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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/util/sequtil/
H A Dsequtil_convert_imp.hpp51 static SIZE_TYPE Convert in Convert()
73 static SIZE_TYPE Convert(const char* src, TCoding src_coding,
80 static SIZE_TYPE Subseq in Subseq()
99 static SIZE_TYPE Subseq(const char* src, TCoding coding,
106 static SIZE_TYPE Pack in Pack()
122 SIZE_TYPE res = Pack(&*src.begin(), length, src_coding, in Pack()
138 static SIZE_TYPE Pack in Pack()
178 static SIZE_TYPE x_Convert2naTo4na(const char* src, TSeqPos pos,
180 static SIZE_TYPE x_Convert2naTo8na(const char* src, TSeqPos pos,
256 SIZE_TYPE Pack(const char* src, TSeqPos length);
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H A Dsequtil_convert.cpp46 SIZE_TYPE CSeqConvert::Convert in Convert()
61 SIZE_TYPE CSeqConvert::Convert in Convert()
76 SIZE_TYPE CSeqConvert::Convert in Convert()
121 SIZE_TYPE CSeqConvert::Subseq in Subseq()
132 SIZE_TYPE CSeqConvert::Subseq in Subseq()
143 SIZE_TYPE CSeqConvert::Subseq in Subseq()
154 SIZE_TYPE CSeqConvert::Subseq in Subseq()
165 SIZE_TYPE CSeqConvert::Subseq in Subseq()
178 SIZE_TYPE CSeqConvert::Pack in Pack()
189 SIZE_TYPE CSeqConvert::Pack in Pack()
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H A Dsequtil_manip.cpp58 static SIZE_TYPE s_2naReverse in s_2naReverse()
102 static SIZE_TYPE s_4naReverse in s_4naReverse()
151 SIZE_TYPE s_Reverse in s_Reverse()
171 SIZE_TYPE CSeqManip::Reverse in Reverse()
183 SIZE_TYPE CSeqManip::Reverse in Reverse()
195 SIZE_TYPE CSeqManip::Reverse in Reverse()
228 SIZE_TYPE s_Complement in s_Complement()
248 SIZE_TYPE CSeqManip::Complement in Complement()
260 SIZE_TYPE CSeqManip::Complement in Complement()
412 SIZE_TYPE s_ReverseComplement in s_ReverseComplement()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/util/sequtil/
H A Dsequtil_convert_imp.hpp51 static SIZE_TYPE Convert in Convert()
73 static SIZE_TYPE Convert(const char* src, TCoding src_coding,
80 static SIZE_TYPE Subseq in Subseq()
99 static SIZE_TYPE Subseq(const char* src, TCoding coding,
106 static SIZE_TYPE Pack in Pack()
122 SIZE_TYPE res = Pack(&*src.begin(), length, src_coding, in Pack()
138 static SIZE_TYPE Pack in Pack()
178 static SIZE_TYPE x_Convert2naTo4na(const char* src, TSeqPos pos,
180 static SIZE_TYPE x_Convert2naTo8na(const char* src, TSeqPos pos,
256 SIZE_TYPE Pack(const char* src, TSeqPos length);
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H A Dsequtil_convert.cpp46 SIZE_TYPE CSeqConvert::Convert in Convert()
61 SIZE_TYPE CSeqConvert::Convert in Convert()
76 SIZE_TYPE CSeqConvert::Convert in Convert()
121 SIZE_TYPE CSeqConvert::Subseq in Subseq()
132 SIZE_TYPE CSeqConvert::Subseq in Subseq()
143 SIZE_TYPE CSeqConvert::Subseq in Subseq()
154 SIZE_TYPE CSeqConvert::Subseq in Subseq()
165 SIZE_TYPE CSeqConvert::Subseq in Subseq()
178 SIZE_TYPE CSeqConvert::Pack in Pack()
189 SIZE_TYPE CSeqConvert::Pack in Pack()
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H A Dsequtil_manip.cpp58 static SIZE_TYPE s_2naReverse in s_2naReverse()
102 static SIZE_TYPE s_4naReverse in s_4naReverse()
151 SIZE_TYPE s_Reverse in s_Reverse()
171 SIZE_TYPE CSeqManip::Reverse in Reverse()
183 SIZE_TYPE CSeqManip::Reverse in Reverse()
195 SIZE_TYPE CSeqManip::Reverse in Reverse()
228 SIZE_TYPE s_Complement in s_Complement()
248 SIZE_TYPE CSeqManip::Complement in Complement()
260 SIZE_TYPE CSeqManip::Complement in Complement()
412 SIZE_TYPE s_ReverseComplement in s_ReverseComplement()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/format/items/
H A Dbasecount_item.hpp62 void GetCounts(SIZE_TYPE& a, SIZE_TYPE& c, SIZE_TYPE& g, SIZE_TYPE& t,
63 SIZE_TYPE& other) const;
64 SIZE_TYPE GetA(void) const { return m_A; } in GetA()
65 SIZE_TYPE GetC(void) const { return m_C; } in GetC()
