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CSeqConvert Class Reference

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#include <util/sequtil/sequtil_convert.hpp>

Classes

class  IPackTarget
 

Public Types

typedef CSeqUtil::ECoding TCoding
 

Static Public Member Functions

static SIZE_TYPE Convert (const CTempString &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst, TCoding dst_coding)
 
static SIZE_TYPE Convert (const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, vector< char > &dst, TCoding dst_coding)
 
static SIZE_TYPE Convert (const vector< char > &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst, TCoding dst_coding)
 
static SIZE_TYPE Convert (const vector< char > &src, TCoding src_coding, TSeqPos pos, TSeqPos length, vector< char > &dst, TCoding dst_coding)
 
static SIZE_TYPE Convert (const char src[], TCoding src_coding, TSeqPos pos, TSeqPos length, char dst[], TCoding dst_coding)
 
static SIZE_TYPE Subseq (const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)
 
static SIZE_TYPE Subseq (const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, vector< char > &dst)
 
static SIZE_TYPE Subseq (const vector< char > &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)
 
static SIZE_TYPE Subseq (const vector< char > &src, TCoding src_coding, TSeqPos pos, TSeqPos length, vector< char > &dst)
 
static SIZE_TYPE Subseq (const char *src, TCoding src_coding, TSeqPos pos, TSeqPos length, char *dst)
 
static SIZE_TYPE Pack (const string &src, TCoding src_coding, vector< char > &dst, TCoding &dst_coding, TSeqPos length=ncbi::numeric_limits< TSeqPos >::max())
 
static SIZE_TYPE Pack (const vector< char > &src, TCoding src_coding, vector< char > &dst, TCoding &dst_coding, TSeqPos length=ncbi::numeric_limits< TSeqPos >::max())
 
static SIZE_TYPE Pack (const char *src, TSeqPos length, TCoding src_coding, char *dst, TCoding &dst_coding)
 
static SIZE_TYPE Pack (const string &src, TCoding src_coding, IPackTarget &dst, TSeqPos length=numeric_limits< TSeqPos >::max())
 
static SIZE_TYPE Pack (const vector< char > &src, TCoding src_coding, IPackTarget &dst, TSeqPos length=numeric_limits< TSeqPos >::max())
 
static SIZE_TYPE Pack (const char *src, TSeqPos length, TCoding src_coding, IPackTarget &dst)
 

Detailed Description

Definition at line 48 of file sequtil_convert.hpp.

Member Typedef Documentation

◆ TCoding

typedef CSeqUtil::ECoding CSeqConvert::TCoding

Definition at line 53 of file sequtil_convert.hpp.

Member Function Documentation

◆ Convert() [1/5]

SIZE_TYPE CSeqConvert::Convert ( const char  src[],
TCoding  src_coding,
TSeqPos  pos,
TSeqPos  length,
char  dst[],
TCoding  dst_coding 
)
static

Definition at line 105 of file sequtil_convert.cpp.

References CSeqConvert_imp::Convert().

◆ Convert() [2/5]

SIZE_TYPE CSeqConvert::Convert ( const CTempString &  src,
TCoding  src_coding,
TSeqPos  pos,
TSeqPos  length,
string &  dst,
TCoding  dst_coding 
)
static

Definition at line 46 of file sequtil_convert.cpp.

References CSeqConvert_imp::Convert().

Referenced by AddLiteral(), CRawSeqToDeltaSeqByLoc::apply_impl(), BOOST_AUTO_TEST_CASE(), CRawSeqToDeltaSeqByLoc::ByAssemblyGapFeatures_impl(), CBlastSeqVectorFromCSeq_data::CBlastSeqVectorFromCSeq_data(), CSeqportUtil_implementation::Convert(), CPepXML::ConvertAA(), ConvertRawToDeltaByNs(), CRawSeqToDeltaByN::DeltaSeqToRaw(), GapLocationsFromNs(), CCleave::GetCleaveAt(), GetCodeBreakCharacter(), GetNcbistdSeq(), CSeqDB::GetSequenceAsString(), CEditingActionFeatTranslExcept::GetValue(), InspectSeqFeat(), NcbieaaToNcbistdaaString(), NcbistdaaToNcbieaaString(), CSeqConvert_imp::CPacker::Pack(), PackSeqData(), s_ConvertTrnaAaToLetter(), s_FixBioseqDeltas(), s_GetAaAsChar(), s_GetQuerySequence(), s_Ncbi2naRevCmp(), s_Ncbi4naRevCmp(), s_ToIupacaa(), CBlastSeqVectorFromCSeq_data::SetCoding(), CWriteDB_Impl::SetMaskedLetters(), CSplitCDSwithTooManyXs::TooManyXs(), WriteDB_EaaToBinary(), WriteDB_IupacaaToBinary(), WriteDB_IupacnaToBinary(), CCDSTranslationProblems::x_GetTranslExceptProblems(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CSingleCDSExceptionPanel::x_SetAminoAcid(), CtRNAProductPanel::x_SetAminoAcid(), CFeatureGenerator::SImplementation::x_SetComment(), CRNAValidator::x_ValidateTrnaCodons(), and CForeignContaminationScreenReportReader::xTrimLiteral().

