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NCBI C++ ToolKit: include/util/range_set.hpp Source File

1 #ifndef UTIL___RANGE_SET__HPP 2 #define UTIL___RANGE_SET__HPP 44 template

<

class

Range,

class

Position>

50  bool operator()

(

const

Range &R1,

const

Range &R2)

const

{

return

R1.GetToOpen() < R2.GetToOpen(); }

61 template

<

class

Position>

78  if

(

r

.NotEmpty() ) {

156

length +=

r

.GetLength();

266  bool

b_contains = it !=

end

() && it->GetFrom() <= pos;

267  return

make_pair(it, b_contains);

273  bool

intersects = it !=

end

() &&

r

.NotEmpty() && it->GetFrom() <

r

.GetToOpen();

274  return

make_pair(it, intersects);

280  bool

contains = it !=

end

() && it->GetFrom() <=

r

.GetFrom() && it->GetToOpen() >=

r

.GetToOpen();

281  return

make_pair(it, contains);

290  if

( it->GetFrom() >= keep_from ) {

295  if

( to_open > keep_from ) {

308  if

( it->GetToOpen() <= trim_at ) {

313  if

( from < trim_at ) {

339  if

( pos_from >

r

.GetPositionMin() ) {

341

it_begin =

find

(pos_from-1);

342  if

( it_begin ==

m_Ranges

.

end

() || it_begin->GetFrom() > pos_to_open ) {

347  if

( it_begin->GetFrom() < pos_from ) {

348

pos_from = it_begin->GetFrom();

352  while

( it_begin !=

m_Ranges

.

end

() && it_begin->GetFrom() <= pos_to_open ) {

353  if

( it_begin->GetToOpen() > pos_to_open ) {

354

pos_to_open = it_begin->GetToOpen();

367  if

( it !=

m_Ranges

.

end

() && it->GetFrom() <

r

.GetFrom() ) {

372  while

( it !=

m_Ranges

.

end

() && it->GetFrom() <

r

.GetToOpen() ) {

375  if

( pos_to_open >

r

.GetToOpen() ) {

386

c_iterator = c.

begin

();

387  while

(my_iterator !=

end

() && c_iterator != c.

end

()) {

390

intersection_ranges.

insert

(intersection);

391  if

(my_iterator->GetTo() < c_iterator->GetTo())

396  m_Ranges

= std::move(intersection_ranges);

405  if

( from_pos <= p && to_pos > p) {

423  const TRange

& rr = *add_it;

439  if

( it->GetFrom() >= stop_pos ) {

const_reverse_iterator rend() const

void x_Subtract(const TRange &r)

PRangeLessPos2< TRange, position_type > TLess

position_type GetFrom() const

pair< const_iterator, bool > x_Intersects(const TRange &r) const

const_iterator end() const

position_type GetCoveredLength(void) const

Returns total length covered by ranges in this collection, i.e.

TThisType & operator+=(const TRange &r)

pair< const_iterator, bool > x_Find(position_type pos) const

set< TRange, TLess > TRanges

TThisType & IntersectWith(const TRange &r)

CRangeSet(const TRange &r)

TThisType & Subtract(const TRange &r)

iterator find_nc(position_type pos)

pair< const_iterator, bool > x_Contains(const TRange &r) const

TThisType & operator-=(const TRange &r)

void x_IntersectWith(const TRange &r)

bool Contains(const TRange &r) const

TRanges::iterator iterator

position_type GetToOpen() const

void x_TrimStartingWith(position_type trim_at)

TThisType & CombineWithAndKeepAbutting(const TThisType &c)

TRanges::const_reverse_iterator const_reverse_iterator

void x_IntersectWith(const TThisType &c)

TRanges::const_iterator const_iterator

position_type GetTo() const

const_iterator find(position_type pos) const

TThisType & CombineWith(const TRange &r)

TRanges::size_type size_type

bool IntersectingWith(const TRange &r) const

TThisType & IntersectWith(const TThisType &c)

TThisType & Subtract(const TThisType &c)

void x_Divide(const position_type &p)

void x_CombineWithAndKeepAbutting(const TThisType &c)

position_type GetLength(void) const

const_reverse_iterator rbegin() const

void x_TrimBefore(position_type keep_from)

TThisType & operator&=(const TRange &r)

COpenRange< position_type > TOpenRange

const_iterator begin() const

void x_Subtract(const TThisType &c)

void x_CombineWith(const TThisType &c)

CRangeSet< position_type > TThisType

TThisType & CombineWith(const TThisType &c)

TRanges::reverse_iterator reverse_iterator

TThisType & DivideAfter(const position_type &p)

If position is in middle of range, divide into two consecutive ranges after this position.

iterator x_CombineWith(const TRange &r)

CRange< position_type > TRange

iterator_bool insert(const value_type &val)

const_iterator begin() const

parent_type::iterator iterator

const_iterator end() const

const_iterator lower_bound(const key_type &key) const

parent_type::size_type size_type

parent_type::const_iterator const_iterator

Include a standard set of the NCBI C++ Toolkit most basic headers.

static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

bool NotEmpty(void) const

TThisType IntersectionWith(const TThisType &r) const

static TThisType GetEmpty(void)

static position_type GetEmptyFrom(void)

static position_type GetEmptyTo(void)

static position_type GetEmptyToOpen(void)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TFrom GetFrom(void) const

Get the From member data.

The NCBI C++/STL use hints.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

bool operator()(const Range &R, Position Pos) const

bool operator()(const Range &R1, const Range &R2) const

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