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NCBI C++ ToolKit: src/algo/gnomon/select_alignments_alt.cpp Source File

47  if

(

a

.Strand() !=

b

.Strand())

49  if

(

Precede

(

a

.Limits(),

b

.Limits())) {

50  if

(

a

.OpenRightEnd() &&

b

.OpenLeftEnd())

52

}

else if

(

Precede

(

b

.Limits(),

a

.Limits())) {

53  if

(

b

.OpenRightEnd() &&

a

.OpenLeftEnd())

62  if

(

a

.Strand() !=

b

.Strand() || !

a

.IntersectingWith(

b

))

return

commonspl;

63  for

(

size_t i

= 1;

i

<

a

.Exons().

size

(); ++

i

) {

64  for

(

size_t

j = 1; j <

b

.Exons().

size

(); ++j) {

65  if

(

a

.Exons()[

i

-1].GetTo() ==

b

.Exons()[j-1].GetTo())

67  if

(

a

.Exons()[

i

].GetFrom() ==

b

.Exons()[j].GetFrom() )

78  if

(

a

.Strand() !=

b

.Strand())

81  if

(

a

.ReadingFrame().NotEmpty() &&

b

.ReadingFrame().NotEmpty()) {

82  if

(!

a

.ReadingFrame().IntersectingWith(

b

.ReadingFrame()) ||

a

.GetCdsInfo().PStops() !=

b

.GetCdsInfo().PStops())

85  if

(

a

.Exons().size() == 1 &&

b

.Exons().size()==1) {

88  int

common_point = (acds & bcds).GetFrom();

89  if

(

a

.FShiftedLen(acds.

GetFrom

(),common_point,

false

)%3 !=

b

.FShiftedLen(bcds.

GetFrom

(),common_point,

false

)%3)

99  while

(amin < (

int

)

a

.Exons().size() &&

a

.Exons()[amin].GetTo() < mutual_min) ++amin;

100  if

(amin == (

int

)

a

.Exons().size())

return false

;

102  int

amax = (

int

)

a

.Exons().size()-1;

103  while

(amax >=0 &&

a

.Exons()[amax].GetFrom() > mutual_max) --amax;

104  if

(amax < 0)

return false

;

107  while

(bmin < (

int

)

b

.Exons().size() &&

b

.Exons()[bmin].GetTo() < mutual_min) ++bmin;

108  if

(bmin == (

int

)

b

.Exons().size())

return false

;

110  int bmax

= (

int

)

b

.Exons().size()-1;

111  while

(

bmax

>=0 &&

b

.Exons()[

bmax

].GetFrom() > mutual_max) --

bmax

;

112  if

(

bmax

< 0)

return false

;

114  if

(amax-amin !=

bmax

-bmin)

return false

;

117  if

(amin != 0 ||

size_t

(amax) !=

a

.Exons().size()-1 || bmin != 0 || size_t(

bmax

) !=

b

.Exons().size()-1)

120  for

( ; amin <= amax; ++amin, ++bmin) {

121  if

(

abs

(

max

(mutual_min,

a

.Exons()[amin].GetFrom())-

max

(mutual_min,

b

.Exons()[bmin].GetFrom())) >= tolerance)

123  if

(

abs

(

min

(mutual_max,

a

.Exons()[amin].GetTo())-

min

(mutual_max,

b

.Exons()[bmin].GetTo())) >= tolerance)

132  if

((!

a

.TrustedmRNA().empty() || !

a

.TrustedProt().empty()) && (!

b

.TrustedmRNA().empty() || !

b

.TrustedProt().empty()))

142  for

(

int i

= 1;

i

< (

int

)algn.

Exons

().size(); ++

i

) {

143  if

(check_in_holes || (algn.

Exons

()[

i

-1].m_ssplice && algn.

Exons

()[

i

].m_fsplice)) {

154  if

(

a

.Strand() !=

b

.Strand() || !

a

.IntersectingWith(

b

))

return false

;

156  for

(

unsigned int i

= 0;

i

<

a

.Exons().

size

(); ++

i

) {

157  for

(

unsigned int

j = 0; j <

b

.Exons().

size

(); ++j) {

158  if

(

a

.Exons()[

i

] ==

b

.Exons()[j])

163  for

(

unsigned int i

= 1;

i

<

a

.Exons().

size

(); ++

i

) {

165  for

(

unsigned int

j = 1; j <

b

.Exons().

size

(); ++j) {

167  if

(introna == intronb)

189  bool

gapfilled =

false

;

191  for

(

int

ie = 0; ie < (

int

)model.

Exons

().size(); ++ie) {

192  if

(model.

Exons

()[ie].Limits().Empty())

198  if

(gapfilled && genome_cds < 45) {

200

model.

AddComment

(

"Most CDS in genomic gap"

);

206

bad_aligns.push_back(*it);

CCDSInfo MapFromOrigToEdited(const CAlignMap &amap) const

bool IsMappedToGenome() const

TSignedSeqRange Cds() const

TSignedSeqRange ReadingFrame() const

const TExons & Exons() const

virtual CAlignMap GetAlignMap() const

TSignedSeqRange TranscriptExon(int i) const

void AddComment(const string &comment)

const CCDSInfo & GetCdsInfo() const

void FilterGenes(TGeneModelList &chains, TGeneModelList &bad_aligns, TGeneModelList &dest)

Filters genes, excluding genes flagged to be skipped.

static bool HaveCommonExonOrIntron(const CGeneModel &a, const CGeneModel &b)

static bool RangeNestedInIntron(TSignedSeqRange r, const CGeneModel &algn, bool check_in_holes=true)

static size_t CountCommonSplices(const CGeneModel &a, const CGeneModel &b)

static bool AreSimilar(const CGeneModel &a, const CGeneModel &b, int tolerance)

static bool BadOverlapTest(const CGeneModel &a, const CGeneModel &b)

bool Precede(TSignedSeqRange l, TSignedSeqRange r)

bool Include(TSignedSeqRange big, TSignedSeqRange small)

list< CGeneModel > TGeneModelList

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

unsigned int

A callback function used to compare two keys in a database.

static constexpr streamsize bmax

const struct ncbi::grid::netcache::search::fields::SIZE size

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

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