Search Toolkit Book for CCDSTranslationProblems
#include <objtools/validator/translation_problems.hpp>
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enum | ECDSTranslationProblem {
eCDSTranslationProblem_FrameNotPartial = 1
, eCDSTranslationProblem_FrameNotConsensus = 2
, eCDSTranslationProblem_NoStop = 4
, eCDSTranslationProblem_StopPartial = 8
,
eCDSTranslationProblem_PastStop = 16
, eCDSTranslationProblem_ShouldStartPartial = 32
, eCDSTranslationProblem_Mismatches = 64
, eCDSTranslationProblem_BadStart = 128
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eCDSTranslationProblem_TooManyX = 256
, eCDSTranslationProblem_UnableToFetch = 512
, eCDSTranslationProblem_NoProtein = 1024
, eCDSTranslationProblem_ShouldBePartialButIsnt = 2048
,
eCDSTranslationProblem_ShouldNotBePartialButIs = 4096
, eCDSTranslationProblem_UnnecessaryException = 8192
, eCDSTranslationProblem_UnqualifiedException = 16384
, eCDSTranslationProblem_ErroneousException = 32768
} |
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enum | ETranslExceptType { eTranslExceptPhase = 0
, eTranslExceptSuspicious
, eTranslExceptUnnecessary
, eTranslExceptUnexpected
} |
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typedef vector< STranslExceptProblem > | TTranslExceptProblems |
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typedef vector< STranslationMismatch > | TTranslationMismatches |
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| CCDSTranslationProblems () |
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| ~CCDSTranslationProblems () |
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void | CalculateTranslationProblems (const CSeq_feat &feat, CBioseq_Handle loc_handle, CBioseq_Handle prot_handle, bool ignore_exceptions, bool far_fetch_cds, bool standalone_annot, bool single_seq, bool is_gpipe, bool is_genomic, bool is_refseq, bool is_nt_or_ng_or_nw, bool is_nc, bool has_accession, CScope *scope) |
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size_t | GetTranslationProblemFlags () const |
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const TTranslExceptProblems & | GetTranslExceptProblems () const |
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const TTranslationMismatches & | GetTranslationMismatches () const |
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bool | HasException () const |
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bool | UnableToTranslate () const |
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bool | HasUnparsedTranslExcept () const |
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size_t | GetInternalStopCodons () const |
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size_t | GetNumNonsenseIntrons () const |
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bool | AltStart () const |
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char | GetTranslStartCharacter () const |
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int | GetRaggedLength () const |
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size_t | GetProtLen () const |
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size_t | GetTransLen () const |
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size_t | GetTranslTerminalX () const |
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size_t | GetProdTerminalX () const |
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static size_t | x_CountNonsenseIntrons (const CSeq_feat &feat, CScope *scope) |
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static bool | x_ProteinHasTooManyXs (const string &transl_prot) |
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static bool | x_IsThreeBaseNonsense (const CSeq_feat &feat, const CSeq_id &id, const CCdregion &cdr, TSeqPos start, TSeqPos stop, ENa_strand strand, CScope *scope) |
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static void | x_GetExceptionFlags (const string &except_text, bool &unclassified_except, bool &mismatch_except, bool &frameshift_except, bool &rearrange_except, bool &product_replaced, bool &mixed_population, bool &low_quality, bool &rna_editing, bool &transcript_or_proteomic) |
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static size_t | x_CheckCDSFrame (const CSeq_feat &feat, CScope *scope) |
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static bool | x_Is5AtEndSpliceSiteOrGap (const CSeq_loc &loc, CScope &scope) |
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static size_t | x_CountTerminalXs (const string &transl_prot, bool skip_stop) |
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static size_t | x_CountTerminalXs (const CSeqVector &prot_vec) |
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static TTranslationMismatches | x_GetTranslationMismatches (const CSeq_feat &feat, const CSeqVector &prot_vec, const string &transl_prot, bool has_accession) |
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static bool | x_JustifiesException (const TTranslExceptProblems &problems) |
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static int | x_CheckForRaggedEnd (const CSeq_feat &feat, CScope *scope) |
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static int | x_CheckForRaggedEnd (const CSeq_loc &, const CCdregion &cdr, CScope *scope) |
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Definition at line 56 of file translation_problems.hpp.
◆ TTranslationMismatches
◆ TTranslExceptProblems
◆ ECDSTranslationProblem
Enumerator |
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eCDSTranslationProblem_FrameNotPartial | |
eCDSTranslationProblem_FrameNotConsensus | |
eCDSTranslationProblem_NoStop | |
eCDSTranslationProblem_StopPartial | |
eCDSTranslationProblem_PastStop | |
eCDSTranslationProblem_ShouldStartPartial | |
eCDSTranslationProblem_Mismatches | |
eCDSTranslationProblem_BadStart | |
eCDSTranslationProblem_TooManyX | |
eCDSTranslationProblem_UnableToFetch | |
eCDSTranslationProblem_NoProtein | |
eCDSTranslationProblem_ShouldBePartialButIsnt | |
eCDSTranslationProblem_ShouldNotBePartialButIs | |
eCDSTranslationProblem_UnnecessaryException | |
eCDSTranslationProblem_UnqualifiedException | |
eCDSTranslationProblem_ErroneousException | |
Definition at line 77 of file translation_problems.hpp.
