iterator for FormatFieldGenericValue objects. More...

#include <individual_field_value_iterator.h>

Inheritance diagram for gamgee::IndividualFieldValueIterator< VALUE_TYPE >:

Public Member Functions
	IndividualFieldValueIterator (const std::shared_ptr< bcf1_t > &body, uint8_t data_ptr, uint8_t end_ptr, const uint8_t num_bytes, const utils::VariantFieldType &type)
	Constructor with bcf1_t structure and start and end pointers of the array/vector. More...

	IndividualFieldValueIterator (const std::shared_ptr< bcf1_t > &body, uint8_t *data_ptr, const uint8_t num_bytes, const utils::VariantFieldType &type)
	Constructor with bcf1_t structure and start pointer of the array/vector. More...

	IndividualFieldValueIterator (const IndividualFieldValueIterator &other)
	copy constructor is only meant for internal STL functions use. It makes a shallow copy of the underlying object which is sufficient for an iterator, but not exactly what a user would expect (user should expect copy constructors to make deep copies). But a deep copied iterator makes no sense. More...

	IndividualFieldValueIterator (IndividualFieldValueIterator &&other) noexcept
	copy constructor is only meant for internal STL functions use. It makes a shallow copy of the underlying object which is sufficient for an iterator, but not exactly what a user would expect (user should expect copy constructors to make deep copies). But a deep copied iterator makes no sense. More...

IndividualFieldValueIterator &	operator= (const IndividualFieldValueIterator &other)
	copy constructor is only meant for internal STL functions use. It makes a shallow copy of the underlying object which is sufficient for an iterator, but not exactly what a user would expect (user should expect copy constructors to make deep copies). But a deep copied iterator makes no sense. More...

IndividualFieldValueIterator &	operator= (IndividualFieldValueIterator &&other) noexcept
	safely moves the data from one VariantField to a new one without making any copies More...

IndividualFieldValueIterator &	operator+= (const int n)
	simple compound assignment operation for random advances (back/forward) to the iterator More...

IndividualFieldValueIterator &	operator-= (const int n)
	simple compound assignment operation for random advances (back/forward) to the iterator More...

bool	operator== (const IndividualFieldValueIterator &other)
	two iterators are equal if they are in exactly the same state (pointing at the same location in memory More...

bool	operator!= (const IndividualFieldValueIterator &other)
	the oposite check of IndividualFieldValueIterator::operator==() More...

bool	operator< (const IndividualFieldValueIterator &other)
	an operator is greater/less than another iterator if it is pointing to a previous element (sample) in the FormatField object. The order is determined by the Variant record. More...

bool	operator> (const IndividualFieldValueIterator &other)
	an operator is greater/less than another iterator if it is pointing to a previous element (sample) in the FormatField object. The order is determined by the Variant record. More...

bool	operator<= (const IndividualFieldValueIterator &other)
	an operator is greater/less than another iterator if it is pointing to a previous element (sample) in the FormatField object. The order is determined by the Variant record. More...

bool	operator>= (const IndividualFieldValueIterator &other)
	an operator is greater/less than another iterator if it is pointing to a previous element (sample) in the FormatField object. The order is determined by the Variant record. More...

VALUE_TYPE	operator* () const noexcept
	direct access to the value of the current sample More...

VALUE_TYPE	read_and_cache_current_pointee () noexcept

IndividualFieldValueIterator &	operator++ () noexcept
	advances to the next sample More...

IndividualFieldValueIterator	operator++ (int) noexcept
	postfix operator to advance iterator to the next position More...

IndividualFieldValueIterator &	operator-- ()
	advances to the previous sample More...

IndividualFieldValueIterator	operator-- (int) noexcept
	postfix operator to retreat iterator to the previous position More...

VALUE_TYPE	operator[] (const uint32_t index) const
	random access to the value of a given index for reading or writing More...

Detailed Description

template<class VALUE_TYPE>
class gamgee::IndividualFieldValueIterator< VALUE_TYPE >

iterator for FormatFieldGenericValue objects.

This iterator will walk through all the values for a sample for a given FormatFieldGenericValue object. For example if you want to iterate over all the GQ values of a Variant record you would do so through this iterator.

Note: implements a random access iterator which gives you full performance on STL algorithms that use iterators (mostly every one); this iterator never makes any copies of the underlying memory. It is implemented with pointer acrobatics behind the scenes for maximum performance while maintaining a friendly interface.

Warning: modifying any elements via this iterator will modify the values in the Variant record.

