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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/wig2table_8cpp_source.html below:

NCBI C++ ToolKit: src/app/wig2table/wig2table.cpp Source File

(

)

;

m_BufferSize(32*1024),

m_Buffer(new char[m_BufferSize]),

m_Pos(m_Buffer.get()),

* start =

;

(

* p = start; p < end; ++p ) {

( *p ==

) {

* start =

;

(

* p = start; p < end; ++p ) {

( c ==

|| c ==

) {

( p < end && c ==

&& *p ==

) {

( c ==

&& *p ==

) {

.append(start, end - start);

(

flag =

; flag; ) {

(

);

(

);

(

rows,

fixed_span)

;

arg_desc->SetUsageContext

);

arg_desc->AddDefaultKey

(

,

,

,

arg_desc->AddDefaultKey

(

,

,

,

arg_desc->AddDefaultKey(

,

,

,

arg_desc->SetConstraint(

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

(name ==

) {

}

(name ==

) {

}

(name ==

) {

(runtime_error,

+ name);

(

= 1;

<

; ++

) {

(

= 1;

<

; ++

) {

range = 255;

(

= 1;

<

; ++

) {

(

[

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

[

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

nv.back().m_Span +=

[

].m_Span;

( nv.size() !=

) {

interval.

(chrom_id);

->SetFeat_type(0);

->SetColumns().push_back(col_id);

col_id->

().SetField_name(

);

->SetColumns().push_back(col_id);

->SetColumns().push_back(col_pos);

->SetColumns().push_back(col_span);

col_span->

().SetField_name(

);

span_ptr = &col_span->

().SetInt();

span_ptr->reserve(

);

->SetColumns().push_back(col_step);

col_step->

().SetField_name(

);

->SetColumns().push_back(col_min);

col_min->

().SetField_name(

);

->SetColumns().push_back(col_step);

col_step->

().SetField_name(

);

->SetColumns().push_back(col_val);

col_val->

().SetField_name(

);

values->reserve(

);

pos.push_back(it->m_Pos);

span_ptr->push_back(it->m_Span);

values->push_back(stat.

(it->m_Value));

values.reserve(

);

pos.push_back(it->m_Pos);

span_ptr->push_back(it->m_Span);

values.push_back(stat.

(it->m_Value));

->SetColumns().push_back(col_val);

col_val->

().SetField_name(

);

values.reserve(

);

pos.push_back(it->m_Pos);

span_ptr->push_back(it->m_Span);

values.push_back(it->m_Value);

graph->

(*graph_loc);

pos = it->m_Pos - start;

= pos / stat.

;

v = stat.

(it->m_Value);

( ; span > 0; span -= stat.

, ++

) {

annot->

().Set().push_back(desc);

annot->

().Set().push_back(desc);

annot->

().Set().push_back(desc);

user.

().SetStr(

);

field->

().SetStr(it->first);

field->

().SetStr(it->second);

user.

().push_back(field);

( c !=

&& c !=

) {

( c ==

|| c ==

) {

(

);

( c ==

|| c ==

) {

(

&& *ptr ==

) {

( ; pos <

; ++pos ) {

(

skip = 0; ; ++skip ) {

( c >=

&& c <=

) {

ret = ret*10 + (c-

);

( (c ==

|| c ==

|| c ==

) && skip ) {

(

);

negate =

, digits =

;

( c >=

&& c <=

) {

ret = ret*10 + (c-

);

( c ==

) {

( c ==

) {

digit_mul = 1;

( c >=

&& c <=

) {

ret += (c-

)*digit_mul;

( (c ==

|| c ==

|| c ==

) && digits ) {

v = strtod(ptr, &endptr);

( endptr == ptr ) {

(

);

( c < '0' || c >

) {

(

);

( name ==

) {

(

==

) {

(

==

) {

(

);

( name ==

) {

( name ==

) {

(

);

(

);

( name ==

) {

( name ==

) {

( name ==

) {

( name ==

) {

.m_Pos = start-1;

.m_Span = span;

.m_Pos += step;

(

);

( name ==

) {

( name ==

) {

.m_Span = span;

(

);

( args[

] ) {

args[

].AsString(),

( !args[

].AsString().

() ) {

(

<<args[

].AsString());

);

);

);

args[

].AsOutputFile()));

( args[

] ) {

( s ==

) {

( s ==

) {

( s ==

) {

( s ==

) {

(

argc,

* argv[])

User-defined methods of the data storage class.

User-defined methods of the data storage class.

IdMapper implementation using hardcoded values.

IdMapper implementation using an external configuration file.

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

void ReadBedLine(CTempString chrom)

void x_GetPos(TSeqPos &v)

bool x_TryGetDouble(double &v)

CTempString x_GetParamValue(void)

string m_TrackDescription

CTempString x_GetWord(void)

CRef< CSeq_annot > MakeGraphAnnot(void)

vector< SValueInfo > TValues

void ResetChromValues(void)

CRef< CSeq_annot > m_Annot

bool x_CommentLine(void) const

void SetChrom(CTempString chrom)

bool x_TryGetPos(TSeqPos &v)

void x_SetTotalLoc(CSeq_loc &loc, CSeq_id &chrom_id)

AutoPtr< IIdMapper > m_IdMapper

void x_GetDouble(double &v)

TTrackParams m_TrackParams

CTempString x_GetParamName(void)

CRef< CSeq_annot > MakeTableAnnot(void)

virtual int Run(void)

Run the application.

