#include <genesis/utils/math/twobit_vector.hpp>

Detailed Description

Definition at line 41 of file twobit_vector.hpp.

Public Member Functions
	TwobitVector ()=default

	TwobitVector (size_t size)
	Constructor that initializes the vector with `size` many zero values. More...

	TwobitVector (TwobitVector &&)=default

	TwobitVector (TwobitVector const &)=default

	~TwobitVector ()=default

void	clear ()
	Clear the vector, so that it contains no data. More...

WordType &	data_at (size_t index)
	Return a single word of the vector. More...

WordType const &	data_at (size_t index) const
	Return a single word of the vector. More...

size_t	data_size () const
	Return the number of words (of type WordType) that are used to store the values in the vector. More...

ValueType	get (size_t index) const
	Get the value at a position in the vector. More...

WordType	hash () const
	Calculate a hash value of the vector, based on its size() and the xor of all its words. More...

void	insert_at (size_t index, ValueType value)
	Insert a value at a position. More...

bool	operator!= (TwobitVector const &other) const
	Inequality operator, opposite of operator==(). More...

TwobitVector &	operator= (TwobitVector &&)=default

TwobitVector &	operator= (TwobitVector const &)=default

bool	operator== (TwobitVector const &other) const
	Equality operator. More...

ValueType	operator[] (size_t index) const
	Alias for get(). More...

void	remove_at (size_t index)
	Remove the value at a position. More...

void	set (size_t index, ValueType value)
	Set a value at a position in the vector. More...

size_t	size () const
	Return the size of the vector, that is, how many values (of type ValueType) it currently holds. More...

bool	validate () const
	Validation function that checks some basic invariants. More...

Public Types
enum	ValueType : WordType { A = 0, C = 1, G = 2, T = 3 }
	Value Type enumeration for the elements of a TwobitVector. More...

using	WordType = uint64_t
	Underlying word type for the bitvector. More...

Static Public Attributes
static const size_t	kValuesPerWord = sizeof( WordType ) * 8 / 2
	Constant that holds the number of values (of tyoe ValueType) that are stored in a single word in the vector. More...

Constructor & Destructor Documentation

◆ TwobitVector() [1/4]

TwobitVector ( )

default

◆ TwobitVector() [2/4]

TwobitVector ( size_t size )

Constructor that initializes the vector with size many zero values.

Definition at line 118 of file twobit_vector.cpp.

◆ ~TwobitVector()

~TwobitVector ( )

default

◆ TwobitVector() [3/4]

TwobitVector ( TwobitVector const & )

default

◆ TwobitVector() [4/4]

TwobitVector ( TwobitVector && )

default

Member Function Documentation

◆ clear()

void clear ( )

Clear the vector, so that it contains no data.

Definition at line 405 of file twobit_vector.cpp.

◆ data_at() [1/2]

TwobitVector::WordType & data_at ( size_t index )

Return a single word of the vector.

This is useful for external functions that want to directly work on the underlying bit representation.

Definition at line 187 of file twobit_vector.cpp.

◆ data_at() [2/2]

TwobitVector::WordType const & data_at ( size_t index ) const

Return a single word of the vector.

This is useful for external functions that want to directly work on the underlying bit representation.

Definition at line 176 of file twobit_vector.cpp.

◆ data_size()

size_t data_size ( ) const

Return the number of words (of type WordType) that are used to store the values in the vector.

Definition at line 140 of file twobit_vector.cpp.

◆ get()

TwobitVector::ValueType get ( size_t index ) const

Get the value at a position in the vector.

Definition at line 149 of file twobit_vector.cpp.

◆ hash()

TwobitVector::WordType hash ( ) const

Calculate a hash value of the vector, based on its size() and the xor of all its words.

This is a simple function, but might just be enough for using it in a hashmap.

Definition at line 198 of file twobit_vector.cpp.

◆ insert_at()

void insert_at	(	size_t	index,
		TwobitVector::ValueType	value
	)

Insert a value at a position.

The size() is increased by one.

Definition at line 290 of file twobit_vector.cpp.

◆ operator!=()

bool operator!= ( TwobitVector const & other ) const

Inequality operator, opposite of operator==().

Definition at line 230 of file twobit_vector.cpp.

◆ operator=() [1/2]

TwobitVector& operator= ( TwobitVector && )

default

◆ operator=() [2/2]

TwobitVector& operator= ( TwobitVector const & )

default

◆ operator==()

bool operator== ( TwobitVector const & other ) const

Equality operator.

Definition at line 214 of file twobit_vector.cpp.

◆ operator[]()

TwobitVector::ValueType operator[] ( size_t index ) const

Alias for get().

Definition at line 165 of file twobit_vector.cpp.

◆ remove_at()

void remove_at ( size_t index )

Remove the value at a position.

The size() is decreased by one.

Definition at line 342 of file twobit_vector.cpp.

◆ set()

void set	(	size_t	index,
		TwobitVector::ValueType	value
	)

Set a value at a position in the vector.

Definition at line 269 of file twobit_vector.cpp.

◆ size()

size_t size ( ) const

Return the size of the vector, that is, how many values (of type ValueType) it currently holds.

Definition at line 131 of file twobit_vector.cpp.

◆ validate()

bool validate ( ) const

Validation function that checks some basic invariants.

This is mainly useful in testing. The function checks whether the vector is correctly sized and contains zero padding at its end.

Definition at line 241 of file twobit_vector.cpp.

Member Typedef Documentation

◆ WordType

using WordType = uint64_t

Underlying word type for the bitvector.

We use 64bit words to store the 2bit values (of type ValueType), so that we get best speed on modern architectures.

Definition at line 55 of file twobit_vector.hpp.

Member Enumeration Documentation

◆ ValueType

enum ValueType : WordType

strong

Value Type enumeration for the elements of a TwobitVector.

The values 0-3 are named A, C, G and T, respectively, in order to ease the use with nucleotide sequences.

The underlying value of the enum is WordType, so that a cast does not need to convert internally.

Enumerator
A
C
G
T

Definition at line 66 of file twobit_vector.hpp.

Member Data Documentation

◆ kValuesPerWord

const size_t kValuesPerWord = sizeof( WordType ) * 8 / 2

static

Constant that holds the number of values (of tyoe ValueType) that are stored in a single word in the vector.

As we use 64bit words, this value is 32.

Definition at line 79 of file twobit_vector.hpp.

The documentation for this class was generated from the following files:

Detailed Description

Public Member Functions

Public Types

Static Public Attributes

Constructor & Destructor Documentation

◆ TwobitVector() [1/4]

◆ TwobitVector() [2/4]

◆ ~TwobitVector()

◆ TwobitVector() [3/4]

◆ TwobitVector() [4/4]

Member Function Documentation

◆ clear()

◆ data_at() [1/2]

◆ data_at() [2/2]

◆ data_size()

◆ get()

◆ hash()

◆ insert_at()

◆ operator!=()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

◆ operator[]()

◆ remove_at()

◆ set()

◆ size()

◆ validate()

Member Typedef Documentation

◆ WordType

Member Enumeration Documentation

◆ ValueType

Member Data Documentation

◆ kValuesPerWord