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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/bedgraph__writer_8cpp_source.html below:

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

66 unsigned int

colCount,

67 unsigned int

uFlags ) :

95 if

(!track.

(annot)) {

111 "BedGraph writer does not support this annotation type."

);

128 int

numRows =

.GetNum_rows();

129 for

(

int row

=0;

< numRows; ++

) {

134 "Processing terminated by user"

);

139 const

vector<CRef<CSeqTable_column> >

=

.GetColumns();

140 for

(

size_t

col = 0; col <

.size(); ++col) {

144 if

(fieldName ==

"Seq-table location"

) {

160 if

(chromId.empty()) {

161

chromId =

"unknown"

;

167 const

vector<CRef<CSeqTable_column> >

=

.GetColumns();

168 for

(

size_t

col = 0; col <

.size(); ++col) {

173 if

(

[col]->TryGetInt(

, chromStart)) {

184 const

vector<CRef<CSeqTable_column> >

=

.GetColumns();

185 for

(

size_t

col = 0; col <

.size(); ++col) {

189 if

(fieldName ==

"span"

) {

190 if

(

[col]->TryGetInt(

, chromEnd)) {

191

chromEnd += chromStart;

199 if

(

[col]->TryGetInt(

, chromEnd)) {

208 double

chromValue(0);

210 const

vector<CRef<CSeqTable_column> >

=

.GetColumns();

211 for

(

size_t

col = 0; col <

.size(); ++col) {

215 if

(fieldName ==

"values"

) {

216 if

(

[col]->TryGetReal(

, chromValue)) {

220 if

(

[col]->TryGetInt(

, intValue)) {

221

chromValue = intValue;

243 const

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

().

();

251

cerr << except.

() << endl;

269

cit != features.end();

275

cerr << except.

() << endl;

310 "Processing terminated by user"

);

320 "BedGraph writer does not support feature locations that are not intervals."

);

324 const string

& scoreStr = feature.

(

"score"

);

325 if

(scoreStr.empty()) {

329 "BedGraph writer only supports features with a \"score\" qualifier."

);

339 "BedGraph writer encountered feature with bad \"score\" qualifier."

);

362 location

.GetId()->GetLabel(&chromId);

363 size_t

chromStep = graph.

();

364 double

scale = graph.

();

370 for

(

size_t

valIndex = 0; valIndex < numValues; ++valIndex) {

375 "Processing terminated by user"

);

380 size_t

recordStart = valIndex * chromStep;

383 size_t

recordEnd = recordStart + chromStep - 1;

401 location

.GetId()->GetLabel(&chromId);

402 size_t

chromStep = graph.

();

403 double

scale = graph.

();

409 for

(

size_t

valIndex = 0; valIndex < numValues; ++valIndex) {

414 "Processing terminated by user"

);

419 size_t

recordStart = valIndex * chromStep;

422 size_t

recordEnd = recordStart + chromStep;

425 double value

=

+ scale*(

unsigned

char)values[valIndex];

441 location

.GetId()->GetLabel(&chromId);

442 size_t

chromStep = graph.

();

443 double

scale = graph.

();

449 for

(

size_t

valIndex = 0; valIndex < numValues; ++valIndex) {

454 "Processing terminated by user"

);

459 size_t

recordStart = valIndex * chromStep;

462 size_t

recordEnd = recordStart + chromStep - 1;

static CRef< CScope > m_Scope

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.

Encapsulation of the BED feature record.

void SetChromId(const string &)

void SetChromStart(size_t)

bool Write(CNcbiOstream &)

void SetChromValue(double)

bool xWriteAnnotFeatureTable(const CBedTrackRecord &, const CSeq_annot &)

bool xWriteSingleGraphReal(const CBedTrackRecord &, const CSeq_graph &)

virtual ~CBedGraphWriter()

bool xWriteSingleGraph(const CBedTrackRecord &, const CSeq_graph &)

bool xWriteAnnotGraphs(const CBedTrackRecord &, const CSeq_annot &)

bool xWriteSingleFeature(const CBedTrackRecord &, const CSeq_feat &)

bool xWriteSingleGraphByte(const CBedTrackRecord &, const CSeq_graph &)

bool xWriteSingleGraphInt(const CBedTrackRecord &, const CSeq_graph &)

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

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

CBedGraphWriter(CScope &scope, CNcbiOstream &ostr, unsigned int colCount=12, unsigned int flags=fNormal)

Constructor.

bool xWriteAnnotSeqTable(const CBedTrackRecord &, const CSeq_annot &)

Encapsulation of a track line in the BED file format.

bool Assign(const CSeq_annot &)

bool Write(CNcbiOstream &)

bool IsSeq_table(void) const

bool IsFtable(void) const

namespace ncbi::objects::

const string & GetNamedQual(const CTempString &qual_name) const

Return a named qualifier.

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

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.

const string & GetMsg(void) const

Get 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.

@ 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 double StringToDouble(const CTempStringEx str, TStringToNumFlags flags=0)

Convert string to double.

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

const TLocation & GetLocation(void) const

Get the Location member data.

const TId & GetId(void) const

Get the Id member data.

TFrom GetFrom(void) const

Get the From member data.

TTo GetTo(void) const

Get the To member data.

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.

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 IsByte(void) const

Check if variant Byte is selected.

const TValues & GetValues(void) const

Get the Values member data.

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 TGraph & GetGraph(void) const

Get the variant data.

const TSeq_table & GetSeq_table(void) const

Get the variant data.

const TFtable & GetFtable(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

#define row(bind, expected)

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