RetroSearch Browse

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blast__tabular_8cpp_source.html below:

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

52

TParent(seq_align, save_xcript)

56

TCoord spaces (0), gaps (0), aln_len (0);

57 if

(seq_align_segs.IsDenseg()) {

61 const CDense_seg

& ds (seq_align_segs.GetDenseg());

64 for

(

size_t i

(0), dim (lens.size());

i

< dim; ++

i

) {

65 if

(starts[2*

i

] == -1 || starts[2*

i

+1] == -1) {

72 else if

(seq_align_segs.IsStd()) {

84 if

(stdsegs.empty()) {

86 "CBlastTabular(): Cannot init off of an empty seq-align."

);

93 if

(locs.size() != 2) {

95 "Unexpected std-seg alignment"

);

100 if

(

> 0 &&

> 0) {

107 if

(

[0] &&

[1]) {

109

ratio = (6*

[0])/

[1];

115

}

else if

(ratio < 12) {

116

scale[0] = scale[1] = 1;

135 if

(

[0] == 0) {

136 if

(

[1] == 0) {

138 "CBlastTabular(): Empty std-segs not expected."

);

142

aln_len += increment;

147 else if

(

[1] == 0) {

149

aln_len += increment;

154

aln_len +=

[0] / scale[0];

166 if

(seq_align.

(

"bit_score"

, score) ==

false

) {

167

score = 2.f * aln_len;

169

SetScore(

float

(score));

171 int

raw_score = (

)score;

173

SetRawScore((TCoord)raw_score);

176 if

(seq_align.

(

"num_ident"

, matches) ==

false

) {

177

matches = aln_len - spaces;

179

SetIdentity(

float

(matches / aln_len));

183

SetMismatches(aln_len - spaces - TCoord(matches));

186 if

(seq_align.

(

"e_value"

, evalue) ==

false

) {

196 const CSeq_loc

& row_loc (*locs[where]);

199 if

(row_loc.

()) {

201 bool

disc_seg_found (

false

);

206

disc_seg_found =

true

;

208 delta

[where] = 1 + row_start - row_stop;

209 prev

[where] = row_stop;

215

disc_seg_found =

true

;

217 delta

[where] = 1 + row_stop - row_start;

218 prev

[where] = row_stop;

221 if

(disc_seg_found) {

223 "CBlastTabular(): discontiguous std-segs not expected"

);

234 const TId

& idsubj,

sstart,

bool

sstrand,

235 const string

& xcript):

236 TParent

(idquery, qstart, qstrand, idsubj, sstart, sstrand, xcript)

243 switch

(xcript[

i

]) {

245 case 'M'

: ++matches; diag =

true

;

break

;

246 case 'I'

:

case 'D'

:

if

(diag) {diag =

false

; ++

; }

break

;

258 class

CLocalSeqIdCreator {

285 class

CBestSeqIdExtractor {

288

m_score_func(score_func) {}

322 const char

* p0 = m8, *p = p0;

323 for

(; *p &&

((

unsigned char

)(*p)); ++p);

324 for

(p0 = p; *p && !

((

unsigned char

)(*p)); ++p);

326 const string

id1 (p0, p - p0);

327 m_Id

.first = seq_id_extractor(id1);

330 for

(; *p &&

((

unsigned char

)(*p)); ++p);

331 for

(p0 = p; *p && !

