/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objmgr/ |
H A D | seq_vector.hpp | 72 CSeqVector(void); 89 CSeqVector(const CBioseq& bioseq, 93 CSeqVector(const CSeqVector& vec); 95 virtual ~CSeqVector(void); 97 CSeqVector& operator= (const CSeqVector& vec); 263 CSeqVector::TMutex& CSeqVector::GetMutex(void) const in GetMutex() 270 CSeqVector::TResidue CSeqVector::operator[] (TSeqPos pos) const in operator []() 284 bool CSeqVector::empty(void) const in empty() 312 CSeqVector::TCoding CSeqVector::GetCoding(void) const in GetCoding() 318 CSeqVector::TResidue CSeqVector::GetGapChar(ECaseConversion case_cvt) const in GetGapChar() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objmgr/ |
H A D | seq_vector.hpp | 72 CSeqVector(void); 89 CSeqVector(const CBioseq& bioseq, 93 CSeqVector(const CSeqVector& vec); 95 virtual ~CSeqVector(void); 97 CSeqVector& operator= (const CSeqVector& vec); 263 CSeqVector::TMutex& CSeqVector::GetMutex(void) const in GetMutex() 270 CSeqVector::TResidue CSeqVector::operator[] (TSeqPos pos) const in operator []() 284 bool CSeqVector::empty(void) const in empty() 312 CSeqVector::TCoding CSeqVector::GetCoding(void) const in GetCoding() 318 CSeqVector::TResidue CSeqVector::GetGapChar(ECaseConversion case_cvt) const in GetGapChar() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/simple/ |
H A D | simple_om.cpp | 101 CSeqVector vec = GetSeqVector(id, strand); in GetIupac() 109 CSeqVector vec = GetSeqVector(id_string, strand); in GetIupac() 117 CSeqVector vec = GetSeqVector(gi, strand); in GetIupac() 125 CSeqVector vec = GetSeqVector(id, strand); in GetIupac() 133 CSeqVector vec = GetSeqVector(loc, strand); in GetIupac() 141 CSeqVector CSimpleOM::GetSeqVector(const CSeq_id& id, ENa_strand strand) in GetSeqVector() 147 CSeqVector CSimpleOM::GetSeqVector(const string& id_string, ENa_strand strand) in GetSeqVector() 153 CSeqVector CSimpleOM::GetSeqVector(TGi gi, ENa_strand strand) in GetSeqVector() 159 CSeqVector CSimpleOM::GetSeqVector(const CSeq_id_Handle& id, ENa_strand strand) in GetSeqVector() 165 CSeqVector CSimpleOM::GetSeqVector(const CSeq_loc& loc, ENa_strand strand) in GetSeqVector() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/simple/ |
H A D | simple_om.cpp | 101 CSeqVector vec = GetSeqVector(id, strand); in GetIupac() 109 CSeqVector vec = GetSeqVector(id_string, strand); in GetIupac() 117 CSeqVector vec = GetSeqVector(gi, strand); in GetIupac() 125 CSeqVector vec = GetSeqVector(id, strand); in GetIupac() 133 CSeqVector vec = GetSeqVector(loc, strand); in GetIupac() 141 CSeqVector CSimpleOM::GetSeqVector(const CSeq_id& id, ENa_strand strand) in GetSeqVector() 147 CSeqVector CSimpleOM::GetSeqVector(const string& id_string, ENa_strand strand) in GetSeqVector() 153 CSeqVector CSimpleOM::GetSeqVector(TGi gi, ENa_strand strand) in GetSeqVector() 159 CSeqVector CSimpleOM::GetSeqVector(const CSeq_id_Handle& id, ENa_strand strand) in GetSeqVector() 165 CSeqVector CSimpleOM::GetSeqVector(const CSeq_loc& loc, ENa_strand strand) in GetSeqVector() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/ |
H A D | seq_vector.cpp | 134 CSeqVector::CSeqVector(void) in CSeqVector() function in CSeqVector 140 CSeqVector::CSeqVector(const CSeqVector& vec) in CSeqVector() function in CSeqVector 152 CSeqVector::CSeqVector(const CBioseq_Handle& bioseq, in CSeqVector() function in CSeqVector 166 CSeqVector::CSeqVector(const CSeqMap& seqMap, CScope& scope, in CSeqVector() function in CSeqVector 179 CSeqVector::CSeqVector(const CSeqMap& seqMap, const CTSE_Handle& top_tse, in CSeqVector() function in CSeqVector 193 CSeqVector::CSeqVector(const CSeq_loc& loc, CScope& scope, in CSeqVector() function in CSeqVector 211 CSeqVector::CSeqVector(const CSeq_loc& loc, const CTSE_Handle& top_tse, in CSeqVector() function in CSeqVector 225 CSeqVector::CSeqVector(const CBioseq& bioseq, in CSeqVector() function in CSeqVector 239 CSeqVector::~CSeqVector(void) in ~CSeqVector() 244 CSeqVector& CSeqVector::operator= (const CSeqVector& vec) in operator =() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/ |
