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Searched defs:state_freq (Results 1 – 14 of 14) sorted by relevance

/dports/biology/iqtree/IQ-TREE-2.0.6/model/
H A Dmodelsubst.cpp122 void ModelSubst::getStateFrequency(double *state_freq, int mixture) { in getStateFrequency()
128 void ModelSubst::setStateFrequency(double *state_freq) { in setStateFrequency()
H A Dmodelsubst.h377 double *state_freq; variable
H A Dpartitionmodel.cpp89 double *state_freq = new double[nstates]; in PartitionModel() local
H A Dmodelmixture.cpp1450 void ModelMixture::getStateFrequency(double *state_freq, int mixture) { in getStateFrequency()
H A Dmodelfactory.cpp544 double *state_freq = new double[model->num_states]; in ModelFactory() local
/dports/biology/iqtree/IQ-TREE-2.0.6/obsolete/
H A Dngs.h419 vector<double*> state_freq; variable
H A Dngs.cpp879 double *state_freq = new double[aln.num_states]; in reportNGSAnalysis() local
/dports/biology/iqtree/IQ-TREE-2.0.6/utils/
H A Deigendecomposition.cpp38 double **rate_params, double *state_freq, in eigensystem()
162 void EigenDecomposition::eigensystem_sym(double **rate_params, double *state_freq, in eigensystem_sym()
313 double *rate_matrix, double *state_freq, double *eval, double *eval_imag, in eigensystem_nonrev()
/dports/biology/iqtree/IQ-TREE-2.0.6/tree/
H A Dphylotreesse.cpp644 double state_freq[nstates]; in computePtnInvar() local
1545 double state_freq[nstates]; in computeMarginalAncestralState() local
H A Dphylokernelnonrev.h618 double state_freq[nstates]; local
1085 double state_freq[nstates]; local
/dports/biology/iqtree/IQ-TREE-2.0.6/alignment/
H A Dalignment.cpp113 double *state_freq = new double[num_states]; in checkAbsentStates() local
170 double *state_freq = new double[num_states]; in checkSeqName() local
3317 double *state_freq = new double[num_states]; in createBootstrapAlignment() local
4003 void Alignment::convertCountToFreq(size_t *state_count, double *state_freq) { in convertCountToFreq()
4051 void Alignment::computeStateFreq (double *state_freq, size_t num_unknown_states) { in computeStateFreq()
4178 double *state_freq = &freq_per_sequence[seq*num_states]; in computeStateFreqPerSequence() local
4372 void Alignment::computeCodonFreq(StateFreqType freq, double *state_freq, double *ntfreq) { in computeCodonFreq()
4530 void Alignment::computeDivergenceMatrix(double *pair_freq, double *state_freq, bool normalize) { in computeDivergenceMatrix()
H A Dsuperalignment.cpp1080 void SuperAlignment::computeDivergenceMatrix(double *pair_freq, double *state_freq, bool normalize)… in computeDivergenceMatrix()
/dports/biology/iqtree/IQ-TREE-2.0.6/main/
H A Dtreetesting.cpp391 double *state_freq = &ptn_state_freq[pattern_index[i]*nstates]; in printSiteStateFreq() local
420 double *state_freq = aln->site_state_freq[pattern_index[i]]; in printSiteStateFreq() local
H A Dphyloanalysis.cpp363 double state_freq[20]; in reportModel() local