Home
last modified time | relevance | path

Searched refs:src_coding (Results 1 – 20 of 20) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/util/sequtil/
H A Dsequtil_convert.cpp48 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 …]
H A Dsequtil_manip.cpp173 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 …]
H A Dsequtil_convert_imp.hpp53 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 …]
H A Dsequtil_convert_imp.cpp62 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 …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/util/sequtil/
H A Dsequtil_convert.cpp48 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 …]
H A Dsequtil_manip.cpp173 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 …]
H A Dsequtil_convert_imp.hpp53 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 …]
H A Dsequtil_convert_imp.cpp62 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 …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/util/sequtil/
H A Dsequtil_convert.hpp72 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 …]
H A Dsequtil_manip.hpp58 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/util/sequtil/
H A Dsequtil_convert.hpp72 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 …]
H A Dsequtil_manip.hpp58 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/
H A Dseq_vector.cpp631 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 …]
H A Dseq_map_ci.cpp905 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/
H A Dseq_vector.cpp631 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 …]
H A Dseq_map_ci.cpp905 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/table2asn/
H A Dfcs_reader.cpp163 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/
H A Dgaps_edit.cpp61 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/edit/
H A Dgaps_edit.cpp61 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/
H A Dgene_model.cpp3181 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()