#include <IndexRangeList.h>

Collaboration diagram for IntaRNA::IndexRangeList:

[legend]

Public Types
typedef List::iterator	iterator

typedef List::const_iterator	const_iterator

typedef List::reverse_iterator	reverse_iterator

typedef List::const_reverse_iterator	const_reverse_iterator

Public Member Functions
	IndexRangeList (const bool allowOverlap=false)

	IndexRangeList (const std::string &stringEncoding, const bool allowOverlap=false, const RnaSequence *seq=NULL, const bool isComplete=false)

	IndexRangeList (const IndexRangeList &toCopy)

virtual	~IndexRangeList ()

bool	covers (const size_t index) const

bool	covers (const size_t from, const size_t to) const

bool	covers (const IndexRange &range) const

bool	overlaps (const IndexRange &range) const

void	push_back (const IndexRange &range)

iterator	insert (const IndexRange &range)

IndexRange &	get (const size_t idx)

const IndexRange &	get (const size_t idx) const

iterator	erase (iterator i)

iterator	begin ()

iterator	end ()

const_iterator	begin () const

const_iterator	end () const

reverse_iterator	rbegin ()

reverse_iterator	rend ()

const_reverse_iterator	rbegin () const

const_reverse_iterator	rend () const

bool	empty () const

size_t	size () const

void	clear ()

bool	isAllowingOverlap () const

void	fromString (const std::string &stringEncoding, const RnaSequence *seq=NULL)

IndexRangeList	shift (const int indexShift, const size_t indexMax) const

IndexRangeList &	reverseInplace (const size_t seqLength)

IndexRangeList	reverse (const size_t seqLength) const

const bool	operator== (const IndexRangeList &r) const

const bool	operator!= (const IndexRangeList &r) const

void	setComplete (const bool isComplete)

bool	isComplete () const

Static Public Attributes
static const std::string	regexString
	regular expression string (without start/end matching)

static const boost::regex	regex
	regular expression that matches valid IndexRangeList string encodings

Protected Types
typedef std::list< IndexRange >	List
	List of ranges.

Protected Attributes
bool	allowOverlap
	whether or not overlapping ranges are allowed

List	list
	the list of indices

bool	listIsComplete
	whether or not the list is complete, i.e. cannot be extended

Friends
std::ostream &	operator<< (std::ostream &out, const IndexRangeList &l)

Detailed Description

Sorted list of ascending ranges that can be constrained to be non-overlapping

Author: Martin Mann

Member Typedef Documentation

◆ const_iterator

typedef List::const_iterator IntaRNA::IndexRangeList::const_iterator

◆ const_reverse_iterator

typedef List::const_reverse_iterator IntaRNA::IndexRangeList::const_reverse_iterator

◆ iterator

typedef List::iterator IntaRNA::IndexRangeList::iterator

◆ List

typedef std::list< IndexRange > IntaRNA::IndexRangeList::List

protected

List of ranges.

◆ reverse_iterator

typedef List::reverse_iterator IntaRNA::IndexRangeList::reverse_iterator

Constructor & Destructor Documentation

◆ IndexRangeList() [1/3]

IntaRNA::IndexRangeList::IndexRangeList ( const bool allowOverlap = false )

inline

empty construction

Parameters

allowOverlap whether or not overlapping ranges are allowed

◆ IndexRangeList() [2/3]

IntaRNA::IndexRangeList::IndexRangeList	(	const std::string &	stringEncoding,
		const bool	allowOverlap = `false`,
		const RnaSequence *	seq = `NULL`,
		const bool	isComplete = `false`
	)

inline

String encoding based construction

Parameters

stringEncoding	the string encoding to be parsed
allowOverlap	whether or not overlapping ranges are allowed
seq	if not NULL, the RnaSequence to be used to shift in/output indices to 0-based internal index positions
isComplete	whether or not the list is complete (no further ranges can be added)

Exceptions

std::runtime_error if stringEncoding does not match regex

◆ IndexRangeList() [3/3]

IntaRNA::IndexRangeList::IndexRangeList ( const IndexRangeList & toCopy )

inline

copy construction

Parameters

toCopy the list to make this a copy of

◆ ~IndexRangeList()

IntaRNA::IndexRangeList::~IndexRangeList ( )

inlinevirtual

destruction

Member Function Documentation

◆ begin() [1/2]

IndexRangeList::iterator IntaRNA::IndexRangeList::begin ( )

inline

Access to the first index range within the list

Returns: the begin of the list

◆ begin() [2/2]

