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A library for working with phylogenetic and population genetic data.
v0.32.0 |
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A library for working with phylogenetic and population genetic data.
v0.32.0 |
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#include <genesis/sequence/functions/signature_specifications.hpp>
Specifications for calculating signatures (like k-mer counts) from Sequences.
This class stores settings needed for signature functions like signature_counts(), signature_frequencies(), signature_symmetrized_frequencies() etc. It mainly stores the alphabet() and k() to use for these calculations.
It also serves as storage and lookup for index tables that are needed by those functions. Thus, the indices are only created once per instance of this class, that is, once per alphabet and k. This saves costs when calculating signatures for many Sequences.
Definition at line 64 of file signature_specifications.hpp.
Public Member Functions | |
| SignatureSpecifications ()=default | |
| SignatureSpecifications (SignatureSpecifications &&)=default | |
| Default move constructor. More... | |
| SignatureSpecifications (SignatureSpecifications const &)=default | |
| Default copy constructor. More... | |
| SignatureSpecifications (std::string const &alphabet, size_t k) | |
| ~SignatureSpecifications ()=default | |
| Default destructor. More... | |
| std::string const & | alphabet () const |
| size_t | char_index (char c) const |
| Return the index of a char within the alphabet(). More... | |
| bool | is_nucleic_acids () const |
Speedup and shortcut to test whether the alphabet() is "ACGT". More... | |
| size_t | k () const |
| std::vector< size_t > const & | kmer_combined_reverse_complement_map () const |
| Get a map from indices of kmer_list() and signature_counts() vectors to a smaller list which combines reverse complementary kmers for nucleic acid sequences. More... | |
| std::vector< std::string > const & | kmer_list () const |
Return the list of all possible k-mers for the given k and alphabet. More... | |
| size_t | kmer_list_size () const |
| std::vector< size_t > const & | kmer_reverse_complement_indices () const |
| Get the indices for each kmer in kmer_list() to its reverse complement in the list. More... | |
| std::vector< std::string > const & | kmer_reverse_complement_list () const |
| size_t | kmer_reverse_complement_list_size (bool with_palindromes=true) const |
| SignatureSpecifications & | operator= (SignatureSpecifications &&)=default |
| Default move assignment. More... | |
| SignatureSpecifications & | operator= (SignatureSpecifications const &)=default |
| Default copy assignment. More... | |
| UnknownCharBehavior | unknown_char_behavior () const |
| SignatureSpecifications & | unknown_char_behavior (UnknownCharBehavior value) |
Public Types | |
| enum | UnknownCharBehavior { kSkip, kThrow } |
| List of policies to decide what to do when a char that is not part of the alphabet occurs while counting kmers. More... | |
Static Public Attributes | |
| static const size_t | InvalidCharIndex = std::numeric_limits<size_t>::max() |
| Value that is used to indicate an invalid (non-alphabet) char when using index_of(). More... | |
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default |
| SignatureSpecifications | ( | std::string const & | alphabet, |
| size_t | k | ||
| ) |
Definition at line 52 of file signature_specifications.cpp.
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default |
Default destructor.
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default |
Default copy constructor.
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default |
Default move constructor.
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inline |
Definition at line 130 of file signature_specifications.hpp.
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inline |
Return the index of a char within the alphabet().
For chars that are not in the alphabet, InvalidCharIndex is returned as an indicator value.
Definition at line 163 of file signature_specifications.hpp.
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inline |
Speedup and shortcut to test whether the alphabet() is "ACGT".
Definition at line 152 of file signature_specifications.hpp.
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inline |
Definition at line 135 of file signature_specifications.hpp.
| std::vector< size_t > const & kmer_combined_reverse_complement_map | ( | ) | const |
Get a map from indices of kmer_list() and signature_counts() vectors to a smaller list which combines reverse complementary kmers for nucleic acid sequences.
Definition at line 122 of file signature_specifications.cpp.
| std::vector< std::string > const & kmer_list | ( | ) | const |
Return the list of all possible k-mers for the given k and alphabet.
Definition at line 80 of file signature_specifications.cpp.
| size_t kmer_list_size | ( | ) | const |
Definition at line 117 of file signature_specifications.cpp.
| std::vector< size_t > const & kmer_reverse_complement_indices | ( | ) | const |
Get the indices for each kmer in kmer_list() to its reverse complement in the list.
Definition at line 174 of file signature_specifications.cpp.
| std::vector< std::string > const & kmer_reverse_complement_list | ( | ) | const |
Definition at line 226 of file signature_specifications.cpp.
| size_t kmer_reverse_complement_list_size | ( | bool | with_palindromes = true | ) | const |
Definition at line 263 of file signature_specifications.cpp.
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default |
Default move assignment.
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default |
Default copy assignment.
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inline |
Definition at line 140 of file signature_specifications.hpp.
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inline |
Definition at line 194 of file signature_specifications.hpp.
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strong |
List of policies to decide what to do when a char that is not part of the alphabet occurs while counting kmers.
| Enumerator | |
|---|---|
| kSkip | Simply ignore the char by skipping it. |
| kThrow | Throw an exception. |
Definition at line 76 of file signature_specifications.hpp.
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static |
Value that is used to indicate an invalid (non-alphabet) char when using index_of().
Definition at line 92 of file signature_specifications.hpp.
1.8.17