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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seq__masker__istat__bin_8cpp_source.html below:

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

50  case eFormat

:

return "file format error"

;

60  Uint4

arg_use_max_count,

62  Uint4

arg_use_min_count,

65

arg_max_count, arg_use_max_count,

66

arg_min_count, arg_use_min_count )

85  char

*

data

(

new char

[skip] );

86

in_stream.read(

data

, skip );

90

streamsize adj( in_stream.tellg() );

92

in_stream.read( (

char

*)&

data

,

sizeof

(

Uint4

) );

95

in_stream.read( (

char

*)&

data

,

sizeof

(

Uint4

) );

98  if

( us == 0 || us > 16 )

107  if

( datalen%(2*

sizeof

(

Uint4

)) != 0 )

114

cdata =

new Uint4

[datalen/

sizeof

(

Uint4

)];

115

in_stream.read( (

char

*)cdata, datalen );

120

in_stream.read( (

char

*)&

data

,

sizeof

(

Uint4

) );

124

in_stream.read( (

char

*)&

data

,

sizeof

(

Uint4

) );

129

in_stream.read( (

char

*)&

data

,

sizeof

(

Uint4

) );

134

in_stream.read( (

char

*)&

data

,

sizeof

(

Uint4

) );

Exceptions that CSeqMaskerIstatBin might throw.

@ eStreamOpenFail

File open failure.

@ eFormat

File format error.

virtual const char * GetErrCodeString() const override

Get a description string for this exception.

CSeqMaskerIstatBin(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 skip=0)

Object constructor.

virtual Uint4 at(Uint4 unit) const

Get the count of the given unit.

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.

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.

void add_info(const Uint4 *arg_unit_data, Uint4 sz)

Add unit counts information to the container.

Uint4 get_info(Uint4 unit) const

Lookup the count value for a given unit.

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.

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

static const streamsize HEADER_LEN

static const streamsize TRAILER_LEN

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