◆ ETranslExceptType
Enumerator |
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eTranslExceptPhase | |
eTranslExceptSuspicious | |
eTranslExceptUnnecessary | |
eTranslExceptUnexpected | |
Definition at line 99 of file translation_problems.hpp.
◆ CCDSTranslationProblems()
CCDSTranslationProblems::CCDSTranslationProblems |
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◆ ~CCDSTranslationProblems()
CCDSTranslationProblems::~CCDSTranslationProblems |
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◆ AltStart()
bool CCDSTranslationProblems::AltStart |
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const |
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◆ CalculateTranslationProblems()
void CCDSTranslationProblems::CalculateTranslationProblems |
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const CSeq_feat & |
feat, |
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CBioseq_Handle |
loc_handle, |
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CBioseq_Handle |
prot_handle, |
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bool |
ignore_exceptions, |
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bool |
far_fetch_cds, |
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bool |
standalone_annot, |
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bool |
single_seq, |
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bool |
is_gpipe, |
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bool |
is_genomic, |
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bool |
is_refseq, |
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bool |
is_nt_or_ng_or_nw, |
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bool |
is_nc, |
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bool |
has_accession, |
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CScope * |
scope |
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) |
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Definition at line 78 of file translation_problems.cpp.
References CalculateEffectiveTranslationLengths(), CSeq_feat_Base::CanGetPartial(), CountInternalStopCodons(), CSeq_data_Base::e_Ncbieaa, NStr::EndsWith(), NStr::Equal(), NStr::EqualNocase(), FeatureHasEnds(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetExcept(), CSeq_feat_Base::GetExcept_text(), GetId(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetPartial(), CSeq_feat_Base::GetProduct(), CSeq_feat_Base::GetQual(), CBioseq_Handle::GetSeqVector(), HasBadStartCodon(), CBioseq_Handle::IsAa(), CSeqFeatData_Base::IsCdregion(), CSeq_feat_Base::IsSetExcept(), CSeq_feat_Base::IsSetExcept_text(), CSeq_feat_Base::IsSetPartial(), CSeq_feat_Base::IsSetProduct(), CSeq_feat_Base::IsSetQual(), ReportTranslationErrors(), CSeqVector::SetCoding(), CSeqVector::size(), and TranslateCodingRegionForValidation().
Referenced by DoesCodingRegionHaveUnnecessaryException(), and CCdregionValidator::x_ValidateTrans().
◆ GetInternalStopCodons()
size_t CCDSTranslationProblems::GetInternalStopCodons |
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const |
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◆ GetNonsenseIntrons()
Definition at line 381 of file translation_problems.cpp.
References eNa_strand_minus, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetLocation(), CSeqFeatData_Base::IsCdregion(), IsPseudo(), IsSameBioseq(), CCdregion_Base::IsSetCode_break(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetExcept(), CSeq_feat_Base::IsSetExcept_text(), and prev().
Referenced by BOOST_AUTO_TEST_CASE(), and CCdregionValidator::ReportShortIntrons().
◆ GetNumNonsenseIntrons()
size_t CCDSTranslationProblems::GetNumNonsenseIntrons |
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const |
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◆ GetProdTerminalX()
size_t CCDSTranslationProblems::GetProdTerminalX |
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const |
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◆ GetProtLen()
size_t CCDSTranslationProblems::GetProtLen |
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const |
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◆ GetRaggedLength()
int CCDSTranslationProblems::GetRaggedLength |
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const |
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◆ GetTranslationMismatches()
◆ GetTranslationProblemFlags()
size_t CCDSTranslationProblems::GetTranslationProblemFlags |
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const |
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◆ GetTransLen()
size_t CCDSTranslationProblems::GetTransLen |
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const |
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◆ GetTranslExceptProblems()
◆ GetTranslStartCharacter()
char CCDSTranslationProblems::GetTranslStartCharacter |
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const |
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◆ GetTranslTerminalX()
size_t CCDSTranslationProblems::GetTranslTerminalX |
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const |
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◆ HasException()
bool CCDSTranslationProblems::HasException |
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const |
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◆ HasUnparsedTranslExcept()
bool CCDSTranslationProblems::HasUnparsedTranslExcept |
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const |
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◆ UnableToTranslate()
bool CCDSTranslationProblems::UnableToTranslate |
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const |
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◆ x_CheckCDSFrame()
Definition at line 498 of file translation_problems.cpp.
References CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, eSeqlocPartial_Nostart, eSeqlocPartial_Start, NStr::Find(), CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetComment(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::IsSetComment(), CCdregion_Base::IsSetFrame(), location, s_PartialAtGapOrNs(), and SeqLocPartialCheck().
◆ x_CheckForRaggedEnd() [1/2]
◆ x_CheckForRaggedEnd() [2/2]
◆ x_CountNonsenseIntrons()
Definition at line 337 of file translation_problems.cpp.
