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CSeqportUtil Class Reference

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#include <objects/seq/seqport_util.hpp>

Classes

struct  CBadIndex
 
struct  CBadSymbol
 
struct  CBadType
 

Public Types

typedef unsigned int TIndex
 
typedef pair< TIndex, TIndex > TPair
 

Static Public Member Functions

static TSeqPos Convert (const CSeq_data &in_seq, CSeq_data *out_seq, CSeq_data::E_Choice to_code, TSeqPos uBeginIdx=0, TSeqPos uLength=0, bool bAmbig=false, Uint4 seed=17734276)
 
static TSeqPos ConvertWithBlastAmbig (const CSeq_data &in_seq, CSeq_data *out_seq, TSeqPos uBeginIdx, TSeqPos uLength, TSeqPos total_length, TSeqPos *out_seq_length, vector< Uint4 > *blast_ambig)
 
static TSeqPos Pack (CSeq_data *in_seq, TSeqPos uLength=ncbi::numeric_limits< TSeqPos >::max())
 
static bool FastValidate (const CSeq_data &in_seq, TSeqPos uBeginIdx=0, TSeqPos uLength=0)
 
static void Validate (const CSeq_data &in_seq, vector< TSeqPos > *badIdx, TSeqPos uBeginIdx=0, TSeqPos uLength=0)
 
static TSeqPos GetAmbigs (const CSeq_data &in_seq, CSeq_data *out_seq, vector< TSeqPos > *out_indices, CSeq_data::E_Choice to_code=CSeq_data::e_Ncbi2na, TSeqPos uBeginIdx=0, TSeqPos uLength=0)
 
static TSeqPos GetCopy (const CSeq_data &in_seq, CSeq_data *out_seq, TSeqPos uBeginIdx=0, TSeqPos uLength=0)
 
static TSeqPos Keep (CSeq_data *in_seq, TSeqPos uBeginIdx=0, TSeqPos uLength=0)
 
static TSeqPos Append (CSeq_data *out_seq, const CSeq_data &in_seq1, TSeqPos uBeginIdx1, TSeqPos uLength1, const CSeq_data &in_seq2, TSeqPos uBeginIdx2, TSeqPos uLength2)
 
static TSeqPos Complement (CSeq_data *in_seq, TSeqPos uBeginIdx=0, TSeqPos uLength=0)
 
static TSeqPos Complement (const CSeq_data &in_seq, CSeq_data *out_seq, TSeqPos uBeginIdx=0, TSeqPos uLength=0)
 
static TSeqPos Reverse (CSeq_data *in_seq, TSeqPos uBeginIdx=0, TSeqPos uLength=0)
 
static TSeqPos Reverse (const CSeq_data &in_seq, CSeq_data *out_seq, TSeqPos uBeginIdx=0, TSeqPos uLength=0)
 
static TSeqPos ReverseComplement (CSeq_data *in_seq, TSeqPos uBeginIdx=0, TSeqPos uLength=0)
 
static TSeqPos ReverseComplement (const CSeq_data &in_seq, CSeq_data *out_seq, TSeqPos uBeginIdx=0, TSeqPos uLength=0)
 
static const string & GetIupacaa3 (TIndex ncbistdaa)
 
static bool IsCodeAvailable (CSeq_data::E_Choice code_type)
 
static bool IsCodeAvailable (ESeq_code_type code_type)
 
static TPair GetCodeIndexFromTo (CSeq_data::E_Choice code_type)
 
static TPair GetCodeIndexFromTo (ESeq_code_type code_type)
 
static const string & GetCode (CSeq_data::E_Choice code_type, TIndex idx)
 
static const string & GetCode (ESeq_code_type code_type, TIndex idx)
 
static const string & GetName (CSeq_data::E_Choice code_type, TIndex idx)
 
static const string & GetName (ESeq_code_type code_type, TIndex idx)
 
static TIndex GetIndex (CSeq_data::E_Choice code_type, const string &code)
 
static TIndex GetIndex (ESeq_code_type code_type, const string &code)
 
static TIndex GetIndexComplement (CSeq_data::E_Choice code_type, TIndex idx)
 
static TIndex GetIndexComplement (ESeq_code_type code_type, TIndex idx)
 
static TIndex GetMapToIndex (CSeq_data::E_Choice from_type, CSeq_data::E_Choice to_type, TIndex from_idx)
 
static TIndex GetMapToIndex (ESeq_code_type from_type, ESeq_code_type to_type, TIndex from_idx)
 

