NCBI C++ ToolKit
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CValidError_graph Class Reference

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#include <objtools/validator/validerror_graph.hpp>

+ Inheritance diagram for CValidError_graph:
+ Collaboration diagram for CValidError_graph:

Public Member Functions

 CValidError_graph (CValidError_imp &imp)
 
 ~CValidError_graph () override
 
void ValidateSeqGraph (const CSeq_graph &graph)
 
void ValidateSeqGraphContext (const CSeq_graph &graph, const CBioseq_set &set)
 
void ValidateSeqGraphContext (const CSeq_graph &graph, const CBioseq &seq)
 
void ValidateGraphsOnBioseq (const CBioseq &seq)
 

Static Public Member Functions

static bool IsSupportedGraphType (const CSeq_graph &graph)
 

Private Member Functions

void x_ValidateMinValues (const CByte_graph &bg, const CSeq_graph &graph)
 
void x_ValidateMaxValues (const CByte_graph &bg, const CSeq_graph &graph)
 
bool x_ValidateGraphLocation (const CSeq_graph &graph)
 
void x_ValidateGraphOrderOnBioseq (const CBioseq &seq, vector< CRef< CSeq_graph > > graph_list)
 
void x_ValidateGraphValues (const CSeq_graph &graph, const CBioseq &seq, int &first_N, int &first_ACGT, size_t &num_bases, size_t &Ns_with_score, size_t &gaps_with_score, size_t &ACGTs_without_score, size_t &vals_below_min, size_t &vals_above_max)
 
void x_ValidateGraphOnDeltaBioseq (const CBioseq &seq)
 
SIZE_TYPE GetUngappedSeqLen (const CBioseq &seq)
 
bool x_GetLitLength (const CDelta_seq &delta, TSeqPos &len)
 
- 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)
 
CCacheImplGetCache ()
 

Additional Inherited Members

- Static Private Member Functions inherited from CValidError_base
static CSeq_entry_Handle GetAppropriateXrefParent (CSeq_entry_Handle seh)
 
- Private Attributes inherited from CValidError_base
CValidError_impm_Imp
 
CScopem_Scope
 

Detailed Description

Definition at line 58 of file validerror_graph.hpp.

Constructor & Destructor Documentation

◆ CValidError_graph()

CValidError_graph::CValidError_graph ( CValidError_imp imp)

Definition at line 48 of file validerror_graph.cpp.

◆ ~CValidError_graph()

CValidError_graph::~CValidError_graph ( )
override

Definition at line 54 of file validerror_graph.cpp.

Member Function Documentation

◆ GetUngappedSeqLen()

SIZE_TYPE CValidError_graph::GetUngappedSeqLen ( const CBioseq seq)
private

◆ IsSupportedGraphType()

bool CValidError_graph::IsSupportedGraphType ( const CSeq_graph graph)
static

◆ ValidateGraphsOnBioseq()

void CValidError_graph::ValidateGraphsOnBioseq ( const CBioseq seq)

◆ ValidateSeqGraph()

void CValidError_graph::ValidateSeqGraph ( const CSeq_graph graph)

◆ ValidateSeqGraphContext() [1/2]

void CValidError_graph::ValidateSeqGraphContext ( const CSeq_graph graph,
const CBioseq seq 
)

◆ ValidateSeqGraphContext() [2/2]

void CValidError_graph::ValidateSeqGraphContext ( const CSeq_graph graph,
const CBioseq_set set 
)

◆ x_GetLitLength()

bool CValidError_graph::x_GetLitLength ( const CDelta_seq delta,
TSeqPos len 
)
private

◆ x_ValidateGraphLocation()

bool CValidError_graph::x_ValidateGraphLocation ( const CSeq_graph graph)
private

◆ x_ValidateGraphOnDeltaBioseq()

void CValidError_graph::x_ValidateGraphOnDeltaBioseq ( const CBioseq seq)
private

◆ x_ValidateGraphOrderOnBioseq()

void CValidError_graph::x_ValidateGraphOrderOnBioseq ( const CBioseq seq,
vector< CRef< CSeq_graph > >  graph_list 
)
private

◆ x_ValidateGraphValues()

void CValidError_graph::x_ValidateGraphValues ( const CSeq_graph graph,
const CBioseq seq,
int first_N,
int first_ACGT,
size_t &  num_bases,
size_t &  Ns_with_score,
size_t &  gaps_with_score,
size_t &  ACGTs_without_score,
size_t &  vals_below_min,
size_t &  vals_above_max 
)
private

◆ x_ValidateMaxValues()

void CValidError_graph::x_ValidateMaxValues ( const CByte_graph bg,
const CSeq_graph graph 
)
private

◆ x_ValidateMinValues()

void CValidError_graph::x_ValidateMinValues ( const CByte_graph bg,
const CSeq_graph graph 
)
private

The documentation for this class was generated from the following files:
Modified on Sat Dec 02 09:21:21 2023 by modify_doxy.py rev. 669887