66 SIZE_TYPE GetG(void) const { return m_G; } in GetG()
67 SIZE_TYPE GetT(void) const { return m_T; } in GetT()
81 (SIZE_TYPE& a, in GetCounts()
82 SIZE_TYPE& c, in GetCounts()
83 SIZE_TYPE& g, in GetCounts()
84 SIZE_TYPE& t, in GetCounts()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/format/items/
H A Dbasecount_item.hpp62 void GetCounts(SIZE_TYPE& a, SIZE_TYPE& c, SIZE_TYPE& g, SIZE_TYPE& t,
63 SIZE_TYPE& other) const;
64 SIZE_TYPE GetA(void) const { return m_A; } in GetA()
65 SIZE_TYPE GetC(void) const { return m_C; } in GetC()
66 SIZE_TYPE GetG(void) const { return m_G; } in GetG()
67 SIZE_TYPE GetT(void) const { return m_T; } in GetT()
81 (SIZE_TYPE& a, in GetCounts()
82 SIZE_TYPE& c, in GetCounts()
83 SIZE_TYPE& g, in GetCounts()
84 SIZE_TYPE& t, in GetCounts()
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/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,
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,
145 virtual SIZE_TYPE GetOverhead(TCoding coding) const = 0;
156 static SIZE_TYPE Pack(const string& src, TCoding src_coding,
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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,
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/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,
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,
145 virtual SIZE_TYPE GetOverhead(TCoding coding) const = 0;
156 static SIZE_TYPE Pack(const string& src, TCoding src_coding,
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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,
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objects/valerr/
H A DValidError.hpp103 SIZE_TYPE TotalSize(void) const;
104 SIZE_TYPE Size(EDiagSev sev) const;
106 SIZE_TYPE InfoSize (void) const;
107 SIZE_TYPE WarningSize (void) const;
108 SIZE_TYPE ErrorSize (void) const;
109 SIZE_TYPE CriticalSize(void) const;
110 SIZE_TYPE FatalSize (void) const;
182 SIZE_TYPE CValidError::TotalSize(void) const in TotalSize()
196 SIZE_TYPE CValidError::InfoSize(void) const in InfoSize()
210 SIZE_TYPE CValidError::ErrorSize(void) const in ErrorSize()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objects/valerr/
H A DValidError.hpp103 SIZE_TYPE TotalSize(void) const;
104 SIZE_TYPE Size(EDiagSev sev) const;
106 SIZE_TYPE InfoSize (void) const;
107 SIZE_TYPE WarningSize (void) const;
108 SIZE_TYPE ErrorSize (void) const;
109 SIZE_TYPE CriticalSize(void) const;
110 SIZE_TYPE FatalSize (void) const;
182 SIZE_TYPE CValidError::TotalSize(void) const in TotalSize()
196 SIZE_TYPE CValidError::InfoSize(void) const in InfoSize()
210 SIZE_TYPE CValidError::ErrorSize(void) const in ErrorSize()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/corelib/impl/
H A Dstringutf8_deprecated.hpp159 const TUnicodeSymbol* src, SIZE_TYPE char_count);
162 const TCharUCS4* src, SIZE_TYPE char_count);
165 const TCharUCS2* src, SIZE_TYPE char_count);
391 SIZE_TYPE GetSymbolCount(void) const;
399 static SIZE_TYPE GetSymbolCount(const CTempString src);
412 static SIZE_TYPE GetValidSymbolCount(const char* src, SIZE_TYPE buf_size);
436 static SIZE_TYPE GetValidBytesCount(const char* src, SIZE_TYPE buf_size);
447 static SIZE_TYPE GetValidBytesCount(const CTempString src);
726 void x_Append(const TChar* src, SIZE_TYPE to = NPOS,
738 static SIZE_TYPE x_BytesNeeded(TUnicodeSymbol ch);
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/corelib/impl/
H A Dstringutf8_deprecated.hpp159 const TUnicodeSymbol* src, SIZE_TYPE char_count);
162 const TCharUCS4* src, SIZE_TYPE char_count);
165 const TCharUCS2* src, SIZE_TYPE char_count);
391 SIZE_TYPE GetSymbolCount(void) const;
399 static SIZE_TYPE GetSymbolCount(const CTempString src);
412 static SIZE_TYPE GetValidSymbolCount(const char* src, SIZE_TYPE buf_size);
436 static SIZE_TYPE GetValidBytesCount(const char* src, SIZE_TYPE buf_size);
