| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/ |
| H A D | psiblast_aux_priv.cpp | 82 _ASSERT(pssm.NotEmpty()); in BEGIN_SCOPE()
258 *retval, pssm.GetByRow(), pssm.GetNumRows(), in GetScores()
259 pssm.GetNumColumns()); in GetScores()
281 *retval, pssm.GetByRow(), pssm.GetNumRows(), in GetFreqRatios()
305 *retval, pssm.GetByRow(), pssm.GetNumRows(), in GetResidueFrequencies()
331 *retval, pssm.GetByRow(), pssm.GetNumRows(), in GetWeightedResidueFrequencies()
487 if (pssm->GetPssm().GetNumRows() != in PsiBlastComputePssmScores()
501 PsiBlastAddAncillaryPssmData(*pssm, in PsiBlastComputePssmScores()
572 if ( !pssm.CanGetPssm() ) { in Pssm()
612 if ( !pssm.HasQuery() ) { in Pssm()
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| H A D | pssm_engine.cpp | 347 CPSIMatrix pssm; in x_CreatePssmFromFreqRatios() local
358 &pssm); in x_CreatePssmFromFreqRatios()
383 CPSIMatrix pssm; in x_CreatePssmFromMsa() local
419 CPSIMatrix pssm; in x_CreatePssmFromCDD() local
426 &pssm, in x_CreatePssmFromCDD()
630 _ASSERT(pssm); in x_PSIMatrix2Asn1()
645 asn1_pssm.SetNumRows(pssm->nrows); in x_PSIMatrix2Asn1()
651 asn1_pssm.SetKappa(pssm->kappa); in x_PSIMatrix2Asn1()
652 asn1_pssm.SetH(pssm->h); in x_PSIMatrix2Asn1()
660 push_back(pssm->pssm[i][j]); in x_PSIMatrix2Asn1()
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| H A D | psiblast_impl.cpp | 59 CPsiBlastImpl::CPsiBlastImpl(CRef<objects::CPssmWithParameters> pssm, in BEGIN_SCOPE()
154 CPssm& pssm = m_Pssm->SetPssm(); in Run() local
155 pssm.SetLambda in Run()
157 pssm.SetKappa in Run()
159 pssm.SetH in Run()
161 pssm.SetLambdaUngapped in Run()
163 pssm.SetKappaUngapped in Run()
165 pssm.SetHUngapped in Run()
174 if (pssm.Empty()) { in SetPssm()
178 CPsiBlastValidate::Pssm(*pssm, true); in SetPssm()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/ |
| H A D | psiblast_aux_priv.cpp | 82 _ASSERT(pssm.NotEmpty()); in BEGIN_SCOPE()
258 *retval, pssm.GetByRow(), pssm.GetNumRows(), in GetScores()
259 pssm.GetNumColumns()); in GetScores()
281 *retval, pssm.GetByRow(), pssm.GetNumRows(), in GetFreqRatios()
305 *retval, pssm.GetByRow(), pssm.GetNumRows(), in GetResidueFrequencies()
331 *retval, pssm.GetByRow(), pssm.GetNumRows(), in GetWeightedResidueFrequencies()
487 if (pssm->GetPssm().GetNumRows() != in PsiBlastComputePssmScores()
501 PsiBlastAddAncillaryPssmData(*pssm, in PsiBlastComputePssmScores()
572 if ( !pssm.CanGetPssm() ) { in Pssm()
612 if ( !pssm.HasQuery() ) { in Pssm()
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| H A D | pssm_engine.cpp | 347 CPSIMatrix pssm; in x_CreatePssmFromFreqRatios() local
358 &pssm); in x_CreatePssmFromFreqRatios()
383 CPSIMatrix pssm; in x_CreatePssmFromMsa() local
419 CPSIMatrix pssm; in x_CreatePssmFromCDD() local
426 &pssm, in x_CreatePssmFromCDD()
630 _ASSERT(pssm); in x_PSIMatrix2Asn1()
645 asn1_pssm.SetNumRows(pssm->nrows); in x_PSIMatrix2Asn1()
651 asn1_pssm.SetKappa(pssm->kappa); in x_PSIMatrix2Asn1()
652 asn1_pssm.SetH(pssm->h); in x_PSIMatrix2Asn1()
660 push_back(pssm->pssm[i][j]); in x_PSIMatrix2Asn1()
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| H A D | psiblast_impl.cpp | 59 CPsiBlastImpl::CPsiBlastImpl(CRef<objects::CPssmWithParameters> pssm, in BEGIN_SCOPE()
154 CPssm& pssm = m_Pssm->SetPssm(); in Run() local
155 pssm.SetLambda in Run()
157 pssm.SetKappa in Run()
