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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/align__shadow_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/align/util/align_shadow.cpp Source File

50 typedef

pair<objects::ENa_strand, objects::ENa_strand> TStrands;

53

TStrands RetrieveStdStrands(

const

objects::CSeq_align& seq_align)

58 const CStd_seg

& stdseg (*(std_list.front()));

69 if

(seq_align.CheckNumRows() != 2) {

71 "Pairwise seq-align required to init align-shadow"

);

74 const bool

is_denseg (seq_align.GetSegs().IsDenseg());

75 const bool

is_stdseg (seq_align.GetSegs().IsStd());

76 if

(!is_denseg && !is_stdseg) {

78 "Must be a dense-seg or std_seg to init align-shadow"

);

81 m_Id

.first.Reset(&seq_align.GetSeq_id(0));

82 m_Id

.second.Reset(&seq_align.GetSeq_id(1));

88

qstrand = seq_align.GetSeqStrand(0);

89

sstrand = seq_align.GetSeqStrand(1);

92 const

TStrands strands (RetrieveStdStrands(seq_align));

93

qstrand = strands.first;

94

sstrand = strands.second;

98 m_Box

[1] = seq_align.GetSeqStart(0);

99 m_Box

[0] = seq_align.GetSeqStop(0);

102 m_Box

[0] = seq_align.GetSeqStart(0);

103 m_Box

[1] = seq_align.GetSeqStop(0);

107 m_Box

[3] = seq_align.GetSeqStart(1);

108 m_Box

[2] = seq_align.GetSeqStop(1);

111 m_Box

[2] = seq_align.GetSeqStart(1);

112 m_Box

[3] = seq_align.GetSeqStop(1);

120 const CDense_seg

& ds (seq_align.GetSegs().GetDenseg());

125 const char

indel[2] = {

'D'

'I'

};

128 for

(

size_t

j: {0,1}) {

130 while

(

< starts.size() && starts[

]==-1)

+= 2;

131 next

[j] = starts[

];

133 next

[j] += lens[

/2];

139 for

(

size_t

ii_lens = 0; ii_lens < lens.size(); ++ii_lens) {

142 for

(

size_t

j: {0,1}) {

143 if

(starts[

+j] != -1) {

146 if

(

[j] != end) {

150 next

[j] = starts[

+j];

152 if

(

[j] != starts[

+j]) {

156 next

[j] = starts[

+j] + lens[ii_lens];

161 if

(starts[

] < 0) {

164 else if

(starts[

+1] < 0) {

171 if

(lens[ii_lens] > 1) {

180 "CAlignShadow(): save_xcript mode not supported " 181 "for seq-align segments other than dense-seg."

);

194 const TId

& idsubj,

TCoord

sstart,

bool

sstrand,

195 const string

& xcript)

197 m_Id

.first = idquery;

198 m_Id

.second = idsubj;

203 TCoord

q = qstart, q0 = q, s = sstart, s0 = s;

204 const int

qinc (qstrand? 1: -1), sinc (sstrand? 1: -1);

206 ITERATE

(

string

, ii, xcript) {

210 case 'M'

case 'R'

229 "CAlignShadow()::CAlignShadow(): " 230 "Unexpected transcript symbol found"

);

245

os << align_shadow.

GetId

(0)->AsFastaString() <<

'\t' 246

<< align_shadow.

GetId

(1)->AsFastaString() <<

'\t'

;

261 case

return m_Id

.first;

262 case

return m_Id

.second;

265 "CAlignShadow::GetId() - argument out of range"

);

286 case

m_Id

.first = id;

break

;

287 case

m_Id

.second = id;

break

;

290 "CAlignShadow::SetId() - argument out of range"

);

311 if

(0 != where && where != 1) {

313 "CAlignShadow::GetStrand() - argument out of range"

);

337 if

(0 != where && where != 1) {

339 "CAlignShadow::SetStrand() - argument out of range"

);

