssemblyMapperAdaptor Status : Stable
public List Bio::EnsEMBL::AssemblyMapper::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 names of another coordinate system. This is the same as the list_ids method but uses seq_region names rather internal IDs. Return type: List of strings. Exceptions : None Caller : General Status : Stable
public List Bio::EnsEMBL::AssemblyMapper::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 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. Return type: List of ints. Exceptions : None Caller : General Status : Stable
public List Bio::EnsEMBL::AssemblyMapper::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] : Dummy placeholder to keep the interface consistent across different mappers Arg [7] : Bio::EnsEMBL::Slice Target slice Arg [8] : (optional) boolean Whether to include the original coordinates or not Example :
Description: Transforms coordinates from one coordinate system to another. Return type: List of Bio::EnsEMBL::Mapper::Coordinate and/or Bio::EnsEMBL::Mapper:Gap objects. Exceptions : Throws if if the specified TO coordinat system is not one of the coordinate systems associated with this assembly mapper. Caller : General Status : Stable
public Bio::EnsEMBL::Mapper Bio::EnsEMBL::AssemblyMapper::mapper | ( | ) |
Arg [1] : None Example :
Description: Retrieves the internal mapper used by this Assembly Mapper. This is unlikely to be useful unless you _really_ know what you are doing. Return type: Bio::EnsEMBL::Mapper Exceptions : None Caller : Internal, AssemblyMapperAdaptor Status : Stable
public Int Bio::EnsEMBL::AssemblyMapper::max_pair_count | ( | ) |
Arg [1] : (optional) int $max_pair_count Example :
Description: Getter/Setter for the number of mapping pairs allowed in the internal cache. This can be used to override the default value (1000) to tune the performance and memory usage for certain scenarios. Higher value means bigger cache, more memory used. Return type: int Exceptions : None Caller : General Status : Stable
public Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor Bio::EnsEMBL::AssemblyMapper::new | ( | ) |
Arg [1] : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor Arg [2] : Bio::EnsEMBL::CoordSystem $asm_cs Arg [3] : Bio::EnsEMBL::CoordSystem $cmp_cs Example :
Description: Creates a new AssemblyMapper Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor Exceptions : Throws if multiple coord_systems are provided Caller : AssemblyMapperAdaptor Status : Stable
public void Bio::EnsEMBL::AssemblyMapper::register_all | ( | ) |
Arg [1] : None Example :
Description: Pre-registers all assembly information in this mapper. The cache size should be set to a sufficiently large value so that all of the information can be stored. This method is useful when *a lot* of mapping will be done in regions which are distributed around the genome. After registration the mapper will consume a lot of memory but will not have to perform any SQL and will be faster. Return type: None Exceptions : None Caller : Specialised programs doing a lot of mapping. Status : Stable
public void Bio::EnsEMBL::AssemblyMapper::register_assembled | ( | ) |
Arg [1] : integer $asm_seq_region The dbID of the sequence region to register. Arg [2] : int $chunk_id The chunk number of the provided seq_region to register. Example :
Description: Flags a given assembled region as registered in this assembly mapper. This should only be called by this class or the AssemblyMapperAdaptor. Do not call this method unless you really know what you are doing. Return type: None Exceptions : Throws on incorrect arguments Caller : Internal, AssemblyMapperAdaptor Status : Stable
public void Bio::EnsEMBL::AssemblyMapper::register_component | ( | ) |
Arg [1] : integer $cmp_seq_region The dbID of the component sequence region to register. Example :
Description: Flags a given component sequence region as registered in this assembly mapper. This should only be called by this class or the AssemblyMapperAdaptor. Return type: None Exceptions : Throws on incorrect arguments Caller : Internal, AssemblyMapperAdaptor Status : Stable
public Int Bio::EnsEMBL::AssemblyMapper::size | ( | ) |
Args : None Example :
Description: Returns the number of pairs currently stored. Return type: int Exceptions : None Caller : General Status : Stable