IntaRNA::UpperBandedMatrix< T > Class Template Reference

#include <Matrix.h>

Public Types
using	value_type = T
	Type of one stored cell.

Public Member Functions
	UpperBandedMatrix ()=default
	UpperBandedMatrix (std::size_t rows, std::size_t columns, std::size_t lower, std::size_t upper)
	UpperBandedMatrix (const UpperBandedMatrix &)=default
UpperBandedMatrix &	operator= (const UpperBandedMatrix &)=default
	UpperBandedMatrix (UpperBandedMatrix &&other) noexcept
UpperBandedMatrix &	operator= (UpperBandedMatrix &&other) noexcept
std::size_t	size1 () const noexcept
std::size_t	size2 () const noexcept
std::size_t	storageSize () const noexcept
T &	operator() (std::size_t i, std::size_t j)
const T &	operator() (std::size_t i, std::size_t j) const
std::span< T >	row (std::size_t i)
std::span< const T >	row (std::size_t i) const
void	clear ()
void	swap (UpperBandedMatrix &other) noexcept
void	resize (std::size_t rows, std::size_t newColumns, std::size_t lower, std::size_t upper, bool preserve=true)

Detailed Description

template<class T>
class IntaRNA::UpperBandedMatrix< T >

Upper band including the diagonal and 'upper' superdiagonals. Stores rows * min(columns, upper+1) cells, never a dense square for a narrow band. Logical (i,j) maps to mdspan[i,j-i] in the owning Matrix. Const access outside the band returns zero; writes must be in the band.

Member Typedef Documentation

value_type

template<class T >

using IntaRNA::UpperBandedMatrix< T >::value_type = T

Type of one stored cell.

Constructor & Destructor Documentation

UpperBandedMatrix() [1/4]

template<class T >

IntaRNA::UpperBandedMatrix< T >::UpperBandedMatrix ( )

default

Construct an empty matrix.

UpperBandedMatrix() [2/4]

template<class T >

IntaRNA::UpperBandedMatrix< T >::UpperBandedMatrix ( std::size_t  rows, std::size_t  columns, std::size_t  lower, std::size_t  upper  )

inline

Allocate a default-initialized upper band.

Parameters

rows	logical row count
columns	logical column count
lower	lower bandwidth; must be zero
upper	number of stored superdiagonals

Exceptions

std::invalid_argument	if lower is not zero
std::length_error	if the storage size overflows

UpperBandedMatrix() [3/4]

template<class T >

IntaRNA::UpperBandedMatrix< T >::UpperBandedMatrix ( const UpperBandedMatrix< T > &  )

default

Copy the shape and values into independent storage.

UpperBandedMatrix() [4/4]

template<class T >

IntaRNA::UpperBandedMatrix< T >::UpperBandedMatrix ( UpperBandedMatrix< T > &&  other )

inlinenoexcept

Take ownership of another matrix and leave it empty.

Parameters

other

matrix whose storage is moved

Member Function Documentation

clear()

template<class T >

void IntaRNA::UpperBandedMatrix< T >::clear ( )

inline

Reset stored cells to default values without changing the shape.

operator()() [1/2]

template<class T >

T & IntaRNA::UpperBandedMatrix< T >::operator() ( std::size_t  i, std::size_t  j  )

inline

Access a cell within the stored upper band.

Parameters

i	zero-based row within the logical shape
j	zero-based column within the logical shape

Returns

mutable reference to the cell

operator()() [2/2]

template<class T >

const T & IntaRNA::UpperBandedMatrix< T >::operator() ( std::size_t  i, std::size_t  j  ) const

inline

Read a logical cell; structural zeros are returned outside stored cells.

Parameters

i	zero-based row within the logical shape
j	zero-based column within the logical shape

Returns

read-only reference to the cell

operator=() [1/2]

template<class T >

UpperBandedMatrix & IntaRNA::UpperBandedMatrix< T >::operator= ( const UpperBandedMatrix< T > &  )

default

Copy the shape and values into independent storage.

Returns

this matrix

operator=() [2/2]

template<class T >

UpperBandedMatrix< T > & IntaRNA::UpperBandedMatrix< T >::operator= ( UpperBandedMatrix< T > &&  other )

inlinenoexcept

Take ownership of another matrix; self-move leaves this matrix unchanged.

Parameters

other

matrix whose storage is moved; emptied on a non-self move

Returns

this matrix

resize()

template<class T >

void IntaRNA::UpperBandedMatrix< T >::resize ( std::size_t  rows, std::size_t  newColumns, std::size_t  lower, std::size_t  upper, bool  preserve = true  )

inline

Resize, preserving overlapping logical cells when requested.

Parameters

rows	new row count
newColumns	new column count
lower	lower bandwidth; must be zero
upper	number of stored superdiagonals
preserve	retain overlapping cells and default-initialize new cells; otherwise callers must overwrite cells before reading

Exceptions

std::length_error	if the storage size overflows
std::invalid_argument	if the requested shape or band is unsupported

row() [1/2]

template<class T >

std::span< T > IntaRNA::UpperBandedMatrix< T >::row ( std::size_t  i )

inline

View the contiguous stored cells (i,i), (i,i+1), ... in one row. Excludes structural zeros and row-end padding. The view aliases this matrix and must not outlive its storage or be retained across resize, move, swap or assignment.

Parameters

i	zero-based row, less than size1()

Returns

mutable stored cells; empty when i >= size2() or the band is empty

row() [2/2]

template<class T >

std::span< const T > IntaRNA::UpperBandedMatrix< T >::row ( std::size_t  i ) const

inline

Read-only view of one stored row, with the same bounds and lifetime as row().

Parameters

i	zero-based row, less than size1()

Returns

read-only stored cells, excluding padding and structural zeros

size1()

template<class T >

std::size_t IntaRNA::UpperBandedMatrix< T >::size1 ( ) const

inlinenoexcept

Number of logical rows.

Returns

logical row count

size2()

template<class T >

std::size_t IntaRNA::UpperBandedMatrix< T >::size2 ( ) const

inlinenoexcept

Number of logical columns.

Returns

logical column count

storageSize()

template<class T >

std::size_t IntaRNA::UpperBandedMatrix< T >::storageSize ( ) const

inlinenoexcept

Number of stored elements, including any band padding.

Returns

stored element count

swap()

template<class T >

void IntaRNA::UpperBandedMatrix< T >::swap ( UpperBandedMatrix< T > &  other )

inlinenoexcept

Exchange shape and owned storage.

Parameters

other

matrix to exchange with

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

• src/IntaRNA/Accessibility.h
• src/IntaRNA/Matrix.h