| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/ |
| H A D | blast_options_cxx.cpp | 299 CBlastOptions::CBlastOptions(EAPILocality locality) in CBlastOptions() function in CBlastOptions
315 CBlastOptions::~CBlastOptions() in ~CBlastOptions()
325 CRef<CBlastOptions> CBlastOptions::Clone() const in Clone()
327 CRef<CBlastOptions> optsRef; in Clone()
333 CBlastOptions::EAPILocality
800 CBlastOptions::operator==(const CBlastOptions& rhs) const in operator ==()
811 CBlastOptions::operator!=(const CBlastOptions& rhs) const in operator !=()
817 CBlastOptions::Validate() const in Validate()
825 CBlastOptions::GetProgram() const in GetProgram()
2533 CBlastOptions::TBlast4Opts *
[all …]
|
| H A D | winmask_filter.hpp | 51 class CBlastOptions;
94 const CBlastOptions * opts_handle);
103 const CBlastOptions * opts);
|
| H A D | blast_objmgr_priv.hpp | 59 class CBlastOptions;
81 CBlastQuerySourceOM(TSeqLocVector & v, const CBlastOptions* opts);
98 CBlastQuerySourceOM(CBlastQueryVector & v, const CBlastOptions* opts);
176 const CBlastOptions* m_Options;
|
| H A D | psiblast_aux_priv.hpp | 66 class CBlastOptions;
84 CConstRef<CBlastOptions> options);
92 const CBlastOptions& opts);
|
| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/ |
| H A D | blast_options_cxx.cpp | 299 CBlastOptions::CBlastOptions(EAPILocality locality) in CBlastOptions() function in CBlastOptions
315 CBlastOptions::~CBlastOptions() in ~CBlastOptions()
325 CRef<CBlastOptions> CBlastOptions::Clone() const in Clone()
327 CRef<CBlastOptions> optsRef; in Clone()
333 CBlastOptions::EAPILocality
800 CBlastOptions::operator==(const CBlastOptions& rhs) const in operator ==()
811 CBlastOptions::operator!=(const CBlastOptions& rhs) const in operator !=()
817 CBlastOptions::Validate() const in Validate()
825 CBlastOptions::GetProgram() const in GetProgram()
2533 CBlastOptions::TBlast4Opts *
[all …]
|
| H A D | winmask_filter.hpp | 51 class CBlastOptions;
94 const CBlastOptions * opts_handle);
103 const CBlastOptions * opts);
|
| H A D | blast_objmgr_priv.hpp | 59 class CBlastOptions;
81 CBlastQuerySourceOM(TSeqLocVector & v, const CBlastOptions* opts);
98 CBlastQuerySourceOM(CBlastQueryVector & v, const CBlastOptions* opts);
176 const CBlastOptions* m_Options;
|
| H A D | psiblast_aux_priv.hpp | 66 class CBlastOptions;
84 CConstRef<CBlastOptions> options);
92 const CBlastOptions& opts);
|
| H A D | blast_nucl_options.cpp | 55 CBlastNucleotideOptionsHandle::CBlastNucleotideOptionsHandle(CRef<CBlastOptions> opt) in CBlastNucleotideOptionsHandle()
76 if (m_Opts->GetLocality() == CBlastOptions::eRemote) { in SetTraditionalBlastnDefaults()
99 if (m_Opts->GetLocality() == CBlastOptions::eRemote) { in SetVecScreenDefaults()
121 if (m_Opts->GetLocality() == CBlastOptions::eRemote) { in SetTraditionalMegablastDefaults()
|
| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/blastinput/ |
| H A D | blast_args.hpp | 103 CBlastOptions& options);
121 CBlastOptions& options);
212 CBlastOptions& options);
231 CBlastOptions& options);
245 CBlastOptions& options);
259 CBlastOptions& options);
272 CBlastOptions& options);
912 CBlastOptions& opts);
1110 CBlastOptions& opts);
1367 CBlastOptions& opts);
[all …]
|
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/blastinput/ |
| H A D | blast_args.hpp | 103 CBlastOptions& options);
121 CBlastOptions& options);
212 CBlastOptions& options);
231 CBlastOptions& options);
245 CBlastOptions& options);
259 CBlastOptions& options);
272 CBlastOptions& options);
912 CBlastOptions& opts);
1110 CBlastOptions& opts);
1367 CBlastOptions& opts);
[all …]
|
| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/api/ |
| H A D | blast_options.hpp | 84 class NCBI_XBLAST_EXPORT CBlastOptions : public CObject class
103 CBlastOptions(EAPILocality locality = eLocal);
106 ~CBlastOptions();
110 CRef<CBlastOptions> Clone() const;
482 bool operator==(const CBlastOptions& rhs) const;
483 bool operator!=(const CBlastOptions& rhs) const;
512 CBlastOptions(const CBlastOptions& bo);
514 CBlastOptions& operator=(const CBlastOptions& bo);
556 void x_DoDeepCopy(const CBlastOptions& opts);
|
| H A D | blast_options_handle.hpp | 85 typedef CBlastOptions::EAPILocality EAPILocality;
96 EAPILocality locality = CBlastOptions::eLocal);
108 EAPILocality locality = CBlastOptions::eLocal);