447 static SIZE_TYPE GetValidBytesCount(const CTempString src);
726 void x_Append(const TChar* src, SIZE_TYPE to = NPOS,
738 static SIZE_TYPE x_BytesNeeded(TUnicodeSymbol ch);
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/corelib/
H A Dncbistr.hpp1375 static int Compare(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n,
1398 static int Compare(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n,
1586 static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n,
1609 static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n,
2022 SIZE_TYPE start, SIZE_TYPE end,
2086 SIZE_TYPE start, SIZE_TYPE end,
2145 SIZE_TYPE start, SIZE_TYPE end,
5165 int NStr::Compare(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, in Compare()
5173 int NStr::Compare(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, in Compare()
5252 bool NStr::Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, in Equal()
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H A Dncbi_xstr.hpp230 …int CompareCase(const basic_string<_TChar>& str, SIZE_TYPE pos, SIZE_TYPE n, const _TChar* pattern) in CompareCase()
236 int CompareCase(const _TChar* str, SIZE_TYPE pos, SIZE_TYPE n, const _TChar* pattern) in CompareCase()
243 …int CompareCase(const basic_string<_TChar>& str, SIZE_TYPE pos, SIZE_TYPE n, const basic_string<_T… in CompareCase()
249 …int CompareCase(const _TChar* str, SIZE_TYPE pos, SIZE_TYPE n, const basic_string<_TChar>& pattern) in CompareCase()
257 …int CompareNocase(const basic_string<_TChar>& str, SIZE_TYPE pos, SIZE_TYPE n, const _TChar* patte… in CompareNocase()
263 int CompareNocase(const _TChar* str, SIZE_TYPE pos, SIZE_TYPE n, const _TChar* pattern) in CompareNocase()
270 …int CompareNocase(const basic_string<_TChar>& str, SIZE_TYPE pos, SIZE_TYPE n, const basic_string<… in CompareNocase()
276 …int CompareNocase(const _TChar* str, SIZE_TYPE pos, SIZE_TYPE n, const basic_string<_TChar>& patte… in CompareNocase()
284 …int Compare(const basic_string<_TChar>& str, SIZE_TYPE pos, SIZE_TYPE n, const _TChar* pattern, EC… in Compare()
290 …int Compare(const _TChar* str, SIZE_TYPE pos, SIZE_TYPE n, const _TChar* pattern, ECase use_case =… in Compare()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/corelib/
H A Dncbistr.hpp1375 static int Compare(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n,
1398 static int Compare(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n,
1586 static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n,
1609 static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n,
2022 SIZE_TYPE start, SIZE_TYPE end,
2086 SIZE_TYPE start, SIZE_TYPE end,
2145 SIZE_TYPE start, SIZE_TYPE end,
5165 int NStr::Compare(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, in Compare()
5173 int NStr::Compare(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, in Compare()
5252 bool NStr::Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, in Equal()
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H A Dncbi_xstr.hpp230 …int CompareCase(const basic_string<_TChar>& str, SIZE_TYPE pos, SIZE_TYPE n, const _TChar* pattern) in CompareCase()
236 int CompareCase(const _TChar* str, SIZE_TYPE pos, SIZE_TYPE n, const _TChar* pattern) in CompareCase()
243 …int CompareCase(const basic_string<_TChar>& str, SIZE_TYPE pos, SIZE_TYPE n, const basic_string<_T… in CompareCase()
249 …int CompareCase(const _TChar* str, SIZE_TYPE pos, SIZE_TYPE n, const basic_string<_TChar>& pattern) in CompareCase()
257 …int CompareNocase(const basic_string<_TChar>& str, SIZE_TYPE pos, SIZE_TYPE n, const _TChar* patte… in CompareNocase()
263 int CompareNocase(const _TChar* str, SIZE_TYPE pos, SIZE_TYPE n, const _TChar* pattern) in CompareNocase()
270 …int CompareNocase(const basic_string<_TChar>& str, SIZE_TYPE pos, SIZE_TYPE n, const basic_string<… in CompareNocase()
