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NCBI C++ ToolKit: include/algo/winmask/seq_masker_istat.hpp Source File

: divisor_( divisor/(8*sizeof(

)) ), cba_( cba )

arg_use_max_count,

arg_use_min_count )

: threshold( arg_threshold ),

textend( arg_textend ),

max_count( arg_max_count ),

use_max_count( arg_use_max_count ),

min_count( arg_min_count ),

use_min_count( arg_use_min_count ),

{

ambig_unit; }

{

opt_data_.

== 0 ? 0 : &opt_data_; }

fmt_gen_algo_ver;

fmt_gen_algo_ver = v;

{ threshold = arg_threshold; }

{ textend = arg_textend; }

{ max_count = arg_max_count; }

{ use_max_count = arg_use_max_count; }

( min_count != 0 && min_count < arg_min_count ) {

<<

<<

<< arg_min_count <<

<<

<< arg_min_count

<<

);

min_count = arg_min_count;

( min_count == 0 ) {

min_count = arg_min_count;

fmt_version.get();

{ use_min_count = arg_use_min_count; }

{ unit_size = arg_unit_size; }

{ ambig_unit = arg_ambig_unit; }

{ opt_data_ = opt_data; }

std::vector< double >

&

()

{

count_map; }

major,

minor,

patch ) {

Defines an interface for accessing the unit counts information.

virtual ~CSeqMaskerIstat()

Object destructor.

void SetStatAlgoVersion(CSeqMaskerVersion const &v)

Set the version of the algorithm used to generate counts.

virtual Uint4 trueat(Uint4 unit) const =0

Get the true count for an n-mer.

void SetFmtEncoding(string const &e)

Set the statistics file format encoding.

void SetCountMap(std::vector< double > const &cm)

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.

std::unique_ptr< CComponentVersionInfo > fmt_version

Format version of the statistics file from which the data was read.

std::vector< double > const & GetCountMap() const

CSeqMaskerIstat(Uint4 arg_threshold, Uint4 arg_textend, Uint4 arg_max_count, Uint4 arg_use_max_count, Uint4 arg_min_count, Uint4 arg_use_min_count)

Object constructor.

void set_textend(Uint4 arg_textend)

Set the value of T_extend.

void set_threshold(Uint4 arg_threshold)

Set the value of T_threshold.

CSeqMaskerWindow::TUnit ambig_unit

virtual Uint4 at(Uint4 unit) const =0

Get the unit count of a given unit.

CSeqMaskerVersion fmt_gen_algo_ver

version of the algorithm used to generate counts

string const & GetMetaData() const

Return the metadata string.

void SetMetaData(string const &md)

Set metadata string.

Uint4 GetMaxCount() const

void set_use_max_count(Uint4 arg_use_max_count)

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

CSeqMaskerIstat(const CSeqMaskerIstat &)

Uint4 get_use_max_count() const

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

void SetMaxCount(Uint4 mc)

CSeqMaskerWindow::TUnit AmbigUnit() const

Get the value of the unit used to represent an ambuguity.

CSeqMaskerIstat & operator=(const CSeqMaskerIstat &)

std::vector< double > count_map

void set_optimization_data(const optimization_data &opt_data)

Set optimization parameters.

Uint4 operator[](Uint4 unit) const

Look up the count value of a given unit.

void SetFmtVersion(string const &name, int major, int minor, int patch)

Set the statistics file format version.

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.

CSeqMaskerVersion const & GetStatAlgoVersion() const

Return the version of the algorithm used to generate counts.

optimization_data opt_data_

virtual Uint1 UnitSize() const =0

Get the unit size.

Uint4 get_use_min_count() const

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

CComponentVersionInfo const * GetFmtVersion() const

Return the format version of the source statistics file.

const optimization_data * get_optimization_data() const

Get the data structure optimization parameters.

string const & GetFmtEncoding() const

Return the encoding of the source statistics file.

void set_unit_size(Uint1 arg_unit_size)

Set the unit size.

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.

Base class for computing and saving unit counts data.

Uint4 TUnit

Integer type used to represent units within a window.

The NCBI C++ standard methods for dealing with std::string.

#define ERR_POST(message)

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

void Warning(CExceptionArgs_Base &args)

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define CComponentVersionInfo

#define NCBI_XALGOWINMASK_EXPORT

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

Defines Limits for the types used in NCBI C/C++ toolkit.

Structure containing information about optimization parameters used.

optimization_data(Uint4 divisor, Uint4 *cba)

Object constructor.

Uint4 divisor_

How many units are represented by one 4-byte word in cba_ array.

Uint4 * cba_

Bit array with zeroes where all corresponding units have counts below t_extend.

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