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CValidError_align Class Reference

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#include <objtools/validator/validerror_align.hpp>

+ Inheritance diagram for CValidError_align:
+ Collaboration diagram for CValidError_align:

Classes

struct  TSegmentGap
 

Public Types

typedef vector< TSegmentGap > TSegmentGapV
 
typedef CSeq_align::C_Segs::TDendiag TDendiag
 
typedef CSeq_align::C_Segs::TDenseg TDenseg
 
typedef CSeq_align::C_Segs::TPacked TPacked
 
typedef CSeq_align::C_Segs::TStd TStd
 

Public Member Functions

 CValidError_align (CValidError_imp &imp)
 
 ~CValidError_align () override
 
void ValidateSeqAlign (const CSeq_align &align, int order=-1)
 

Static Public Member Functions

static TSegmentGapV FindSegmentGaps (const TPacked &packed)
 
static TSegmentGapV FindSegmentGaps (const TDenseg &std_segs)
 
static TSegmentGapV FindSegmentGaps (const TStd &denseg, CScope *scope)
 
static TSegmentGapV FindSegmentGaps (const TDendiag &dendiags)
 

Private Types

typedef CSeq_align::C_Segs::TDisc TDisc
 

Private Member Functions

void x_ValidateAlignPercentIdentity (const CSeq_align &align, bool internal_gaps)
 
void x_ValidateDendiag (const TDendiag &dendiags, const CSeq_align &align)
 
void x_ValidateDenseg (const TDenseg &denseg, const CSeq_align &align)
 
void x_ValidateStd (const TStd &stdsegs, const CSeq_align &align)
 
void x_ValidatePacked (const TPacked &packed, const CSeq_align &align)
 
template<typename T >
bool x_ValidateDim (T &obj, const CSeq_align &align, size_t part=0)
 
void x_ValidateStrand (const TDenseg &denseg, const CSeq_align &align)
 
void x_ValidateStrand (const TStd &std_segs, const CSeq_align &align)
 
void x_ValidateFastaLike (const TDenseg &denseg, const CSeq_align &align)
 
void x_ReportSegmentGaps (const TSegmentGapV &seggaps, const CSeq_align &align)
 
void x_ValidateSegmentGap (const TDenseg &denseg, const CSeq_align &align)
 
void x_ValidateSegmentGap (const TPacked &packed, const CSeq_align &align)
 
void x_ValidateSegmentGap (const TStd &std_segs, const CSeq_align &align)
 
void x_ValidateSegmentGap (const TDendiag &dendiags, const CSeq_align &align)
 
void x_ValidateSeqId (const CSeq_align &align)
 
void x_GetIds (const CSeq_align &align, vector< CRef< CSeq_id > > &ids)
 
void x_ReportAlignErr (const CSeq_align &align, const CSeq_id &id, const CSeq_id &id_context, size_t segment, size_t pos, EErrType et, EDiagSev sev, const string &prefix, const string &message)
 
void x_ReportSumLenStart (const CSeq_align &align, const CSeq_id &id, const CSeq_id &id_context, size_t segment, size_t pos)
 
void x_ReportStartMoreThanBiolen (const CSeq_align &align, const CSeq_id &id, const CSeq_id &id_context, size_t segment, size_t pos)
 
void x_ValidateSeqLength (const TDenseg &denseg, const CSeq_align &align)
 
void x_ValidateSeqLength (const TPacked &packed, const CSeq_align &align)
 
void x_ValidateSeqLength (const TStd &std_segs, const CSeq_align &align)
 
void x_ValidateSeqLength (const CDense_diag &dendiag, size_t dendiag_num, const CSeq_align &align)
 
- Private Member Functions inherited from CValidError_base
 CValidError_base (CValidError_imp &imp)
 
virtual ~CValidError_base ()
 
void PostErr (EDiagSev sv, EErrType et, const string &msg, const CSerialObject &obj)
 
void PostErr (EDiagSev sv, EErrType et, const string &msg, const CSeq_feat &ft)
 
void PostErr (EDiagSev sv, EErrType et, const string &msg, const CBioseq &sq)
 
void PostErr (EDiagSev sv, EErrType et, const string &msg, const CSeq_entry &ctx, const CSeqdesc &ds)
 
void PostErr (EDiagSev sv, EErrType et, const string &msg, const CBioseq_set &set)
 
void PostErr (EDiagSev sv, EErrType et, const string &msg, const CSeq_annot &annot)
 
void PostErr (EDiagSev sv, EErrType et, const string &msg, const CSeq_graph &graph)
 
void PostErr (EDiagSev sv, EErrType et, const string &msg, const CBioseq &sq, const CSeq_graph &graph)
 
void PostErr (EDiagSev sv, EErrType et, const string &msg, const CSeq_align &align)
 
void PostErr (EDiagSev sv, EErrType et, const string &msg, const CSeq_entry &entry)
 
