NCBI C++ ToolKit
Public Types | Static Public Member Functions | List of all members
CSeqManip Class Reference

Search Toolkit Book for CSeqManip

#include <util/sequtil/sequtil_manip.hpp>

Public Types

typedef CSeqUtil::TCoding TCoding
 

Static Public Member Functions

static SIZE_TYPE Reverse (const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)
 
static SIZE_TYPE Reverse (const vector< char > &src, TCoding src_coding, TSeqPos pos, TSeqPos length, vector< char > &dst)
 
static SIZE_TYPE Reverse (const char *src, TCoding src_coding, TSeqPos pos, TSeqPos length, char *dst)
 
static SIZE_TYPE Complement (const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)
 
static SIZE_TYPE Complement (const vector< char > &src, TCoding src_coding, TSeqPos pos, TSeqPos length, vector< char > &dst)
 
static SIZE_TYPE Complement (const char *src, TCoding src_coding, TSeqPos pos, TSeqPos length, char *dst)
 
static SIZE_TYPE ReverseComplement (const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)
 
static SIZE_TYPE ReverseComplement (const vector< char > &src, TCoding src_coding, TSeqPos pos, TSeqPos length, vector< char > &dst)
 
static SIZE_TYPE ReverseComplement (const char *src, TCoding src_coding, TSeqPos pos, TSeqPos length, char *dst)
 
static SIZE_TYPE ReverseComplement (string &src, TCoding src_coding, TSeqPos pos, TSeqPos length)
 
static SIZE_TYPE ReverseComplement (vector< char > &src, TCoding src_coding, TSeqPos pos, TSeqPos length)
 
static SIZE_TYPE ReverseComplement (char *src, TCoding src_coding, TSeqPos pos, TSeqPos length)
 

Detailed Description

Definition at line 50 of file sequtil_manip.hpp.

Member Typedef Documentation

◆ TCoding

typedef CSeqUtil::TCoding CSeqManip::TCoding

Definition at line 55 of file sequtil_manip.hpp.

Member Function Documentation

◆ Complement() [1/3]

SIZE_TYPE CSeqManip::Complement ( const char *  src,
TCoding  src_coding,
TSeqPos  pos,
TSeqPos  length,
char *  dst 
)
static

Definition at line 373 of file sequtil_manip.cpp.

References _ASSERT, convert_1_to_1(), CSeqUtil::e_Iupacna, CSeqUtil::e_Ncbi2na, CSeqUtil::e_Ncbi2na_expand, CSeqUtil::e_Ncbi4na, CSeqUtil::e_Ncbi4na_expand, CSeqUtil::e_Ncbi8na, CIupacnaCmp::GetTable(), C8naCmp::GetTable(), NCBI_THROW, s_Ncbi2naComplement(), s_Ncbi2naExpandComplement(), and s_Ncbi4naComplement().

◆ Complement() [2/3]

SIZE_TYPE CSeqManip::Complement ( const string &  src,
TCoding  src_coding,
TSeqPos  pos,
TSeqPos  length,
string &  dst 
)
static

Definition at line 248 of file sequtil_manip.cpp.

References s_Complement().

Referenced by CSeqportUtil_implementation::Complement(), CGuiObjectInfoSeq_align::GetSeqString(), CSequenceTrack::GetTooltip(), s_Complement(), s_ComputeTraceback(), CPaintSequence::UpdateData(), CCdsGlyph::x_Draw(), CAlignGlyph::x_DrawAlignRowSequence(), CAlignGlyph::x_DrawUnalignedRowSequence(), and CSequenceTrack::x_RenderSequence().

◆ Complement() [3/3]

SIZE_TYPE CSeqManip::Complement ( const vector< char > &  src,
TCoding  src_coding,
TSeqPos  pos,
TSeqPos  length,
vector< char > &  dst 
)
static

Definition at line 260 of file sequtil_manip.cpp.

References s_Complement().

◆ Reverse() [1/3]

SIZE_TYPE CSeqManip::Reverse ( const char *  src,
TCoding  src_coding,
TSeqPos  pos,
TSeqPos  length,
char *  dst 
)
static

Definition at line 195 of file sequtil_manip.cpp.

References _ASSERT, CSeqUtil::e_Ncbi2na, CSeqUtil::e_Ncbi4na, NCBI_THROW, s_2naReverse(), and s_4naReverse().

◆ Reverse() [2/3]

SIZE_TYPE CSeqManip::Reverse ( const string &  src,
TCoding  src_coding,
TSeqPos  pos,
TSeqPos  length,
string &  dst 
)
static

Definition at line 171 of file sequtil_manip.cpp.

References s_Reverse().

Referenced by CGuiObjectInfoSeq_align::GetSeqString(), IAlnGraphicDataSource::GetSeqString(), CSeqportUtil_implementation::Reverse(), s_Reverse(), CAlignGlyph::x_DrawAlignRowSequence(), CAlignGlyph::x_DrawUnalignedRowSequence(), and CURLTooltipHandler::x_ReverseSequence().

