| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/oligofar/ |
| H A D | cscoreparam.hpp | 28 double GetMismatchPenalty() const { return m_mismatchPenalty; } in GetMismatchPenalty() function in CScoreParam
56 m_identityTbl[i] = p*GetIdentityScore() - (1.0 - p)*GetMismatchPenalty(); in x_InitSubjIdentityTable()
63 …] = pow( 10.0, -double(i)/10 ) * (GetIdentityScore() - GetMismatchPenalty()) + GetMismatchPenalty(… in x_InitScoreForPhrap()
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| H A D | cscore-impl.hpp | 76 return q & s ? m_scoreParam->GetIdentityScore( s ) : -m_scoreParam->GetMismatchPenalty(); in Score()
141 double mi = - m_scoreParam->GetMismatchPenalty() / 255 / 3; in Score()
159 fill( m_scoretbl, m_scoretbl + 1024, - sp->GetMismatchPenalty() ); in CDibaseScore_Base()
185 -TSuper::m_scoreParam->GetMismatchPenalty(); in GetScore()
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| H A D | caligner-alignwindow.cpp | 110 double xs = id + m_scoreParam->GetMismatchPenalty(); in AlignWindow()
174 m_penalty += k * (m_scoreParam->GetIdentityScore() + m_scoreParam->GetMismatchPenalty()); in AdjustWindowBoundary()
183 m_penalty += k * (m_scoreParam->GetIdentityScore() + m_scoreParam->GetMismatchPenalty()); in AdjustWindowBoundary()
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| H A D | cguidesam.cpp | 114 double mm = m_scoreParam->GetMismatchPenalty(); in AddSingle()
125 double mm = m_scoreParam->GetMismatchPenalty(); in AddPair()
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| H A D | caligner-aligndiag.cpp | 72 double mi = m_scoreParam->GetMismatchPenalty(); in AlignDiag()
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| H A D | caligner.hpp | 231 …entionPenalty() + m_scoreParam->GetIdentityScore() - m_scoreParam->GetMismatchPenalty() ) * u.GetC… in AppendTranscriptItem()
235 …entionPenalty() + m_scoreParam->GetIdentityScore() - m_scoreParam->GetMismatchPenalty() ) * m_tran… in AppendTranscriptItem()
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| H A D | cguidefile.cpp | 41 m_mismatchPenalty = (-sc.GetMismatchPenalty())/sc.GetIdentityScore() - 1; in SetMismatchPenalty()
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| H A D | caligner-alignwintwodiag.cpp | 23 double mm = m_scoreParam->GetMismatchPenalty(); in AlignWinTwoDiag()
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| H A D | cbatch.cpp | 72 double mm = m_scoringFactory->GetScoreParam()->GetMismatchPenalty(); in x_Rehash()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/api/ |
| H A D | magicblast_options.hpp | 153 int GetMismatchPenalty() const { return m_Opts->GetMismatchPenalty(); } in GetMismatchPenalty() function in CMagicBlastOptionsHandle
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| H A D | blast_nucl_options.hpp | 189 int GetMismatchPenalty() const { return m_Opts->GetMismatchPenalty(); } in GetMismatchPenalty() function in CBlastNucleotideOptionsHandle
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| H A D | blast_options.hpp | 409 int GetMismatchPenalty() const;
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/api/ |
| H A D | magicblast_options.hpp | 153 int GetMismatchPenalty() const { return m_Opts->GetMismatchPenalty(); } in GetMismatchPenalty() function in CMagicBlastOptionsHandle
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| H A D | blast_nucl_options.hpp | 189 int GetMismatchPenalty() const { return m_Opts->GetMismatchPenalty(); } in GetMismatchPenalty() function in CBlastNucleotideOptionsHandle
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| H A D | blast_options.hpp | 409 int GetMismatchPenalty() const;
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/format/ |
| H A D | data4xmlformat.hpp | 142 int GetMismatchPenalty(void) const { in GetMismatchPenalty() function in CCmdLineBlastXMLReportData
143 return m_Options.GetMismatchPenalty(); in GetMismatchPenalty()
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| H A D | data4xml2format.hpp | 129 int GetMismatchPenalty(void) const { in GetMismatchPenalty() function in CCmdLineBlastXML2ReportData
130 return m_Options->GetMismatchPenalty(); in GetMismatchPenalty()
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| H A D | blastxml_format.hpp | 75 virtual int GetMismatchPenalty(void) const = 0;
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| H A D | blastxml2_format.hpp | 74 virtual int GetMismatchPenalty(void) const = 0;
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/format/ |
| H A D | data4xmlformat.hpp | 142 int GetMismatchPenalty(void) const { in GetMismatchPenalty() function in CCmdLineBlastXMLReportData
143 return m_Options.GetMismatchPenalty(); in GetMismatchPenalty()
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| H A D | data4xml2format.hpp | 129 int GetMismatchPenalty(void) const { in GetMismatchPenalty() function in CCmdLineBlastXML2ReportData
130 return m_Options->GetMismatchPenalty(); in GetMismatchPenalty()
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| H A D | blastxml_format.hpp | 75 virtual int GetMismatchPenalty(void) const = 0;
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| H A D | blastxml2_format.hpp | 74 virtual int GetMismatchPenalty(void) const = 0;
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/ |
| H A D | search_strategy_unit_test.cpp | 88 BOOST_REQUIRE_EQUAL(blastn_opts->GetMismatchPenalty(), -2); in BOOST_AUTO_TEST_CASE()
150 BOOST_REQUIRE_EQUAL(blastn_opts->GetMismatchPenalty(), -3); in BOOST_AUTO_TEST_CASE()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/ |
| H A D | search_strategy_unit_test.cpp | 88 BOOST_REQUIRE_EQUAL(blastn_opts->GetMismatchPenalty(), -2); in BOOST_AUTO_TEST_CASE()
150 BOOST_REQUIRE_EQUAL(blastn_opts->GetMismatchPenalty(), -3); in BOOST_AUTO_TEST_CASE()
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