H A D | seq_vector.cpp | 134 CSeqVector::CSeqVector(void) in CSeqVector() function in CSeqVector 140 CSeqVector::CSeqVector(const CSeqVector& vec) in CSeqVector() function in CSeqVector 152 CSeqVector::CSeqVector(const CBioseq_Handle& bioseq, in CSeqVector() function in CSeqVector 166 CSeqVector::CSeqVector(const CSeqMap& seqMap, CScope& scope, in CSeqVector() function in CSeqVector 179 CSeqVector::CSeqVector(const CSeqMap& seqMap, const CTSE_Handle& top_tse, in CSeqVector() function in CSeqVector 193 CSeqVector::CSeqVector(const CSeq_loc& loc, CScope& scope, in CSeqVector() function in CSeqVector 211 CSeqVector::CSeqVector(const CSeq_loc& loc, const CTSE_Handle& top_tse, in CSeqVector() function in CSeqVector 225 CSeqVector::CSeqVector(const CBioseq& bioseq, in CSeqVector() function in CSeqVector 239 CSeqVector::~CSeqVector(void) in ~CSeqVector() 244 CSeqVector& CSeqVector::operator= (const CSeqVector& vec) in operator =() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/ |
H A D | prot_prop.cpp | 41 TSeqPos CProtProp::AACount(CSeqVector& v, vector<TSeqPos>& aacount) in BEGIN_SCOPE() 52 CSeqVector::TResidue res = *vit; in BEGIN_SCOPE() 59 double CProtProp::GetProteinPI(CSeqVector& v) in GetProteinPI() 67 CSeqVector::TResidue nter = v[0]; in GetProteinPI() 68 CSeqVector::TResidue cter = v[v.size() - 1]; in GetProteinPI() 106 CSeqVector::TResidue nter, in GetProteinCharge() 107 CSeqVector::TResidue cter, in GetProteinCharge()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/test/objmgr/ |
H A D | seqvec_bench.cpp | 207 CSeqVector vec = handle.GetSeqVector(coding, strand); in Run() 225 CSeqVector vec = handle.GetSeqVector(coding, strand); in Run() 251 CSeqVector vec = handle.GetSeqVector(coding, strand); in Run() 265 CSeqVector vec = handle.GetSeqVector(coding, strand); in Run() 280 CSeqVector vec = handle.GetSeqVector(coding, strand); in Run() 296 CSeqVector vec = handle.GetSeqVector(coding, strand); in Run() 312 CSeqVector vec = handle.GetSeqVector(coding, strand); in Run() 338 CSeqVector vec = handle.GetSeqVector(coding, strand); in Run() 352 CSeqVector vec = handle.GetSeqVector(coding, strand); in Run() 353 ITERATE ( CSeqVector, iter, vec ) { in Run() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/sequence/ |
H A D | prot_prop.hpp | 48 static TSeqPos AACount(CSeqVector& v, vector<TSeqPos>& aacount); 51 static double GetProteinPI(CSeqVector& v); 56 CSeqVector::TResidue nter, 57 CSeqVector::TResidue cter,
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/alnmgr/ |
H A D | alnvec.hpp | 51 typedef map<TNumrow, CRef<CSeqVector> > TSeqVectorCache; 54 typedef CSeqVector::TResidue TResidue; 177 CSeqVector& x_GetSeqVector (TNumrow row) const; 178 CSeqVector& x_GetConsensusSeqVector(void) const; 230 typedef CSeqVector::TResidue TResidue; 254 CSeqVector::TResidue CAlnVec::GetResidue(TNumrow row, TSeqPos aln_pos) const in GetResidue() 261 CSeqVector& seq_vec = x_GetSeqVector(row); in GetResidue() 298 CSeqVector& seq_vec = x_GetSeqVector(row); in GetSeqString() 307 CSeqVector& seq_vec = x_GetSeqVector(row); in GetSeqString() 358 CSeqVector::TResidue CAlnVec::GetGapChar(TNumrow row) const in GetGapChar() [all …]
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H A D | alnseq.hpp | 170 CSeqVector& GetPlusStrandSeqVector(void) in GetPlusStrandSeqVector() 173 m_PlusStrandSeqVector = new CSeqVector in GetPlusStrandSeqVector() 180 CSeqVector& GetMinusStrandSeqVector(void) in GetMinusStrandSeqVector() 183 m_MinusStrandSeqVector = new CSeqVector in GetMinusStrandSeqVector() 214 CRef<CSeqVector> m_PlusStrandSeqVector; 215 CRef<CSeqVector> m_MinusStrandSeqVector;
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/alnmgr/ |