◆ Convert() [3/5]

SIZE_TYPE CSeqConvert::Convert ( const string &  src,
TCoding  src_coding,
TSeqPos  pos,
TSeqPos  length,
vector< char > &  dst,
TCoding  dst_coding 
)
static

Definition at line 61 of file sequtil_convert.cpp.

References CSeqConvert_imp::Convert().

◆ Convert() [4/5]

SIZE_TYPE CSeqConvert::Convert ( const vector< char > &  src,
TCoding  src_coding,
TSeqPos  pos,
TSeqPos  length,
string &  dst,
TCoding  dst_coding 
)
static

Definition at line 76 of file sequtil_convert.cpp.

References CSeqConvert_imp::Convert().

◆ Convert() [5/5]

SIZE_TYPE CSeqConvert::Convert ( const vector< char > &  src,
TCoding  src_coding,
TSeqPos  pos,
TSeqPos  length,
vector< char > &  dst,
TCoding  dst_coding 
)
static

Definition at line 91 of file sequtil_convert.cpp.

References CSeqConvert_imp::Convert().

◆ Pack() [1/6]

SIZE_TYPE CSeqConvert::Pack ( const char *  src,
TSeqPos  length,
TCoding  src_coding,
char *  dst,
TCoding &  dst_coding 
)
static

Definition at line 199 of file sequtil_convert.cpp.

References CSeqConvert_imp::Pack().

◆ Pack() [2/6]

SIZE_TYPE CSeqConvert::Pack ( const char *  src,
TSeqPos  length,
TCoding  src_coding,
IPackTarget &  dst 
)
static

Definition at line 222 of file sequtil_convert.cpp.

References CSeqConvert_imp::Pack().

◆ Pack() [3/6]

SIZE_TYPE CSeqConvert::Pack ( const string &  src,
TCoding  src_coding,
IPackTarget &  dst,
TSeqPos  length = numeric_limits<TSeqPos>::max() 
)
static

Definition at line 210 of file sequtil_convert.cpp.

References CSeqConvert_imp::Pack().

◆ Pack() [4/6]

SIZE_TYPE CSeqConvert::Pack ( const string &  src,
TCoding  src_coding,
vector< char > &  dst,
TCoding &  dst_coding,
TSeqPos  length = ncbi::numeric_limits<TSeqPos>::max() 
)
static

Definition at line 178 of file sequtil_convert.cpp.

References CSeqConvert_imp::Pack().

Referenced by CDelta_ext::AddAndSplit(), and CSeqportUtil_implementation::Pack().

◆ Pack() [5/6]

SIZE_TYPE CSeqConvert::Pack ( const vector< char > &  src,
TCoding  src_coding,
IPackTarget &  dst,
TSeqPos  length = numeric_limits<TSeqPos>::max() 
)
static

Definition at line 216 of file sequtil_convert.cpp.

References CSeqConvert_imp::Pack().

◆ Pack() [6/6]

SIZE_TYPE CSeqConvert::Pack ( const vector< char > &  src,
TCoding  src_coding,
vector< char > &  dst,
TCoding &  dst_coding,
TSeqPos  length = ncbi::numeric_limits<TSeqPos>::max() 
)
static

Definition at line 189 of file sequtil_convert.cpp.

References CSeqConvert_imp::Pack().

◆ Subseq() [1/5]

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

Definition at line 165 of file sequtil_convert.cpp.

References CSeqConvert_imp::Subseq().

◆ Subseq() [2/5]

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

Definition at line 121 of file sequtil_convert.cpp.

References CSeqConvert_imp::Subseq().

◆ Subseq() [3/5]

SIZE_TYPE CSeqConvert::Subseq ( const string &  src,
TCoding  src_coding,
TSeqPos  pos,
TSeqPos  length,
vector< char > &  dst 
)
static

Definition at line 132 of file sequtil_convert.cpp.

References CSeqConvert_imp::Subseq().

◆ Subseq() [4/5]

SIZE_TYPE CSeqConvert::Subseq ( const vector< char > &  src,
TCoding  src_coding,
TSeqPos  pos,
TSeqPos  length,
string &  dst 
)
static

Definition at line 143 of file sequtil_convert.cpp.

References CSeqConvert_imp::Subseq().

◆ Subseq() [5/5]

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

Definition at line 154 of file sequtil_convert.cpp.

References CSeqConvert_imp::Subseq().

The documentation for this class was generated from the following files:
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Modified on Sun Apr 28 04:45:03 2024 by modify_doxy.py rev. 669887