◆ Reverse() [3/3]

SIZE_TYPE CSeqManip::Reverse ( const vector< char > &  src,
TCoding  src_coding,
TSeqPos  pos,
TSeqPos  length,
vector< char > &  dst 
)
static

Definition at line 183 of file sequtil_manip.cpp.

References s_Reverse().

◆ ReverseComplement() [1/6]

SIZE_TYPE CSeqManip::ReverseComplement ( char *  src,
TCoding  src_coding,
TSeqPos  pos,
TSeqPos  length 
)
static

Definition at line 701 of file sequtil_manip.cpp.

References _ASSERT, CSeqUtil::e_Iupacna, CSeqUtil::e_Ncbi2na, CSeqUtil::e_Ncbi2na_expand, CSeqUtil::e_Ncbi4na, CSeqUtil::e_Ncbi4na_expand, CSeqUtil::e_Ncbi8na, CIupacnaCmp::GetTable(), C8naCmp::GetTable(), NCBI_THROW, revcmp(), s_Ncbi2naExpandRevCmp(), s_Ncbi2naRevCmp(), and s_Ncbi4naRevCmp().

◆ ReverseComplement() [2/6]

SIZE_TYPE CSeqManip::ReverseComplement ( const char *  src,
TCoding  src_coding,
TSeqPos  pos,
TSeqPos  length,
char *  dst 
)
static

Definition at line 565 of file sequtil_manip.cpp.

References _ASSERT, copy_1_to_1_reverse(), CSeqUtil::e_Iupacna, CSeqUtil::e_Ncbi2na, CSeqUtil::e_Ncbi2na_expand, CSeqUtil::e_Ncbi4na, CSeqUtil::e_Ncbi4na_expand, CSeqUtil::e_Ncbi8na, CIupacnaCmp::GetTable(), C8naCmp::GetTable(), NCBI_THROW, s_Ncbi2naExpandRevCmp(), s_Ncbi2naRevCmp(), and s_Ncbi4naRevCmp().

◆ ReverseComplement() [3/6]

SIZE_TYPE CSeqManip::ReverseComplement ( const string &  src,
TCoding  src_coding,
TSeqPos  pos,
TSeqPos  length,
string &  dst 
)
static

Definition at line 432 of file sequtil_manip.cpp.

References s_ReverseComplement().

Referenced by CDefaultSpotIdDetector::AddSpotId(), CBlastDBExtractor::ExtractSeqData(), CDensegGraphicDataSource::GetAlnSeqString(), CProjectedMappingInfo::GetAnchorSequence(), CProductStringBuilder::GetProductString(), CPaintAlignment::GetSegments(), CAlnWriter::GetSegString(), CGuiObjectInfoSeq_align::GetSeqString(), IAlnGraphicDataSource::GetSeqString(), CDensegGraphicDataSource::GetSeqString(), CBamAlignIterator::GetShortBioseq(), CSeqportUtil_implementation::ReverseComplement(), s_GetQuerySequence(), s_GetSplicedSegIdentityMismatch(), s_GetSpliceSiteOrientation(), s_ReverseComplement(), s_TokenizeTRnaString(), CPaintSequence::TranslateCDS(), CPaintSequence::UpdateData(), CProductStringBuilder::x_AddExon(), CBlastSeqVectorFromCSeq_data::x_ComplementData(), CSGAlignStatJob::x_CreatePileUpGraphs(), CAlignGlyph::x_DrawAlignRowSequence(), CCdsGlyph::x_DrawProtSeqWithMapping(), CFeatGlyph::x_DrawRNAProductSequence(), CAlignGlyph::x_DrawUnalignedRowSequence(), CSFTranslationJob::x_Execute(), CGuiObjectInfoSeq_feat::x_GetSplicedSeqTitle(), CURLTooltipHandler::x_ReverseSequence(), and CSequenceSearchJob::x_SearchSequence().

◆ ReverseComplement() [4/6]

SIZE_TYPE CSeqManip::ReverseComplement ( const vector< char > &  src,
TCoding  src_coding,
TSeqPos  pos,
TSeqPos  length,
vector< char > &  dst 
)
static

Definition at line 444 of file sequtil_manip.cpp.

References s_ReverseComplement().

◆ ReverseComplement() [5/6]

SIZE_TYPE CSeqManip::ReverseComplement ( string &  src,
TCoding  src_coding,
TSeqPos  pos,
TSeqPos  length 
)
static

Definition at line 622 of file sequtil_manip.cpp.

References s_ReverseComplement().

◆ ReverseComplement() [6/6]

SIZE_TYPE CSeqManip::ReverseComplement ( vector< char > &  src,
TCoding  src_coding,
TSeqPos  pos,
TSeqPos  length 
)
static

Definition at line 633 of file sequtil_manip.cpp.

References s_ReverseComplement().

The documentation for this class was generated from the following files:
Generated by doxygen 1.9.0
Modified on Fri Sep 20 14:57:13 2024 by modify_doxy.py rev. 669887