CCacheImpl & GetCache ()
 

Static Private Member Functions

static bool AlignmentScorePercentIdOk (const CSeq_align &align)
 
static bool IsTpaAlignment (const CDense_seg &denseg, CScope &scope)
 
static bool IsTpaAlignment (const CSparseAln &sparse_aln, CScope &scope)
 
- Static Private Member Functions inherited from CValidError_base
static CSeq_entry_Handle GetAppropriateXrefParent (CSeq_entry_Handle seh)
 

Additional Inherited Members

- Private Attributes inherited from CValidError_base
CValidError_imp & m_Imp
 
CScope * m_Scope
 

Detailed Description

Definition at line 62 of file validerror_align.hpp.

Member Typedef Documentation

◆ TDendiag

typedef CSeq_align::C_Segs::TDendiag CValidError_align::TDendiag

Definition at line 77 of file validerror_align.hpp.

◆ TDenseg

typedef CSeq_align::C_Segs::TDenseg CValidError_align::TDenseg

Definition at line 78 of file validerror_align.hpp.

◆ TDisc

typedef CSeq_align::C_Segs::TDisc CValidError_align::TDisc
private

Definition at line 88 of file validerror_align.hpp.

◆ TPacked

typedef CSeq_align::C_Segs::TPacked CValidError_align::TPacked

Definition at line 79 of file validerror_align.hpp.

◆ TSegmentGapV

typedef vector<TSegmentGap> CValidError_align::TSegmentGapV

Definition at line 75 of file validerror_align.hpp.

◆ TStd

typedef CSeq_align::C_Segs::TStd CValidError_align::TStd

Definition at line 80 of file validerror_align.hpp.

Constructor & Destructor Documentation

◆ CValidError_align()

CValidError_align::CValidError_align ( CValidError_imp &  imp)

Definition at line 70 of file validerror_align.cpp.

◆ ~CValidError_align()

CValidError_align::~CValidError_align ( )
override

Definition at line 76 of file validerror_align.cpp.

Member Function Documentation

◆ AlignmentScorePercentIdOk()

bool CValidError_align::AlignmentScorePercentIdOk ( const CSeq_align &  align)
staticprivate

Definition at line 238 of file validerror_align.cpp.

References NStr::EqualNocase(), CSeq_align_Base::GetScore(), CSeq_align_Base::IsSetScore(), and ITERATE.

Referenced by x_ValidateAlignPercentIdentity().

◆ FindSegmentGaps() [1/4]

CValidError_align::TSegmentGapV CValidError_align::FindSegmentGaps ( const TDendiag &  dendiags)
static

Definition at line 1209 of file validerror_align.cpp.

References NStr::IsBlank(), ITERATE, and label.

◆ FindSegmentGaps() [2/4]

CValidError_align::TSegmentGapV CValidError_align::FindSegmentGaps ( const TDenseg &  std_segs)
static

Definition at line 1055 of file validerror_align.cpp.

References CSeq_id::eContent, NStr::IsBlank(), and label.

◆ FindSegmentGaps() [3/4]

CValidError_align::TSegmentGapV CValidError_align::FindSegmentGaps ( const TPacked &  packed)
static

Definition at line 1118 of file validerror_align.cpp.

References CSeq_id::eContent, i, NStr::IsBlank(), and label.

Referenced by x_ValidateAlignPercentIdentity(), and x_ValidateSegmentGap().

◆ FindSegmentGaps() [4/4]

CValidError_align::TSegmentGapV CValidError_align::FindSegmentGaps ( const TStd &  denseg,
CScope *  scope 
)
static

Definition at line 1166 of file validerror_align.cpp.

References CSeq_id::eContent, GetLength(), NStr::IsBlank(), ITERATE, label, and len.

◆ IsTpaAlignment() [1/2]

bool CValidError_align::IsTpaAlignment ( const CDense_seg &  denseg,
CScope &  scope 
)
staticprivate

Definition at line 258 of file validerror_align.cpp.

