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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/wiggle__writer_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/writers/wiggle_writer.cpp Source File

59 #define ROUND(x) int( floor((x)+0.5) ) 69

m_uTrackSize(uTrackSize == 0 ? size_t( -1 ) : uTrackSize)

80

m_uTrackSize(uTrackSize == 0 ? size_t( -1 ) : uTrackSize)

130  const

list< CRef<CSeq_graph> >& graphs = annot.

GetData

().

GetGraph

();

131

list< CRef<CSeq_graph> >::const_iterator it = graphs.begin();

132  while

( it != graphs.end() ) {

183  m_Os

<<

"track type=wiggle_0"

<<

'\n'

;

191  string

strTrackLine(

"track type=wiggle_0"

);

193  const

list<CRef< CAnnotdesc > >&

data

= descr.

Get

();

194

list< CRef< CAnnotdesc > >::const_iterator it =

data

.begin();

195  while

( it !=

data

.end() ) {

196  if

( (*it)->IsName() ) {

197

strTrackLine +=

" name=\""

;

198

strTrackLine += (*it)->GetName();

199

strTrackLine +=

"\""

;

201  if

( ! (*it)->IsUser() ) {

217  const

vector< CRef< CUser_field > >& fields = user.

GetData

();

218  for

(

size_t

u=0; u < fields.size(); ++u ) {

220

strTrackLine +=

" "

;

222

strTrackLine +=

"="

;

229  m_Os

<< strTrackLine <<

'\n'

;

239  string

strFixedStep(

"fixedStep"

);

252  switch

( pId->

Which

() ) {

272

strFixedStep +=

string

(

" chrom="

);

273

strFixedStep += strChrom;

276  string

strStart(

" start="

);

281

uFrom =

location

.GetInt().GetFrom();;

285

strFixedStep += strStart;

288  string

strSpan(

" span="

);

289  string

strStep(

" step="

);

293

strFixedStep += strStep;

295

strFixedStep += strSpan;

297  m_Os

<< strFixedStep <<

'\n'

;

304  size_t

uStartRecord )

316  double

dA = graph.

GetA

();

317  double

dB = graph.

GetB

();

321  for

(

size_t

u=0; u + uStartRecord < uNumVals && u <

m_uTrackSize

; ++u ) {

327  "Processing terminated by user"

);

330  int

iVal = (

unsigned

char)values[u + uStartRecord];

340  size_t

uStartRecord )

352  double

dA = graph.

GetA

();

353  double

dB = graph.

GetB

();

357  for

(

size_t

u=0; u + uStartRecord < uNumVals && u <

m_uTrackSize

; ++u ) {

363  "Processing terminated by user"

);

366  double

dVal = values[u + uStartRecord];

367  m_Os

<< (dA*dVal+dB) <<

'\n'

;

376  size_t

uStartRecord )

388  double

dA = graph.

GetA

();

389  double

dB = graph.

GetB

();

393  for

(

size_t

u=0; u + uStartRecord < uNumVals && u <

m_uTrackSize

; ++u ) {

399  "Processing terminated by user"

);

402  double

dVal = values[u + uStartRecord];

403  m_Os

<< ( dA*dVal+dB ) <<

'\n'

;

412  size_t

uStartRecord )

423  for

(

size_t

u=0; u + uStartRecord < uNumVals && u <

m_uTrackSize

; ++u ) {

424  int

iVal = (

unsigned

char)values[u + uStartRecord];

435  size_t

uStartRecord )

446  for

(

size_t

u=0; u + uStartRecord < uNumVals && u <

m_uTrackSize

; ++u ) {

447  int

iVal = (

unsigned

char)values[u + uStartRecord];

458  size_t

uStartRecord )

469  for

(

size_t

u=0; u + uStartRecord < uNumVals && u <

m_uTrackSize

; ++u ) {

470  int

iVal = (

unsigned

char)values[u + uStartRecord];

495  int

span(0), start(0), step(0);

519

span = start = step = 0;

531

step = currentIn - start;

533  int

numRows =

table

.GetNum_rows();

534  for

(

int i

=1;

i

< numRows-1; ++

i

) {

539  if

(nextIn-currentIn != step) {

560  int

numRows =

table

.GetNum_rows();

