NCBI C++ ToolKit
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#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>
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Typedefs | |
typedef CStaticArraySet< const char *, PCase_CStr > | TBypassMrnaTransCheckSet |
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 CStaticArraySet<const char*, PCase_CStr> TBypassMrnaTransCheckSet |
Definition at line 972 of file translation_problems.cpp.
enum EMRNAException |
Enumerator | |
---|---|
eMRNAExcept_Biological | |
eMRNAExcept_RNAEditing | |
eMRNAExcept_Unclassified | |
eMRNAExcept_Mismatch | |
eMRNAExcept_ProductReplaced |
Definition at line 956 of file translation_problems.cpp.
DEFINE_STATIC_ARRAY_MAP | ( | TBypassMrnaTransCheckSet | , |
sc_BypassMrnaTransCheck | , | ||
sc_BypassMrnaTransCheckText | |||
) |
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 | ||
) |
Definition at line 1000 of file translation_problems.cpp.
References _ASSERT, CSeq_feat_Base::CanGetExcept(), CSeq_feat_Base::CanGetExcept_text(), CSeq_feat_Base::CanGetProduct(), CSeq_feat_Base::CanGetPseudo(), CBioseq_Handle::eCoding_Iupac, eMRNAExcept_Biological, eMRNAExcept_Mismatch, eMRNAExcept_ProductReplaced, eMRNAExcept_RNAEditing, eMRNAExcept_Unclassified, eMRNAProblem_ErroneousException, eMRNAProblem_Mismatch, eMRNAProblem_PolyATail100, eMRNAProblem_PolyATail95, eMRNAProblem_ProductReplaced, eMRNAProblem_TranscriptLenLess, eMRNAProblem_TranscriptLenMore, eMRNAProblem_TransFail, eMRNAProblem_UnableToFetch, eMRNAProblem_UnnecessaryException, CSeq_feat_Base::GetExcept(), CSeq_feat_Base::GetExcept_text(), GetId(), CSeq_feat_Base::GetLocation(), CSeqVector_CI::GetPos(), CSeq_feat_Base::GetProduct(), CSeq_feat_Base::GetPseudo(), InterpretMrnaException(), min(), nuc, CConstRef< C, Locker >::Reset(), rna, and CSeqVector::size().
Referenced by DoesmRNAHaveUnnecessaryException(), and CRNAValidator::x_ValidateRnaTrans().
Definition at line 976 of file translation_problems.cpp.
References eMRNAExcept_Biological, eMRNAExcept_Mismatch, eMRNAExcept_ProductReplaced, eMRNAExcept_RNAEditing, eMRNAExcept_Unclassified, NStr::FindNoCase(), ITERATE, and NPOS.
Referenced by GetMRNATranslationProblems().
Definition at line 625 of file translation_problems.cpp.
References NStr::Compare(), NStr::FindNoCase(), CSeq_feat_Base::GetExcept_text(), CGb_qual_Base::GetQual(), CSeq_feat_Base::GetQual(), CSeq_feat_Base::IsSetExcept(), CSeq_feat_Base::IsSetExcept_text(), CGb_qual_Base::IsSetQual(), CSeq_feat_Base::IsSetQual(), and NPOS.
Referenced by CCDSTranslationProblems::x_GetTranslExceptProblems().
Definition at line 963 of file translation_problems.cpp.