159 pssm.SetH in Run()
161 pssm.SetLambdaUngapped in Run()
163 pssm.SetKappaUngapped in Run()
165 pssm.SetHUngapped in Run()
174 if (pssm.Empty()) { in SetPssm()
178 CPsiBlastValidate::Pssm(*pssm, true); in SetPssm()
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| /dports/biology/ncbi-toolkit/ncbi/algo/blast/core/ |
| H A D | blast_psi.c | 69 PSIMatrix* pssm);
98 PSIMatrix** pssm) in PSICreatePssm() argument
336 if (pssm) { in s_PSICreatePssmFromFrequencyRatiosCleanUp()
337 *pssm = PSIMatrixFree(*pssm); in s_PSICreatePssmFromFrequencyRatiosCleanUp()
429 if (pssm) { in s_PSICreatePssmCleanUp()
430 *pssm = PSIMatrixFree(*pssm); in s_PSICreatePssmCleanUp()
446 ASSERT(pssm); in s_PSISavePssm()
448 _PSICopyMatrix_int(pssm->pssm, internal_pssm->pssm, in s_PSISavePssm()
449 pssm->ncols, pssm->nrows); in s_PSISavePssm()
554 if ( !(retval->pssm) ) { in PSIMatrixNew()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/ |
| H A D | blast_psi.c | 69 PSIMatrix* pssm);
98 PSIMatrix** pssm) in PSICreatePssm() argument
336 if (pssm) { in s_PSICreatePssmFromFrequencyRatiosCleanUp()
337 *pssm = PSIMatrixFree(*pssm); in s_PSICreatePssmFromFrequencyRatiosCleanUp()
429 if (pssm) { in s_PSICreatePssmCleanUp()
430 *pssm = PSIMatrixFree(*pssm); in s_PSICreatePssmCleanUp()
446 ASSERT(pssm); in s_PSISavePssm()
448 _PSICopyMatrix_int(pssm->pssm, internal_pssm->pssm, in s_PSISavePssm()
449 pssm->ncols, pssm->nrows); in s_PSISavePssm()
554 if ( !(retval->pssm) ) { in PSIMatrixNew()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/ |
| H A D | blast_psi.c | 69 PSIMatrix* pssm);
98 PSIMatrix** pssm) in PSICreatePssm() argument
336 if (pssm) { in s_PSICreatePssmFromFrequencyRatiosCleanUp()
337 *pssm = PSIMatrixFree(*pssm); in s_PSICreatePssmFromFrequencyRatiosCleanUp()
429 if (pssm) { in s_PSICreatePssmCleanUp()
430 *pssm = PSIMatrixFree(*pssm); in s_PSICreatePssmCleanUp()
446 ASSERT(pssm); in s_PSISavePssm()
448 _PSICopyMatrix_int(pssm->pssm, internal_pssm->pssm, in s_PSISavePssm()
449 pssm->ncols, pssm->nrows); in s_PSISavePssm()
554 if ( !(retval->pssm) ) { in PSIMatrixNew()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/app/blast/ |
| H A D | psiblast_app.cpp | 153 if (pssm) { in s_GetQueryBioseq()
238 if (pssm.NotEmpty()) { in x_RunLocalPsiBlastIterations()
307 pssm = in x_RunLocalPsiBlastIterations()
320 SavePssmToFile(pssm, &itr); in x_RunLocalPsiBlastIterations()
361 else if (!pssm.Empty()) in DoIterations()
388 if (pssm.Empty()) { in SavePssmToFile()
509 if (pssm.Empty()) in Run()
519 pssm, in Run()
531 pssm.Reset(); in Run()
535 _ASSERT(pssm->HasQuery()); in Run()
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| H A D | deltablast_app.cpp | 130 if (pssm.Empty()) { in SavePssmToFile()
143 CBlastFormatUtil::PrintAsciiPssm(*pssm, in SavePssmToFile()
303 CRef<CPssmWithParameters> pssm; in Run() local
314 pssm = rmt_blast->GetPSSM(); in Run()
328 pssm = deltablast->GetPssm(); in Run()
353 SavePssmToFile(pssm); in Run()
397 SavePssmToFile(pssm); in Run()
405 SavePssmToFile(pssm); in Run()
530 psiblast->SetPssm(pssm); in DoPsiBlastIterations()
533 SavePssmToFile(pssm); in DoPsiBlastIterations()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/blast/ |
| H A D | psiblast_app.cpp | 153 if (pssm) { in s_GetQueryBioseq()
238 if (pssm.NotEmpty()) { in x_RunLocalPsiBlastIterations()