Static Private Member Functions

static CSeqportUtil_implementation & x_GetImplementation (void)
 

Detailed Description

Definition at line 51 of file seqport_util.hpp.

Member Typedef Documentation

◆ TIndex

typedef unsigned int CSeqportUtil::TIndex

Definition at line 56 of file seqport_util.hpp.

◆ TPair

typedef pair<TIndex, TIndex> CSeqportUtil::TPair

Definition at line 57 of file seqport_util.hpp.

Member Function Documentation

◆ Append()

TSeqPos CSeqportUtil::Append ( CSeq_data *  out_seq,
const CSeq_data &  in_seq1,
TSeqPos  uBeginIdx1,
TSeqPos  uLength1,
const CSeq_data &  in_seq2,
TSeqPos  uBeginIdx2,
TSeqPos  uLength2 
)
static

Definition at line 1010 of file seqport_util.cpp.

References CSeqportUtil_implementation::Append(), and x_GetImplementation().

Referenced by variation_ref::CVariationUtil::s_CatLiterals(), and variation::CVariationUtil::s_CatLiterals().

◆ Complement() [1/2]

TSeqPos CSeqportUtil::Complement ( const CSeq_data &  in_seq,
CSeq_data *  out_seq,
TSeqPos  uBeginIdx = 0,
TSeqPos  uLength = 0 
)
static

Definition at line 1035 of file seqport_util.cpp.

References CSeqportUtil_implementation::Complement(), and x_GetImplementation().

◆ Complement() [2/2]

TSeqPos CSeqportUtil::Complement ( CSeq_data *  in_seq,
TSeqPos  uBeginIdx = 0,
TSeqPos  uLength = 0 
)
static

Definition at line 1025 of file seqport_util.cpp.

References CSeqportUtil_implementation::Complement(), and x_GetImplementation().

◆ Convert()

TSeqPos CSeqportUtil::Convert ( const CSeq_data &  in_seq,
CSeq_data *  out_seq,
CSeq_data::E_Choice  to_code,
TSeqPos  uBeginIdx = 0,
TSeqPos  uLength = 0,
bool  bAmbig = false,
Uint4  seed = 17734276 
)
static

Definition at line 917 of file seqport_util.cpp.

References CSeqportUtil_implementation::Convert(), seed, and x_GetImplementation().

Referenced by BOOST_AUTO_TEST_CASE(), CBlastFormattingMatrix::CBlastFormattingMatrix(), CountNs(), CountNucleotides(), FindGeneticCode(), CPssm::GetQuerySequenceData(), CWinMaskDemoApplication::Run(), CNmer_repeatsApplication::Run(), s_GetQuerySequenceData(), s_GetRnaRefLabel(), CFeatureItem::x_AddQualsVariation(), CValidError_bioseq::x_CountAdjacentNs(), variation::CVariationUtil::x_InferNAfromAA(), variation_ref::CVariationUtil::x_ProtToPrecursor(), variation_ref::CHgvsParser::x_SeqLiteralToStr(), variation::CHgvsParser::x_SeqLiteralToStr(), CSequenceDataTester::x_TestSingleNucleotide_Remote(), and CSequenceDataTester::x_TestSingleProtein_Remote().

◆ ConvertWithBlastAmbig()

TSeqPos CSeqportUtil::ConvertWithBlastAmbig ( const CSeq_data &  in_seq,
CSeq_data *  out_seq,
TSeqPos  uBeginIdx,
TSeqPos  uLength,
TSeqPos  total_length,
TSeqPos *  out_seq_length,
vector< Uint4 > *  blast_ambig 
)
static

Definition at line 931 of file seqport_util.cpp.

