an abstract class for Digester objects. More...
#include <digester.hpp>
Public Member Functions | |
| Digester (const char *seq, size_t len, unsigned k, size_t start=0, MinimizedHashType minimized_h=MinimizedHashType::CANON) | |
| Digester (const std::string &seq, unsigned k, size_t start=0, MinimizedHashType minimized_h=MinimizedHashType::CANON) | |
| bool | get_is_valid_hash () |
| unsigned | get_k () |
| size_t | get_len () |
| bool | roll_one () |
| moves the internal pointer to the next valid k-mer. Time Complexity: O(1) | |
| virtual void | roll_minimizer (unsigned amount, std::vector< uint32_t > &vec)=0 |
| gets the positions, as defined by get_pos(), of minimizers up to the amount specified | |
| virtual void | roll_minimizer (unsigned amount, std::vector< std::pair< uint32_t, uint32_t > > &vec)=0 |
| gets the positions (pair.first), as defined by get_pos(), and the hashes (pair.second) of minimizers up to the amount specified | |
| size_t | get_pos () |
| uint64_t | get_chash () |
| uint64_t | get_fhash () |
| uint64_t | get_rhash () |
| virtual void | new_seq (const char *seq, size_t len, size_t start) |
| replaces the current sequence with the new one. It's like starting over with a completely new seqeunce | |
| virtual void | new_seq (const std::string &seq, size_t pos) |
| replaces the current sequence with the new one. It's like starting over with a completely new sequence | |
| void | append_seq (const char *seq, size_t len) |
| simulates the appending of a new sequence to the end of the old sequence. The old sequence will no longer be stored, but the rolling hashes will be able to preceed as if the sequences were appended. Can only be called when you've reached the end of the current sequence i.e. if you're current sequence is ACTGAC, and you have reached the end of this sequence, and you call append_seq with the sequence CCGGCCGG, then the minimizers you will get after calling append_seq plus the minimizers you got from going through ACTGAC, will be equivalent to the minimizers you would have gotten from rolling across ACTGACCCGGCCGG | |
| void | append_seq (const std::string &seq) |
| simulates the appending of a new sequence to the end of the old sequence. The old sequence will no longer be stored, but the rolling hashes will be able to preceed as if the sequences were appended. Can only be called when you've reached the end of the current sequence i.e. if you're current sequence is ACTGAC, and you have reached the end of this sequence, and you call append_seq with the sequence CCGGCCGG, then the minimizers you will get after calling append_seq plus the minimizers you got from going through ACTGAC, will be equivalent to the minimizers you would have gotten from rolling across ACTGACCCGGCCGG | |
| MinimizedHashType | get_minimized_h () |
| const char * | get_sequence () |
Detailed Description
class digest::Digester< P >
an abstract class for Digester objects.
- Template Parameters
-
a BadCharPolicy enum value. The policy to adopt when handling non-ACTG characters.
Constructor & Destructor Documentation
◆ Digester() [1/2]
|
inline |
- Parameters
-
seq const char pointer pointing to the c-string of DNA sequence to be hashed. len length of seq. k kmer size. start 0-indexed position in seq to start hashing from. minimized_h whether we are minimizing the canonical, forward, or reverse hash
- Exceptions
-
BadConstructionException Thrown if k is less than 4, or if the starting position is after the end of the string
◆ Digester() [2/2]
|
inline |
- Parameters
-
seq const string of the DNA sequence to be hashed. k kmer size. start 0-indexed position in seq to start hashing from. minimized_h whether we are minimizing the canonical, forward, or reverse hash
- Exceptions
-
BadConstructionException Thrown if k is less than 4, or if the starting position is after the end of the string
Member Function Documentation
◆ append_seq() [1/2]
|
inline |
simulates the appending of a new sequence to the end of the old sequence. The old sequence will no longer be stored, but the rolling hashes will be able to preceed as if the sequences were appended. Can only be called when you've reached the end of the current sequence i.e. if you're current sequence is ACTGAC, and you have reached the end of this sequence, and you call append_seq with the sequence CCGGCCGG, then the minimizers you will get after calling append_seq plus the minimizers you got from going through ACTGAC, will be equivalent to the minimizers you would have gotten from rolling across ACTGACCCGGCCGG
- Parameters
-
seq const C string of DNA sequence to be appended len length of the sequence
- Exceptions
-
NotRolledTillEndException Thrown when the internal iterator is not at the end of the current sequence
◆ append_seq() [2/2]
|
inline |
simulates the appending of a new sequence to the end of the old sequence. The old sequence will no longer be stored, but the rolling hashes will be able to preceed as if the sequences were appended. Can only be called when you've reached the end of the current sequence i.e. if you're current sequence is ACTGAC, and you have reached the end of this sequence, and you call append_seq with the sequence CCGGCCGG, then the minimizers you will get after calling append_seq plus the minimizers you got from going through ACTGAC, will be equivalent to the minimizers you would have gotten from rolling across ACTGACCCGGCCGG
- Parameters
-
seq const std string of DNA sequence to be appended
- Exceptions
-
NotRolledTillEndException Thrown when the internal iterator is not at the end of the current sequence
◆ get_chash()
|
inline |
- Returns
- uint64_t, the canonical hash of the kmer that was rolled over when roll_one was last called (roll_minimizer() calls roll_one() internally).