References count, eNa_strand_minus, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetLocation(), CSeqFeatData_Base::IsCdregion(), IsPseudo(), IsSameBioseq(), CCdregion_Base::IsSetCode_break(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetExcept(), CSeq_feat_Base::IsSetExcept_text(), and prev().
◆ x_CountTerminalXs() [1/2]
size_t CCDSTranslationProblems::x_CountTerminalXs |
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const CSeqVector & |
prot_vec | ) |
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staticprivate |
◆ x_CountTerminalXs() [2/2]
size_t CCDSTranslationProblems::x_CountTerminalXs |
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const string & |
transl_prot, |
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bool |
skip_stop |
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◆ x_GetCdTransErrors()
◆ x_GetExceptionFlags()
void CCDSTranslationProblems::x_GetExceptionFlags |
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const string & |
except_text, |
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bool & |
unclassified_except, |
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bool & |
mismatch_except, |
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bool & |
frameshift_except, |
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bool & |
rearrange_except, |
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bool & |
product_replaced, |
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bool & |
mixed_population, |
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bool & |
low_quality, |
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bool & |
rna_editing, |
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bool & |
transcript_or_proteomic |
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) |
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staticprivate |
◆ x_GetTranslationMismatches()
◆ x_GetTranslExceptProblems()
Definition at line 644 of file translation_problems.cpp.
References CCdregion_Base::CanGetCode(), Compare(), CSeqConvert::Convert(), CCode_break_Base::C_Aa::e_Ncbi8aa, CSeqUtil::e_Ncbi8aa, CCode_break_Base::C_Aa::e_Ncbieaa, CSeqUtil::e_Ncbieaa, CCode_break_Base::C_Aa::e_Ncbistdaa, CSeqUtil::e_Ncbistdaa, CBioseq_Handle::eCoding_Iupac, eContained, eExtreme_Biological, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, eOffset_FromEnd, eOffset_FromStart, NStr::Equal(), NStr::EqualNocase(), eSame, fCompareOverlapping, CSeqTranslator::fIs5PrimePartial, CSeqFeatData_Base::GetCdregion(), CCdregion_Base::GetCode(), CCdregion_Base::GetCode_break(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), GetLength(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetPartial(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CSeqFeatData_Base::IsCdregion(), CCdregion_Base::IsSetCode(), CCdregion_Base::IsSetCode_break(), CSeq_feat_Base::IsSetData(), CCdregion_Base::IsSetFrame(), CSeq_feat_Base::IsSetPartial(), len, LocationOffset(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), str(), CSeqTranslator::Translate(), and x_LeuCUGstart().
◆ x_Is5AtEndSpliceSiteOrGap()
Definition at line 833 of file translation_problems.cpp.
References ConsistentWithA(), ConsistentWithC(), ConsistentWithG(), ConsistentWithT(), CBioseq_Handle::eCoding_Iupac, eExtreme_Biological, eNa_strand_minus, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetSeqVector(), CSeq_loc::GetStart(), CSeq_loc::GetStrand(), CSeqVector::IsInGap(), and IsResidue().
◆ x_IsThreeBaseNonsense()
◆ x_JustifiesException() [1/2]
bool CCDSTranslationProblems::x_JustifiesException |
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const |
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◆ x_JustifiesException() [2/2]
◆ x_ProteinHasTooManyXs()
bool CCDSTranslationProblems::x_ProteinHasTooManyXs |
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const string & |
transl_prot | ) |
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staticprivate |
◆ x_Reset()
void CCDSTranslationProblems::x_Reset |
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void |
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◆ m_AltStart
bool CCDSTranslationProblems::m_AltStart |
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◆ m_HasDashXStart
bool CCDSTranslationProblems::m_HasDashXStart |
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◆ m_HasException
bool CCDSTranslationProblems::m_HasException |
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◆ m_InternalStopCodons
size_t CCDSTranslationProblems::m_InternalStopCodons |
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◆ m_Mismatches
◆ m_NumNonsenseIntrons
size_t CCDSTranslationProblems::m_NumNonsenseIntrons |
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◆ m_ProblemFlags
size_t CCDSTranslationProblems::m_ProblemFlags |
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◆ m_ProdTerminalX
size_t CCDSTranslationProblems::m_ProdTerminalX |
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◆ m_ProtLen
size_t CCDSTranslationProblems::m_ProtLen |
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◆ m_RaggedLength
int CCDSTranslationProblems::m_RaggedLength |
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◆ m_TransLen
size_t CCDSTranslationProblems::m_TransLen |
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◆ m_TranslExceptProblems
◆ m_TranslStart
char CCDSTranslationProblems::m_TranslStart |
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◆ m_TranslTerminalX
size_t CCDSTranslationProblems::m_TranslTerminalX |
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◆ m_UnableToTranslate
bool CCDSTranslationProblems::m_UnableToTranslate |
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◆ m_UnparsedTranslExcept
bool CCDSTranslationProblems::m_UnparsedTranslExcept |
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The documentation for this class was generated from the following files: