ensembl-hive
2.6
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Public Member Functions | |
public Bio::EnsEMBL::Mapper | new () |
public void | flush () |
public | map_coordinates () |
public List | map_insert () |
public | fastmap () |
public | add_map_coordinates () |
public | add_indel_coordinates () |
public Bio::EnsEMBL::Mapper::Unit | map_indel () |
public | add_Mapper () |
public | list_pairs () |
public | to () |
public | from () |
protected | _dump () |
protected | _sort () |
protected | _merge_pairs () |
protected | _is_sorted () |
protected | _build_immutable_tree () |
Generic mapper to provide coordinate transforms between two disjoint coordinate systems. This mapper is intended to be 'context neutral' - in that it does not contain any code relating to any particular coordinate system. This is provided in, for example, Bio::EnsEMBL::AssemblyMapper. Mappings consist of pairs of 'to-' and 'from-' contigs with coordinates on each. Orientation is abbreviated to 'ori', The contig pair hash is divided into mappings per seq_region, the code below makes assumptions about how to filter these results, thus the comparisons for some properties are absent in the code but implicit by data structure. The assembly mapping hash '_pair_last' orders itself by the target seq region and looks like this: 1 => ARRAY(0x1024c79c0) 0 Bio::EnsEMBL::Mapper::Pair=HASH(0x1024d6198) 'from' => Bio::EnsEMBL::Mapper::Unit=HASH(0x1025edf98) 'end' => 4 'id' => 4 'start' => 1 'ori' => 1 'to' => Bio::EnsEMBL::Mapper::Unit=HASH(0x1025edf68) 'end' => 4 'id' => 1 'start' => 1 1 Bio::EnsEMBL::Mapper::Pair=HASH(0x1026c20f0) 'from' => Bio::EnsEMBL::Mapper::Unit=HASH(0x1025ee3a0) 'end' => 12 'id' => 4 'start' => 9 'ori' => 1 'to' => Bio::EnsEMBL::Mapper::Unit=HASH(0x1025ee370) 'end' => 4 'id' => 1 'start' => 1 2 => ARRAY(0x1025ee460) 0 Bio::EnsEMBL::Mapper::Pair=HASH(0x1025ee400) 'from' => Bio::EnsEMBL::Mapper::Unit=HASH(0x1025ee2c8) 'end' => 8 'id' => 4 'start' => 5 'ori' => 1 'to' => Bio::EnsEMBL::Mapper::Unit=HASH(0x1025ee2b0) 'end' => 4 'id' => 2 'start' => 1 1 Bio::EnsEMBL::Mapper::Pair=HASH(0x1025ee658) 'from' => Bio::EnsEMBL::Mapper::Unit=HASH(0x1025eea48) 'end' => 16 'id' => 4 'start' => 13 'ori' => 1 'to' => Bio::EnsEMBL::Mapper::Unit=HASH(0x1025eea18) 'end' => 4 'id' => 2 'start' => 1 The other mapping hash available is the reverse sense, putting the 'from' seq_region as the sorting key. Here is an excerpt. 0 HASH(0x102690bb8) 4 => ARRAY(0x1025ee028) 0 Bio::EnsEMBL::Mapper::Pair=HASH(0x1024d6198) 'from' => Bio::EnsEMBL::Mapper::Unit=HASH(0x1025edf98) 'end' => 4 'id' => 4 'start' => 1 'ori' => 1 'to' => Bio::EnsEMBL::Mapper::Unit=HASH(0x1025edf68) 'end' => 4 'id' => 1 'start' => 1 1 Bio::EnsEMBL::Mapper::Pair=HASH(0x1025ee400) 'from' => Bio::EnsEMBL::Mapper::Unit=HASH(0x1025ee2c8) 'end' => 8 'id' => 4 'start' => 5 'ori' => 1 'to' => Bio::EnsEMBL::Mapper::Unit=HASH(0x1025ee2b0) 'end' => 4 'id' => 2 'start' => 1
protected Bio::EnsEMBL::Mapper::_build_immutable_tree | ( | ) |
Undocumented method
protected Bio::EnsEMBL::Mapper::_dump | ( | ) |
Undocumented method
protected Bio::EnsEMBL::Mapper::_is_sorted | ( | ) |
Undocumented method
protected Bio::EnsEMBL::Mapper::_merge_pairs | ( | ) |
Undocumented method
protected Bio::EnsEMBL::Mapper::_sort | ( | ) |
Undocumented method
public Bio::EnsEMBL::Mapper::add_indel_coordinates | ( | ) |
Arg 1 int $id id of 'source' sequence Arg 2 int $start start coordinate of 'source' sequence Arg 3 int $end end coordinate of 'source' sequence Arg 4 int $strand relative orientation of source and target (+/- 1) Arg 5 int $id id of 'targe' sequence Arg 6 int $start start coordinate of 'targe' sequence Arg 7 int $end end coordinate of 'targe' sequence Function stores details of mapping between two regions: 'source' and 'target'. Returns 1 if the pair was added, 0 if it was already in. Used when adding an indel Returntype int 0,1 Exceptions none Caller Bio::EnsEMBL::Mapper
public Bio::EnsEMBL::Mapper::add_map_coordinates | ( | ) |
Arg 1 int $id id of 'source' sequence Arg 2 int $start start coordinate of 'source' sequence Arg 3 int $end end coordinate of 'source' sequence Arg 4 int $strand relative orientation of source and target (+/- 1) Arg 5 int $id id of 'target' sequence Arg 6 int $start start coordinate of 'target' sequence Arg 7 int $end end coordinate of 'target' sequence Function Stores details of mapping between 'source' and 'target' regions. Returntype none Exceptions none Caller Bio::EnsEMBL::Mapper
public Bio::EnsEMBL::Mapper::add_Mapper | ( | ) |
Arg 1 Bio::EnsEMBL::Mapper $mapper2 Example $mapper->add_Mapper($mapper2) Function add all the map coordinates from $mapper to this mapper. This object will contain mapping pairs from both the old object and $mapper2. Returntype int 0,1 Exceptions throw if 'to' and 'from' from both Bio::EnsEMBL::Mappers are incompatible Caller $mapper->methodname()