146 typedef CBlastOptions::EAPILocality EAPILocality;
160 const CBlastOptions& GetOptions() const { return *m_Opts; } in GetOptions()
169 CBlastOptions& SetOptions() { return *m_Opts; } in SetOptions()
329 CBlastOptionsHandle(CRef<CBlastOptions> opt);
335 CRef<CBlastOptions> m_Opts;
|
| H A D | prelim_stage.hpp | 61 CRef<CBlastOptions> options,
68 CRef<CBlastOptions> options,
76 CRef<CBlastOptions> options,
150 CRef<CBlastOptions> options,
165 CRef<CBlastOptions> m_Options;
|
| H A D | traceback_stage.hpp | 61 CRef<CBlastOptions> opts,
71 CRef<CBlastOptions> opts,
97 CRef<CBlastOptions> opts,
113 CRef<CBlastOptions> m_Options;
|
| H A D | query_data.hpp | 135 class CBlastOptions;
152 CRef<ILocalQueryData> MakeLocalQueryData(const CBlastOptions* opts);
164 x_MakeLocalQueryData(const CBlastOptions* opts) = 0;
|
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/api/ |
| H A D | blast_options.hpp | 84 class NCBI_XBLAST_EXPORT CBlastOptions : public CObject class
103 CBlastOptions(EAPILocality locality = eLocal);
106 ~CBlastOptions();
110 CRef<CBlastOptions> Clone() const;
482 bool operator==(const CBlastOptions& rhs) const;
483 bool operator!=(const CBlastOptions& rhs) const;
512 CBlastOptions(const CBlastOptions& bo);
514 CBlastOptions& operator=(const CBlastOptions& bo);
556 void x_DoDeepCopy(const CBlastOptions& opts);
|
| H A D | blast_options_handle.hpp | 85 typedef CBlastOptions::EAPILocality EAPILocality;
96 EAPILocality locality = CBlastOptions::eLocal);
108 EAPILocality locality = CBlastOptions::eLocal);
146 typedef CBlastOptions::EAPILocality EAPILocality;
160 const CBlastOptions& GetOptions() const { return *m_Opts; } in GetOptions()
169 CBlastOptions& SetOptions() { return *m_Opts; } in SetOptions()
329 CBlastOptionsHandle(CRef<CBlastOptions> opt);
335 CRef<CBlastOptions> m_Opts;
|
| H A D | prelim_stage.hpp | 61 CRef<CBlastOptions> options,
68 CRef<CBlastOptions> options,
76 CRef<CBlastOptions> options,
150 CRef<CBlastOptions> options,
165 CRef<CBlastOptions> m_Options;
|
| H A D | traceback_stage.hpp | 61 CRef<CBlastOptions> opts,
71 CRef<CBlastOptions> opts,
97 CRef<CBlastOptions> opts,
113 CRef<CBlastOptions> m_Options;
|
| H A D | query_data.hpp | 135 class CBlastOptions;
152 CRef<ILocalQueryData> MakeLocalQueryData(const CBlastOptions* opts);
164 x_MakeLocalQueryData(const CBlastOptions* opts) = 0;
|
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/format/ |
| H A D | data4xml2format.hpp | 64 CConstRef<blast::CBlastOptions> opts,
72 CConstRef<blast::CBlastOptions> opts,
80 CConstRef<blast::CBlastOptions> opts,
88 CConstRef<blast::CBlastOptions> opts,
211 CConstRef<blast::CBlastOptions> m_Options;
248 void x_InitCommon(const blast::CSearchResults & results, CConstRef<blast::CBlastOptions> opts);
|
| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/format/ |
| H A D | data4xml2format.hpp | 64 CConstRef<blast::CBlastOptions> opts,
72 CConstRef<blast::CBlastOptions> opts,
80 CConstRef<blast::CBlastOptions> opts,
88 CConstRef<blast::CBlastOptions> opts,
211 CConstRef<blast::CBlastOptions> m_Options;
248 void x_InitCommon(const blast::CSearchResults & results, CConstRef<blast::CBlastOptions> opts);
|
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/ |
| H A D | queryinfo_unit_test.cpp | 63 const CBlastOptions& kOpts = opts->GetOptions(); in BOOST_AUTO_TEST_CASE()
88 const CBlastOptions& kOpts = opts->GetOptions(); in BOOST_AUTO_TEST_CASE()
112 const CBlastOptions& kOpts = opts->GetOptions(); in BOOST_AUTO_TEST_CASE()
136 const CBlastOptions& kOpts = opts->GetOptions(); in BOOST_AUTO_TEST_CASE()
160 const CBlastOptions& kOpts = opts->GetOptions(); in BOOST_AUTO_TEST_CASE()
197 const CBlastOptions& kOpts = opts->GetOptions(); in BOOST_AUTO_TEST_CASE()
|
| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/ |
| H A D | queryinfo_unit_test.cpp | 63 const CBlastOptions& kOpts = opts->GetOptions(); in BOOST_AUTO_TEST_CASE()
88 const CBlastOptions& kOpts = opts->GetOptions(); in BOOST_AUTO_TEST_CASE()
112 const CBlastOptions& kOpts = opts->GetOptions(); in BOOST_AUTO_TEST_CASE()
136 const CBlastOptions& kOpts = opts->GetOptions(); in BOOST_AUTO_TEST_CASE()
160 const CBlastOptions& kOpts = opts->GetOptions(); in BOOST_AUTO_TEST_CASE()
197 const CBlastOptions& kOpts = opts->GetOptions(); in BOOST_AUTO_TEST_CASE()
|