307 pssm = in x_RunLocalPsiBlastIterations()
320 SavePssmToFile(pssm, &itr); in x_RunLocalPsiBlastIterations()
361 else if (!pssm.Empty()) in DoIterations()
388 if (pssm.Empty()) { in SavePssmToFile()
509 if (pssm.Empty()) in Run()
519 pssm, in Run()
531 pssm.Reset(); in Run()
535 _ASSERT(pssm->HasQuery()); in Run()
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| H A D | deltablast_app.cpp | 130 if (pssm.Empty()) { in SavePssmToFile()
143 CBlastFormatUtil::PrintAsciiPssm(*pssm, in SavePssmToFile()
303 CRef<CPssmWithParameters> pssm; in Run() local
314 pssm = rmt_blast->GetPSSM(); in Run()
328 pssm = deltablast->GetPssm(); in Run()
353 SavePssmToFile(pssm); in Run()
397 SavePssmToFile(pssm); in Run()
405 SavePssmToFile(pssm); in Run()
530 psiblast->SetPssm(pssm); in DoPsiBlastIterations()
533 SavePssmToFile(pssm); in DoPsiBlastIterations()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/cn3d/ |
| H A D | cn3d_pssm.cpp | 103 pssm = pm.make(); in BEGIN_SCOPE()
106 if (!pssm->GetPssm().IsSetQuery() || !pssm->GetPssm().GetQuery().IsSeq()) in BEGIN_SCOPE()
119 oosa << *pssm; in BEGIN_SCOPE()
214 if (!pssm->GetPssm().IsSetFinalData()) in UnpackMatrix()
216 unsigned int nScores = pssm->GetPssm().GetNumRows() * pssm->GetPssm().GetNumColumns(); in UnpackMatrix()
217 …if (pssm->GetPssm().GetNumRows() != 28 || pssm->GetPssm().GetFinalData().GetScores().size() != nSc… in UnpackMatrix()
224 scaledMatrix.resize(pssm->GetPssm().GetNumColumns()); in UnpackMatrix()
225 for (i=0; (int)i<pssm->GetPssm().GetNumColumns(); ++i) in UnpackMatrix()
236 if (pssm->GetPssm().GetByRow()) { in UnpackMatrix()
244 if ((int)r == pssm->GetPssm().GetNumRows()) { in UnpackMatrix()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/api/ |
| H A D | pssm_engine.hpp | 227 x_PSIMatrix2Asn1(const PSIMatrix* pssm,
259 GetScores(const objects::CPssmWithParameters& pssm);
266 GetFreqRatios(const objects::CPssmWithParameters& pssm);
273 GetInformationContent(const objects::CPssmWithParameters& pssm,
282 GetGaplessColumnWeights(const objects::CPssmWithParameters& pssm,
291 GetResidueFrequencies(const objects::CPssmWithParameters& pssm);
299 GetWeightedResidueFrequencies(const objects::CPssmWithParameters& pssm);
306 GetSigma(const objects::CPssmWithParameters& pssm, vector<double>& retval);
313 GetIntervalSizes(const objects::CPssmWithParameters& pssm,
321 GetNumMatchingSeqs(const objects::CPssmWithParameters& pssm,
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/api/ |
| H A D | pssm_engine.hpp | 227 x_PSIMatrix2Asn1(const PSIMatrix* pssm,
259 GetScores(const objects::CPssmWithParameters& pssm);
266 GetFreqRatios(const objects::CPssmWithParameters& pssm);
273 GetInformationContent(const objects::CPssmWithParameters& pssm,
282 GetGaplessColumnWeights(const objects::CPssmWithParameters& pssm,
291 GetResidueFrequencies(const objects::CPssmWithParameters& pssm);
299 GetWeightedResidueFrequencies(const objects::CPssmWithParameters& pssm);
306 GetSigma(const objects::CPssmWithParameters& pssm, vector<double>& retval);
313 GetIntervalSizes(const objects::CPssmWithParameters& pssm,
321 GetNumMatchingSeqs(const objects::CPssmWithParameters& pssm,
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/ |
| H A D | pssmenginefreqratios_unit_test.cpp | 91 auto_ptr< CNcbiMatrix<int> > pssm in BOOST_AUTO_TEST_CASE() local
