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Searched refs:CSeqVector (Results 1 – 25 of 294) sorted by relevance

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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objmgr/
H A Dseq_vector.hpp72 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objmgr/
H A Dseq_vector.hpp72 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/simple/
H A Dsimple_om.cpp101 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/simple/
H A Dsimple_om.cpp101 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/
H A Dseq_vector.cpp134 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 =()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/
H A Dseq_vector.cpp134 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 =()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/
H A Dprot_prop.cpp41 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/test/objmgr/
H A Dseqvec_bench.cpp207 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/sequence/
H A Dprot_prop.hpp48 static TSeqPos AACount(CSeqVector& v, vector<TSeqPos>& aacount);
51 static double GetProteinPI(CSeqVector& v);
56 CSeqVector::TResidue nter,
57 CSeqVector::TResidue cter,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/alnmgr/
H A Dalnvec.hpp51 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()
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H A Dalnseq.hpp170 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;
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/alnmgr/
H A Dalnvec.hpp51 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()
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H A Dalnseq.hpp170 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;
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/validator/
H A Dsplice_problems.hpp135 …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…
H A Dutilities.hpp77 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…
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/simple/
H A Dsimple_om.hpp85 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,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/simple/
H A Dsimple_om.hpp85 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,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/variation/
H A Dvariation_utils.hpp108 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);
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/app/winmasker/
H A Dwin_mask_sdust_masker.cpp76 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 ()()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/winmasker/
H A Dwin_mask_sdust_masker.cpp76 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 ()()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/util/
H A Dseq_trimmer.cpp55 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/util/
H A Dseq_trimmer.cpp55 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/format/items/
H A Dsequence_item.hpp62 const CSeqVector& GetSequence(void) const;
74 CSeqVector m_Sequence;
83 const CSeqVector& CSequenceItem::GetSequence(void) const in GetSequence()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/format/items/
H A Dsequence_item.hpp62 const CSeqVector& GetSequence(void) const;
74 CSeqVector m_Sequence;
83 const CSeqVector& CSequenceItem::GetSequence(void) const in GetSequence()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/
H A Dsplice_problems.cpp55 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()
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