((

unsigned char

)(*p)); ++p);

334 const string

id2 (p0, p - p0);

335 m_Id

.second = seq_id_extractor(id2);

338 if

(

.first.IsNull() ||

.second.IsNull()) {

341 "Unable to recognize sequence IDs in " 345 for

(; *p &&

((

unsigned char

)(*p)); ++p);

474 double

identity100, evalue, score;

477

>>

a

>>

b

>> c >> d >> evalue >> score;

479 if

(iss.fail() ==

false

) {

486 if

(

a

> 0 &&

b

> 0 && c > 0 && d > 0) {

495 "Coordinates in m8 string are expected to be one-based: " 506 "Failed to init from m8 string: " 518 #ifdef ALGO_ALIGN_UTIL_BT_MM_INCLUDED 531 bool

m =

false

, mm =

false

;

532 TCoord

mcnt = 0, mmcnt = 0;

536 if

(c ==

'D'

|| c ==

'I'

) {

539

matches += mcnt == 0? 1: mcnt;

543

mismatches += mcnt == 0? 1: mmcnt;

547 else if

(c ==

'M'

) {

551 else if

(c ==

'R'

) {

555 else if

(

'0'

<= c && c <=

'9'

) {

557

mcnt = 10*mcnt + c -

'0'

;

560

mmcnt = 10*mmcnt + c -

'0'

;

565 "Unexpected transcript symbol."

);

569

matches += mcnt == 0? 1: mcnt;

572

mismatches += mmcnt == 0? 1: mmcnt;

576 SetLength

(matches + mismatches + indels);

584 const double

kq = double(trlen_new) / trlen_old;

595 const double

kq = double(query_span_new) / query_span_old;

TCoord GetQueryStart(void) const

TCoord GetSubjStop(void) const

std::pair< TId, TId > m_Id

static string s_RunLengthDecode(const string &in)

virtual void Modify(Uint1 point, TCoord new_pos)

TCoord GetSubjStart(void) const

void SetSubjStart(TCoord pos)

TCoord GetQueryStop(void) const

void SetQueryStart(TCoord pos)

void SetSubjStop(TCoord pos)

TCoord GetQuerySpan(void) const

const TTranscript & GetTranscript(void) const

void SetQueryStop(TCoord pos)

void SetMismatches(TCoord mismatches)

void SetLength(TCoord length)

float GetScore(void) const

void SetRawScore(TCoord score)

void SetEValue(double evalue)

void SetScore(float score)

virtual void Modify(Uint1 where, TCoord new_pos)

TCoord GetLength(void) const

TCoord GetGaps(void) const

virtual void x_PartialSerialize(CNcbiOstream &os) const

int(* SCORE_FUNC)(const CRef< objects::CSeq_id > &id)

Construct CBlastTabular from m8 line, use score_func to select seq-id from FASTA-style ids.

void SetIdentity(float identity)

float GetIdentity(void) const

virtual void x_PartialDeserialize(const char *m8)

TCoord GetMismatches(void) const

void x_Deserialize(const char *m8, F seq_id_extractor)

double GetEValue(void) const

static void sx_MineSegment(size_t where, const objects::CStd_seg::TLoc &locs, TSeqPos *delta, TSeqPos *prev)

TCoord GetRawScore(void) const

void SetGaps(TCoord gaps)

bool GetNamedScore(const string &id, int &score) const

Get score.

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

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

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

static SIZE_TYPE ParseFastaIds(CBioseq::TId &ids, const CTempString &s, bool allow_partial_failure=false)

Parse an entire set of |-delimited FASTA-style IDs, appending the results to IDS.

ENa_strand GetStrand(void) const

Get the location's strand.

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

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

void Reset(void)

Reset reference object.

uint8_t Uint1

1-byte (8-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

TStr & SetStr(void)

Select the variant.

vector< CRef< CSeq_loc > > TLoc

list< CRef< CStd_seg > > TStd

vector< TSignedSeqPos > TStarts

const TSegs & GetSegs(void) const

Get the Segs member data.

TFrom GetFrom(void) const

Get the From member data.

TLocal & SetLocal(void)

Select the variant.

TTo GetTo(void) const

Get the To member data.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

list< CRef< CSeq_id > > TId

unsigned int

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

#define F(x)

Make a parametrized function appear to have only one variable.

Useful/utility classes and methods.

Int4 delta(size_t dimension_, const Int4 *score_)

static const sljit_gpr r1

static const sljit_gpr r0

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4