/dports/biology/lamarc/lamarc-2.1.8/src/postlike/ |
H A D | plforces.h | 43 TreeSummary *m_pTreedata; // non-owning pointer 130 const TreeSummary * treedata); 134 const TreeSummary * treedata); 137 const TreeSummary * treedata, 141 const TreeSummary * treedata, 180 const TreeSummary * treedata); 184 const TreeSummary * treedata); 232 const TreeSummary * treedata); 565 const TreeSummary *treedata); 569 const TreeSummary *treedata); [all …]
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H A D | plforces.cpp | 57 double DiseasePL::lnWait (const vector < double >¶m, const TreeSummary * treedata) in lnWait() 82 const TreeSummary * treedata) in lnPoint() 120 const TreeSummary * treedata) in lnPoint() 340 const TreeSummary * treedata) in lnPoint() 499 const TreeSummary * treedata) in lnPoint() 851 const TreeSummary * treedata) in lnPoint() 1394 double DivMigPL::lnWait(const vector<double>& param, const TreeSummary* treedata) in lnWait() 1430 const TreeSummary * treedata) in lnPoint() 1705 const TreeSummary* treedata) in lnPoint() 2213 const TreeSummary *treedata) in lnPoint() [all …]
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H A D | likelihood.h | 37 class TreeSummary; variable 100 const TreeSummary *treedata); 111 const TreeSummary* treedata); 130 const vector<TreeSummary*> *data); 134 const vector<TreeSummary*> *pGenealogies,
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H A D | derivatives.cpp | 60 … const vector<TreeSummary*> *pGenealogies, const long& whichparam) in DCalc_sumG_BasicNumerator() 308 const vector<TreeSummary*> *pGenealogies = in DCalculate() 363 const vector<TreeSummary*> *pGenealogies = in DCalculate()
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H A D | likelihood.cpp | 360 const vector<TreeSummary*> *pGenealogies) in Calc_sumG_ProbGP_over_ProbGPo() 364 vector<TreeSummary*>::const_iterator currentGenealogy; in Calc_sumG_ProbGP_over_ProbGPo() 411 …lc_lnProbGP(const DoubleVec1d& param, const DoubleVec1d& lparam, const TreeSummary *pThisGenealogy) in Calc_lnProbGP() 436 …lc_lnProbGS(const DoubleVec1d& param, const DoubleVec1d& lparam, const TreeSummary *pThisGenealogy) in Calc_lnProbGS() 541 vector<TreeSummary*> genealogies = pTreeCollector->treeSummaries; in Setup() 749 TreeSummary* tr(m_data[rep]->treeSummaries[tree]); in GeyerLike() 798 TreeSummary* tr(m_data[rep]->treeSummaries[tree]); in GeyerStart()
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/dports/biology/lamarc/lamarc-2.1.8/src/tree/ |
H A D | treesum.h | 72 class TreeSummary 75 TreeSummary & operator=(const TreeSummary & src); // undefined 99 TreeSummary(); // used only to prototype 100 TreeSummary(const TreeSummary & src); 101 virtual TreeSummary * Clone() const; 102 virtual ~TreeSummary(); 162 class RecTreeSummary : public TreeSummary 172 virtual TreeSummary * Clone() const;
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H A D | treesum.cpp | 62 TreeSummary::TreeSummary() in TreeSummary() function in TreeSummary 86 TreeSummary::TreeSummary(const TreeSummary & src) in TreeSummary() function in TreeSummary 101 TreeSummary * TreeSummary::Clone() const in Clone() 103 return new TreeSummary(*this); in Clone() 108 TreeSummary::~TreeSummary() in ~TreeSummary() 119 void TreeSummary::Compress() in Compress() 138 void TreeSummary::Summarize(const Tree & tree) in Summarize() 358 void TreeSummary::CacheSummaries() in CacheSummaries() 446 : TreeSummary() in RecTreeSummary() 462 : TreeSummary(src), in RecTreeSummary() [all …]
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H A D | branch.h | 64 class TreeSummary; variable 220 virtual void ScoreEvent(TreeSummary & summary, BranchBuffer & ks) const = 0; 286 virtual void ScoreEvent(TreeSummary & summary, BranchBuffer & ks) const; 287 virtual void ScoreEvent(TreeSummary & summary, BranchBuffer & ks, long & s) const; 325 virtual void ScoreEvent(TreeSummary & summary, BranchBuffer & ks) const; 378 virtual void ScoreEvent(TreeSummary & summary, BranchBuffer & ks) const; 456 virtual void ScoreEvent(TreeSummary & summary, BranchBuffer & ks) const; 486 virtual void ScoreEvent(TreeSummary & summary, BranchBuffer & ks) const; 518 virtual void ScoreEvent(TreeSummary & summary, BranchBuffer & ks) const; 548 virtual void ScoreEvent(TreeSummary & summary, BranchBuffer & ks) const; [all …]
