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Searched refs:nIntNodes (Results 1 – 10 of 10) sorted by relevance

/dports/biology/mrbayes/MrBayes-3.2.7/src/
H A Dmbbeagle.c800 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()
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H A Dbest.c266 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()
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H A Dutils.c2024 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()
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H A Dmcmc.c5464 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()
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H A Dbayes.h598 …int nIntNodes; /*!< number of interior nodes in tree (excluding lower root in… member
649 int nIntNodes; /*!< number of interior nodes in tree */ member
H A Dsumpt.c3282 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()
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H A Dproposal.c4248 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()
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H A Dcommand.c8487 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()
H A Dmodel.c11924 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()
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H A Dlikelihood.c7706 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()