References CSeqportUtil_implementation::Convert(), CSeq_data_Base::e_Ncbi2na, and x_GetImplementation().

◆ FastValidate()

bool CSeqportUtil::FastValidate ( const CSeq_data &  in_seq,
TSeqPos  uBeginIdx = 0,
TSeqPos  uLength = 0 
)
static

Definition at line 954 of file seqport_util.cpp.

References CSeqportUtil_implementation::FastValidate(), and x_GetImplementation().

◆ GetAmbigs()

TSeqPos CSeqportUtil::GetAmbigs ( const CSeq_data &  in_seq,
CSeq_data *  out_seq,
vector< TSeqPos > *  out_indices,
CSeq_data::E_Choice  to_code = CSeq_data::e_Ncbi2na,
TSeqPos  uBeginIdx = 0,
TSeqPos  uLength = 0 
)
static

Definition at line 975 of file seqport_util.cpp.

References CSeqportUtil_implementation::GetAmbigs(), and x_GetImplementation().

Referenced by CTestSingleAln_All::RunTest(), and s_CountAmbiguities().

◆ GetCode() [1/2]

const string & CSeqportUtil::GetCode ( CSeq_data::E_Choice  code_type,
TIndex  idx 
)
static

Definition at line 1115 of file seqport_util.cpp.

References CSeqportUtil_implementation::GetCodeOrName(), and x_GetImplementation().

Referenced by GetDNAConv(), GetProteinConv(), s_GetRnaRefLabel(), and variation::CHgvsParser::s_hgvsaa2ncbieaa().

◆ GetCode() [2/2]

const string & CSeqportUtil::GetCode ( ESeq_code_type  code_type,
TIndex  idx 
)
static

Definition at line 1122 of file seqport_util.cpp.

References CSeqportUtil_implementation::GetCodeOrName(), and x_GetImplementation().

◆ GetCodeIndexFromTo() [1/2]

CSeqportUtil::TPair CSeqportUtil::GetCodeIndexFromTo ( CSeq_data::E_Choice  code_type)
static

Definition at line 1103 of file seqport_util.cpp.

References CSeqportUtil_implementation::GetCodeIndexFromTo(), and x_GetImplementation().

Referenced by GetDNAConv(), GetProteinConv(), and CSeqVectorTypes::sx_GetConvertTable().

◆ GetCodeIndexFromTo() [2/2]

CSeqportUtil::TPair CSeqportUtil::GetCodeIndexFromTo ( ESeq_code_type  code_type)
static

Definition at line 1109 of file seqport_util.cpp.

References CSeqportUtil_implementation::GetCodeIndexFromTo(), and x_GetImplementation().

◆ GetCopy()

TSeqPos CSeqportUtil::GetCopy ( const CSeq_data &  in_seq,
CSeq_data *  out_seq,
TSeqPos  uBeginIdx = 0,
TSeqPos  uLength = 0 
)
static

Definition at line 988 of file seqport_util.cpp.

References CSeqportUtil_implementation::GetCopy(), and x_GetImplementation().

◆ GetIndex() [1/2]

CSeqportUtil::TIndex CSeqportUtil::GetIndex ( CSeq_data::E_Choice  code_type,
const string &  code 
)
static

Definition at line 1143 of file seqport_util.cpp.

References CSeqportUtil_implementation::GetIndex(), and x_GetImplementation().

Referenced by CPssmInputTestData::SetupQueryAlignedWithInternalGaps(), and CAlnMultiRenderer::x_GetRowTooltip().

◆ GetIndex() [2/2]

CSeqportUtil::TIndex CSeqportUtil::GetIndex ( ESeq_code_type  code_type,
const string &  code 
)
static

Definition at line 1150 of file seqport_util.cpp.

References CSeqportUtil_implementation::GetIndex(), and x_GetImplementation().