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H A D | branch.cpp | 820 void BBranch::ScoreEvent(TreeSummary &, BranchBuffer &) const in ScoreEvent() argument 828 void BBranch::ScoreEvent(TreeSummary &, BranchBuffer &, long &) const in ScoreEvent() argument 960 void TBranch::ScoreEvent(TreeSummary &, BranchBuffer &) const in ScoreEvent() argument 968 void TBranch::ScoreEvent(TreeSummary &, BranchBuffer &, long &) const in ScoreEvent() argument 1195 void CBranch::ScoreEvent(TreeSummary & summary, BranchBuffer & ks) const in ScoreEvent() 1221 void CBranch::ScoreEvent(TreeSummary & summary, BranchBuffer & ks, long & s) const in ScoreEvent() 1469 void MBranch::ScoreEvent(TreeSummary & summary, BranchBuffer & ks) const in ScoreEvent() 1555 void DivMigBranch::ScoreEvent(TreeSummary & summary, BranchBuffer & ks) const in ScoreEvent() 1641 void DBranch::ScoreEvent(TreeSummary & summary, BranchBuffer & ks) const in ScoreEvent() 1710 void EBranch::ScoreEvent(TreeSummary & summary, BranchBuffer & ks) const in ScoreEvent() [all …]
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H A D | collector.cpp | 57 vector<TreeSummary*>::iterator treeiter; in ~TreeCollector() 112 vector<TreeSummary*>::iterator treesum = treeSummaries.begin(); in CorrectForFatalAttraction() 158 void TreeCollector::AddTreeSummary(TreeSummary* ts) in AddTreeSummary() 171 vector<TreeSummary*>::const_iterator treesum = treeSummaries.begin(); in TreeCount()
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H A D | collector.h | 71 vector<TreeSummary*> treeSummaries; // public for speed of access 78 virtual void AddTreeSummary(TreeSummary* ts);
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H A D | tree.h | 54 class TreeSummary; // return type of SummarizeTree() variable 183 TreeSummary * SummarizeTree() const; 195 void ScoreStick(TreeSummary & treesum) const;
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H A D | chain.cpp | 443 TreeSummary* trsum = m_chainstate.GetTree()->SummarizeTree(); in DoOneChain() 572 TreeSummary* hotsum = hot.m_chainstate.GetTree()->SummarizeTree(); in SwapTemperatureIdentities() 573 TreeSummary* coldsum = cold.m_chainstate.GetTree()->SummarizeTree(); in SwapTemperatureIdentities()
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H A D | arranger.cpp | 1014 TreeSummary * trsum = chstate.GetTree()->SummarizeTree(); in AcceptAndSynchronize() 1147 TreeSummary * trsum = chstate.GetTree()->SummarizeTree(); in AcceptAndSynchronize() 1293 double StairArranger::LnPBrownStickParams(const DoubleVec1d & param, const TreeSummary * partialtre… in LnPBrownStickParams() 1348 TreeSummary * newtrsum = chstate.GetTree()->SummarizeTree(); in AcceptAndSynchronize() 1349 TreeSummary * oldtrsum = chstate.GetOldTree()->SummarizeTree(); in AcceptAndSynchronize()
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H A D | tree.cpp | 229 TreeSummary * Tree::SummarizeTree() const in SummarizeTree() 231 TreeSummary * treesum = registry.GetProtoTreeSummary().Clone(); in SummarizeTree() 1141 void Tree::ScoreStick(TreeSummary & treesum) const in ScoreStick()
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H A D | arranger.h | 369 … double LnPBrownStickParams(const DoubleVec1d & param, const TreeSummary * partialtreedata) const;
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/dports/biology/lamarc/lamarc-2.1.8/src/control/ |
H A D | registry.h | 56 class TreeSummary; variable 76 const TreeSummary& GetProtoTreeSummary() const; 104 void Register(TreeSummary* treesum); 146 TreeSummary* protoTreeSummary;
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H A D | registry.cpp | 109 const TreeSummary& Registry::GetProtoTreeSummary() const in GetProtoTreeSummary() 281 void Registry::Register(TreeSummary* treesum) in Register()
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H A D | sumfilehandler.cpp | 485 TreeSummary* ts = registry.GetProtoTreeSummary().Clone(); in ReadInChainSum()
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H A D | chainmanager.cpp | 1749 TreeSummary * trsum = tree.SummarizeTree(); in DoSingleChainPosterior()
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/dports/biology/lamarc/lamarc-2.1.8/src/force/ |
H A D | forcesummary.h | 59 class TreeSummary; variable 125 TreeSummary* CreateProtoTreeSummary() const;
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H A D | timemanager.h | 25 class TreeSummary; variable 59 virtual void ScoreStick(TreeSummary& treesum) const; 158 virtual void ScoreStick(TreeSummary& treesum) const;
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H A D | forcesummary.cpp | 150 TreeSummary* ForceSummary::CreateProtoTreeSummary() const in CreateProtoTreeSummary() 162 TreeSummary* treesum; in CreateProtoTreeSummary() 169 treesum = new TreeSummary(); in CreateProtoTreeSummary()
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H A D | timemanager.cpp | 99 void TimeManager::ScoreStick(TreeSummary&) const in ScoreStick() 1235 void StickTimeManager::ScoreStick(TreeSummary& treesum) const in ScoreStick()
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/dports/www/gitlab-workhorse/gitlab-foss-0a901d60f8ae4a60c04ae82e6e9c3a03e9321417/lib/gitlab/ |
H A D | tree_summary.rb | 4 class TreeSummary class
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