NCBI C++ ToolKit
Functions | Variables
seq_vector.cpp File Reference
#include <ncbi_pch.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/seq_vector_ci.hpp>
#include <corelib/ncbimtx.hpp>
#include <objmgr/impl/data_source.hpp>
#include <objects/seq/seqport_util.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objmgr/seq_map.hpp>
#include <objmgr/objmgr_exception.hpp>
#include <objmgr/impl/seq_vector_cvt.hpp>
#include <algorithm>
#include <map>
#include <vector>
#include <util/random_gen.hpp>
+ Include dependency graph for seq_vector.cpp:

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Functions

static void x_Append8To8 (string &dst_str, const string &src_str, size_t src_pos, size_t count)
 
static void x_Append8To8 (string &dst_str, const vector< char > &src_str, size_t src_pos, size_t count)
 
static void x_AppendGapTo8 (string &dst_str, size_t count, char gap)
 
static void x_Append8To4 (string &dst, char &dst_c, TSeqPos dst_pos, const char *src, size_t count)
 
static void x_Append4To4 (string &dst, char &dst_c, TSeqPos dst_pos, const vector< char > &src, TSeqPos src_pos, TSeqPos count)
 
static void x_AppendGapTo4 (string &dst_str, char &dst_c, TSeqPos dst_pos, TSeqPos count, char gap)
 
static void x_Append8To2 (string &dst_str, char &dst_c, TSeqPos dst_pos, const char *buffer, TSeqPos count)
 
static void x_Append2To2 (string &dst, char &dst_c, TSeqPos dst_pos, const vector< char > &src, TSeqPos src_pos, TSeqPos count)
 
static void x_AppendRandomTo2 (string &dst_str, char &dst_c, TSeqPos dst_pos, TSeqPos src_pos, TSeqPos count, INcbi2naRandomizer &randomizer, char gap)
 
static void x_AppendAnyTo8 (string &dst_str, const CSeq_data &data, TSeqPos dataPos, TSeqPos total_count, const char *table=0, bool reverse=false)
 
static void x_AppendAnyTo4 (string &dst_str, char &dst_c, TSeqPos dst_pos, const CSeq_data &data, TSeqPos dataPos, TSeqPos total_count, const char *table, bool reverse)
 
static void x_AppendAnyTo2 (string &dst_str, char &dst_c, TSeqPos dst_pos, const CSeq_data &data, TSeqPos dataPos, TSeqPos total_count, const char *table, bool reverse, INcbi2naRandomizer *randomizer, TSeqPos randomizer_pos)
 
 DEFINE_STATIC_FAST_MUTEX (s_ConvertTableMutex2)
 

Variables

static const size_t kBufferSize = 1024
 

Function Documentation

◆ DEFINE_STATIC_FAST_MUTEX()

DEFINE_STATIC_FAST_MUTEX ( s_ConvertTableMutex2  )

◆ x_Append2To2()

static void x_Append2To2 ( string dst,
char &  dst_c,
TSeqPos  dst_pos,
const vector< char > &  src,
TSeqPos  src_pos,
TSeqPos  count 
)
static

Definition at line 542 of file seq_vector.cpp.

References _ASSERT, buffer, copy_2bit(), kBufferSize, min(), and x_Append8To2().

Referenced by CSeqVector::x_GetPacked2naSeqData().

◆ x_Append4To4()

static void x_Append4To4 ( string dst,
char &  dst_c,
TSeqPos  dst_pos,
const vector< char > &  src,
TSeqPos  src_pos,
TSeqPos  count 
)
static

Definition at line 411 of file seq_vector.cpp.

References _ASSERT.

Referenced by CSeqVector::x_GetPacked4naSeqData().

◆ x_Append8To2()

static void x_Append8To2 ( string dst_str,
char &  dst_c,
TSeqPos  dst_pos,
const char *  buffer,
TSeqPos  count 
)
static

Definition at line 491 of file seq_vector.cpp.

References _ASSERT, buffer, and kBufferSize.

Referenced by x_Append2To2(), x_AppendAnyTo2(), and x_AppendRandomTo2().

◆ x_Append8To4()

static void x_Append8To4 ( string dst,
char &  dst_c,
TSeqPos  dst_pos,
const char *  src,
size_t  count 
)
static

Definition at line 387 of file seq_vector.cpp.

References _ASSERT.

Referenced by x_AppendAnyTo4().

◆ x_Append8To8() [1/2]

static void x_Append8To8 ( string dst_str,
const string src_str,
size_t  src_pos,
size_t  count 
)
inlinestatic

Definition at line 354 of file seq_vector.cpp.

References _ASSERT.

Referenced by CSeqVector::x_GetPacked8SeqData().

◆ x_Append8To8() [2/2]

static void x_Append8To8 ( string dst_str,
const vector< char > &  src_str,
size_t  src_pos,
size_t  count 
)
inlinestatic

Definition at line 366 of file seq_vector.cpp.

References _ASSERT.

◆ x_AppendAnyTo2()

static void x_AppendAnyTo2 ( string dst_str,
char &  dst_c,
TSeqPos  dst_pos,
const CSeq_data data,
TSeqPos  dataPos,
TSeqPos  total_count,
const char *  table,
bool  reverse,
INcbi2naRandomizer randomizer,
TSeqPos  randomizer_pos 
)
static

◆ x_AppendAnyTo4()

static void x_AppendAnyTo4 ( string dst_str,
char &  dst_c,
TSeqPos  dst_pos,
const CSeq_data data,
TSeqPos  dataPos,
TSeqPos  total_count,
const char *  table,
bool  reverse 
)
static

◆ x_AppendAnyTo8()

static void x_AppendAnyTo8 ( string dst_str,
const CSeq_data data,
TSeqPos  dataPos,
TSeqPos  total_count,
const char *  table = 0,
bool  reverse = false 
)
static

◆ x_AppendGapTo4()

static void x_AppendGapTo4 ( string dst_str,
char &  dst_c,
TSeqPos  dst_pos,
TSeqPos  count,
char  gap 
)
static

Definition at line 466 of file seq_vector.cpp.

References _ASSERT.

Referenced by CSeqVector::x_GetPacked4naSeqData().

◆ x_AppendGapTo8()

static void x_AppendGapTo8 ( string dst_str,
size_t  count,
char  gap 
)
inlinestatic

Definition at line 378 of file seq_vector.cpp.

Referenced by CSeqVector::x_GetPacked8SeqData().

◆ x_AppendRandomTo2()

static void x_AppendRandomTo2 ( string dst_str,
char &  dst_c,
TSeqPos  dst_pos,
TSeqPos  src_pos,
TSeqPos  count,
INcbi2naRandomizer randomizer,
char  gap 
)
static

Variable Documentation

◆ kBufferSize

const size_t kBufferSize = 1024
static
Modified on Tue Feb 27 05:54:38 2024 by modify_doxy.py rev. 669887