References CSeqdesc_Base::e_User, NStr::EqualNocase(), CScope::GetBioseqHandle(), CDense_seg_Base::GetDim(), CDense_seg_Base::GetIds(), CObject_id_Base::GetStr(), CUser_object_Base::GetType(), CSeqdesc_Base::GetUser(), CUser_object_Base::IsSetType(), CObject_id_Base::IsStr(), row, and s_GetNumIdsToUse().

Referenced by x_ValidateAlignPercentIdentity().

◆ IsTpaAlignment() [2/2]

bool CValidError_align::IsTpaAlignment ( const CSparseAln &  sparse_aln,
CScope &  scope 
)
staticprivate

Definition at line 285 of file validerror_align.cpp.

References CSeqdesc_Base::e_User, NStr::EqualNocase(), CScope::GetBioseqHandle(), CSparseAln::GetDim(), CSparseAln::GetSeqId(), CObject_id_Base::GetStr(), CUser_object_Base::GetType(), CSeqdesc_Base::GetUser(), CUser_object_Base::IsSetType(), CObject_id_Base::IsStr(), and row.

◆ ValidateSeqAlign()

void CValidError_align::ValidateSeqAlign ( const CSeq_align &  align,
int  order = -1 
)

Definition at line 88 of file validerror_align.cpp.

References CSeq_align_Base::C_Segs::e_Dendiag, CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Disc, CSeq_align_Base::C_Segs::e_not_set, CSeq_align_Base::C_Segs::e_Packed, CSeq_align_Base::C_Segs::e_Sparse, CSeq_align_Base::C_Segs::e_Spliced, CSeq_align_Base::C_Segs::e_Std, eDiag_Error, eDiag_Warning, eErr_SEQ_ALIGN_NullSegs, eErr_SEQ_ALIGN_Segtype, eErr_SEQ_ALIGN_UnexpectedAlignmentType, CSeq_align_Base::eType_global, CSeq_align_Base::eType_partial, CSeq_align_set_Base::Get(), CSeq_align_Base::C_Segs::GetDendiag(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::C_Segs::GetDisc(), GetInvalidSeqAlignTypeStr(), CSeq_align_Base::C_Segs::GetPacked(), CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::GetStd(), CSeq_align_Base::GetType(), CValidError_imp::IsGenomic(), CValidError_imp::IsGpipe(), CSeq_align_Base::IsSetSegs(), CSeq_align_Base::IsSetType(), ITERATE, CValidError_base::m_Imp, CValidError_base::PostErr(), CSeq_align_Base::C_Segs::Which(), x_ValidateAlignPercentIdentity(), x_ValidateDendiag(), x_ValidateDenseg(), x_ValidatePacked(), and x_ValidateStd().

Referenced by CValidError_imp::Validate(), and CValidError_annot::ValidateSeqAnnot().

◆ x_GetIds()

void CValidError_align::x_GetIds ( const CSeq_align &  align,
vector< CRef< CSeq_id > > &  ids 
)
private

Definition at line 1296 of file validerror_align.cpp.

References copy(), CSeq_align_Base::C_Segs::e_Dendiag, CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Packed, CSeq_align_Base::C_Segs::e_Std, CSeq_align_Base::C_Segs::GetDendiag(), CSeq_align_Base::C_Segs::GetDenseg(), GetId(), CDense_seg_Base::GetIds(), CPacked_seg_Base::GetIds(), CSeq_align_Base::C_Segs::GetPacked(), CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::GetStd(), ITERATE, CValidError_base::m_Scope, and CSeq_align_Base::C_Segs::Which().

Referenced by x_ValidateSeqId().

◆ x_ReportAlignErr()

void CValidError_align::x_ReportAlignErr ( const CSeq_align &  align,
const CSeq_id &  id,
const CSeq_id &  id_context,
size_t  segment,
size_t  pos,
EErrType  et,
EDiagSev  sev,
const string &  prefix,
const string &  message 
)
private

Definition at line 1349 of file validerror_align.cpp.

References CValidError_base::PostErr(), prefix, and s_DescribeSegment().

Referenced by x_ReportStartMoreThanBiolen(), x_ReportSumLenStart(), and x_ValidateSeqLength().

◆ x_ReportSegmentGaps()

void CValidError_align::x_ReportSegmentGaps ( const TSegmentGapV &  seggaps,
const CSeq_align &  align 
)
private

Definition at line 1090 of file validerror_align.cpp.

