Searched refs:nIntNodes (Results 1 – 10 of 10) sorted by relevance
/dports/biology/mrbayes/MrBayes-3.2.7/src/ |
H A D | mbbeagle.c | 800 for (i=0; i<t->nIntNodes; i++) in TreeCondLikes_Beagle_No_Rescale() 901 for (i=0; i<t->nIntNodes; i++) in TreeCondLikes_Beagle_Rescale_All() 957 opJ = op + j * t->nIntNodes; in TreeCondLikes_Beagle_Rescale_All() 984 t->nIntNodes, in TreeCondLikes_Beagle_Rescale_All() 1012 for (i=0; i<t->nIntNodes; i++) in TreeCondLikes_Beagle_Always_Rescale() 2175 for (i=0; i<t->nIntNodes; i++) in TreeCondLikes_BeagleMultiPartition_No_Rescale() 2256 opJ = i + j*t->nIntNodes; in TreeCondLikes_BeagleMultiPartition_No_Rescale() 2321 for (i=0; i<t->nIntNodes; i++) in TreeCondLikes_BeagleMultiPartition_Rescale_All() 2406 opJ = i + j*t->nIntNodes; in TreeCondLikes_BeagleMultiPartition_Rescale_All() 2467 for (i=0; i<t->nIntNodes; i++) in TreeCondLikes_BeagleMultiPartition_Always_Rescale() [all …]
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H A D | best.c | 266 for (i=0; i<speciesTree->nIntNodes; i++) in GetDepthMatrix() 322 for (i=0; i<speciesTree->nIntNodes; i++) in GetMeanDist() 344 (*mean) = distSum / speciesTree->nIntNodes; in GetMeanDist() 406 for (i=0; i<geneTrees[w]->nIntNodes; i++) { in GetMinDepthMatrix() 422 for (j=0; j<geneTrees[w]->nIntNodes; j++) { in GetMinDepthMatrix() 530 polyTree->nIntNodes = 1; in GetSpeciesTreeFromMinDepths() 562 polyTree->nIntNodes++; in GetSpeciesTreeFromMinDepths() 601 assert (polyTree->nIntNodes == numSpecies - 1); in GetSpeciesTreeFromMinDepths() 865 for (i=0; i<geneTree->nIntNodes; i++) in LnPriorProbGeneTree() 970 for (i=0; i<speciesTree->nIntNodes; i++) in LnProposalProbSpeciesTree() [all …]
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H A D | utils.c | 2024 t->nIntNodes = 0; in AllocateTree() 2176 if (t1->nIntNodes != t2->nIntNodes) in AreTopologiesSame() 2239 if (t1->nIntNodes != t2->nIntNodes) in AreTreesSame() 2358 pt->nIntNodes = 1; in BuildConstraintTree() 2487 pt->nIntNodes++; in BuildConstraintTree() 3060 to->nIntNodes = from->nIntNodes; in CopyToPolyTreeFromPolyTree() 3149 assert (to->nIntNodes == from->nIntNodes); in CopyToSpeciesTreeFromPolyTree() 3414 to->nIntNodes = from->nIntNodes; in CopyToTreeFromTree() 3614 pt->nIntNodes--; in Deroot() 6266 pt->nIntNodes = 0; in ResetPolyTree() [all …]
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H A D | mcmc.c | 5464 for (i=0; i<t->nIntNodes; i++) in GibbsSampleGamma() 5840 nIntNodes = GetTree(m->brlens, 0, 0)->nIntNodes; in InitChainCondLikes() 6120 nIntNodes = GetTree(m->brlens,0,0)->nIntNodes; in InitChainCondLikes() 6158 clIndex += nIntNodes; in InitChainCondLikes() 6923 nIntNodes = GetTree(m->brlens,0,0)->nIntNodes; in InitParsSets() 8400 n = t->nIntNodes+1; in LnBirthDeathPriorPrRandom() 8418 for (i=0; i<t->nIntNodes; i++) in LnBirthDeathPriorPrRandom() 8467 n = t->nIntNodes+1; in LnBirthDeathPriorPrDiversity() 8485 for (i=0; i<t->nIntNodes; i++) in LnBirthDeathPriorPrDiversity() 8542 n = t->nIntNodes+1; in LnBirthDeathPriorPrCluster() [all …]
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H A D | bayes.h | 598 …int nIntNodes; /*!< number of interior nodes in tree (excluding lower root in… member 649 int nIntNodes; /*!< number of interior nodes in tree */ member