◆ GetIndexComplement() [1/2]

CSeqportUtil::TIndex CSeqportUtil::GetIndexComplement ( CSeq_data::E_Choice  code_type,
TIndex  idx 
)
static

Definition at line 1157 of file seqport_util.cpp.

References CSeqportUtil_implementation::GetIndexComplement(), and x_GetImplementation().

Referenced by CSeqVectorTypes::sx_GetConvertTable().

◆ GetIndexComplement() [2/2]

CSeqportUtil::TIndex CSeqportUtil::GetIndexComplement ( ESeq_code_type  code_type,
TIndex  idx 
)
static

Definition at line 1164 of file seqport_util.cpp.

References CSeqportUtil_implementation::GetIndexComplement(), and x_GetImplementation().

◆ GetIupacaa3()

const string & CSeqportUtil::GetIupacaa3 ( TIndex  ncbistdaa)
static

Definition at line 1088 of file seqport_util.cpp.

References CSeqportUtil_implementation::GetIupacaa3(), and x_GetImplementation().

Referenced by s_GetRnaRefLabel(), and variation::CHgvsParser::s_hgvsaa2ncbieaa().

◆ GetMapToIndex() [1/2]

CSeqportUtil::TIndex CSeqportUtil::GetMapToIndex ( CSeq_data::E_Choice  from_type,
CSeq_data::E_Choice  to_type,
TIndex  from_idx 
)
static

Definition at line 1171 of file seqport_util.cpp.

References CSeqportUtil_implementation::GetMapToIndex(), and x_GetImplementation().

Referenced by CWriteUtil::GetAaName(), GetAAName(), IsStopCodon(), variation::CHgvsParser::s_hgvsaa2ncbieaa(), and CSeqVectorTypes::sx_GetConvertTable().

◆ GetMapToIndex() [2/2]

CSeqportUtil::TIndex CSeqportUtil::GetMapToIndex ( ESeq_code_type  from_type,
ESeq_code_type  to_type,
TIndex  from_idx 
)
static

Definition at line 1179 of file seqport_util.cpp.

References CSeqportUtil_implementation::GetMapToIndex(), and x_GetImplementation().

◆ GetName() [1/2]

const string & CSeqportUtil::GetName ( CSeq_data::E_Choice  code_type,
TIndex  idx 
)
static

Definition at line 1129 of file seqport_util.cpp.

References CSeqportUtil_implementation::GetCodeOrName(), and x_GetImplementation().

Referenced by CAlnMultiRenderer::x_GetRowTooltip().

◆ GetName() [2/2]

const string & CSeqportUtil::GetName ( ESeq_code_type  code_type,
TIndex  idx 
)
static

Definition at line 1136 of file seqport_util.cpp.

References CSeqportUtil_implementation::GetCodeOrName(), and x_GetImplementation().

◆ IsCodeAvailable() [1/2]

bool CSeqportUtil::IsCodeAvailable ( CSeq_data::E_Choice  code_type)
static

Definition at line 1093 of file seqport_util.cpp.

References CSeqportUtil_implementation::IsCodeAvailable(), and x_GetImplementation().

Referenced by CSeqVectorTypes::sx_GetConvertTable().

◆ IsCodeAvailable() [2/2]

bool CSeqportUtil::IsCodeAvailable ( ESeq_code_type  code_type)
static

Definition at line 1098 of file seqport_util.cpp.

References CSeqportUtil_implementation::IsCodeAvailable(), and x_GetImplementation().

◆ Keep()

TSeqPos CSeqportUtil::Keep ( CSeq_data *  in_seq,
TSeqPos  uBeginIdx = 0,
TSeqPos  uLength = 0 
)
static

Definition at line 1000 of file seqport_util.cpp.

References CSeqportUtil_implementation::Keep(), and x_GetImplementation().

Referenced by variation::CVariationUtil::s_SpliceLiterals().

◆ Pack()

TSeqPos CSeqportUtil::Pack ( CSeq_data *  in_seq,
TSeqPos  uLength = ncbi::numeric_limits<TSeqPos>::max() 
)
static

Definition at line 945 of file seqport_util.cpp.