IndexRangeList::const_iterator IntaRNA::IndexRangeList::begin ( ) const

inline

Constant access to the first index range within the list

Returns: the begin of the list

◆ clear()

void IntaRNA::IndexRangeList::clear ( )

inline

Removes all stored elements

◆ covers() [1/3]

bool IntaRNA::IndexRangeList::covers ( const IndexRange & range ) const

checks whether or not a given index range is completely covered by one of the stored index ranges

Parameters

range the index range of interest

Returns: true if range is within one of the index ranges (including boundaries); false otherwise

◆ covers() [2/3]

bool IntaRNA::IndexRangeList::covers	(	const size_t	from,
		const size_t	to
	)		const

inline

checks whether or not a given index range is completely covered by one of the stored index ranges

Parameters

from	the start index of the range of interest
to	the end index of the range of interest

Returns: true if [from,to] is within one of the index ranges (including boundaries); false otherwise

◆ covers() [3/3]

bool IntaRNA::IndexRangeList::covers ( const size_t index ) const

checks whether or not a given index is covered by one of the stored index ranges

Parameters

index the index to check

Returns: true if index is within one of the index ranges (including boundaries); false otherwise

◆ empty()

bool IntaRNA::IndexRangeList::empty ( ) const

inline

Whether or not an index range is present

Returns: true if no index range is stored; false otherwise

◆ end() [1/2]

IndexRangeList::iterator IntaRNA::IndexRangeList::end ( )

inline

Access to the end of the index range iteration

Returns: the end of the list

◆ end() [2/2]

IndexRangeList::const_iterator IntaRNA::IndexRangeList::end ( ) const

inline

Constant access to the end of the index range iteration

Returns: the end of the list

◆ erase()

IndexRangeList::iterator IntaRNA::IndexRangeList::erase ( IndexRangeList::iterator i )

inline

removes an element from the list

Parameters

i	the iterator pointing to the element to delete

◆ fromString()

void IntaRNA::IndexRangeList::fromString	(	const std::string &	stringEncoding,
		const RnaSequence *	seq = `NULL`
	)

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

Parameters

stringEncoding	the interval list string encoding
seq	if not NULL, the RnaSequence to be used to shift in/output indices to 0-based internal index positions

Exceptions

std::runtime_error if stringEncoding does not match regex

◆ get() [1/2]

IndexRange & IntaRNA::IndexRangeList::get ( const size_t idx )

access to the stored range with the given index

Parameters

idx	the index of the range within the list to access

Returns: the range for index idx

Exceptions

std::runtime_error if idx >= this.size()

◆ get() [2/2]

const IndexRange & IntaRNA::IndexRangeList::get ( const size_t idx ) const

Constant access to the stored range with the given index

Parameters

idx	the index of the range within the list to access

Returns: the range for index idx (const access)

Exceptions

std::runtime_error if idx >= this.size()

◆ insert()

iterator IntaRNA::IndexRangeList::insert ( const IndexRange & range )

adds an ascending range to the according position of the sorted list. Insertion of duplicates is avoided.

Parameters

range the ascending index range to add

Returns: iterator to the inserted (or already present) element

◆ isAllowingOverlap()

bool IntaRNA::IndexRangeList::isAllowingOverlap ( ) const

inline

Whether or not index ranges are allowed to overlap

Returns: true if ranges are allowed to overlap; false otherwise

◆ isComplete()

bool IntaRNA::IndexRangeList::isComplete ( ) const

inline

Whether or not the list is complete, i.e. cannot be extended

Returns: true if the list is complete; false otherwise

◆ operator!=()

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

inline

Checks whether or not two range lists are inequivalent

Parameters

r	the range list to compare to

Returns: list != r.list

◆ operator==()

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

inline

Checks whether or not two range lists are equivalent

Parameters

r	the range list to compare to

Returns: list == r.list

◆ overlaps()

bool IntaRNA::IndexRangeList::overlaps ( const IndexRange & range ) const

checks whether or not a given ascending index range is overlapping with at least one of the stored index ranges

Parameters

range the range to check

Returns: true if range is within one of the index ranges (including boundaries); false otherwise

◆ push_back()

void IntaRNA::IndexRangeList::push_back ( const IndexRange & range )

adds an ascending range to the end of the list. NOTE: if the insertion would violate range sorting, an exception is raised

Parameters

range the ascending index range to add (from should be > rbegin()->to)

◆ rbegin() [1/2]