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H A D | sumpt.c | 3282 t->nIntNodes = 1; in ConTree() 3421 t->nIntNodes++; in ConTree() 6395 if (t->nNodes - t->nIntNodes != numTranslates) in DoSumtTree() 6454 sumtParams.numTaxa = t->nNodes - t->nIntNodes; in DoSumtTree() 6483 if (t->nNodes - t->nIntNodes != sumtParams.numTaxa) in DoSumtTree() 6486 … spacer, sumtParams.numTaxa, t->name, sumtParams.curFileName, t->nNodes-t->nIntNodes); in DoSumtTree() 8037 k = t->nNodes - t->nIntNodes; in ShowConTree() 8038 for (i=0; i<t->nIntNodes; i++) in ShowConTree() 8420 orderLen = t->nIntNodes - 1; in StoreSumtTree() 8488 theTree->nIntNodes = sumtParams.numTaxa - 1; in TreeProb() [all …]
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H A D | proposal.c | 4248 for (i=t->nIntNodes-2; i>=0; i--) in Move_ExtSSClock() 4314 for (i=t->nIntNodes-1; i>=0; i--) in Move_ExtSSClock() 4400 for (i=t->nIntNodes-1; i>=0; i--) in Move_ExtSSClock() 4443 for (i=t->nIntNodes-1; i>=0; i--) in Move_ExtSSClock() 7627 for (i=0; i<t->nIntNodes-1; i++) in Move_NNIClock() 7713 for (i=0; i<t->nIntNodes-1; i++) in Move_NNIClock() 9264 subtree->nIntNodes = nSubTerminals - 2; in Move_ParsEraser1() 9276 subtree1->nIntNodes = nSubTerminals - 2; in Move_ParsEraser1() 9292 tInfo.vertex = tInfo.leaf + t->nNodes - t->nIntNodes; in Move_ParsEraser1() 9302 for (i=0; i<t->nIntNodes; i++) in Move_ParsEraser1() [all …]
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H A D | command.c | 8487 t->nIntNodes = t->nNodes; in DoTreeParm() 8491 t->nIntNodes--; in DoTreeParm() 8496 if (t->isRooted == NO && t->nNodes-t->nIntNodes == t->nIntNodes + 1) in DoTreeParm() 8498 if ((t->isRooted == YES && t->nNodes-t->nIntNodes != t->nIntNodes + 1) || in DoTreeParm() 8499 (t->isRooted == NO && t->nNodes-t->nIntNodes != t->nIntNodes + 2)) in DoTreeParm() 8502 if (t->isRooted == YES && t->nNodes-t->nIntNodes == t->nIntNodes + 2) in DoTreeParm()
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H A D | model.c | 11924 for (i=0; i<t->nIntNodes; i++) in DoesTreeSatisfyConstraints() 11966 for (i=0; i<t->nIntNodes; i++) in DoesTreeSatisfyConstraints() 11978 if (i==t->nIntNodes) in DoesTreeSatisfyConstraints() 12022 for (i=0; i<t->nIntNodes; i++) in DoesTreeSatisfyConstraints() 12033 if (i==t->nIntNodes) in DoesTreeSatisfyConstraints() 12052 for (i=0; i<t->nIntNodes; i++) in DoesTreeSatisfyConstraints() 12063 if (i!=t->nIntNodes) in DoesTreeSatisfyConstraints() 12124 if (tree->nIntNodes != constraintTree->nIntNodes) in FillTreeParams() 13001 tree->nIntNodes = numSpecies - 1; in InitializeChainTrees() 13006 tree->nIntNodes = numLocalTaxa - 1; in InitializeChainTrees() [all …]
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H A D | likelihood.c | 7706 for (i=t->nIntNodes-1; i>=0; i--) in Likelihood_Pars() 7718 for (i=0; i<t->nIntNodes; i++) in Likelihood_Pars() 7872 for (i=0; i<t->nIntNodes; i++) in Likelihood_ParsStd() 8033 for (i=0; i<tree->nIntNodes; i++) in LaunchLogLikeForDivision()
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