97 for (size_t i = 0; i < pssm->GetCols(); i++) { in BOOST_AUTO_TEST_CASE()
98 for (size_t j = 0; j < pssm->GetRows(); j++) { in BOOST_AUTO_TEST_CASE()
105 BOOST_REQUIRE_MESSAGE((*pssm)(j, i) == BLAST_SCORE_MIN, in BOOST_AUTO_TEST_CASE()
116 << " actual=" << NStr::IntToString((*pssm)(j, i)); in BOOST_AUTO_TEST_CASE()
118 (score-1 <= (*pssm)(j, i) || (*pssm)(j, i) <= score+1, in BOOST_AUTO_TEST_CASE()
138 const CPssm & pssm = pssm_w_param->GetPssm(); in BOOST_AUTO_TEST_CASE() local
139 BOOST_REQUIRE(pssm.IsSetIntermediateData()); in BOOST_AUTO_TEST_CASE()
140 BOOST_REQUIRE(pssm.GetIntermediateData().IsSetWeightedResFreqsPerPos()); in BOOST_AUTO_TEST_CASE()
141 list<double> freq_ratios = pssm.GetIntermediateData().GetWeightedResFreqsPerPos(); 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 | pssmenginefreqratios_unit_test.cpp | 91 auto_ptr< CNcbiMatrix<int> > pssm in BOOST_AUTO_TEST_CASE() local
97 for (size_t i = 0; i < pssm->GetCols(); i++) { in BOOST_AUTO_TEST_CASE()
98 for (size_t j = 0; j < pssm->GetRows(); j++) { in BOOST_AUTO_TEST_CASE()
105 BOOST_REQUIRE_MESSAGE((*pssm)(j, i) == BLAST_SCORE_MIN, in BOOST_AUTO_TEST_CASE()
116 << " actual=" << NStr::IntToString((*pssm)(j, i)); in BOOST_AUTO_TEST_CASE()
118 (score-1 <= (*pssm)(j, i) || (*pssm)(j, i) <= score+1, in BOOST_AUTO_TEST_CASE()
138 const CPssm & pssm = pssm_w_param->GetPssm(); in BOOST_AUTO_TEST_CASE() local
139 BOOST_REQUIRE(pssm.IsSetIntermediateData()); in BOOST_AUTO_TEST_CASE()
140 BOOST_REQUIRE(pssm.GetIntermediateData().IsSetWeightedResFreqsPerPos()); in BOOST_AUTO_TEST_CASE()
141 list<double> freq_ratios = pssm.GetIntermediateData().GetWeightedResFreqsPerPos(); in BOOST_AUTO_TEST_CASE()
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| /dports/biology/ncbi-toolkit/ncbi/algo/blast/api/ |
| H A D | blast_input.c | 440 PssmPtr pssm = NULL; in s_PosReadAsnCheckpoint() local
464 pssm = scoremat->pssm; in s_PosReadAsnCheckpoint()
465 if (pssm == NULL) { in s_PosReadAsnCheckpoint()
470 freqs = pssm->intermediateData; in s_PosReadAsnCheckpoint()
483 if (pssm->numRows != BLASTAA_SIZE) { in s_PosReadAsnCheckpoint()
489 if (!pssm->query || !pssm->query->data.ptrvalue) { in s_PosReadAsnCheckpoint()
496 if (pssm->numColumns != bsp->length) { in s_PosReadAsnCheckpoint()
578 if (pssm->byRow == FALSE) { in s_PosReadAsnCheckpoint()
594 if (j < pssm->numRows) in s_PosReadAsnCheckpoint()
613 if (i < pssm->numColumns) in s_PosReadAsnCheckpoint()
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| /dports/biology/ncbi-toolkit/ncbi/demo/ |
| H A D | formatrpsdb.c | 304 PssmPtr pssm = seq->pssm; in RPSUpdateStatistics() local
407 if (pssm->byRow == FALSE) { in RPSUpdateStatistics()
524 PssmPtr pssm = seq->pssm; in RPSUpdatePSSM() local
660 PssmPtr pssm = seq->pssm; in RPSAddFirstSequence() local
748 PssmPtr pssm; in RPSAddSequence() local
752 pssm = seq->pssm; in RPSAddSequence()
753 if (pssm == NULL) { in RPSAddSequence()
1051 PssmPtr pssm = NULL; in Main() local
1149 pssm = sequence->pssm; in Main()
1150 if (pssm == NULL) { in Main()
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| /dports/biology/py-biopython/biopython-1.79/Bio/motifs/ |
| H A D | thresholds.py | 17 def __init__(self, motif=None, precision=10 ** 3, pssm=None, background=None): argument
19 if pssm is None:
25 self.min_score = min(0.0, pssm.min)
26 self.interval = max(0.0, pssm.max) - self.min_score