343 const Uint1

i1 (where << 1), i2 (i1 + 1);

345 if

(

m_Box

[i1] == g_UndefCoord ||

m_Box

[i2] == g_UndefCoord) {

347 "CAlignShadow::SetStrand() -start and/or stop not yet set"

);

350 const bool

cur_strand (

GetStrand

(where));

351 if

(strand != cur_strand) {

409 if

(0 != where && where != 1) {

411 "CAlignShadow::GetStart() - argument out of range"

);

415 return m_Box

[where << 1];

422 if

(0 != where && where != 1) {

424 "CAlignShadow::GetStop() - argument out of range"

);

428 return m_Box

[(where << 1) | 1];

459 if

(0 != where && where != 1) {

461 "CAlignShadow::GetStart() - argument out of range"

);

472 if

(0 != where && where != 1) {

474 "CAlignShadow::GetStop() - argument out of range"

);

512 if

(0 != where && where != 1) {

514 "CAlignShadow::GetMin() - argument out of range"

);

518 Uint1

i1 = where << 1, i2 = i1 + 1;

526 if

(0 != where && where != 1) {

528 "CAlignShadow::GetMax() - argument out of range"

);

532 Uint1

i1 = where << 1, i2 = i1 + 1;

540 if

(0 != where && where != 1) {

542 "CAlignShadow::SetMin() - argument out of range"

);

546 const Uint1

i1 (where << 1), i2 (i1 + 1);

548 if

(

m_Box

[i1] == g_UndefCoord ||

m_Box

[i2] == g_UndefCoord) {

550 "CAlignShadow::SetMin() - start and/or stop not yet set"

);

562 "CAlignShadow::SetMin() - new position is invalid"

);

572 if

(0 != where && where != 1) {

574 "CAlignShadow::SetMax() - argument out of range"

);

578 const Uint1

i1 (where << 1), i2 (i1 + 1);

580 if

(

m_Box

[i1] == g_UndefCoord ||

m_Box

[i2] == g_UndefCoord) {

582 "CAlignShadow::SetMax() - start and/or stop not yet set"

);

594 "CAlignShadow::SetMax() - new position is invalid"

);

681 m_Box

[0] += shift_query;

682 m_Box

[1] += shift_query;

683 m_Box

[2] += shift_subj;

684 m_Box

[3] += shift_subj;

716 bool

newpos_invalid =

false

;

718 if

(new_pos < qmin || new_pos > qmax) {

719

newpos_invalid =

true

;

723 if

(new_pos < smin || new_pos > smax) {

724

newpos_invalid =

true

;

728 if

(newpos_invalid) {

730 "CAlignShadow::Modify(): requested new position invalid"

);

733 const bool

same_strands = qstrand == sstrand;

741 Int1

dq = (qstrand? +1: -1), ds = (sstrand? +1: -1);

745 bool

need_trace =

true

;

747 if

(q == new_pos) need_trace =

false

;

750 if

(s == new_pos) need_trace =

false

;

753 const bool

point_is_start((point%2) ^ (

GetStrand

(point/2)? 1: 0));

761 case 'M'

case 'R'

: q += dq; s += ds;

break

;

762 case 'D'

: q += dq;

break

;

763 case 'I'

: s += ds;

break

;

766 "CAlignShadow::Modify(): unexpected transcript symbol"

);

770 if

(point_is_start) {

772 if

(q == new_pos)

break

;

775 if

(s == new_pos)

break

;

780 if

(q == new_pos + dq)

break

;

783 if

(s == new_pos + ds)

break

;

788 if

(!point_is_start && n1 > 0) {

790 case 'M'

case 'R'

: q -= dq; s -= ds;

break

;

791 case 'D'

: q -= dq;

break

;

792 case 'I'

: s -= ds;

break

;

817 "CAlignShadow::Modify(): Invalid end point requested."