AutoPtr< CObjectOStream > m_Output

void ReadVariableStep(void)

CRef< CSeq_graph > MakeGraph(void)

void x_Error(const char *msg)

SStat x_PreprocessValues(void)

void DumpChromValues(void)

virtual void Init(void)

Initialize the application.

void AddValue(const SValueInfo &value)

double EstimateSize(size_t rows, bool fixed_span) const

bool x_TryGetDoubleSimple(double &v)

CRef< CSeq_table > MakeTable(void)

map< string, string > TTrackParams

AutoPtr< CWigBufferedLineReader > m_Input

CRef< CSeq_id > x_MakeChromId(void)

CRef< CSeq_annot > MakeAnnot(void)

AutoPtr< IReader > m_Reader

Uint8 GetLineNumber(void) const

CWigBufferedLineReader & operator++(void)

CWigBufferedLineReader(const string &filename)

read from the file, "-" (but not "./-") means standard input

CT_POS_TYPE GetPosition(void) const

virtual ~CWigBufferedLineReader()

AutoArray< char > m_Buffer

CTempStringEx operator*(void) const

virtual void MapObject(CSerialObject &)=0

Map all embedded IDs in a given object at once.

void reset(element_type *p=0, EOwnership ownership=eTakeOwnership)

Reset will delete the old pointer (if owned), set content to the new value, and assume the ownership ...

unsigned int TSeqPos

Type for sequence locations and lengths.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

element_type * get(void) const

Get pointer.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

element_type * release(void)

Release will release ownership of pointer to caller.

@ fPreOpen

Open file right away; for eInputFile, eOutputFile, eIOFile.

@ eInputFile

Name of file (must exist and be readable)

@ eDouble

Convertible into a floating point number (double)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

#define ERR_FATAL(message)

Posting fatal error and abort.

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

@ eDiag_Warning

Warning message.

#define NCBI_THROW(exception_class, err_code, message)

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

void Warning(CExceptionArgs_Base &args)

#define THROW1_TRACE(exception_class, exception_arg)

Throw trace.

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

uint64_t Uint8

8-byte (64-bit) unsigned integer

ERW_Result

Result codes for I/O operations.

virtual ERW_Result Read(void *buf, size_t count, size_t *bytes_read=0)=0

Read as many as "count" bytes into a buffer pointed to by the "buf" argument.

@ eRW_NotImplemented

Action / information is not available.

@ eRW_Eof

End of data, should be considered permanent.

@ eRW_Error

Unrecoverable error, no retry possible.

@ eRW_Timeout

Timeout expired, try again later.

@ eRW_Success

Everything is okay, I/O completed.

CTempStringEx substr(size_type pos) const

Obtain a substring from this string, beginning at a given offset.

const char * data(void) const

Return a pointer to the array represented.

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

void clear(void)

Clear value to an empty string.

static unsigned int StringToUInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned int.

bool HasZeroAtEnd(void) const

CTempStringEx & assign(const char *str, size_type len)

Assign new values to the content of the a string.

size_type size(void) const

Return the length of the represented array.

const_iterator begin() const

Return an iterator to the string's starting position.

TData & SetData(void)

Assign a value to Data data member.

void SetLabel(TLabel &value)

Assign a value to Label data member.

void SetType(TType &value)

Assign a value to Type data member.

void SetData(TData &value)

Assign a value to Data data member.

void SetHeader(THeader &value)

Assign a value to Header data member.

void SetData(TData &value)

Assign a value to Data data member.

void SetDefault(TDefault &value)

Assign a value to Default data member.

@ eField_id_location_id

location Seq-id

@ eField_id_location_from

interval from

void SetTo(TTo value)

Assign a value to To data member.

void SetId(TId &value)

Assign a value to Id data member.

void SetFrom(TFrom value)

Assign a value to From data member.

void SetA(TA value)

Assign a value to A data member.

void SetMin(TMin value)

Assign a value to Min data member.

void SetTitle(const TTitle &value)

Assign a value to Title data member.

void SetNumval(TNumval value)

Assign a value to Numval data member.

void SetComp(TComp value)

Assign a value to Comp data member.

TValues & SetValues(void)

Assign a value to Values data member.

void SetGraph(TGraph &value)

Assign a value to Graph data member.

void SetB(TB value)

Assign a value to B data member.

void SetMax(TMax value)

Assign a value to Max data member.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

void SetAxis(TAxis value)

Assign a value to Axis data member.

TTitle & SetTitle(void)

Select the variant.

void SetData(TData &value)

Assign a value to Data data member.

void SetDesc(TDesc &value)

Assign a value to Desc data member.

TName & SetName(void)

Select the variant.

TUser & SetUser(void)

Select the variant.

unsigned int

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

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

constexpr auto sort(_Init &&init)

constexpr bool empty(list< Ts... >) noexcept

const struct ncbi::grid::netcache::search::fields::SIZE size

Magic spell ;-) needed for some weird compilers... very empiric.

const GenericPointer< typename T::ValueType > T2 value

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

void SetFirstValue(double v)

void AddSpan(TSeqPos span)

void SetFirstSpan(TSeqPos span)

int AsByte(double v) const

bool operator<(const SValueInfo &v) const

TSeqPos GetEnd(void) const

int main(int argc, const char *argv[])

static ESerialDataFormat s_GetFormat(const string &name)

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