27 self.n_points = precision * pssm.length
28 self.ic = pssm.mean(background)
34 if pssm is None:
38 for position in range(pssm.length):
41 lo = pssm[:, position]
44 mo = pow(2, pssm[letter, position]) * bg
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/app/blastdb/ |
| H A D | makeprofiledb.cpp | 610 if(!pssm.IsSetQuery() || (0 == pssm.GetQueryLength())) in x_CheckInputScoremat()
616 if(!pssm.IsSetNumRows() || !pssm.IsSetNumColumns()) in x_CheckInputScoremat()
622 if((int) (pssm.GetQueryLength()) != pssm.GetNumColumns()) in x_CheckInputScoremat()
657 if(pssm.IsSetFinalData()) in x_CheckInputScoremat()
864 CPssm & pssm = seq.SetPssm(); in x_RPSUpdateStatistics() local
1000 if(pssm.IsSetQuery()) in x_UpdateCobalt()
1002 if(pssm.GetQuery().IsSeq()) in x_UpdateCobalt()
1048 if (pssm.GetByRow() == FALSE) { in x_UpdateFreqRatios()
1554 if(!pssm.IsSetIntermediateData()|| !pssm.GetIntermediateData().IsSetWeightedResFreqsPerPos()) in x_CreateDeltaList()
1615 if(pssm.GetByRow()) in x_UpdateDelta()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/blastdb/ |
| H A D | makeprofiledb.cpp | 610 if(!pssm.IsSetQuery() || (0 == pssm.GetQueryLength())) in x_CheckInputScoremat()
616 if(!pssm.IsSetNumRows() || !pssm.IsSetNumColumns()) in x_CheckInputScoremat()
622 if((int) (pssm.GetQueryLength()) != pssm.GetNumColumns()) in x_CheckInputScoremat()
657 if(pssm.IsSetFinalData()) in x_CheckInputScoremat()
864 CPssm & pssm = seq.SetPssm(); in x_RPSUpdateStatistics() local
1000 if(pssm.IsSetQuery()) in x_UpdateCobalt()
1002 if(pssm.GetQuery().IsSeq()) in x_UpdateCobalt()
1048 if (pssm.GetByRow() == FALSE) { in x_UpdateFreqRatios()
1554 if(!pssm.IsSetIntermediateData()|| !pssm.GetIntermediateData().IsSetWeightedResFreqsPerPos()) in x_CreateDeltaList()
1615 if(pssm.GetByRow()) in x_UpdateDelta()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/struct_util/ |
| H A D | su_pssm.cpp | 445 if (!pssm.GetPssm().IsSetFinalData()) in ConvertPSSMToBLASTMatrix()
447 unsigned int nScores = pssm.GetPssm().GetNumRows() * pssm.GetPssm().GetNumColumns(); in ConvertPSSMToBLASTMatrix()
448 …if (pssm.GetPssm().GetNumRows() != 28 || pssm.GetPssm().GetFinalData().GetScores().size() != nScor… in ConvertPSSMToBLASTMatrix()
452 …BLAST_Matrix *matrix = new BLAST_Matrix(pssm.GetPssm().GetNumColumns() + 1, pssm.GetPssm().GetNumR… in ConvertPSSMToBLASTMatrix()
455 matrix->is_prot = pssm.GetPssm().GetIsProtein(); in ConvertPSSMToBLASTMatrix()
458 if (pssm.GetPssm().GetFinalData().IsSetKappa()) in ConvertPSSMToBLASTMatrix()
472 if (pssm.GetPssm().GetByRow()) { in ConvertPSSMToBLASTMatrix()
480 if ((int)c == pssm.GetPssm().GetNumRows()) { in ConvertPSSMToBLASTMatrix()
522 CRef < CPssmWithParameters > pssm = engine.Run(); in CreateBlastMatrix() local
528 oosa << *pssm; in CreateBlastMatrix()
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| /dports/biology/mmseqs2/MMseqs2-13-45111/src/alignment/ |
| H A D | PSSMCalculator.h | 13 const char * pssm; member
17 Profile(char * pssm, float * prob, float * neffM, std::string consensus) in Profile()
18 : pssm(pssm), prob(prob), neffM(neffM), consensus(consensus) {}; in Profile()
61 char * pssm; variable
91 …void computeLogPSSM(char *pssm, const float *profile, float bitFactor, size_t queryLength, float s…
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