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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seq__masker__istat__ascii_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/winmask/seq_masker_istat_ascii.cpp Source File

:

;

:

;

arg_use_max_count,

arg_use_min_count,

arg_max_count, arg_use_max_count,

arg_min_count, arg_use_min_count )

(

) + name );

linenum = start_line;

(

( 0 );

< start_line; ++

) getline( input_stream, line );

( input_stream )

getline( input_stream, line );

( line.length() == 0 )

;

( line[0] ==

)

;

name_end = line.find_first_of(

, 0 );

val_start = line.find_first_not_of(

, name_end );

( name_end ==

|| val_start ==

)

<<

<< linenum;

name = line.substr( 1, name_end - 1 );

( name ==

)

unit_start = line.find_first_not_of(

, 0 );

unit_end = line.find_first_of(

, unit_start );

cnt_start = line.find_first_not_of(

, unit_end );

( unit_start ==

|| unit_end ==

|| cnt_start ==

)

<<

<< linenum;

unit_end - unit_start),

(

< ambig_len ) {

bad_param +=

;

bad_param +=

;

bad_param +=

;

bad_param +=

;

( !bad_param.empty() )

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

Exceptions that CSeqMaskerIstatAscii might throw.

@ eStreamOpenFail

File open failure.

@ eParam

Unknown parameter name.

virtual const char * GetErrCodeString() const override

Get a description string for this exception.

CSeqMaskerUsetSimple uset

virtual Uint4 at(Uint4 unit) const

Get the count of the given unit.

CSeqMaskerIstatAscii(const string &name, Uint4 arg_threshold, Uint4 arg_textend, Uint4 arg_max_count, Uint4 arg_use_max_count, Uint4 arg_min_count, Uint4 arg_use_min_count, Uint4 start_line=0)

Object constructor.

virtual Uint4 trueat(Uint4 unit) const

Get the true count for an n-mer.

Defines an interface for accessing the unit counts information.

Uint4 get_min_count() const

Get the value of T_low.

void set_use_min_count(Uint4 arg_use_min_count)

Set the count value for units with actual counts below T_low.

void set_textend(Uint4 arg_textend)

Set the value of T_extend.

void set_threshold(Uint4 arg_threshold)

Set the value of T_threshold.

void set_use_max_count(Uint4 arg_use_max_count)

Set the count value for units with actual counts above T_high.

Uint4 get_use_max_count() const

Get the count value for units with actual counts above T_high.

Uint4 get_textend() const

Get the value of T_extend.

void set_ambig_unit(const CSeqMaskerWindow::TUnit &arg_ambig_unit)

Set the ambiguity unit value.

Uint4 get_max_count() const

Get the current value of T_high.

Uint4 get_use_min_count() const

Get the count value for units with actual counts below T_low.

void set_min_count(Uint4 arg_min_count)

Set the value of T_low.

Uint4 get_threshold() const

Get the value of T_threshold.

void set_max_count(Uint4 arg_max_count)

Set the value of T_high.

void set_unit_size(Uint1 arg_unit_size)

Set the unit size.

Uint4 get_info(Uint4 unit) const

Lookup the count value for a given unit.

void add_info(Uint4 unit, Uint4 count)

Add information about the given unit.

static const char * str(char *buf, int n)

TErrCode GetErrCode(void) const

Get error code.

#define NCBI_THROW(exception_class, err_code, message)

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

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

NCBI_NS_STD::string::size_type SIZE_TYPE

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

Convert string to unsigned int.

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

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