References eDiag_Error, eErr_SEQ_ALIGN_SegmentGap, ITERATE, CValidError_base::PostErr(), and NStr::SizetToString().

Referenced by x_ValidateSegmentGap().

◆ x_ReportStartMoreThanBiolen()

void CValidError_align::x_ReportStartMoreThanBiolen ( const CSeq_align &  align,
const CSeq_id &  id,
const CSeq_id &  id_context,
size_t  segment,
size_t  pos 
)
private

Definition at line 1378 of file validerror_align.cpp.

References eDiag_Error, eErr_SEQ_ALIGN_StartMorethanBiolen, kAlignmentTooLong, and x_ReportAlignErr().

Referenced by x_ValidateSeqLength().

◆ x_ReportSumLenStart()

void CValidError_align::x_ReportSumLenStart ( const CSeq_align &  align,
const CSeq_id &  id,
const CSeq_id &  id_context,
size_t  segment,
size_t  pos 
)
private

Definition at line 1365 of file validerror_align.cpp.

References eDiag_Error, eErr_SEQ_ALIGN_SumLenStart, kAlignmentTooLong, and x_ReportAlignErr().

Referenced by x_ValidateSeqLength().

◆ x_ValidateAlignPercentIdentity()

void CValidError_align::x_ValidateAlignPercentIdentity ( const CSeq_align &  align,
bool  internal_gaps 
)
private

Definition at line 413 of file validerror_align.cpp.

References AlignmentScorePercentIdOk(), BuildAln(), column, CreateAnchoredAlnVec(), eDiag_Warning, eErr_SEQ_ALIGN_PercentIdentity, NStr::Equal(), FindSegmentGaps(), CSparseAln::GetAlnPosFromSeqPos(), CSparseAln::GetAlnRange(), CSparseAln::GetAlnSeqString(), CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CSparseAln::GetDim(), COpenRange< Position >::GetLength(), CSeq_align_Base::GetSegs(), CSparseAln::GetSeqAlnStart(), CSparseAln::GetSeqAlnStop(), CSparseAln::GetSeqPosFromAlnPos(), CSeq_align_Base::C_Segs::GetStd(), NStr::IsBlank(), CSeq_align_Base::C_Segs::IsDenseg(), CSeq_align_Base::IsSetSegs(), CSeq_align_Base::C_Segs::IsStd(), IsTpaAlignment(), CValidError_base::m_Scope, match(), NStr::NumericToString(), CValidError_base::PostErr(), CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::push_back(), row, s_AmbiguousMatch(), s_CalculateMatchingColumns(), s_DensegHasAccessionWithZeroVersion(), s_FixZeroVersions(), s_GetNumIdsToUse(), and tmp.

Referenced by ValidateSeqAlign().

◆ x_ValidateDendiag()

void CValidError_align::x_ValidateDendiag ( const TDendiag &  dendiags,
const CSeq_align &  align 
)
private

Definition at line 676 of file validerror_align.cpp.

References context, eDiag_Error, eErr_SEQ_ALIGN_SegsDimMismatch, eErr_SEQ_ALIGN_SegsDimSeqIdNotMatch, NStr::Find(), CDense_diag_Base::GetDim(), CDense_diag_Base::GetIds(), CDense_diag_Base::GetStarts(), CDense_diag_Base::GetStrands(), CValidError_imp::IsRemoteFetch(), CDense_diag_Base::IsSetStrands(), ITERATE, label, CValidError_base::m_Imp, CValidError_base::PostErr(), NStr::SizetToString(), x_ValidateDim(), x_ValidateSegmentGap(), x_ValidateSeqId(), and x_ValidateSeqLength().

Referenced by ValidateSeqAlign().

◆ x_ValidateDenseg()

void CValidError_align::x_ValidateDenseg ( const TDenseg &  denseg,
const CSeq_align &  align 
)
private

Definition at line 582 of file validerror_align.cpp.

References context, eDiag_Error, eErr_SEQ_ALIGN_AlignDimSeqIdNotMatch, eErr_SEQ_ALIGN_SegsNumsegMismatch, eErr_SEQ_ALIGN_SegsStartsMismatch, NStr::Find(), CValidError_imp::IsRemoteFetch(), label, CValidError_base::m_Imp, CValidError_base::PostErr(), NStr::SizetToString(), x_ValidateDim(), x_ValidateFastaLike(), x_ValidateSegmentGap(), x_ValidateSeqId(), x_ValidateSeqLength(), and x_ValidateStrand().

