/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/util/sequtil/ |
H A D | sequtil_convert.cpp | 48 TCoding src_coding, in Convert() argument 54 return CSeqConvert_imp::Convert(src, src_coding, in Convert() 63 TCoding src_coding, in Convert() argument 69 return CSeqConvert_imp::Convert(src, src_coding, in Convert() 78 TCoding src_coding, in Convert() argument 84 return CSeqConvert_imp::Convert(src, src_coding, in Convert() 93 TCoding src_coding, in Convert() argument 107 TCoding src_coding, in Convert() argument 180 TCoding src_coding, in Pack() argument 191 TCoding src_coding, in Pack() argument [all …]
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H A D | sequtil_manip.cpp | 173 TCoding src_coding, in Reverse() argument 197 TCoding src_coding, in Reverse() argument 204 switch ( src_coding ) { in Reverse() 375 TCoding src_coding, in Complement() argument 382 switch ( src_coding ) { in Complement() 567 TCoding src_coding, in ReverseComplement() argument 574 switch ( src_coding ) { in ReverseComplement() 624 TCoding src_coding, in ReverseComplement() argument 635 TCoding src_coding, in ReverseComplement() argument 703 TCoding src_coding, in ReverseComplement() argument [all …]
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H A D | sequtil_convert_imp.hpp | 53 TCoding src_coding, in Convert() argument 59 _ASSERT(!OutOfRange(pos, src, src_coding)); in Convert() 65 AdjustLength(src, src_coding, pos, length); in Convert() 68 return Convert(&*src.begin(), src_coding, pos, length, in Convert() 73 static SIZE_TYPE Convert(const char* src, TCoding src_coding, 108 TCoding src_coding, in Pack() argument 117 AdjustLength(src, src_coding, 0, length); in Pack() 122 SIZE_TYPE res = Pack(&*src.begin(), length, src_coding, in Pack() 140 TCoding src_coding, in Pack() argument 148 AdjustLength(src, src_coding, 0, length); in Pack() [all …]
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H A D | sequtil_convert_imp.cpp | 62 TCoding src_coding, in Convert() argument 69 _ASSERT(CSeqUtil::GetCodingType(src_coding) == in Convert() 77 if ( src_coding == dst_coding ) { in Convert() 78 return Subseq(src, src_coding, pos, length, dst); in Convert() 82 switch ( src_coding ) { in Convert() 1048 TCoding src_coding, in Pack() argument 1068 switch (src_coding) { in Pack() 1074 return Convert(src, src_coding, 0, length, in Pack() 1110 GetBytesNeeded(src_coding, length)); in Pack() 1309 TCoding src_coding, in x_HasAmbig() argument [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/util/sequtil/ |
H A D | sequtil_convert.cpp | 48 TCoding src_coding, in Convert() argument 54 return CSeqConvert_imp::Convert(src, src_coding, in Convert() 63 TCoding src_coding, in Convert() argument 69 return CSeqConvert_imp::Convert(src, src_coding, in Convert() 78 TCoding src_coding, in Convert() argument 84 return CSeqConvert_imp::Convert(src, src_coding, in Convert() 93 TCoding src_coding, in Convert() argument 107 TCoding src_coding, in Convert() argument 180 TCoding src_coding, in Pack() argument 191 TCoding src_coding, in Pack() argument [all …]
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H A D | sequtil_manip.cpp | 173 TCoding src_coding, in Reverse() argument 197 TCoding src_coding, in Reverse() argument 204 switch ( src_coding ) { in Reverse() 375 TCoding src_coding, in Complement() argument 382 switch ( src_coding ) { in Complement() 567 TCoding src_coding, in ReverseComplement() argument 574 switch ( src_coding ) { in ReverseComplement() 624 TCoding src_coding, in ReverseComplement() argument 635 TCoding src_coding, in ReverseComplement() argument 703 TCoding src_coding, in ReverseComplement() argument [all …]