Constructor & Destructor Documentation

template<class VALUE_TYPE >

gamgee::IndividualFieldValueIterator< VALUE_TYPE >::IndividualFieldValueIterator	(	const std::shared_ptr< bcf1_t > &	body,
		uint8_t *	data_ptr,
		uint8_t *	end_ptr,
		const uint8_t	num_bytes,
		const utils::VariantFieldType &	type
	)

inlineexplicit

Constructor with bcf1_t structure and start and end pointers of the array/vector.

Parameters

body	a pointer to the bcf1_t data structure to be held as a shared pointer
data_ptr	the byte array containing the value(s) for this sample
end_ptr	pointer to the end of the byte array
num_bytes	number of bytes in each value
type	the encoding of the value

Note: this constructor is probably only used by IndividualFieldValue::begin() and IndividualFieldValue::end()

template<class VALUE_TYPE >

gamgee::IndividualFieldValueIterator< VALUE_TYPE >::IndividualFieldValueIterator	(	const std::shared_ptr< bcf1_t > &	body,
		uint8_t *	data_ptr,
		const uint8_t	num_bytes,
		const utils::VariantFieldType &	type
	)

inlineexplicit

Constructor with bcf1_t structure and start pointer of the array/vector.

Parameters

body	a pointer to the bcf1_t data structure to be held as a shared pointer
data_ptr	the byte array containing the value(s) for this sample
num_bytes	number of bytes in each value
type	the encoding of the value

Note: this constructor is probably only used by IndividualFieldValue::begin() and IndividualFieldValue::end()

template<class VALUE_TYPE >

gamgee::IndividualFieldValueIterator< VALUE_TYPE >::IndividualFieldValueIterator ( const IndividualFieldValueIterator< VALUE_TYPE > & other )

inline

copy constructor is only meant for internal STL functions use. It makes a shallow copy of the underlying object which is sufficient for an iterator, but not exactly what a user would expect (user should expect copy constructors to make deep copies). But a deep copied iterator makes no sense.

Warning: does not deep copy the underlying data! (but the copied iterator will be able to navigate independentely).

template<class VALUE_TYPE >

gamgee::IndividualFieldValueIterator< VALUE_TYPE >::IndividualFieldValueIterator ( IndividualFieldValueIterator< VALUE_TYPE > && other )

inlinenoexcept

copy constructor is only meant for internal STL functions use. It makes a shallow copy of the underlying object which is sufficient for an iterator, but not exactly what a user would expect (user should expect copy constructors to make deep copies). But a deep copied iterator makes no sense.

Warning: does not deep copy the underlying data! (but the copied iterator will be able to navigate independentely).

Member Function Documentation

template<class VALUE_TYPE >

bool gamgee::IndividualFieldValueIterator< VALUE_TYPE >::operator!= ( const IndividualFieldValueIterator< VALUE_TYPE > & other )

inline

the oposite check of IndividualFieldValueIterator::operator==()

template<class VALUE_TYPE >

VALUE_TYPE gamgee::IndividualFieldValueIterator< VALUE_TYPE >::operator* ( ) const

inlinenoexcept

direct access to the value of the current sample

Returns: the value in its native type

template<class VALUE_TYPE >

IndividualFieldValueIterator& gamgee::IndividualFieldValueIterator< VALUE_TYPE >::operator++ ( )

inlinenoexcept

advances to the next sample

Note: mainly designed for iterators

Warning: does not check for bounds exception, you should verify whether or not you've reached the end by comparing the result of operator* with end(). This is the STL way.

Returns: modified iterator

template<class VALUE_TYPE >

IndividualFieldValueIterator gamgee::IndividualFieldValueIterator< VALUE_TYPE >::operator++ ( int )

inlinenoexcept

postfix operator to advance iterator to the next position

Note: mainly designed for iterators

Warning: does not check for bounds exception, you should verify whether or not you've reached the end by comparing the result of operator* with end(). This is the STL way.

Returns: copy of iterator at current position (before the increment)

template<class VALUE_TYPE >

IndividualFieldValueIterator& gamgee::IndividualFieldValueIterator< VALUE_TYPE >::operator+= ( const int n )

inline

simple compound assignment operation for random advances (back/forward) to the iterator

Parameters

n	how much to advance (negative numbers to go the other direction)

Warning: there is no boundary check in this operator

template<class VALUE_TYPE >

IndividualFieldValueIterator& gamgee::IndividualFieldValueIterator< VALUE_TYPE >::operator-- ( )

inline

advances to the previous sample

Note: mainly designed for iterators

Warning: does not check for bounds exception, you should verify whether or not you've reached the end by comparing the result of operator* with end(). This is the STL way.

