RetroSearch Browse

);

225 while

(curIt != readerData.end()) {

226 auto

line(curIt->mData);

231

pos += fixedStepInfo.

mStep

;

241

TReaderData::const_iterator& curIt,

251 while

(curIt != readerData.end()) {

252 auto

line(curIt->mData);

274

(m_iFlags & fAsByte) ? (ret += rows) : (ret += 8*rows);

288 for

(

size_t i

= 1;

; ++

) {

304 for

(

size_t i

= 1;

; ++

) {

315 const int

range = 255;

326 for

(

size_t i

= 1;

; ++

) {

327 if

(

m_Values

[

].m_Pos == nv.back().GetEnd() &&

328 m_Values

[

].m_Value == nv.back().m_Value ) {

329

nv.back().m_Span +=

m_Values

[

].m_Span;

335 if

( nv.size() !=

) {

371

interval.

SetId

(chrom_id);

384 table

->SetFeat_type(0);

391 table

->SetColumns().push_back(col_id);

392

col_id->

().SetField_name(

"Seq-table location"

);

398 table

->SetColumns().push_back(col_id);

407

seq_id.reserve(

);

410

seq_id.push_back(pId);

417 table

->SetColumns().push_back(col_pos);

432 table

->SetColumns().push_back(col_span);

433

col_span->

().SetField_name(

"span"

);

438

span_ptr = &col_span->

SetData

().SetInt();

439

span_ptr->reserve(

);

445 table

->SetColumns().push_back(col_step);

446

col_step->

().SetField_name(

"value_gap"

);

452 table

->SetColumns().push_back(col_min);

453

col_min->

().SetField_name(

"value_min"

);

457 table

->SetColumns().push_back(col_step);

458

col_step->

().SetField_name(

"value_step"

);

462 table

->SetColumns().push_back(col_val);

463

col_val->

().SetField_name(

"values"

);

466

values.reserve(

);

468

pos.push_back(it->m_Pos);

470

span_ptr->push_back(it->m_Span);

472

values.push_back(stat.

AsByte

(it->m_Value));

477 table

->SetColumns().push_back(col_val);

478

col_val->

().SetField_name(

"values"

);

480

values.reserve(

);

483

pos.push_back(it->m_Pos);

485

span_ptr->push_back(it->m_Span);

487

values.push_back(it->m_Value);

502

graph->

SetLoc

(*graph_loc);

510 if

(!trackName.empty()) {

535 TSeqPos

pos = it->m_Pos - start;

539 size_t i

= pos / stat.

m_Span

;

540 int

v = stat.

AsByte

(it->m_Value);

541 for

( ; span > 0; span -= stat.

m_Span

, ++

) {

554 const char

* ptr = line.c_str();

556 for

(

size_t len

= line.size(); skip <

; ++skip ) {

558 if

( c !=

' '

&& c !=

'\t'

) {

562

line = line.substr(skip);

563 return

!line.empty();

571 const char

* ptr = line.c_str();

573 for

(

size_t len

= line.size(); skip <

; ++skip ) {

575 if

( c ==

' '

|| c ==

'\t'

) {

582 "Identifier expected"

);

585 string

word(ptr, skip);

586

line = line.substr(skip);

595 const char

* ptr = line.c_str();

597 for

(

size_t len

= line.size(); skip <

; ++skip ) {

600 string

name(ptr, skip);

601

line = line.substr(skip+1);

604 if

( c ==

' '

|| c ==

'\t'

) {

619 const char

* ptr = line.c_str();

620 size_t len

= line.size();

621 if

(

&& *ptr ==

'"'

) {

623 for

( ; pos <

; ++pos ) {

626 string value

(ptr, pos);

627

line = line.substr(pos+1);

647 "Integer value expected"

);

649 char

c = line.c_str()[0];

650 if

( c < '0' || c >

'9'

) {

655 const char

* ptr = line.c_str();

656 for

(

size_t

skip = 0; ; ++skip ) {

658 if

( c >=

'0'

&& c <=

'9'

) {

659

ret = ret*10 + (c-

'0'

);

661 else if

( (c ==

' '

|| c ==

'\t'

|| c ==

'\0'

) && skip ) {

662

line = line.substr(skip);

679 const char

* ptr = line.c_str();

681 bool

negate =

false

, digits =

false

;

693 if

( c >=

'0'

&& c <=

'9'

) {

695

ret = ret*10 + (c-

'0'

);

697 else if

( c ==

'.'

) {

701 else if

( c ==

'\0'

) {

716 double

digit_mul = 1;

719 if

( c >=

'0'

&& c <=

'9'

) {

722

ret += (c-

'0'

)*digit_mul;

724 else if

( (c ==

' '

|| c ==

'\t'

|| c ==

'\0'

) && digits ) {

726

v = (negate ? -ret : ret);

744 const char

* ptr = line.c_str();

746

v = strtod(ptr, &endptr);

747 if

( endptr == ptr ) {

750 "Floating point value expected"

);

756 "Extra text on line"

);

802 const string

& chrom)

847 "Invalid track type"

);

854

TReaderData::const_iterator& curIt,

858 auto

firstLine(curIt->mData);

874

TReaderData::const_iterator& curIt,

878 auto

firstLine(curIt->mData);

893 const string

& directive,

901 "Track \"type=wiggle_0\" is required"

);

909 auto

line(directive.substr(

string

(

"fixedStep"

).size() + 1));

911

fixedStepInfo.

Reset

();

915 if

(name ==

"chrom"

) {

919 if

(name ==

"start"

) {

921 if

(0 == fixedStepInfo.

) {

924 "Bad start value: must be positive. Assuming \"start=1\""

);

926

fixedStepInfo.

= 1;

930 if

(name ==

"step"

) {

934 if

(name ==

"span"

) {

940 "Bad parameter name. Ignored"

);

943 if

(fixedStepInfo.

mChrom

.empty()) {

946 "Missing chrom parameter"

);

949 if

(fixedStepInfo.