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H A D | sequtil_convert_imp.hpp | 53 TCoding src_coding, in Convert() argument 59 _ASSERT(!OutOfRange(pos, src, src_coding)); in Convert() 65 AdjustLength(src, src_coding, pos, length); in Convert() 68 return Convert(&*src.begin(), src_coding, pos, length, in Convert() 73 static SIZE_TYPE Convert(const char* src, TCoding src_coding, 108 TCoding src_coding, in Pack() argument 117 AdjustLength(src, src_coding, 0, length); in Pack() 122 SIZE_TYPE res = Pack(&*src.begin(), length, src_coding, in Pack() 140 TCoding src_coding, in Pack() argument 148 AdjustLength(src, src_coding, 0, length); in Pack() [all …]
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H A D | sequtil_convert_imp.cpp | 62 TCoding src_coding, in Convert() argument 69 _ASSERT(CSeqUtil::GetCodingType(src_coding) == in Convert() 77 if ( src_coding == dst_coding ) { in Convert() 78 return Subseq(src, src_coding, pos, length, dst); in Convert() 82 switch ( src_coding ) { in Convert() 1048 TCoding src_coding, in Pack() argument 1068 switch (src_coding) { in Pack() 1074 return Convert(src, src_coding, 0, length, in Pack() 1110 GetBytesNeeded(src_coding, length)); in Pack() 1309 TCoding src_coding, in x_HasAmbig() argument [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/util/sequtil/ |
H A D | sequtil_convert.hpp | 72 static SIZE_TYPE Convert(const CTempString& src, TCoding src_coding, 77 static SIZE_TYPE Convert(const string& src, TCoding src_coding, 92 static SIZE_TYPE Convert(const char src[], TCoding src_coding, 101 static SIZE_TYPE Subseq(const string& src, TCoding src_coding, 104 static SIZE_TYPE Subseq(const string& src, TCoding src_coding, 107 static SIZE_TYPE Subseq(const vector<char>& src, TCoding src_coding, 113 static SIZE_TYPE Subseq(const char* src, TCoding src_coding, 124 static SIZE_TYPE Pack(const string& src, TCoding src_coding, 127 static SIZE_TYPE Pack(const vector<char>& src, TCoding src_coding, 156 static SIZE_TYPE Pack(const string& src, TCoding src_coding, [all …]
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H A D | sequtil_manip.hpp | 58 static SIZE_TYPE Reverse(const string& src, TCoding src_coding, 61 static SIZE_TYPE Reverse(const vector<char>& src, TCoding src_coding, 64 static SIZE_TYPE Reverse(const char* src, TCoding src_coding, 69 static SIZE_TYPE Complement(const string& src, TCoding src_coding, 72 static SIZE_TYPE Complement(const vector<char>& src, TCoding src_coding, 75 static SIZE_TYPE Complement(const char* src, TCoding src_coding, 82 static SIZE_TYPE ReverseComplement(const string& src, TCoding src_coding, 88 static SIZE_TYPE ReverseComplement(const char* src, TCoding src_coding, 93 static SIZE_TYPE ReverseComplement(string& src, TCoding src_coding, 95 static SIZE_TYPE ReverseComplement(vector<char>& src, TCoding src_coding, [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/util/sequtil/ |
H A D | sequtil_convert.hpp | 72 static SIZE_TYPE Convert(const CTempString& src, TCoding src_coding, 77 static SIZE_TYPE Convert(const string& src, TCoding src_coding, 92 static SIZE_TYPE Convert(const char src[], TCoding src_coding, 101 static SIZE_TYPE Subseq(const string& src, TCoding src_coding, 104 static SIZE_TYPE Subseq(const string& src, TCoding src_coding, 107 static SIZE_TYPE Subseq(const vector<char>& src, TCoding src_coding, 113 static SIZE_TYPE Subseq(const char* src, TCoding src_coding, 124 static SIZE_TYPE Pack(const string& src, TCoding src_coding, 127 static SIZE_TYPE Pack(const vector<char>& src, TCoding src_coding, 156 static SIZE_TYPE Pack(const string& src, TCoding src_coding, [all …]
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H A D | sequtil_manip.hpp | 58 static SIZE_TYPE Reverse(const string& src, TCoding src_coding, 61 static SIZE_TYPE Reverse(const vector<char>& src, TCoding src_coding, 64 static SIZE_TYPE Reverse(const char* src, TCoding src_coding, 69 static SIZE_TYPE Complement(const string& src, TCoding src_coding, 72 static SIZE_TYPE Complement(const vector<char>& src, TCoding src_coding, 75 static SIZE_TYPE Complement(const char* src, TCoding src_coding, 82 static SIZE_TYPE ReverseComplement(const string& src, TCoding src_coding, 88 static SIZE_TYPE ReverseComplement(const char* src, TCoding src_coding, 93 static SIZE_TYPE ReverseComplement(string& src, TCoding src_coding, 95 static SIZE_TYPE ReverseComplement(vector<char>& src, TCoding src_coding, [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/ |
