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

= 1024L*1024L;

: out_stream( os ), alloc( alloc ), metadata( metadata ),

fmt_gen_algo_ver( StatAlgoVersion ),

.push_back( unit );

string::size_type pos = name.find_first_of(

);

real_name = name.substr( 0, pos );

(

ind = 0;

ind <

(

)/

(

* ); ++ind )

( real_name ==

[ind] )

(

<<

<< real_name );

vector< Uint4 >::size_type size_type;

(

<< divisor <<

<<

(total/(2048*divisor)) <<

);

size_type

= (size_type)( total/divisor );

( std::exception & e )

fill( *cba, *cba +

, 0 );

( size_type

= 0;

<

.size(); ++

)

& word = (*cba)[unit/divisor];

word |= (1ULL<<(unit%divisor));

& word1 = (*cba)[rcunit/divisor];

word1 |= (1ULL<<(rcunit%divisor));

sz = (k < 32 ? (1ULL<<k) : 0x80000000ULL);

(

= 0;

<= u - k; ++

)

fill( ht, ht + sz, 0 );

j !=

.end(); ++j )

mxcoll[

] = *max_element( ht, ht + sz );

( tc > 0 ) avcoll[

] = (double)

/tc;

avcoll[

] = 0;

* minav = min_element( avcoll, avcoll + u - k + 1 );

roff = (minav - avcoll);

max_coll = mxcoll[roff];

(

);

roff( 0 ), max_coll( 0 );

(

= 0;

< k + 2; ++

) emem *= 2;

(

(

* ) <=

(

) ) {

( k > 8*

(

* ) - 4 )

k = 8*

(

* ) - 4;

);

b0( 0 ), bc( 0 );

sz = (k < 32 ? (1ULL<<k) : 0x80000000ULL);

( (1ULL<<bc) <= max_coll )

( (1ULL<<b0) <=

)

);

(

<<

<< (

)k <<

<<

<< (

)roff <<

<<

<< 2*

+ (1ULL<<(k+2)) <<

);

fill( htp, htp + sz, 0 );

j !=

.end(); ++j )

coll_mask = ((1ULL<<bc) - 1);

pair< Uint4, Uint1 >

ccount = (htp[

.first]&coll_mask);

htp[

.first] += hsb;

( (htp[

.first]&~coll_mask) == 0 )

htp[

.first] += ((vend - 1)<<bc);

htp[

.first] -= (1ULL<<bc);

vtp[htp[

.first]>>bc]

p = {

, k, roff, bc, htp, vtp, cba };

:

;

Exceptions that CSeqMaskerOstatOpt might throw.

@ eMemory

Memory allocation problem.

virtual const char * GetErrCodeString() const override

Get a description string for this exception.

virtual void doSetUnitCount(Uint4 unit, Uint4 count)

Set count information for the given unit.

Uint1 UnitSize() const

Get the unit size value in bases.

virtual void doFinalize()

Generate a hash function and dump the optimized unit counts data to the output stream.

CSeqMaskerOstatOpt(CNcbiOstream &os, Uint2 sz, bool alloc, string const &metadata)

Object constructor.

virtual void write_out(const params &p) const =0

Dump the unit counts data to the output stream according to the requested format.

virtual void doSetUnitSize(Uint4 us)

Set the unit size value.

const vector< Uint4 > & GetParams() const

Get the values of masking parameters.

Uint1 findBestRoff(Uint1 k, Uint1 &max_coll, Uint4 &M, Uint4 *ht)

void createCacheBitArray(Uint4 **cba)

Base class for computing and saving unit counts data.

static const char * PARAMS[]

Algorithm parameter names.

virtual void doSetUnitSize(Uint4 us)

virtual void doSetParam(const string &, Uint4)

CSeqMaskerOstat(CNcbiOstream &os, bool alloc, string const &metadata)

Object constructor.

static pair< Uint4, Uint1 > hash_code(Uint4 unit, Uint1 k, Uint1 roff)

Compute a hash code of a unit.

static Uint4 reverse_complement(Uint4 seq, Uint1 size)

Reverse complement of a unit.

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

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 ...

element_type * get(void) const

Get pointer.

#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...

void Error(CExceptionArgs_Base &args)

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.

void Warning(CExceptionArgs_Base &args)

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

uint16_t Uint2

2-byte (16-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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

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

const GenericPointer< typename T::ValueType > T2 value

Miscellaneous common-use basic types and functionality.

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

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

static const unsigned long MB

static const unsigned long GROW_CHUNK

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

Parameters of the optimized data structure.

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