| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/alnmgr/ |
| H A D | alnvec.hpp | 54 typedef CSeqVector::TResidue TResidue; typedef in CAlnVec
117 void SetGapChar(TResidue gap_char);
123 void SetEndChar(TResidue gap_char);
191 TResidue m_GapChar;
193 TResidue m_EndChar;
230 typedef CSeqVector::TResidue TResidue; typedef in CAlnVecPrinter
233 TResidue m_OrigGapChar;
236 TResidue m_OrigEndChar;
257 return (TResidue) 0; // out of range in GetResidue()
339 void CAlnVec::SetGapChar(TResidue gap_char) in SetGapChar()
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| H A D | aln_explorer.hpp | 53 typedef objects::CSeqVector::TResidue TResidue; typedef in IAlnExplorer
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| H A D | sparse_aln.hpp | 72 void SetGapChar(TResidue gap_char);
314 TResidue m_GapChar;
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/alnmgr/ |
| H A D | alnvec.hpp | 54 typedef CSeqVector::TResidue TResidue; typedef in CAlnVec
117 void SetGapChar(TResidue gap_char);
123 void SetEndChar(TResidue gap_char);
191 TResidue m_GapChar;
193 TResidue m_EndChar;
230 typedef CSeqVector::TResidue TResidue; typedef in CAlnVecPrinter
233 TResidue m_OrigGapChar;
236 TResidue m_OrigEndChar;
257 return (TResidue) 0; // out of range in GetResidue()
339 void CAlnVec::SetGapChar(TResidue gap_char) in SetGapChar()
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| H A D | aln_explorer.hpp | 53 typedef objects::CSeqVector::TResidue TResidue; typedef in IAlnExplorer
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| H A D | sparse_aln.hpp | 72 void SetGapChar(TResidue gap_char);
314 TResidue m_GapChar;
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/ |
| H A D | prot_prop.cpp | 52 CSeqVector::TResidue res = *vit; in BEGIN_SCOPE()
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/include/objmgr/ |
| H A D | seq_vector_ci.hpp | 57 typedef unsigned char TResidue; typedef in CSeqVectorTypes
59 typedef TResidue value_type;
63 typedef const TResidue* pointer;
64 typedef const TResidue& reference;
73 static TResidue sx_GetGapChar(TCoding coding,
199 TResidue operator*(void) const;
212 TResidue GetGapChar(void) const;
469 CSeqVector_CI::TResidue CSeqVector_CI::operator*(void) const in operator *()
622 CSeqVector_CI::TResidue CSeqVector_CI::GetGapChar(void) const in GetGapChar()
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| H A D | seq_vector.hpp | 110 TResidue operator[] (TSeqPos pos) const;
164 TResidue GetGapChar(ECaseConversion case_cvt = eCaseConversion_none) const;
270 CSeqVector::TResidue CSeqVector::operator[] (TSeqPos pos) const in operator []()
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 D | seq_vector_ci.hpp | 57 typedef unsigned char TResidue; typedef in CSeqVectorTypes
59 typedef TResidue value_type;
63 typedef const TResidue* pointer;
64 typedef const TResidue& reference;
73 static TResidue sx_GetGapChar(TCoding coding,
199 TResidue operator*(void) const;
212 TResidue GetGapChar(void) const;
469 CSeqVector_CI::TResidue CSeqVector_CI::operator*(void) const in operator *()
622 CSeqVector_CI::TResidue CSeqVector_CI::GetGapChar(void) const in GetGapChar()
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| H A D | seq_vector.hpp | 110 TResidue operator[] (TSeqPos pos) const;
164 TResidue GetGapChar(ECaseConversion case_cvt = eCaseConversion_none) const;
270 CSeqVector::TResidue CSeqVector::operator[] (TSeqPos pos) const in operator []()
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/include/algo/sequence/ |
| H A D | prot_prop.hpp | 56 CSeqVector::TResidue nter,
57 CSeqVector::TResidue cter,
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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()
646 const CSeqVector::TResidue residue = seqvec[pos]; in x_CountAmbigInRange()
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| H A D | bioseqgaps_ci.cpp | 202 const CSeqVector::TResidue gap_residue = seqvec.GetGapChar(); in x_FindNextGapOnBioseq()
208 const CSeqVector::TResidue residue = seqvec[curr_pos]; in x_FindNextGapOnBioseq()
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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()
646 const CSeqVector::TResidue residue = seqvec[pos]; in x_CountAmbigInRange()
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| H A D | bioseqgaps_ci.cpp | 202 const CSeqVector::TResidue gap_residue = seqvec.GetGapChar(); in x_FindNextGapOnBioseq()
208 const CSeqVector::TResidue residue = seqvec[curr_pos]; in x_FindNextGapOnBioseq()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/ |
| H A D | gnomon_seq.hpp | 61 inline EResidue fromACGT(TResidue c) in fromACGT()
83 inline TResidue toACGT(EResidue c) in toACGT()
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| H A D | gnomon_seq.cpp | 75 const TResidue codons[4][4] = {"ATG", "TAA", "TAG", "TGA"};
76 const TResidue rev_codons[4][4] = {"CAT", "TTA", "CTA", "TCA"};
91 static Res _fromACGT(TResidue x) in _fromACGT()
100 static EResidue _fromACGT(TResidue x) in _fromACGT()
120 template bool IsStartCodon<TResidue>(const TResidue * seq, int strand);
144 template bool IsStopCodon<TResidue>(const TResidue * seq, int strand);
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/streamtest/ |
| H A D | process_seqvector.hpp | 195 CSeqVector::TResidue res = *sv_iter; in SeqEntryProcess()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/ |
| H A D | gnomon_model.hpp | 68 typedef objects::CSeqVectorTypes::TResidue TResidue; // unsigned char typedef
70 typedef vector<TResidue> CResidueVec;
852 inline TResidue Complement(TResidue c) in Complement()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/ |
| H A D | translation_problems.cpp | 601 CSeqVectorTypes::TResidue p_res = prot_vec[i]; in x_GetTranslationMismatches()
602 CSeqVectorTypes::TResidue t_res = transl_prot[i]; in x_GetTranslationMismatches()
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| H A D | utilities.cpp | 1232 CSeqVector::TResidue res = vec[stop + 1]; in s_PartialAtGapOrNs()
1244 CSeqVector::TResidue res = vec[start - 1]; in s_PartialAtGapOrNs()
2621 CSeqVectorTypes::TResidue p_res = prot_vec[i]; in GetMismatches()
2622 CSeqVectorTypes::TResidue t_res = transl_prot[i]; in GetMismatches()
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| H A D | validerror_graph.cpp | 394 CSeqVector::TResidue res = *seq_iter; in x_ValidateGraphValues()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/alnmgr/ |
| H A D | sparse_aln.cpp | 244 void CSparseAln::SetGapChar(TResidue gap_char) in SetGapChar()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/alnmgr/ |
| H A D | sparse_aln.cpp | 244 void CSparseAln::SetGapChar(TResidue gap_char) in SetGapChar()
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