#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:

Go to the SVN repository for this file.

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(), count, 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, and count.

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, count, 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, and count.

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, and count.

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, and count.

◆ 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

Definition at line 752 of file seq_vector.cpp.

References _ASSERT, buffer, copy_2bit_any(), copy_4bit_any(), copy_8bit_any(), count, data, CSeq_data_Base::e_Iupacaa, CSeq_data_Base::e_Iupacna, CSeq_data_Base::e_Ncbi2na, CSeq_data_Base::e_Ncbi4na, CSeq_data_Base::e_Ncbi8aa, CSeq_data_Base::e_Ncbi8na, CSeq_data_Base::e_Ncbieaa, CSeq_data_Base::e_Ncbistdaa, kBufferSize, min(), NCBI_THROW_FMT, INcbi2naRandomizer::RandomizeData(), table, total_count, and x_Append8To2().

Referenced by CSeqVector::x_GetPacked2naSeqData().

◆ 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

Definition at line 687 of file seq_vector.cpp.

References _ASSERT, buffer, copy_2bit_any(), copy_4bit_any(), copy_8bit_any(), count, data, CSeq_data_Base::e_Iupacaa, CSeq_data_Base::e_Iupacna, CSeq_data_Base::e_Ncbi2na, CSeq_data_Base::e_Ncbi4na, CSeq_data_Base::e_Ncbi8aa, CSeq_data_Base::e_Ncbi8na, CSeq_data_Base::e_Ncbieaa, CSeq_data_Base::e_Ncbistdaa, kBufferSize, min(), NCBI_THROW_FMT, table, total_count, and x_Append8To4().

Referenced by CSeqVector::x_GetPacked4naSeqData().

◆ 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

Definition at line 624 of file seq_vector.cpp.

References _ASSERT, buffer, copy_2bit_any(), copy_4bit_any(), copy_8bit_any(), count, data, CSeq_data_Base::e_Iupacaa, CSeq_data_Base::e_Iupacna, CSeq_data_Base::e_Ncbi2na, CSeq_data_Base::e_Ncbi4na, CSeq_data_Base::e_Ncbi8aa, CSeq_data_Base::e_Ncbi8na, CSeq_data_Base::e_Ncbieaa, CSeq_data_Base::e_Ncbistdaa, kBufferSize, min(), NCBI_THROW_FMT, table, and total_count.

Referenced by CSeqVector::x_GetPacked8SeqData().

◆ 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, and count.

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.

References count.

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

Definition at line 601 of file seq_vector.cpp.

References _ASSERT, buffer, count, kBufferSize, min(), INcbi2naRandomizer::RandomizeData(), and x_Append8To2().

Referenced by CSeqVector::x_GetPacked2naSeqData().

Variable Documentation

◆ kBufferSize

const size_t kBufferSize = 1024

static

Definition at line 351 of file seq_vector.cpp.

Referenced by x_Append2To2(), x_Append8To2(), x_AppendAnyTo2(), x_AppendAnyTo4(), x_AppendAnyTo8(), and x_AppendRandomTo2().

Functions

Variables

Function Documentation

◆ DEFINE_STATIC_FAST_MUTEX()

◆ x_Append2To2()

◆ x_Append4To4()

◆ x_Append8To2()

◆ x_Append8To4()

◆ x_Append8To8() [1/2]

◆ x_Append8To8() [2/2]

◆ x_AppendAnyTo2()

◆ x_AppendAnyTo4()

◆ x_AppendAnyTo8()

◆ x_AppendGapTo4()

◆ x_AppendGapTo8()

◆ x_AppendRandomTo2()

Variable Documentation

◆ kBufferSize