);

821 if

( point_is_start ) {

822

xcript = xcript.substr(n1, xcript.size() - n1);

837 TCoord

qlen = 1 + qmax - qmin, slen = 1 + smax - smin;

838 double

k = double(qlen) / slen;

839 Int4

delta_q, delta_s;

844

delta_q = new_pos - qmin;

846 if

( smin + delta_s > smax ) {

847

delta_s = smax - smin;

862

delta_q = qmax - new_pos;

864 if

( smin + delta_s > smax ) {

865

delta_s = smax - smin;

880

delta_s = new_pos - smin;

882 if

( qmin + delta_q > qmax ) {

883

delta_q = qmax - qmin;

898

delta_s = smax - new_pos;

900 if

( qmin + delta_q > qmax ) {

901

delta_q = qmax - qmin;

916 "CAlignShadow::Modify(): invalid end requested"

);

925 const size_t

dim (

.size());

930 const char

* p (

.data());

934 for

(

size_t

k (1); k < dim; ++k) {

970 if

(

'0'

<= c && c <=

'9'

) {

971 N

* 10 + c -

'0'

;

975 out

.append(

- 1,

);

978 out

.push_back(

= c);

982 out

.append(

- 1,

);

CNcbiOstream & operator<<(CNcbiOstream &os, const CAlignShadow &align_shadow)

void SetId(Uint1 where, const TId &id)

bool GetQueryStrand(void) const

void SetQueryMax(TCoord pos)

TCoord GetQueryStart(void) const

void SetQueryMin(TCoord pos)

TCoord GetSubjStop(void) const

void SetStop(Uint1 where, TCoord pos)

std::pair< TId, TId > m_Id

const TCoord * GetBox(void) const

static string s_RunLengthDecode(const string &in)

TCoord GetMin(Uint1 where) const

virtual void Modify(Uint1 point, TCoord new_pos)

const TId & GetSubjId(void) const

void SetMax(Uint1 where, TCoord pos)

void SetSubjStrand(bool strand)

void SetQueryStrand(bool strand)

void Shift(Int4 shift_query, Int4 shift_subj)

TCoord GetQueryMin(void) const

void SetSubjId(const TId &id)

TCoord GetSubjStart(void) const

bool GetSubjStrand(void) const

void SetSubjStart(TCoord pos)

void SetSubjMin(TCoord pos)

void SetMin(Uint1 where, TCoord pos)

TCoord GetMax(Uint1 where) const

void SetStart(Uint1 where, TCoord pos)

TCoord GetStop(Uint1 where) const

const TId & GetId(Uint1 where) const

TCoord GetQueryStop(void) const

void SetQueryStart(TCoord pos)

virtual void x_PartialSerialize(CNcbiOstream &os) const

const TId & GetQueryId(void) const

TCoord GetSubjMin(void) const

static string s_RunLengthEncode(const string &in)

void SetSubjStop(TCoord pos)

TCoord GetQueryMax(void) const

TCoord GetQuerySpan(void) const

void SetBox(const TCoord box[4])

void SetQueryId(const TId &id)

void SetStrand(Uint1 where, bool strand)

void SetSubjMax(TCoord pos)

TCoord GetSubjMax(void) const

const TTranscript & GetTranscript(void) const

TCoord GetSubjSpan(void) const

TCoord GetStart(Uint1 where) const

void SetQueryStop(TCoord pos)

bool GetStrand(Uint1 where) const

std::ofstream out("events_result.xml")

main entry point for tests

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

uint8_t Uint1

1-byte (8-bit) unsigned integer

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

int8_t Int1

1-byte (8-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

vector< CRef< CSeq_loc > > TLoc

list< CRef< CStd_seg > > TStd

const TStarts & GetStarts(void) const

Get the Starts member data.

vector< ENa_strand > TStrands

const TLens & GetLens(void) const

Get the Lens member data.

vector< TSignedSeqPos > TStarts

const TStrands & GetStrands(void) const

Get the Strands member data.

ENa_strand

strand of nucleic acid

std::istream & in(std::istream &in_, double &x_)

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

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