H A D | alnvec.hpp | 51 typedef map<TNumrow, CRef<CSeqVector> > TSeqVectorCache; 54 typedef CSeqVector::TResidue TResidue; 177 CSeqVector& x_GetSeqVector (TNumrow row) const; 178 CSeqVector& x_GetConsensusSeqVector(void) const; 230 typedef CSeqVector::TResidue TResidue; 254 CSeqVector::TResidue CAlnVec::GetResidue(TNumrow row, TSeqPos aln_pos) const in GetResidue() 261 CSeqVector& seq_vec = x_GetSeqVector(row); in GetResidue() 298 CSeqVector& seq_vec = x_GetSeqVector(row); in GetSeqString() 307 CSeqVector& seq_vec = x_GetSeqVector(row); in GetSeqString() 358 CSeqVector::TResidue CAlnVec::GetGapChar(TNumrow row) const in GetGapChar() [all …]
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H A D | alnseq.hpp | 170 CSeqVector& GetPlusStrandSeqVector(void) in GetPlusStrandSeqVector() 173 m_PlusStrandSeqVector = new CSeqVector in GetPlusStrandSeqVector() 180 CSeqVector& GetMinusStrandSeqVector(void) in GetMinusStrandSeqVector() 183 m_MinusStrandSeqVector = new CSeqVector in GetMinusStrandSeqVector() 214 CRef<CSeqVector> m_PlusStrandSeqVector; 215 CRef<CSeqVector> m_MinusStrandSeqVector;
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/validator/ |
H A D | splice_problems.hpp | 135 …void ValidateDonorAcceptorPair(ENa_strand strand, TSeqPos stop, const CSeqVector& vec_donor, TSeqP… 136 TSeqPos start, const CSeqVector& vec_acceptor, TSeqPos seq_len_acceptor); 139 …ESpliceSiteRead ReadDonorSpliceSite(ENa_strand strand, TSeqPos stop, const CSeqVector& vec, TSeqPo… 140 …ESpliceSiteRead ReadDonorSpliceSite(ENa_strand strand, TSeqPos stop, const CSeqVector& vec, TSeqPo… 141 …ESpliceSiteRead ReadAcceptorSpliceSite(ENa_strand strand, TSeqPos start, const CSeqVector& vec, TS… 142 …ESpliceSiteRead ReadAcceptorSpliceSite(ENa_strand strand, TSeqPos start, const CSeqVector& vec, TS…
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H A D | utilities.hpp | 77 CSeqVector GetSequenceFromLoc(const CSeq_loc& loc, CScope& scope, 80 CSeqVector GetSequenceFromFeature(const CSeq_feat& feat, CScope& scope, 171 (const CSeqVector& vec, 246 CRef<CSeqVector> MakeSeqVectorForResidueCounting(const CBioseq_Handle& bsh); 247 bool HasBadProteinStart(const CSeqVector& sv); 250 size_t CountProteinStops(const CSeqVector& sv); 256 vector<TSeqPos> GetMismatches(const CSeq_feat& feat, const CSeqVector& prot_vec, const string& tran… 257 void CalculateEffectiveTranslationLengths(const string& transl_prot, const CSeqVector& prot_vec, si…
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/simple/ |
H A D | simple_om.hpp | 85 static CSeqVector GetSeqVector(const CSeq_id& id, 87 static CSeqVector GetSeqVector(const string& id_string, 89 static CSeqVector GetSeqVector(const CSeq_id_Handle& id, 91 static CSeqVector GetSeqVector(TGi gi, 93 static CSeqVector GetSeqVector(const CSeq_loc& loc,
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/simple/ |
H A D | simple_om.hpp | 85 static CSeqVector GetSeqVector(const CSeq_id& id, 87 static CSeqVector GetSeqVector(const string& id_string, 89 static CSeqVector GetSeqVector(const CSeq_id_Handle& id, 91 static CSeqVector GetSeqVector(TGi gi, 93 static CSeqVector GetSeqVector(const CSeq_loc& loc,
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/variation/ |
H A D | variation_utils.hpp | 108 static TSeqPos GetSeqSize(CSeqVector &seqvec); 109 … static CRef<CSeqVector> PrefetchSequence(CScope &scope, const CSeq_id &seq_id,ENa_strand strand); 110 static string GetSeq(int pos, int length, CSeqVector &seqvec); 113 static CCache<string,CRef<CSeqVector> > m_cache; 147 CSeqVector &seqvec, int& rotation_counter, const CVariation_inst::TType type) in ProcessShift() 199 CSeqVector &seqvec, int& rotation_counter, const CVariation_inst::TType type); 214 CSeqVector &seqvec, int& rotation_counter, const CVariation_inst::TType type); 232 CSeqVector &seqvec, int& rotation_counter, const CVariation_inst::TType type); 246 CSeqVector &seqvec, int& rotation_counter, const CVariation_inst::TType type);
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/app/winmasker/ |
