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Searched refs:TreeSummary (Results 1 – 25 of 25) sorted by relevance

/dports/biology/lamarc/lamarc-2.1.8/src/postlike/
H A Dplforces.h43 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);
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H A Dplforces.cpp57 double DiseasePL::lnWait (const vector < double >&param, 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()
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H A Dlikelihood.h37 class TreeSummary; variable
100 const TreeSummary *treedata);
111 const TreeSummary* treedata);
130 const vector<TreeSummary*> *data);
134 const vector<TreeSummary*> *pGenealogies,
H A Dderivatives.cpp60 … 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()
H A Dlikelihood.cpp360 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()
/dports/biology/lamarc/lamarc-2.1.8/src/tree/
H A Dtreesum.h72 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;
H A Dtreesum.cpp62 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()
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H A Dbranch.h64 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;
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H A Dbranch.cpp820 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()
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H A Dcollector.cpp57 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()
H A Dcollector.h71 vector<TreeSummary*> treeSummaries; // public for speed of access
78 virtual void AddTreeSummary(TreeSummary* ts);
H A Dtree.h54 class TreeSummary; // return type of SummarizeTree() variable
183 TreeSummary * SummarizeTree() const;
195 void ScoreStick(TreeSummary & treesum) const;
H A Dchain.cpp443 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()
H A Darranger.cpp1014 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()
H A Dtree.cpp229 TreeSummary * Tree::SummarizeTree() const in SummarizeTree()
231 TreeSummary * treesum = registry.GetProtoTreeSummary().Clone(); in SummarizeTree()
1141 void Tree::ScoreStick(TreeSummary & treesum) const in ScoreStick()
H A Darranger.h369 … double LnPBrownStickParams(const DoubleVec1d & param, const TreeSummary * partialtreedata) const;
/dports/biology/lamarc/lamarc-2.1.8/src/control/
H A Dregistry.h56 class TreeSummary; variable
76 const TreeSummary& GetProtoTreeSummary() const;
104 void Register(TreeSummary* treesum);
146 TreeSummary* protoTreeSummary;
H A Dregistry.cpp109 const TreeSummary& Registry::GetProtoTreeSummary() const in GetProtoTreeSummary()
281 void Registry::Register(TreeSummary* treesum) in Register()
H A Dsumfilehandler.cpp485 TreeSummary* ts = registry.GetProtoTreeSummary().Clone(); in ReadInChainSum()
H A Dchainmanager.cpp1749 TreeSummary * trsum = tree.SummarizeTree(); in DoSingleChainPosterior()
/dports/biology/lamarc/lamarc-2.1.8/src/force/
H A Dforcesummary.h59 class TreeSummary; variable
125 TreeSummary* CreateProtoTreeSummary() const;
H A Dtimemanager.h25 class TreeSummary; variable
59 virtual void ScoreStick(TreeSummary& treesum) const;
158 virtual void ScoreStick(TreeSummary& treesum) const;
H A Dforcesummary.cpp150 TreeSummary* ForceSummary::CreateProtoTreeSummary() const in CreateProtoTreeSummary()
162 TreeSummary* treesum; in CreateProtoTreeSummary()
169 treesum = new TreeSummary(); in CreateProtoTreeSummary()
H A Dtimemanager.cpp99 void TimeManager::ScoreStick(TreeSummary&) const in ScoreStick()
1235 void StickTimeManager::ScoreStick(TreeSummary& treesum) const in ScoreStick()
/dports/www/gitlab-workhorse/gitlab-foss-0a901d60f8ae4a60c04ae82e6e9c3a03e9321417/lib/gitlab/
H A Dtree_summary.rb4 class TreeSummary class