276 …int CompareNocase(const _TChar* str, SIZE_TYPE pos, SIZE_TYPE n, const basic_string<_TChar>& patte… in CompareNocase()
284 …int Compare(const basic_string<_TChar>& str, SIZE_TYPE pos, SIZE_TYPE n, const _TChar* pattern, EC… in Compare()
290 …int Compare(const _TChar* str, SIZE_TYPE pos, SIZE_TYPE n, const _TChar* pattern, ECase use_case =… in Compare()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/util/xregexp/
H A Dregexp_template_tester.cpp266 SIZE_TYPE* num = NULL; in x_GetLine()
322 SIZE_TYPE CRegexpTemplateTester::x_ParseVar(CTempString str, SIZE_TYPE pos) const in x_ParseVar()
324 SIZE_TYPE len = str.length(); in x_ParseVar()
347 SIZE_TYPE CRegexpTemplateTester::x_ParseVarName(CTempString str, SIZE_TYPE pos) const in x_ParseVarName()
349 SIZE_TYPE len = str.length(); in x_ParseVarName()
357 SIZE_TYPE start = pos; in x_ParseVarName()
373 SIZE_TYPE last = 0; in x_SubstituteVars()
445 SIZE_TYPE len = str.length(); in x_Op_Set()
492 SIZE_TYPE pop; in x_Op_Test()
593 SIZE_TYPE op_num = 0; in x_Op_Skip()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/util/xregexp/
H A Dregexp_template_tester.cpp266 SIZE_TYPE* num = NULL; in x_GetLine()
322 SIZE_TYPE CRegexpTemplateTester::x_ParseVar(CTempString str, SIZE_TYPE pos) const in x_ParseVar()
324 SIZE_TYPE len = str.length(); in x_ParseVar()
347 SIZE_TYPE CRegexpTemplateTester::x_ParseVarName(CTempString str, SIZE_TYPE pos) const in x_ParseVarName()
349 SIZE_TYPE len = str.length(); in x_ParseVarName()
357 SIZE_TYPE start = pos; in x_ParseVarName()
373 SIZE_TYPE last = 0; in x_SubstituteVars()
445 SIZE_TYPE len = str.length(); in x_Op_Set()
492 SIZE_TYPE pop; in x_Op_Test()
593 SIZE_TYPE op_num = 0; in x_Op_Skip()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/html/
H A Dpage.cpp44 const SIZE_TYPE kBufferSize = 4096;
384 m_TemplateSize = (SIZE_TYPE)size; in x_LoadTemplate()
399 str.append(buf, (SIZE_TYPE)is.gcount()); in x_LoadTemplate()
428 str.append(buf, (SIZE_TYPE)is.gcount()); in x_PrintTemplate()
429 SIZE_TYPE pos = str.rfind('\n'); in x_PrintTemplate()
470 SIZE_TYPE start = 0) in s_Find()
588 size = (SIZE_TYPE)x_size; in x_LoadTemplateLib()
605 SIZE_TYPE len = s.length(); in x_LoadTemplateLib()
676 SIZE_TYPE te_size = strlen(kTagEnd); in x_LoadTemplateLib()
677 SIZE_TYPE tse_size = strlen(kTagStartEnd); in x_LoadTemplateLib()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/html/
H A Dpage.cpp44 const SIZE_TYPE kBufferSize = 4096;
384 m_TemplateSize = (SIZE_TYPE)size; in x_LoadTemplate()
399 str.append(buf, (SIZE_TYPE)is.gcount()); in x_LoadTemplate()
428 str.append(buf, (SIZE_TYPE)is.gcount()); in x_PrintTemplate()
429 SIZE_TYPE pos = str.rfind('\n'); in x_PrintTemplate()
470 SIZE_TYPE start = 0) in s_Find()
588 size = (SIZE_TYPE)x_size; in x_LoadTemplateLib()
605 SIZE_TYPE len = s.length(); in x_LoadTemplateLib()
676 SIZE_TYPE te_size = strlen(kTagEnd); in x_LoadTemplateLib()
677 SIZE_TYPE tse_size = strlen(kTagStartEnd); in x_LoadTemplateLib()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/corelib/
H A Dncbistr.cpp65 return end ? (SIZE_TYPE)(end - start) : (SIZE_TYPE) 0; in s_DiffPtr()
135 int NStr::CompareCase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, in CompareCase()
158 int NStr::CompareCase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, in CompareCase()
219 int NStr::CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, in CompareNocase()
248 int NStr::CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, in CompareNocase()
2421 SIZE_TYPE n_copy = min((SIZE_TYPE) n, buf_size); in DoubleToString()
3394 SIZE_TYPE start_pos, SIZE_TYPE max_replace, in Replace()
4027 SIZE_TYPE i; in XmlEncode()
4112 SIZE_TYPE i; in HtmlEncode()
4990 static SIZE_TYPE s_EndOfTag(const string& str, SIZE_TYPE start) in s_EndOfTag()
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