H A D | win_mask_sdust_masker.cpp | 76 const objects::CSeqVector & data, const TMaskList & exclude_ranges ) in operator ()() 81 CSeqVector::const_iterator start_it = data.begin(); in operator ()() 82 CSeqVector::const_iterator current_it = data.begin(); in operator ()() 83 CSeqVector::const_iterator end_it = data.end(); in operator ()()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/winmasker/ |
H A D | win_mask_sdust_masker.cpp | 76 const objects::CSeqVector & data, const TMaskList & exclude_ranges ) in operator ()() 81 CSeqVector::const_iterator start_it = data.begin(); in operator ()() 82 CSeqVector::const_iterator current_it = data.begin(); in operator ()() 83 CSeqVector::const_iterator end_it = data.end(); in operator ()()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/util/ |
H A D | seq_trimmer.cpp | 55 const static CSeqVector::TResidue kFirstCharInLookupTable = 'A'; 56 const static CSeqVector::TResidue kLastCharInLookupTable = 'Z'; 71 const CSeqVector::TResidue(&input_table)[InputSize], in s_SetAmbigLookupTableFromArray() 75 const CSeqVector::TResidue chInputChar = input_table[input_idx]; in s_SetAmbigLookupTableFromArray() 195 const static CSeqVector::TResidue arrNucCertainBases[] = { in CSequenceAmbigTrimmer() 200 const static CSeqVector::TResidue arrProtAmbigBases[] = { in CSequenceAmbigTrimmer() 363 const CSeqVector & seqvec, in x_FindWhereToTrim() 498 const CSeqVector & seqvec, in x_EdgeSeqMapGapAdjust() 573 const CSeqVector & seqvec, in x_CountAmbigInRange() 646 const CSeqVector::TResidue residue = seqvec[pos]; in x_CountAmbigInRange() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/util/ |
H A D | seq_trimmer.cpp | 55 const static CSeqVector::TResidue kFirstCharInLookupTable = 'A'; 56 const static CSeqVector::TResidue kLastCharInLookupTable = 'Z'; 71 const CSeqVector::TResidue(&input_table)[InputSize], in s_SetAmbigLookupTableFromArray() 75 const CSeqVector::TResidue chInputChar = input_table[input_idx]; in s_SetAmbigLookupTableFromArray() 195 const static CSeqVector::TResidue arrNucCertainBases[] = { in CSequenceAmbigTrimmer() 200 const static CSeqVector::TResidue arrProtAmbigBases[] = { in CSequenceAmbigTrimmer() 363 const CSeqVector & seqvec, in x_FindWhereToTrim() 498 const CSeqVector & seqvec, in x_EdgeSeqMapGapAdjust() 573 const CSeqVector & seqvec, in x_CountAmbigInRange() 646 const CSeqVector::TResidue residue = seqvec[pos]; in x_CountAmbigInRange() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/format/items/ |
H A D | sequence_item.hpp | 62 const CSeqVector& GetSequence(void) const; 74 CSeqVector m_Sequence; 83 const CSeqVector& CSequenceItem::GetSequence(void) const in GetSequence()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/format/items/ |
H A D | sequence_item.hpp | 62 const CSeqVector& GetSequence(void) const; 74 CSeqVector m_Sequence; 83 const CSeqVector& CSequenceItem::GetSequence(void) const in GetSequence()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/ |
H A D | splice_problems.cpp | 55 const CSeqVector& vec_donor, in ValidateDonorAcceptorPair() 58 const CSeqVector& vec_acceptor, in ValidateDonorAcceptorPair() 160 const CSeqVector& vec, in ReadAcceptorSpliceSite() 222 const CSeqVector& vec, in ReadAcceptorSpliceSite() 391 CSeqVector vec = bsh_si.GetSeqVector(CBioseq_Handle::eCoding_Iupac); in ValidateSpliceExon() 483 CSeqVector vec = bsh_head.GetSeqVector (CBioseq_Handle::eCoding_Iupac); in ValidateSpliceMrna() 509 CSeqVector vec_head = bsh_head.GetSeqVector(CBioseq_Handle::eCoding_Iupac); in ValidateSpliceMrna() 510 CSeqVector vec_tail = bsh_tail.GetSeqVector(CBioseq_Handle::eCoding_Iupac); in ValidateSpliceMrna() 534 CSeqVector vec = bsh_head.GetSeqVector (CBioseq_Handle::eCoding_Iupac); in ValidateSpliceMrna() 564 CSeqVector vec = bsh_head.GetSeqVector(CBioseq_Handle::eCoding_Iupac); in ValidateSpliceCdregion() [all …]
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