IndexRangeList::reverse_iterator IntaRNA::IndexRangeList::rbegin ( )

inline

Access to the last index range within the list

Returns: the begin of the list

◆ rbegin() [2/2]

IndexRangeList::const_reverse_iterator IntaRNA::IndexRangeList::rbegin ( ) const

inline

Constant access to the last index range within the list

Returns: the begin of the list

◆ rend() [1/2]

IndexRangeList::reverse_iterator IntaRNA::IndexRangeList::rend ( )

inline

Access to the end of the reversed index range iteration

Returns: the end of the list

◆ rend() [2/2]

IndexRangeList::const_reverse_iterator IntaRNA::IndexRangeList::rend ( ) const

inline

Constant access to the end of the reversed index range iteration

Returns: the end of the list

◆ reverse()

IndexRangeList IntaRNA::IndexRangeList::reverse ( const size_t seqLength ) const

inline

Reverses all indices for the given sequence length, i.e. (newIdx = seqLength-1-oldIdx)

◆ reverseInplace()

IndexRangeList & IntaRNA::IndexRangeList::reverseInplace ( const size_t seqLength )

Reverses all indices for the given sequence length, i.e. (newIdx = seqLength-1-oldIdx)

◆ setComplete()

void IntaRNA::IndexRangeList::setComplete ( const bool isComplete )

inline

Sets whether or not the list is complete, i.e. cannot be extended

Parameters

isComplete true if the list is complete; false otherwise

◆ shift()

IndexRangeList IntaRNA::IndexRangeList::shift	(	const int	indexShift,
		const size_t	indexMax
	)		const

shifts all indices by the given value and returns all intervals within the boundaries [0,indexMax] including indexMax

Parameters

indexShift	the shift to be applied to all index range boundaries
indexMax	the maximal value any index in the returned list can have

Returns: a new range list with shifted ranges where all ranges shifted to indices below 0 are (I) removed if range'.to < 0 or (II) cut to range'.from = 0; the same holds respectively for upper bound violations exceeding indexMax.

◆ size()

size_t IntaRNA::IndexRangeList::size ( ) const

inline

The number of index ranges stored

Returns: the number of stored index ranges

Friends And Related Symbol Documentation

◆ operator<<

std::ostream & operator<<	(	std::ostream &	out,
		const IndexRangeList &	l
	)

friend

Prints the boundaries of the list's ranges to stream

Parameters

out	the ostream to write to
l	the IndexRangeList object to add

Returns: the altered stream out

Member Data Documentation

◆ allowOverlap

bool IntaRNA::IndexRangeList::allowOverlap

protected

whether or not overlapping ranges are allowed

◆ list

List IntaRNA::IndexRangeList::list

protected

the list of indices

◆ listIsComplete

bool IntaRNA::IndexRangeList::listIsComplete

protected

whether or not the list is complete, i.e. cannot be extended

◆ regex

const boost::regex IntaRNA::IndexRangeList::regex

static

regular expression that matches valid IndexRangeList string encodings

◆ regexString

const std::string IntaRNA::IndexRangeList::regexString

static

regular expression string (without start/end matching)

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

src/IntaRNA/IndexRangeList.h

Public Types

Public Member Functions

Static Public Attributes

Protected Types

Protected Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ const_iterator

◆ const_reverse_iterator

◆ iterator

◆ List

◆ reverse_iterator

Constructor & Destructor Documentation

◆ IndexRangeList() [1/3]

◆ IndexRangeList() [2/3]

◆ IndexRangeList() [3/3]

◆ ~IndexRangeList()

Member Function Documentation

◆ begin() [1/2]

◆ begin() [2/2]

◆ clear()

◆ covers() [1/3]

◆ covers() [2/3]

◆ covers() [3/3]

◆ empty()

◆ end() [1/2]

◆ end() [2/2]

◆ erase()

◆ fromString()

◆ get() [1/2]

◆ get() [2/2]

◆ insert()

◆ isAllowingOverlap()

◆ isComplete()

◆ operator!=()

◆ operator==()

◆ overlaps()

◆ push_back()

◆ rbegin() [1/2]

◆ rbegin() [2/2]

◆ rend() [1/2]

◆ rend() [2/2]

◆ reverse()

◆ reverseInplace()

◆ setComplete()

◆ shift()

◆ size()

Friends And Related Symbol Documentation

◆ operator<<

Member Data Documentation

◆ allowOverlap

◆ list

◆ listIsComplete

◆ regex

◆ regexString