public Bio::EnsEMBL::Mapper::fastmap | ( | ) |
Arg 1 string $id id of 'source' sequence Arg 2 int $start start coordinate of 'source' sequence Arg 3 int $end end coordinate of 'source' sequence Arg 4 int $strand raw contig orientation (+/- 1) Arg 5 int $type nature of transform - gives the type of coordinates to be transformed *from* Function inferior map method. Will only do ungapped unsplit mapping. Will return id, start, end strand in a list. Returntype list of results Exceptions none Caller Bio::EnsEMBL::AssemblyMapper
public void Bio::EnsEMBL::Mapper::flush | ( | ) |
Args : none Example :
Description: removes all cached information out of this mapper Returntype : none Exceptions : none Caller : AssemblyMapper, ChainedAssemblyMapper
public Bio::EnsEMBL::Mapper::from | ( | ) |
Arg 1 Bio::EnsEMBL::Mapper::Unit $id id of 'source' sequence Function accessor method form the 'source' and 'target' in a Mapper::Pair Returntype Bio::EnsEMBL::Mapper::Unit Exceptions none Caller Bio::EnsEMBL::Mapper
public Bio::EnsEMBL::Mapper::list_pairs | ( | ) |
Arg 1 int $id id of 'source' sequence Arg 2 int $start start coordinate of 'source' sequence Arg 3 int $end end coordinate of 'source' sequence Arg 4 string $type nature of transform - gives the type of coordinates to be transformed *from* Function list all pairs of mappings in a region Returntype list of Bio::EnsEMBL::Mapper::Pair Exceptions none Caller Bio::EnsEMBL::Mapper
public Bio::EnsEMBL::Mapper::map_coordinates | ( | ) |
Arg 1 string $id id of 'source' sequence Arg 2 int $start start coordinate of 'source' sequence Arg 3 int $end end coordinate of 'source' sequence Arg 4 int $strand raw contig orientation (+/- 1) Arg 5 string $type nature of transform - gives the type of coordinates to be transformed *from* Arg 6 boolean (0 or 1) $include_original_region option to include original input coordinate region mappings in the result Arg 7 int $cdna_coding_start cdna coding start Function generic map method Returntype if $include_original_region == 0 array of mappped Bio::EnsEMBL::Mapper::Coordinate and/or Bio::EnsEMBL::Mapper::Gap if $include_original_region == 1 hash of mapped and original Bio::EnsEMBL::Mapper::Coordinate and/or Bio::EnsEMBL::Mapper::Gap Exceptions none Caller Bio::EnsEMBL::Mapper
public Bio::EnsEMBL::Mapper::Unit Bio::EnsEMBL::Mapper::map_indel | ( | ) |
Arg [1] : string $id Arg [2] : int $start - start coord. Since this is an indel should always be one greater than end. Arg [3] : int $end - end coord. Since this is an indel should always be one less than start. Arg [4] : int $strand (0, 1, -1) Arg [5] : string $type - the coordinate system name the coords are from. Example :
Description: This is in internal function which handles the special mapping case for indels (start = end +1). It will be used to map from a coordinate system with a gap to another that contains an insertion. It will be mainly used by the Variation API. Returntype : Bio::EnsEMBL::Mapper::Unit objects Exceptions : none Caller : general
public List Bio::EnsEMBL::Mapper::map_insert | ( | ) |
Arg [1] : string $id Arg [2] : int $start - start coord. Since this is an insert should always be one greater than end. Arg [3] : int $end - end coord. Since this is an insert should always be one less than start. Arg [4] : int $strand (0, 1, -1) Arg [5] : string $type - the coordinate system name the coords are from. Arg [6] : boolean $fastmap - if specified, this is being called from the fastmap call. The mapping done is not any faster for inserts, but the return value is different. Example :
Description: This is in internal function which handles the special mapping case for inserts (start = end +1). This function will be called automatically by the map function so there is no reason to call it directly. Returntype : list of Bio::EnsEMBL::Mapper::Coordinate and/or Gap objects Exceptions : none Caller : map_coordinates()
public Bio::EnsEMBL::Mapper Bio::EnsEMBL::Mapper::new | ( | ) |
Arg [1] : string $from The name of the 'from' coordinate system Arg [2] : string $to The name of the 'to' coordinate system Arg [3] : (optional) Bio::EnsEMBL::CoordSystem $from_cs The 'from' coordinate system Arg [4] : (optional) Bio::EnsEMBL::CoordSystem $to_cs Example :
Description: Constructor. Creates a new Bio::EnsEMBL::Mapper object. Returntype : Bio::EnsEMBL::Mapper Exceptions : none Caller : general
public Bio::EnsEMBL::Mapper::to | ( | ) |
Arg 1 Bio::EnsEMBL::Mapper::Unit $id id of 'source' sequence Function accessor method form the 'source' and 'target' in a Mapper::Pair Returntype Bio::EnsEMBL::Mapper::Unit Exceptions none Caller Bio::EnsEMBL::Mapper