Returns: modified iterator

template<class VALUE_TYPE >

IndividualFieldValueIterator gamgee::IndividualFieldValueIterator< VALUE_TYPE >::operator-- ( int )

inlinenoexcept

postfix operator to retreat iterator to the previous position

Note: mainly designed for iterators

Warning: does not check for bounds exception, you should verify whether or not you've reached the end by comparing the result of operator* with end(). This is the STL way.

Returns: copy of iterator at current position (before the decrement)

template<class VALUE_TYPE >

IndividualFieldValueIterator& gamgee::IndividualFieldValueIterator< VALUE_TYPE >::operator-= ( const int n )

inline

simple compound assignment operation for random advances (back/forward) to the iterator

Parameters

n	how much to advance (negative numbers to go the other direction)

Warning: there is no boundary check in this operator

template<class VALUE_TYPE >

bool gamgee::IndividualFieldValueIterator< VALUE_TYPE >::operator< ( const IndividualFieldValueIterator< VALUE_TYPE > & other )

inline

an operator is greater/less than another iterator if it is pointing to a previous element (sample) in the FormatField object. The order is determined by the Variant record.

template<class VALUE_TYPE >

bool gamgee::IndividualFieldValueIterator< VALUE_TYPE >::operator<= ( const IndividualFieldValueIterator< VALUE_TYPE > & other )

inline

an operator is greater/less than another iterator if it is pointing to a previous element (sample) in the FormatField object. The order is determined by the Variant record.

template<class VALUE_TYPE >

IndividualFieldValueIterator& gamgee::IndividualFieldValueIterator< VALUE_TYPE >::operator= ( const IndividualFieldValueIterator< VALUE_TYPE > & other )

inline

copy constructor is only meant for internal STL functions use. It makes a shallow copy of the underlying object which is sufficient for an iterator, but not exactly what a user would expect (user should expect copy constructors to make deep copies). But a deep copied iterator makes no sense.

Warning: does not deep copy the underlying data! (but the copied iterator will be able to navigate independentely).

template<class VALUE_TYPE >

IndividualFieldValueIterator& gamgee::IndividualFieldValueIterator< VALUE_TYPE >::operator= ( IndividualFieldValueIterator< VALUE_TYPE > && other )

inlinenoexcept

safely moves the data from one VariantField to a new one without making any copies

Parameters

other another VariantField object

template<class VALUE_TYPE >

bool gamgee::IndividualFieldValueIterator< VALUE_TYPE >::operator== ( const IndividualFieldValueIterator< VALUE_TYPE > & other )

inline

two iterators are equal if they are in exactly the same state (pointing at the same location in memory

template<class VALUE_TYPE >

bool gamgee::IndividualFieldValueIterator< VALUE_TYPE >::operator> ( const IndividualFieldValueIterator< VALUE_TYPE > & other )

inline

an operator is greater/less than another iterator if it is pointing to a previous element (sample) in the FormatField object. The order is determined by the Variant record.

template<class VALUE_TYPE >

bool gamgee::IndividualFieldValueIterator< VALUE_TYPE >::operator>= ( const IndividualFieldValueIterator< VALUE_TYPE > & other )

inline

an operator is greater/less than another iterator if it is pointing to a previous element (sample) in the FormatField object. The order is determined by the Variant record.

template<class VALUE_TYPE >

VALUE_TYPE gamgee::IndividualFieldValueIterator< VALUE_TYPE >::operator[] ( const uint32_t index ) const

inline

random access to the value of a given index for reading or writing

Parameters

index must be between 0 and the number of indices for this record but no boundary check is done in this implementation

Note: implementation guarantees this operation to be O(1)

Warning: does not check for bounds exception, you should verify whether or not you've reached the end by comparing the result of operator* with end(). This is the STL way.

Returns: the value in it's native type

template<class VALUE_TYPE >

VALUE_TYPE gamgee::IndividualFieldValueIterator< VALUE_TYPE >::read_and_cache_current_pointee ( )

inlinenoexcept

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

gamgee/variant/individual_field_value_iterator.h

Public Member Functions

Detailed Description

template<class VALUE_TYPE> class gamgee::IndividualFieldValueIterator< VALUE_TYPE >

Constructor & Destructor Documentation

Member Function Documentation

template<class VALUE_TYPE>
class gamgee::IndividualFieldValueIterator< VALUE_TYPE >