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NCBI C++ ToolKit: include/objtools/alnmgr/aln_rng_coll_oper.hpp Source File

1 #ifndef OBJTOOLS_ALNMGR__ALN_RNG_COLL_OPER__HPP 2 #define OBJTOOLS_ALNMGR__ALN_RNG_COLL_OPER__HPP 47 template

<

class

TAlnRng>

59  typename

TAlnRngColl::const_iterator subtrahend_it = subtrahend.

begin

();

60  ITERATE

(

typename

TAlnRngColl, minuend_it, minuend) {

70

TAlnRngCollExt subtrahend_ext(subtrahend);

71

subtrahend_ext.UpdateIndex();

73  typename

TAlnRngCollExt::const_iterator subtrahend_ext_it = subtrahend_ext.begin();

74

TAlnRngCollExt diff_on_first_ext(difference_on_first);

75

diff_on_first_ext.UpdateIndex();

76  ITERATE

(

typename

TAlnRngCollExt, minuend_it, diff_on_first_ext) {

85 template

<

class

Range>

91  return r

.GetFirstToOpen() <= pos;

95  return

pos <

r

.GetFirstToOpen();

99  return r1

.GetFirstToOpen() <=

r2

.GetFirstToOpen();

103  return r

->GetFirstToOpen() <= pos;

107  return

pos <

r

->GetFirstToOpen();

111  return r1

->GetFirstToOpen() <=

r2

->GetFirstToOpen();

116 template

<

class

Iter,

class

T,

class

Compare>

129 template

<

class

TAlnRng>

131  const

TAlnRng& minuend,

140

minuend.GetFirstFrom(),

143  if

(r_it == subtrahend.

end

()) {

144

difference.

insert

(minuend);

150

trim = (r_it->

GetFirstFrom

() <= minuend.GetFirstFrom());

161  if

((

int

)

r

.GetLength() <= 0) {

165  if

(r_it == subtrahend.

end

()) {

186

difference.

insert

(tmp_r);

192 template

<

class

TAlnRng>

200  return

p.second->GetSecondTo() < pos;

205  return

pos < p.second->GetSecondTo();

210  return

p1.second->GetSecondTo() < p2.second->GetSecondTo();

215 template

<

class

TAlnRng>

217  const

TAlnRng& minuend,

222  if

(minuend.GetSecondFrom() < 0) {

223

difference.

insert

(minuend);

230

subtrahend_ext.end(),

231

minuend.GetSecondFrom(),

234  if

(r_it == subtrahend_ext.end()) {

235

difference.

insert

(minuend);

241

trim = (r_it->second->GetSecondFrom() <= minuend.GetSecondFrom());

250

trim = r_it->second->GetSecondToOpen() -

r

.GetSecondFrom();

252  if

((

int

)

r

.GetLength() <= 0) {

256  if

(r_it == subtrahend_ext.end()) {

264

trim =

r

.GetSecondToOpen() - r_it->second->GetSecondFrom();

277

difference.

insert

(tmp_r);

283 template

<

class

TAlnRng>

286

rng.SetLength(rng.GetLength() - trim);

287

rng.SetFirstFrom(rng.GetFirstFrom() + trim);

288  if

(rng.IsDirect()) {

289

rng.SetSecondFrom(rng.GetSecondFrom() + trim);

294 template

<

class

TAlnRng>

297  if

(rng.IsReversed()) {

298

rng.SetSecondFrom(rng.GetSecondFrom() + trim);

300

rng.SetLength(rng.GetLength() - trim);

303 template

<

class

TAlnRng>

306

rng.SetLength(rng.GetLength() - trim);

307

rng.SetSecondFrom(rng.GetSecondFrom() + trim);

308  if

(rng.IsDirect()) {

309

rng.SetFirstFrom(rng.GetFirstFrom() + trim);

313 template

<

class

TAlnRng>

316  if

(rng.IsReversed()) {

317

rng.SetFirstFrom(rng.GetFirstFrom() + trim);

319

rng.SetLength(rng.GetLength() - trim);

void TrimSecondTo(TAlnRng &rng, int trim)

void SubtractAlnRngCollections(const CAlignRangeCollection< TAlnRng > &minuend, const CAlignRangeCollection< TAlnRng > &subtrahend, CAlignRangeCollection< TAlnRng > &difference)

Subtract one range collection from another.

void TrimFirstFrom(TAlnRng &rng, int trim)

void TrimFirstTo(TAlnRng &rng, int trim)

void SubtractOnFirst(const TAlnRng &minuend, const CAlignRangeCollection< TAlnRng > &subtrahend, CAlignRangeCollection< TAlnRng > &difference, typename CAlignRangeCollection< TAlnRng >::const_iterator &r_it)

Iter scan_to_lower_bound(Iter first, Iter last, const T &value, Compare comp)

void SubtractOnSecond(const TAlnRng &minuend, const CAlignRangeCollExtender< CAlignRangeCollection< TAlnRng > > &subtrahend_ext, CAlignRangeCollection< TAlnRng > &difference, typename CAlignRangeCollExtender< CAlignRangeCollection< TAlnRng > >::const_iterator &r_it)

void TrimSecondFrom(TAlnRng &rng, int trim)

class CAlignRangeCollection<TAlignRange> represent a sorted collection of TAlignRange.

TAlignRangeVector::const_iterator const_iterator

int GetPolicyFlags() const

position_type GetFirstToOpen() const

position_type GetFirstFrom() const

const_iterator insert(const TAlignRange &r)

const_iterator end() const

const_iterator begin() const

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

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static DLIST_TYPE *DLIST_NAME() last(DLIST_LIST_TYPE *list)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

sequence::ECompare Compare(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)

Returns the sequence::ECompare containment relationship between CSeq_locs.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

double value_type

The numeric datatype used by the parser.

const GenericPointer< typename T::ValueType > T2 value

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

static const sljit_gpr r1

static const sljit_gpr r2

TAlnRng::position_type position_type

CAlignRangeCollExtender< CAlignRangeCollection< TAlnRng > >::TFrom2Range::value_type value_type

bool operator()(const value_type &p, position_type pos)

bool operator()(const Range &r1, const Range &r2)

bool operator()(const Range &r, position_type pos)

bool operator()(const Range *r1, const Range *r2)

Range::position_type position_type

bool operator()(const Range *r, position_type pos)

bool operator()(position_type pos, const Range *r)

bool operator()(position_type pos, const Range &r)

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