References CSeqportUtil_implementation::Pack(), and x_GetImplementation().

Referenced by CDelta_ext::AddLiteral(), AddLiteral(), CFastaReader::AssembleSeq(), DeltaBioseqPack(), g_ConvertDeltaToRawSeq(), RawBioseqPack(), CUpdateSeq_Input::s_ConvertDeltaToRawBioseq(), CSequenceUpdater::s_UpdateSeqInst(), SeqLocToBioseq(), CSeqUtils::SeqLocToBioseq(), UpdateSeqLength(), CFeatureGenerator::SImplementation::x_CollectMrnaSequence(), CPhrap_Seq::x_FillSeqData(), CAlnReader::x_GetSeqInst(), CUpdateSeq_Input::x_ReadAccession(), CSequenceUpdater::x_ReplaceSequence(), and CVectorTrimPanel::x_SetSeqData().

◆ Reverse() [1/2]

TSeqPos CSeqportUtil::Reverse ( const CSeq_data &  in_seq,
CSeq_data *  out_seq,
TSeqPos  uBeginIdx = 0,
TSeqPos  uLength = 0 
)
static

Definition at line 1056 of file seqport_util.cpp.

References CSeqportUtil_implementation::Reverse(), and x_GetImplementation().

◆ Reverse() [2/2]

TSeqPos CSeqportUtil::Reverse ( CSeq_data *  in_seq,
TSeqPos  uBeginIdx = 0,
TSeqPos  uLength = 0 
)
static

Definition at line 1046 of file seqport_util.cpp.

References CSeqportUtil_implementation::Reverse(), and x_GetImplementation().

◆ ReverseComplement() [1/2]

TSeqPos CSeqportUtil::ReverseComplement ( const CSeq_data &  in_seq,
CSeq_data *  out_seq,
TSeqPos  uBeginIdx = 0,
TSeqPos  uLength = 0 
)
static

Definition at line 1077 of file seqport_util.cpp.

References CSeqportUtil_implementation::ReverseComplement(), and x_GetImplementation().

◆ ReverseComplement() [2/2]

TSeqPos CSeqportUtil::ReverseComplement ( CSeq_data *  in_seq,
TSeqPos  uBeginIdx = 0,
TSeqPos  uLength = 0 
)
static

Definition at line 1067 of file seqport_util.cpp.

References CSeqportUtil_implementation::ReverseComplement(), and x_GetImplementation().

Referenced by variation::CVariationUtil::FlipStrand(), ReverseComplement(), variation::CHgvsParser::x_AsHgvsExpression(), CPhrap_Seq::x_FillSeqData(), and variation_ref::CHgvsParser::x_SeqLiteralToStr().

◆ Validate()

void CSeqportUtil::Validate ( const CSeq_data &  in_seq,
vector< TSeqPos > *  badIdx,
TSeqPos  uBeginIdx = 0,
TSeqPos  uLength = 0 
)
static

Definition at line 964 of file seqport_util.cpp.

References CSeqportUtil_implementation::Validate(), and x_GetImplementation().

Referenced by CFastaReader::AssembleSeq(), CValidError_bioseq::ValidateDelta(), variation_ref::CHgvsParser::x_raw_seq(), and variation::CHgvsParser::x_raw_seq().

◆ x_GetImplementation()

CSeqportUtil_implementation & CSeqportUtil::x_GetImplementation ( void  )
staticprivate

Definition at line 904 of file seqport_util.cpp.

References sx_Implementation.

Referenced by Append(), Complement(), Convert(), ConvertWithBlastAmbig(), FastValidate(), GetAmbigs(), GetCode(), GetCodeIndexFromTo(), GetCopy(), GetIndex(), GetIndexComplement(), GetIupacaa3(), GetMapToIndex(), GetName(), IsCodeAvailable(), Keep(), Pack(), Reverse(), ReverseComplement(), and Validate().

The documentation for this class was generated from the following files:
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Modified on Fri Sep 20 14:58:25 2024 by modify_doxy.py rev. 669887