H A D | seq_vector.cpp | 631 CSeq_data::E_Choice src_coding = data.Which(); in x_AppendAnyTo8() local 640 switch ( src_coding ) { in x_AppendAnyTo8() 695 CSeq_data::E_Choice src_coding = data.Which(); in x_AppendAnyTo4() local 704 switch ( src_coding ) { in x_AppendAnyTo4() 761 CSeq_data::E_Choice src_coding = data.Which(); in x_AppendAnyTo2() local 770 switch ( src_coding ) { in x_AppendAnyTo2() 845 TCoding src_coding = data.Which(); in x_GetPacked8SeqData() local 848 if ( dst_coding != src_coding || reverse || in x_GetPacked8SeqData() 871 switch ( src_coding ) { in x_GetPacked8SeqData() 938 TCoding src_coding = data.Which(); in x_GetPacked4naSeqData() local [all …]
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H A D | seq_map_ci.cpp | 905 CSeq_data::E_Choice src_coding = data->Which(); in GetSequence() local 917 switch ( src_coding ) { in GetSequence() 931 CSeq_data::SelectionName(src_coding)); in GetSequence()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/ |
H A D | seq_vector.cpp | 631 CSeq_data::E_Choice src_coding = data.Which(); in x_AppendAnyTo8() local 640 switch ( src_coding ) { in x_AppendAnyTo8() 695 CSeq_data::E_Choice src_coding = data.Which(); in x_AppendAnyTo4() local 704 switch ( src_coding ) { in x_AppendAnyTo4() 761 CSeq_data::E_Choice src_coding = data.Which(); in x_AppendAnyTo2() local 770 switch ( src_coding ) { in x_AppendAnyTo2() 845 TCoding src_coding = data.Which(); in x_GetPacked8SeqData() local 848 if ( dst_coding != src_coding || reverse || in x_GetPacked8SeqData() 871 switch ( src_coding ) { in x_GetPacked8SeqData() 938 TCoding src_coding = data.Which(); in x_GetPacked4naSeqData() local [all …]
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H A D | seq_map_ci.cpp | 905 CSeq_data::E_Choice src_coding = data->Which(); in GetSequence() local 917 switch ( src_coding ) { in GetSequence() 931 CSeq_data::SelectionName(src_coding)); in GetSequence()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/table2asn/ |
H A D | fcs_reader.cpp | 163 CSeqUtil::TCoding src_coding = xGetCoding(lit.GetSeq_data().Which()); in xTrimLiteral() local 202 … CSeqConvert::Convert(*encoded_vec, src_coding, 0, lit.GetLength(), decoded, CSeqUtil::e_Iupacna); in xTrimLiteral() 207 … CSeqConvert::Convert(*encoded_str, src_coding, 0, lit.GetLength(), decoded, CSeqUtil::e_Iupacna); in xTrimLiteral() 212 … CSeqConvert::Convert(decoded, CSeqUtil::e_Iupacna, 0, decoded.length(), *encoded_vec, src_coding); in xTrimLiteral() 217 … CSeqConvert::Convert(decoded, CSeqUtil::e_Iupacna, 0, decoded.length(), *encoded_str, src_coding); in xTrimLiteral()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/ |
H A D | gaps_edit.cpp | 61 CSeqUtil::TCoding src_coding = CSeqUtil::e_not_set; in Make_Iupacna() local 68 src_coding = CSeqUtil::e_##x; \ in Make_Iupacna() 69 CSeqConvert::Convert(src, src_coding, 0, len, decoded, dst_coding); \ in Make_Iupacna()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/edit/ |
H A D | gaps_edit.cpp | 61 CSeqUtil::TCoding src_coding = CSeqUtil::e_not_set; in Make_Iupacna() local 68 src_coding = CSeqUtil::e_##x; \ in Make_Iupacna() 69 CSeqConvert::Convert(src, src_coding, 0, len, decoded, dst_coding); \ in Make_Iupacna()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/ |
H A D | gene_model.cpp | 3181 CSeqUtil::ECoding src_coding = CSeqUtil::e_Ncbieaa; in x_HandleCdsExceptions() local 3186 src_coding = CSeqUtil::e_Ncbieaa; in x_HandleCdsExceptions() 3191 src_coding = CSeqUtil::e_Ncbistdaa; in x_HandleCdsExceptions() 3196 src_coding = CSeqUtil::e_Ncbi8aa; in x_HandleCdsExceptions() 3205 CSeqConvert::Convert(src, src_coding, 0, 1, in x_HandleCdsExceptions()
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