567  for

(

int i

=1;

i

< numRows; ++

i

) {

575  const

vector<CRef<CSeqTable_column> >

columns

=

table

.GetColumns();

576  for

(

size_t

u = 0; u <

columns

.size(); ++u) {

580  if

(fieldName ==

"span"

) {

581  for

(

size_t i

=0;

i

< numRows; ++

i

) {

583  if

(!

columns

[u]->TryGetInt(

i

, curspan)) {

589  else if

(curspan != span) {

603  const string

& chromId,

613  string

chrom(chromId);

621  m_Os

<<

"fixedStep chrom="

<< chrom <<

" span="

<< span <<

622  " start="

<< (start+1) <<

" step="

<< step <<

'\n'

;

625  int

numRows =

table

.GetNum_rows();

626  for

(

int i

=0;

i

< numRows; ++

i

) {

632  "Processing terminated by user"

);

647  const string

& chromId,

656  string

chrom(chromId);

664  m_Os

<<

"variableStep chrom="

<< chrom <<

" span="

<< span <<

'\n'

;

667  int

numRows =

table

.GetNum_rows();

668  for

(

int i

=0;

i

< numRows; ++

i

) {

674  "Processing terminated by user"

);

685  m_Os

<< (posIn+1) <<

'\t'

<<

value

<<

'\n'

;

706  int

numRows =

table

.GetNum_rows();

709  for

(

int i

=0;

i

< numRows; ++

i

) {

715  "Processing terminated by user"

);

722  auto

idIt = bestIdCache.

find

(chrom);

723  if

(idIt != bestIdCache.

end

()) {

724

chrom = idIt->second;

730

bestIdCache[chrom] = bestId;

734

bestIdCache[chrom] = chrom;

752 #define BED_AS_VARSTEP 1 754  auto

span = posOut - posIn;

755  if

(span != lastSpan) {

756  m_Os

<<

"variableStep chrom="

<< chrom <<

" span="

<< span <<

'\n'

;

759  m_Os

<< posIn+1 <<

'\t'

<<

value

<<

'\n'

;

761  m_Os

<< chrom <<

'\t'

<< (posIn + 1) <<

'\t'

<< (posOut + 1) <<

'\t'

<<

value

<<

'\n'

;

774  const

vector<CRef<CSeqTable_column> >

columns

=

table

.GetColumns();

775  for

(

size_t

u = 0; u <

columns

.size(); ++u) {

779  if

(fieldName ==

"Seq-table location"

) {

814  const

vector<CRef<CSeqTable_column> >

columns

=

table

.GetColumns();

815  for

(

size_t

u = 0; u <

columns

.size(); ++u) {

820  return

(

columns

[u]->TryGetInt(index, posIn));

835  const

vector<CRef<CSeqTable_column> >

columns

=

table

.GetColumns();

836  for

(

size_t

u = 0; u <

columns

.size(); ++u) {

840  if

(fieldName ==

"span"

) {

841  if

(!

columns

[u]->TryGetInt(index, posOut)) {

851  return

(

columns

[u]->TryGetInt(index, posOut));

865  const

vector<CRef<CSeqTable_column> >

columns

=

table

.GetColumns();

866  for

(

size_t

u = 0; u <

columns

.size(); ++u) {

870  if

(fieldName ==

"values"

) {

873  if

(!

columns

[u]->TryGetInt(index, intValue)) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

bool IsSeq_table(void) const

bool xWriteSingleGraphRecordsReal(const CSeq_graph &, size_t)

bool xIsVariableStepData(const CSeq_table &, string &, int &)

bool xWriteAnnotGraphs(const CSeq_annot &)

bool xWriteTrackLine(const CAnnot_descr &)

bool xWriteSingleGraphRecordsByte(const CSeq_graph &, size_t)

bool xWriteSingleGraphRecordsInt(const CSeq_graph &, size_t)

bool xTableGetValue(const CSeq_table &, int, double &)

bool xTableGetPosIn(const CSeq_table &, int, int &)

bool WriteAnnot(const CSeq_annot &, const string &="", const string &="") override

Write a raw Seq-annot to the internal output stream.

