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USING_SCOPE (objects) USING_SCOPE (gnomon) EKozakStrength s_GetKozakStrength (const CSeqVector &vec, TSeqPos pos) string s_KozakStrengthToString (EKozakStrength strength) static CSeqVector s_GetCdregionPlusUpstream (CFeat_CI feat_iter, const CSeqTestContext *ctx, TSeqPos &upstream_length) CConstRef< CGenetic_code > s_GetCode (const CCdregion &cdr) static void s_CdsFlags (const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result) static void s_InframeUpstreamStart (const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result) static void s_InframeUpstreamStop (const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result) static void s_CodingPropensity (const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result) static void s_CdsLength (const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result) static void s_Utrs (const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result) static void s_CdsStartCodon (const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result) static void s_CdsStopCodon (const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result) TSeqPos CodeBreakPosInCds (const CCode_break &code_break, const CSeq_feat &feat, CScope &scope) static bool s_IsSelenocysteine (const CCode_break &code_break) static bool s_IsSelenocysteine (TSeqPos pos_in_cds, CFeat_CI feat_iter, CScope &scope) static void s_PrematureStopCodon (const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result) static CConstRef< CSeq_id > s_FindLatest (const CSeq_id &id, CScope &scope) static void s_CompareProtProdToTrans (const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result) void TestStrongKozakUorfs (const CBioseq_Handle bsh, CSeq_test_result &result) static void s_Code_break (const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result) static void s_OrfExtension (const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result) static TSeqPos s_CountAmbiguities (const CSeqVector &vec) static void s_CdsCountAmbiguities (const CSeq_id &id, const CSeqTestContext *ctx, CFeat_CI feat_iter, CSeq_test_result &result) ◆ EKozakStrength ◆ CodeBreakPosInCds() ◆ s_CdsCountAmbiguities() ◆ s_CdsFlags() ◆ s_CdsLength() ◆ s_CdsStartCodon()Definition at line 425 of file xcript_tests.cpp.
References ctx, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Handle::GetData(), CSeqVector::GetSeqData(), CGen_code_table::GetTransTable(), CTrans_table::IsOrfStart(), result, s_GetCdregionPlusUpstream(), s_GetCode(), s_GetKozakStrength(), s_KozakStrengthToString(), CTrans_table::SetCodonState(), and CSeqVector::SetIupacCoding().
Referenced by CTestTranscript_CdsStartCodon::RunTest().
◆ s_CdsStopCodon()Definition at line 461 of file xcript_tests.cpp.
References ctx, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Handle::GetData(), CMappedFeat::GetLocation(), CSeqVector::GetSeqData(), CGen_code_table::GetTransTable(), CTrans_table::IsOrfStop(), result, s_GetCode(), CTrans_table::SetCodonState(), CSeqVector::SetIupacCoding(), and CSeqVector::size().
Referenced by CTestTranscript_CdsStopCodon::RunTest().
◆ s_Code_break()Definition at line 883 of file xcript_tests.cpp.
References CodeBreakPosInCds(), count, ctx, CSeqFeatData_Base::GetCdregion(), CCdregion_Base::GetCode_break(), CSeq_feat_Handle::GetData(), CMappedFeat::GetOriginalFeature(), CCdregion_Base::IsSetCode_break(), ITERATE, result, and s_IsSelenocysteine().
Referenced by CTestTranscript_Code_break::RunTest().
◆ s_CodingPropensity() ◆ s_CompareProtProdToTrans()Definition at line 612 of file xcript_tests.cpp.
References CSeq_id::AsFastaString(), CSeq_feat_Base::CanGetProduct(), ctx, CSerialObject::Equals(), GetId(), CMappedFeat::GetOriginalFeature(), CSeq_feat_Base::GetProduct(), CBioseq_Handle::GetSeqVector(), i, max(), min(), result, s_FindLatest(), CSeqVector::SetIupacCoding(), CSeqVector::size(), and CSeqTranslator::Translate().
Referenced by CTestTranscript_CompareProtProdToTrans::RunTest().
◆ s_CountAmbiguities() ◆ s_FindLatest() ◆ s_GetCdregionPlusUpstream()Definition at line 157 of file xcript_tests.cpp.
References ctx, eNa_strand_minus, CSeq_loc_CI::GetEmbeddingSeq_loc(), GetId(), GetLength(), CMappedFeat::GetLocation(), GetStart(), GetStop(), GetStrand(), CSeq_loc::SetInt(), and CSeq_loc::SetMix().
Referenced by s_CdsStartCodon(), s_InframeUpstreamStart(), s_InframeUpstreamStop(), and s_OrfExtension().
◆ s_GetCode() ◆ s_GetKozakStrength() ◆ s_InframeUpstreamStart() ◆ s_InframeUpstreamStop()Definition at line 266 of file xcript_tests.cpp.
References ctx, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Handle::GetData(), CGen_code_table::GetTransTable(), i, CTrans_table::IsOrfStop(), result, s_GetCdregionPlusUpstream(), s_GetCode(), CTrans_table::SetCodonState(), and CSeqVector::SetIupacCoding().
Referenced by CTestTranscript_InframeUpstreamStop::RunTest().
◆ s_IsSelenocysteine() [1/2]Definition at line 496 of file xcript_tests.cpp.
References CCode_break_Base::C_Aa::e_Ncbi8aa, CCode_break_Base::C_Aa::e_Ncbieaa, CCode_break_Base::C_Aa::e_Ncbistdaa, CCode_break_Base::C_Aa::e_not_set, CCode_break_Base::GetAa(), CCode_break_Base::C_Aa::GetNcbi8aa(), CCode_break_Base::C_Aa::GetNcbieaa(), CCode_break_Base::C_Aa::GetNcbistdaa(), and CCode_break_Base::C_Aa::Which().
Referenced by s_Code_break(), s_IsSelenocysteine(), and s_PrematureStopCodon().
◆ s_IsSelenocysteine() [2/2] ◆ s_KozakStrengthToString() ◆ s_OrfExtension() ◆ s_PrematureStopCodon()Definition at line 531 of file xcript_tests.cpp.
References ctx, CCdregion_Base::eFrame_not_set, CCdregion_Base::eFrame_one, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Handle::GetData(), CCdregion_Base::GetFrame(), CMappedFeat::GetLocation(), CGen_code_table::GetTransTable(), i, CTrans_table::IsOrfStop(), kInvalidSeqPos, result, s_GetCode(), s_IsSelenocysteine(), CTrans_table::SetCodonState(), CSeqVector::SetIupacCoding(), and CSeqVector::size().
Referenced by CTestTranscript_PrematureStopCodon::RunTest().
◆ s_Utrs() ◆ TestStrongKozakUorfs() ◆ USING_SCOPE() [1/2] ◆ USING_SCOPE() [2/2]RetroSearch is an open source project built by @garambo | Open a GitHub Issue
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