Referenced by ValidateSeqAlign().

◆ x_ValidateDim()

template<typename T >
bool CValidError_align::x_ValidateDim ( T &  obj,
const CSeq_align &  align,
size_t  part = 0 
)
private

Definition at line 796 of file validerror_align.cpp.

References eDiag_Error, eErr_SEQ_ALIGN_AlignDimOne, eErr_SEQ_ALIGN_SegsDimOne, GetAccessionFromObjects(), CScope::GetBioseqHandle(), CBioseq_Handle::GetCompleteBioseq(), GetReportableSeqIdForAlignment(), label, CValidError_base::m_Scope, CValidError_base::PostErr(), NStr::SizetToString(), and version.

Referenced by x_ValidateDendiag(), x_ValidateDenseg(), x_ValidatePacked(), and x_ValidateStd().

◆ x_ValidateFastaLike()

void CValidError_align::x_ValidateFastaLike ( const TDenseg &  denseg,
const CSeq_align &  align 
)
private

Definition at line 988 of file validerror_align.cpp.

References context, eDiag_Warning, eErr_SEQ_ALIGN_FastaLike, CSeq_align_Base::eType_global, CSeq_align_Base::eType_partial, CScope::GetBioseqHandle(), CSeq_align_Base::GetType(), CValidError_base::m_Scope, CValidError_base::PostErr(), s_GetNumIdsToUse(), and s_PercentBioseqMatch().

Referenced by x_ValidateDenseg().

◆ x_ValidatePacked()

void CValidError_align::x_ValidatePacked ( const TPacked &  packed,
const CSeq_align &  align 
)
private

Definition at line 641 of file validerror_align.cpp.

References eDiag_Error, eErr_SEQ_ALIGN_AlignDimSeqIdNotMatch, eErr_SEQ_ALIGN_SegsDimMismatch, CValidError_imp::IsRemoteFetch(), CValidError_base::m_Imp, CValidError_base::PostErr(), NStr::SizetToString(), x_ValidateDim(), x_ValidateSegmentGap(), x_ValidateSeqId(), and x_ValidateSeqLength().

Referenced by ValidateSeqAlign().

◆ x_ValidateSegmentGap() [1/4]

void CValidError_align::x_ValidateSegmentGap ( const TDendiag &  dendiags,
const CSeq_align &  align 
)
private

Definition at line 1236 of file validerror_align.cpp.

References FindSegmentGaps(), and x_ReportSegmentGaps().

◆ x_ValidateSegmentGap() [2/4]

void CValidError_align::x_ValidateSegmentGap ( const TDenseg &  denseg,
const CSeq_align &  align 
)
private

Definition at line 1109 of file validerror_align.cpp.

References FindSegmentGaps(), and x_ReportSegmentGaps().

Referenced by x_ValidateDendiag(), x_ValidateDenseg(), x_ValidatePacked(), and x_ValidateStd().

◆ x_ValidateSegmentGap() [3/4]

void CValidError_align::x_ValidateSegmentGap ( const TPacked &  packed,
const CSeq_align &  align 
)
private

Definition at line 1157 of file validerror_align.cpp.

References FindSegmentGaps(), and x_ReportSegmentGaps().

◆ x_ValidateSegmentGap() [4/4]

void CValidError_align::x_ValidateSegmentGap ( const TStd &  std_segs,
const CSeq_align &  align 
)
private

Definition at line 1200 of file validerror_align.cpp.

References FindSegmentGaps(), CValidError_base::m_Scope, and x_ReportSegmentGaps().

◆ x_ValidateSeqId()

void CValidError_align::x_ValidateSeqId ( const CSeq_align &  align)
private

Definition at line 1251 of file validerror_align.cpp.

References eDiag_Error, eErr_SEQ_ALIGN_NucProtMixture, eErr_SEQ_ALIGN_SeqIdProblem, CScope::GetBioseqHandle(), CBioseq_Handle::IsAa(), CBioseq_Handle::IsNa(), ITERATE, CValidError_base::m_Scope, CValidError_base::PostErr(), and x_GetIds().

Referenced by x_ValidateDendiag(), x_ValidateDenseg(), x_ValidatePacked(), and x_ValidateStd().

◆ x_ValidateSeqLength() [1/4]

void CValidError_align::x_ValidateSeqLength ( const CDense_diag &  dendiag,
size_t  dendiag_num,
const CSeq_align &  align 
)
private

Definition at line 1400 of file validerror_align.cpp.

References CDense_diag_Base::GetDim(), CDense_diag_Base::GetIds(), CDense_diag_Base::GetLen(), GetLength(), CDense_diag_Base::GetStarts(), len, CValidError_base::m_Scope, x_ReportStartMoreThanBiolen(), and x_ReportSumLenStart().

◆ x_ValidateSeqLength() [2/4]

void CValidError_align::x_ValidateSeqLength ( const TDenseg &  denseg,
const CSeq_align &  align 
)
private

Definition at line 1433 of file validerror_align.cpp.

References eDiag_Error, eErr_SEQ_ALIGN_DensegLenStart, eNa_strand_minus, GetLength(), CValidError_base::m_Scope, minus(), CValidError_base::PostErr(), s_DescribeSegment(), and x_ReportSumLenStart().

Referenced by x_ValidateDendiag(), x_ValidateDenseg(), x_ValidatePacked(), and x_ValidateStd().

◆ x_ValidateSeqLength() [3/4]

void CValidError_align::x_ValidateSeqLength ( const TPacked &  packed,
const CSeq_align &  align 
)
private

Definition at line 1501 of file validerror_align.cpp.

References CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), i, label, CValidError_base::m_Scope, x_ReportStartMoreThanBiolen(), and x_ReportSumLenStart().

◆ x_ValidateSeqLength() [4/4]

void CValidError_align::x_ValidateSeqLength ( const TStd &  std_segs,
const CSeq_align &  align 
)
private

Definition at line 1541 of file validerror_align.cpp.

References eDiag_Error, eErr_SEQ_ALIGN_EndLessthanZero, eErr_SEQ_ALIGN_EndMorethanBiolen, eErr_SEQ_ALIGN_LenMorethanBiolen, eErr_SEQ_ALIGN_StartLessthanZero, CRange_Base::GetFrom(), GetId(), CSeq_loc::GetId(), CStd_seg_Base::GetIds(), GetLength(), CStd_seg_Base::GetLoc(), CRange_Base::GetTo(), CSeq_loc::GetTotalRange(), CSeq_loc_Base::IsEmpty(), CSeq_loc_Base::IsNull(), IsOneBioseq(), CStd_seg_Base::IsSetIds(), CSeq_loc_Base::IsWhole(), ITERATE, kAlignmentTooLong, CValidError_base::m_Scope, NStr::UIntToString(), x_ReportAlignErr(), and x_ReportStartMoreThanBiolen().

◆ x_ValidateStd()

void CValidError_align::x_ValidateStd ( const TStd &  stdsegs,
const CSeq_align &  align 
)
private

Definition at line 741 of file validerror_align.cpp.

References context, eDiag_Error, eErr_SEQ_ALIGN_SegsDimMismatch, eErr_SEQ_ALIGN_SegsDimSeqIdNotMatch, NStr::Find(), CStd_seg_Base::GetDim(), CStd_seg_Base::GetIds(), CStd_seg_Base::GetLoc(), CValidError_imp::IsRemoteFetch(), CStd_seg_Base::IsSetIds(), ITERATE, label, CValidError_base::m_Imp, CValidError_base::PostErr(), NStr::SizetToString(), x_ValidateDim(), x_ValidateSegmentGap(), x_ValidateSeqId(), x_ValidateSeqLength(), and x_ValidateStrand().

Referenced by ValidateSeqAlign().

◆ x_ValidateStrand() [1/2]

void CValidError_align::x_ValidateStrand ( const TDenseg &  denseg,
const CSeq_align &  align 
)
private

Definition at line 846 of file validerror_align.cpp.

References eDiag_Error, eErr_SEQ_ALIGN_StrandRev, eNa_strand_other, eNa_strand_unknown, CValidError_base::PostErr(), and NStr::SizetToString().

Referenced by x_ValidateDenseg(), and x_ValidateStd().

◆ x_ValidateStrand() [2/2]

void CValidError_align::x_ValidateStrand ( const TStd &  std_segs,
const CSeq_align &  align 
)
private

Definition at line 901 of file validerror_align.cpp.

References eDiag_Error, eErr_SEQ_ALIGN_StrandRev, eExtreme_Positional, eNa_strand_other, eNa_strand_unknown, GetId(), CSeq_loc::GetStart(), GetStrand(), NStr::IntToString(), IsOneBioseq(), ITERATE, CValidError_base::m_Scope, and CValidError_base::PostErr().

The documentation for this class was generated from the following files:
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