/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/util/sequtil/ |
H A D | sequtil_convert_imp.hpp | 51 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); [all …]
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H A D | sequtil_convert.cpp | 46 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() [all …]
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H A D | sequtil_manip.cpp | 58 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() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/util/sequtil/ |
H A D | sequtil_convert_imp.hpp | 51 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); [all …]
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H A D | sequtil_convert.cpp | 46 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() [all …]
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H A D | sequtil_manip.cpp | 58 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() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/format/items/ |
H A D | basecount_item.hpp | 62 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() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/format/items/ |
H A D | basecount_item.hpp | 62 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() [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, 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, [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, 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, [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/objects/valerr/ |
H A D | ValidError.hpp | 103 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() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objects/valerr/ |
H A D | ValidError.hpp | 103 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() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/corelib/impl/ |
H A D | stringutf8_deprecated.hpp | 159 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); [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/corelib/impl/ |
H A D | stringutf8_deprecated.hpp | 159 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); [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/corelib/ |
H A D | ncbistr.hpp | 1375 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() [all …]
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H A D | ncbi_xstr.hpp | 230 …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() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/corelib/ |
H A D | ncbistr.hpp | 1375 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() [all …]
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H A D | ncbi_xstr.hpp | 230 …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() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/util/xregexp/ |
H A D | regexp_template_tester.cpp | 266 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() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/util/xregexp/ |
H A D | regexp_template_tester.cpp | 266 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() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/html/ |
H A D | page.cpp | 44 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() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/html/ |
H A D | page.cpp | 44 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() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/corelib/ |
H A D | ncbistr.cpp | 65 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() [all …]
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