bool xWriteTableFixedStep(const CSeq_table &, const string &, int, int, int)

bool WriteFooter() override

Write a file trailer.

bool xWriteSingleGraph(const CSeq_graph &)

bool xTableGetChromName(const CSeq_table &, int, string &)

bool xWriteTableVariableStep(const CSeq_table &, const string &, int)

bool xTableGetPosOut(const CSeq_table &, int, int, int &)

bool xWriteTableBedStyle(const CSeq_table &)

bool xWriteSingleGraphFixedStep(const CSeq_graph &, size_t)

~CWiggleWriter() override

bool xWriteDefaultTrackLine()

bool xWriteAnnotTable(const CSeq_annot &)

bool xContainsDataInt(const CSeq_graph &, size_t)

bool xContainsDataByte(const CSeq_graph &, size_t)

CWiggleWriter(CScope &, CNcbiOstream &, size_t=0)

bool xIsFixedStepData(const CSeq_table &, string &, int &, int &, int &)

bool xContainsDataReal(const CSeq_graph &, size_t)

Defines and provides stubs for a general interface to a variety of file formatters.

bool GetBestId(CSeq_id_Handle idh, CScope &scope, string &best_id) const

const_iterator end() const

const_iterator find(const key_type &key) const

static const char location[]

static const column_t columns[]

#define NCBI_THROW(exception_class, err_code, message)

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

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

@ eContent

Untagged human-readable accession or the like.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

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.

const TStr & GetStr(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

bool CanGetType(void) const

Check if it is safe to call GetType method.

const TData & GetData(void) const

Get the Data member data.

bool CanGetData(void) const

Check if it is safe to call GetData method.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TLabel & GetLabel(void) const

Get the Label member data.

const TType & GetType(void) const

Get the Type member data.

TField_id GetField_id(void) const

Get the Field_id member data.

bool IsSetField_name(void) const

any column can be identified by ASN.1 text locator string with omitted object type.

bool IsSetField_id(void) const

Check if a value has been assigned to Field_id data member.

const TField_name & GetField_name(void) const

Get the Field_name member data.

@ eField_id_location_id

location Seq-id

@ eField_id_location_to

interval to

@ eField_id_location_from

interval from

E_Choice Which(void) const

Which variant is currently selected.

const TLocal & GetLocal(void) const

Get the variant data.

bool CanGetComp(void) const

Check if it is safe to call GetComp method.

bool CanGetValues(void) const

Check if it is safe to call GetValues method.

bool CanGetNumval(void) const

Check if it is safe to call GetNumval method.

bool CanGetValues(void) const

Check if it is safe to call GetValues method.

bool CanGetA(void) const

Check if it is safe to call GetA method.

const TInt & GetInt(void) const

Get the variant data.

const TGraph & GetGraph(void) const

Get the Graph member data.

bool IsInt(void) const

Check if variant Int is selected.

const TValues & GetValues(void) const

Get the Values member data.

TB GetB(void) const

Get the B member data.

const TByte & GetByte(void) const

Get the variant data.

bool CanGetLoc(void) const

Check if it is safe to call GetLoc method.

const TReal & GetReal(void) const

Get the variant data.

bool IsReal(void) const

Check if variant Real is selected.

const TValues & GetValues(void) const

Get the Values member data.

bool CanGetGraph(void) const

Check if it is safe to call GetGraph method.

bool IsByte(void) const

Check if variant Byte is selected.

bool CanGetValues(void) const

Check if it is safe to call GetValues method.

const TValues & GetValues(void) const

Get the Values member data.

bool CanGetB(void) const

Check if it is safe to call GetB method.

const TLoc & GetLoc(void) const

Get the Loc member data.

TNumval GetNumval(void) const

Get the Numval member data.

TA GetA(void) const

Get the A member data.

TComp GetComp(void) const

Get the Comp member data.

const Tdata & Get(void) const

Get the member data.

const TGraph & GetGraph(void) const

Get the variant data.

const TDesc & GetDesc(void) const

Get the Desc member data.

bool CanGetDesc(void) const

Check if it is safe to call GetDesc method.

const TSeq_table & GetSeq_table(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

const GenericPointer< typename T::ValueType > T2 value

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