◆ get_fhash()
|
inline |
- Returns
- uint64_t, the forward hash of the kmer that was rolled over when roll_one was last called (roll_minimizer() calls roll_one() internally).
◆ get_is_valid_hash()
|
inline |
- Returns
- bool, true if values of the 3 hashes are meaningful, false otherwise, i.e. the object wasn't able to initialize with a valid hash or roll_one() was called when already at end of sequence
◆ get_k()
|
inline |
- Returns
- unsigned, the value of k (kmer size)
◆ get_len()
|
inline |
- Returns
- size_t, the length of the sequence
◆ get_minimized_h()
|
inline |
- Returns
- unsigned, a number representing the hash you are minimizing, 0 for canoncial, 1 for forward, 2 for reverse
◆ get_pos()
|
inline |
- Returns
- current index of the first character of the current kmer that has been hashed. Sequences that have been appended onto each other count as 1 big sequence, i.e. if you first had a sequence of length 10 and then appended another sequence of length 20, and the index of the first character of the current k-mer is at index 4, 0-indexed, in the second sequence, then it will return 14
◆ get_rhash()
|
inline |
- Returns
- uint64_t, the reverse hash of the kmer that was rolled over when roll_one was last called (roll_minimizer() calls roll_one() internally).
◆ get_sequence()
|
inline |
- Returns
- const char* representation of the sequence
◆ new_seq() [1/2]
|
inlinevirtual |
replaces the current sequence with the new one. It's like starting over with a completely new seqeunce
- Parameters
-
seq const char pointer to new sequence to be hashed len length of the new sequence start position in new sequence to start from
- Exceptions
-
BadConstructionException thrown if the starting position is greater than the length of the string
Reimplemented in digest::WindowMin< P, T >.
◆ new_seq() [2/2]
|
inlinevirtual |
replaces the current sequence with the new one. It's like starting over with a completely new sequence
- Parameters
-
seq const std string reference to the new sequence to be hashed start position in new sequence to start from
- Exceptions
-
BadConstructionException thrown if the starting position is greater than the length of the string
Reimplemented in digest::WindowMin< P, T >.
◆ roll_minimizer() [1/2]
|
pure virtual |
gets the positions (pair.first), as defined by get_pos(), and the hashes (pair.second) of minimizers up to the amount specified
- Parameters
-
amount number of minimizers you want to generate vec a reference to a vector of a pair of uint32_t, the positions and hashes returned will go there
Implemented in digest::ModMin< P >, digest::Syncmer< P, T >, and digest::WindowMin< P, T >.
◆ roll_minimizer() [2/2]
|
pure virtual |
gets the positions, as defined by get_pos(), of minimizers up to the amount specified
- Parameters
-
amount number of minimizers you want to generate vec a reference to a vector of uint32_t, the positions returned will go there
Implemented in digest::ModMin< P >, digest::Syncmer< P, T >, and digest::WindowMin< P, T >.
◆ roll_one()
|
inline |
moves the internal pointer to the next valid k-mer.
Time Complexity: O(1)
- Returns
- bool, true if we were able generate a valid hash, false otherwise
The documentation for this class was generated from the following file:
- include/digest/digester.hpp
