NCBI C++ ToolKit
Typedefs | Enumerations | Functions | Variables
translation_problems.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbistr.hpp>
#include <objtools/validator/translation_problems.hpp>
#include <objtools/validator/utilities.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/util/sequence.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqfeat/Code_break.hpp>
#include <objects/seqfeat/Gb_qual.hpp>
#include <objects/seqfeat/Genetic_code.hpp>
#include <util/sequtil/sequtil_convert.hpp>
+ Include dependency graph for translation_problems.cpp:

Go to the source code of this file.

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Typedefs

typedef CStaticArraySet< const char *, PCase_CStrTBypassMrnaTransCheckSet
 

Enumerations

enum  EMRNAException {
  eMRNAExcept_Biological = 1 , eMRNAExcept_RNAEditing = 2 , eMRNAExcept_Unclassified = 4 , eMRNAExcept_Mismatch = 8 ,
  eMRNAExcept_ProductReplaced = 16
}
 

Functions

static bool x_LeuCUGstart (const CSeq_feat &feat)
 
 DEFINE_STATIC_ARRAY_MAP (TBypassMrnaTransCheckSet, sc_BypassMrnaTransCheck, sc_BypassMrnaTransCheckText)
 
size_t InterpretMrnaException (const string &except_text)
 
size_t GetMRNATranslationProblems (const CSeq_feat &feat, size_t &mismatches, bool ignore_exceptions, CBioseq_Handle nuc, CBioseq_Handle rna, bool far_fetch, bool is_gpipe, bool is_genomic, CScope *scope)
 

Variables

static const char *const sc_BypassMrnaTransCheckText []
 

Typedef Documentation

◆ TBypassMrnaTransCheckSet

Definition at line 972 of file translation_problems.cpp.

Enumeration Type Documentation

◆ EMRNAException

Enumerator
eMRNAExcept_Biological 
eMRNAExcept_RNAEditing 
eMRNAExcept_Unclassified 
eMRNAExcept_Mismatch 
eMRNAExcept_ProductReplaced 

Definition at line 956 of file translation_problems.cpp.

Function Documentation

◆ DEFINE_STATIC_ARRAY_MAP()

DEFINE_STATIC_ARRAY_MAP ( TBypassMrnaTransCheckSet  ,
sc_BypassMrnaTransCheck  ,
sc_BypassMrnaTransCheckText   
)

◆ GetMRNATranslationProblems()

size_t GetMRNATranslationProblems ( const CSeq_feat feat,
size_t &  mismatches,
bool  ignore_exceptions,
CBioseq_Handle  nuc,
CBioseq_Handle  rna,
bool  far_fetch,
bool  is_gpipe,
bool  is_genomic,
CScope scope 
)

◆ InterpretMrnaException()

size_t InterpretMrnaException ( const string except_text)

◆ x_LeuCUGstart()

static bool x_LeuCUGstart ( const CSeq_feat feat)
static

Variable Documentation

◆ sc_BypassMrnaTransCheckText

const char* const sc_BypassMrnaTransCheckText[]
static
Initial value:
= {
"RNA editing",
"adjusted for low-quality genome",
"annotated by transcript or proteomic data",
"artificial frameshift",
"reasons given in citation",
"transcribed product replaced",
"unclassified transcription discrepancy",
}

Definition at line 963 of file translation_problems.cpp.

Modified on Sat May 25 14:21:01 2024 by modify_doxy.py rev. 669887