IntaRNA::IndexRange Class Reference

#include <IndexRange.h>

Public Member Functions
	IndexRange (const size_t from=0, const size_t to=NA_INDEX)
	IndexRange (const std::string &stringEncoding, const RnaSequence *seq)
virtual	~IndexRange ()
bool	isAscending () const
bool	isDescending () const
IndexRange	operator+ (const int shift) const
IndexRange	operator- (const int shift) const
const bool	operator< (const IndexRange &r) const
const bool	operator== (const IndexRange &r) const
const bool	operator!= (const IndexRange &r) const
void	fromString (const std::string &stringEncoding, const RnaSequence *seq)
std::vector< IndexRange >	overlappingWindows (const size_t windowWidth, const size_t windowOverlap) const

Public Attributes
size_t	from
	the start of the index range
size_t	to
	the end of the index range

Static Public Attributes
static const size_t	LAST_INDEX
static const size_t	NA_INDEX
	placeholder for not-defined values
static constexpr const char *	regexString = R"((0|-?[123456789]\d*)-(0|-?[123456789]\d*))"
	regular expression that matches valid IndexRange string encodings
static const boost::regex	regex
	regular expression that matches valid IndexRange string encodings

Friends
std::ostream &	operator<< (std::ostream &out, const IndexRange &range)

Detailed Description

Defines an index region with functionality similar to pair

Author

Martin Mann

Constructor & Destructor Documentation

IndexRange() [1/2]

IntaRNA::IndexRange::IndexRange ( const size_t  from = 0, const size_t  to = NA_INDEX  )

inline

Creates a range

Parameters

from	the start index (default 0)
to	the end index (default NA_INDEX)

IndexRange() [2/2]

IntaRNA::IndexRange::IndexRange ( const std::string &  stringEncoding, const RnaSequence *  seq  )

inline

Creates a range from a string encoding

Parameters

stringEncoding	string encoding of the range as produced by the ostream operator
seq	if not NULL, the RnaSequence to be used to shift the indices of the input string from in/output positions to internal indices

~IndexRange()

virtual IntaRNA::IndexRange::~IndexRange ( )

inlinevirtual

destruction

Member Function Documentation

fromString()

void IntaRNA::IndexRange::fromString ( const std::string &  stringEncoding, const RnaSequence *  seq  )

inline

updates the range data from a valid string encoding (matching regex)

Parameters

stringEncoding

the interval string encoding

Exceptions

std::runtime_error

if stringEncoding does not match regex

isAscending()

bool IntaRNA::IndexRange::isAscending ( ) const

inline

Checks whether or not the range encoding is ascending.

Returns

from <= to

isDescending()

bool IntaRNA::IndexRange::isDescending ( ) const

inline

Checks whether or not the range encoding is descending.

Returns

from >= to

operator!=()

const bool IntaRNA::IndexRange::operator!= ( const IndexRange &  r ) const

inline

Checks whether or not two ranges are different

Parameters

r	the range to compare to

Returns

!( this == r)

operator+()

IndexRange IntaRNA::IndexRange::operator+ ( const int  shift ) const

inline

Adds the given shift to the index range but ensure that the minimal value is 0.

Parameters

r	the range to be added to
shift	the shift to be added to r

Returns

an altered range or (NA_INDEX,NA_INDEX) if the range falls completely below zero or changing from to the lower bound of 0.

operator-()

IndexRange IntaRNA::IndexRange::operator- ( const int  shift ) const

inline

Substracts the given shift to the index range but ensure that the minimal value is 0.

Parameters

r	the range to be altered
shift	the shift to be substracted from r

Returns

an altered range or (NA_INDEX,NA_INDEX) if the range falls completely below zero or changing from to the lower bound of 0.

operator<()

const bool IntaRNA::IndexRange::operator< ( const IndexRange &  r ) const

inline

Checks whether or not the start of this range preceeds the given range.

Parameters

r	the range to compare to

Returns

(from<r.from) || (from==r.from && to<r.to)

operator==()

const bool IntaRNA::IndexRange::operator== ( const IndexRange &  r ) const

inline

Checks whether or not two ranges are equivalent

Parameters

r	the range to compare to

Returns

( from == r.from && to == r.to )

overlappingWindows()

std::vector< IndexRange > IntaRNA::IndexRange::overlappingWindows	(	const size_t	windowWidth,
		const size_t	windowOverlap
	)		const

Computes an overlapping window decomposition of this IndexRange

Parameters

windowWidth	the width of a window
windowOverlap	the amount of overlap between two windows

Returns

a vector of overlapping IndexRanges covering this IndexRange

Friends And Related Symbol Documentation

operator<<

std::ostream & operator<< ( std::ostream &  out, const IndexRange &  range  )

friend

Prints the range's boundaries to stream

Parameters

out	the ostream to write to
range	the IndexRange object to add

Returns

the altered stream out

Member Data Documentation

from

size_t IntaRNA::IndexRange::from

the start of the index range

LAST_INDEX

const size_t IntaRNA::IndexRange::LAST_INDEX

static

placeholder to define the whole range (without explicit naming the last index) is defined

NA_INDEX

const size_t IntaRNA::IndexRange::NA_INDEX

static

placeholder for not-defined values

regex

const boost::regex IntaRNA::IndexRange::regex

static

regular expression that matches valid IndexRange string encodings

regexString

constexpr const char* IntaRNA::IndexRange::regexString = R"((0|-?[123456789]\d*)-(0|-?[123456789]\d*))"

staticconstexpr

regular expression that matches valid IndexRange string encodings

to

size_t IntaRNA::IndexRange::to

the end of the index range

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

• src/IntaRNA/IndexRange.h