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 | flush () |
public Int | size () |
public List | map () |
public | fastmap () |
public List | list_ids () |
public List | list_seq_regions () |
public Bio::EnsEMBL::Mapper | first_last_mapper () |
public Bio::EnsEMBL::Mapper | first_middle_mapper () |
public Bio::EnsEMBL::Mapper | last_middle_mapper () |
public Bio::EnsEMBL::CoordSystem | first_CoordSystem () |
public Bio::EnsEMBL::CoordSystem | middle_CoordSystem () |
public Bio::EnsEMBL::CoordSystem | last_CoordSystem () |
public Bio::EnsEMBL::Mapper::RangeRegistry | first_registry () |
public Bio::EnsEMBL::Mapper::RangeRegistry | last_registry () |
public Bio::EnsEMBL::Mapper | mapper () |
public Bio::EnsEMBL::CoordSystem | assembled_CoordSystem () |
public Bio::EnsEMBL::CoordSystem | component_CoordSystem () |
public Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor | adaptor () |
The ChainedAssemblyMapper is an extension of the regular AssemblyMapper that allows for mappings between coordinate systems that require multi-step mapping. For example if explicit mappings are defined between the following coordinate systems, chromosome <-> contig contig <-> clone the ChainedAssemblyMapper would be able to perform implicit mapping between the chromosome and clone coordinate systems. This should be transparent to the user of this module, and users should not even realise that they are using a chained assembly mapper as opposed to a normal assembly mapper.
Definition at line 54 of file ChainedAssemblyMapper.pm.
public Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor Bio::EnsEMBL::ChainedAssemblyMapper::adaptor | ( | ) |
Arg [1] : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor $adaptor Description: get/set for this objects database adaptor Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::ChainedAssemblyMapper::assembled_CoordSystem | ( | ) |
Args : none Example :
Description: return the first CoordSystem. Returntype : Bio::EnsEMBL::CoordSystem Exceptions : none Caller : internal Status : Stable
public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::ChainedAssemblyMapper::component_CoordSystem | ( | ) |
Args : none Example :
Description: return the last CoordSystem. Returntype : Bio::EnsEMBL::CoordSystem Exceptions : none Caller : internal Status : Stable
public Bio::EnsEMBL::ChainedAssemblyMapper::fastmap | ( | ) |
Undocumented method
public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::ChainedAssemblyMapper::first_CoordSystem | ( | ) |
Args : none Example :
Description: return the CoordSystem. Returntype : Bio::EnsEMBL::CoordSystem Exceptions : none Caller : internal Status : Stable
public Bio::EnsEMBL::Mapper Bio::EnsEMBL::ChainedAssemblyMapper::first_last_mapper | ( | ) |
Args : none Example :
Description: return the mapper. Returntype : Bio::EnsEMBL::Mapper Exceptions : none Caller : internal Status : Stable
public Bio::EnsEMBL::Mapper Bio::EnsEMBL::ChainedAssemblyMapper::first_middle_mapper | ( | ) |
Args : none Example :
Description: return the mapper. Returntype : Bio::EnsEMBL::Mapper Exceptions : none Caller : internal Status : Stable
public Bio::EnsEMBL::Mapper::RangeRegistry Bio::EnsEMBL::ChainedAssemblyMapper::first_registry | ( | ) |
Args : none Example :
Description: return the Registry. Returntype : Bio::EnsEMBL::Mapper::RangeRegistry Exceptions : none Caller : internal Status : Stable
public Bio::EnsEMBL::ChainedAssemblyMapper::flush | ( | ) |
Undocumented method
public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::ChainedAssemblyMapper::last_CoordSystem | ( | ) |
Args : none Example :
Description: return the CoordSystem. Returntype : Bio::EnsEMBL::CoordSystem Exceptions : none Caller : internal Status : Stable
public Bio::EnsEMBL::Mapper Bio::EnsEMBL::ChainedAssemblyMapper::last_middle_mapper | ( | ) |
Args : none Example :
Description: return the mapper. Returntype : Bio::EnsEMBL::Mapper Exceptions : none Caller : internal Status : Stable
public Bio::EnsEMBL::Mapper::RangeRegistry Bio::EnsEMBL::ChainedAssemblyMapper::last_registry | ( | ) |
Args : none Example :
Description: return the Registry. Returntype : Bio::EnsEMBL::Mapper::RangeRegistry Exceptions : none Caller : internal Status : Stable
public List Bio::EnsEMBL::ChainedAssemblyMapper::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 : none Caller : general Status : Stable
public List Bio::EnsEMBL::ChainedAssemblyMapper::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_ids method but uses seq_region names rather internal ids Returntype : List of strings Exceptions : none Caller : general Status : Stable
public List Bio::EnsEMBL::ChainedAssemblyMapper::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] : (optional) fastmap Arg [7] : (optional) Bio::Ensembl::Slice The slice to transform TO Arg [8] : (optional) boolean Whether to include the original coordinates or not 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 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::ChainedAssemblyMapper::mapper | ( | ) |
Args : none Example :
Description: return the first_last_mapper. Returntype : Bio::EnsEMBL::Mapper Exceptions : none Caller : internal Status : Stable
public Int Bio::EnsEMBL::ChainedAssemblyMapper::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 (6000) to tune the performance and memory usage for certain scenarios. Higher value = bigger cache, more memory used Returntype : int Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::ChainedAssemblyMapper::middle_CoordSystem | ( | ) |
Args : none Example :
Description: return the CoordSystem. Returntype : Bio::EnsEMBL::CoordSystem Exceptions : none Caller : internal Status : Stable
public Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor Bio::EnsEMBL::ChainedAssemblyMapper::new | ( | ) |
Arg [1] : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor Arg [2] : Bio::EnsEMBL::CoordSystem $src_cs Arg [3] : Bio::EnsEMBL::CoordSystem $int_cs Arg [4] : Bio::EnsEMBL::CoordSystem $dst_cs Example :
Description: Creates a new AssemblyMapper Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor Exceptions : thrown if wrong number of coord_systems are provided Caller : AssemblyMapperAdaptor Status : Stable
public void Bio::EnsEMBL::ChainedAssemblyMapper::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. Returntype : none Exceptions : none Caller : specialised programs doing a lot of mapping Status : Stable
public Int Bio::EnsEMBL::ChainedAssemblyMapper::size | ( | ) |
Args : none Example :
Description: return the number of pairs currently stored. Returntype : int Exceptions : none Caller : general Status : Stable