/dports/biology/lamarc/lamarc-2.1.8/src/datalike/ |
H A D | locuscell.cpp | 18 LocusCell::LocusCell(const vector<Cell_ptr>& src) in LocusCell() function in LocusCell 25 LocusCell::LocusCell(const LocusCell& src) in LocusCell() function in LocusCell 32 LocusCell::LocusCell(const vector<LocusCell>& src) in LocusCell() function in LocusCell 47 LocusCell& LocusCell::operator=(const LocusCell& src) in operator =() 55 LocusCell& LocusCell::operator+=(const LocusCell& src) in operator +=() 67 LocusCell& LocusCell::operator*=(double mult) in operator *=() 78 bool LocusCell::operator==(const LocusCell& src) const in operator ==() 91 void LocusCell::DeepCopyCells(const vector<Cell_ptr>& src) in DeepCopyCells() 104 bool LocusCell::DiffersFrom(const LocusCell& other, long marker) const in DiffersFrom() 109 void LocusCell::SetAllCategoriesTo(DoubleVec1d& state, long marker) in SetAllCategoriesTo()
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H A D | locuscell.h | 28 class LocusCell 36 LocusCell() {}; in LocusCell() function 37 LocusCell(const std::vector<Cell_ptr>& src); 38 LocusCell(const LocusCell& src); 39 LocusCell(const vector<LocusCell>& src); 40 ~LocusCell() {}; in ~LocusCell() 42 LocusCell& operator=(const LocusCell& src); 43 LocusCell& operator+=(const LocusCell& src); 44 LocusCell& operator*=(double mult); 45 bool operator==(const LocusCell& src) const; [all …]
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H A D | haplotypes.h | 20 class LocusCell; variable 31 vector<vector<LocusCell> > m_haplotype_dlcells; //Phase 2 48 vector<LocusCell> ChooseNewHaplotypes(); 49 vector<LocusCell> ChooseRandomHaplotypes(); 50 vector<LocusCell> ChooseFirstHaplotypes(); 51 vector<LocusCell> ChooseNextHaplotypes();
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H A D | datatype.h | 97 virtual LocusCell CreateDLCell(const Locus& locus) const = 0; 98 virtual LocusCell CreateInitializedDLCell(const Locus& locus, 134 virtual LocusCell CreateDLCell(const Locus& locus) const; 135 virtual LocusCell CreateInitializedDLCell(const Locus& locus, 154 virtual LocusCell CreateDLCell(const Locus& locus) const; 155 virtual LocusCell CreateInitializedDLCell(const Locus& locus, 172 virtual LocusCell CreateDLCell(const Locus& locus) const; 173 virtual LocusCell CreateInitializedDLCell(const Locus& locus,
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H A D | haplotypes.cpp | 65 vector<LocusCell> resolution; in ConvertAllelesToDLCells() 89 vector<vector<LocusCell> >::iterator dlList = m_haplotype_dlcells.begin(); in CollapseHaplotypeDLs() 92 vector<vector<LocusCell> >::iterator dlComp = dlList; in CollapseHaplotypeDLs() 170 vector<LocusCell> Haplotypes::ChooseNewHaplotypes() in ChooseNewHaplotypes() 193 vector<LocusCell> Haplotypes::ChooseRandomHaplotypes() in ChooseRandomHaplotypes() 206 vector<LocusCell> Haplotypes::ChooseFirstHaplotypes() in ChooseFirstHaplotypes() 219 vector<LocusCell> Haplotypes::ChooseNextHaplotypes() in ChooseNextHaplotypes() 226 vector<LocusCell> blankcells; in ChooseNextHaplotypes()
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H A D | datatype.cpp | 365 LocusCell DNASeqType::CreateDLCell(const Locus& locus) const in CreateDLCell() 374 return LocusCell(newcells); in CreateDLCell() 379 LocusCell DNASeqType::CreateInitializedDLCell(const Locus& locus, in CreateInitializedDLCell() 390 return LocusCell(newcells); in CreateInitializedDLCell() 418 LocusCell SNPDataType::CreateDLCell(const Locus& locus) const in CreateDLCell() 431 return LocusCell(newcells); in CreateDLCell() 436 LocusCell SNPDataType::CreateInitializedDLCell(const Locus& locus, in CreateInitializedDLCell() 455 return LocusCell(newcells); in CreateInitializedDLCell() 468 LocusCell AlleleType::CreateDLCell(const Locus& locus) const in CreateDLCell() 478 return LocusCell(newcells); in CreateDLCell() [all …]
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H A D | locus.h | 73 LocusCell m_protoCell; 75 vector<LocusCell> m_tipcells; // dim: tips (LS DEBUG: phase 2) 116 LocusCell GetProtoCell() const { return m_protoCell; }; in GetProtoCell() 117 vector<LocusCell> GetTipCells() const { return m_tipcells; }; in GetTipCells()
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H A D | region.cpp | 742 vector<vector<LocusCell> > tipcells(ntips); in CreateTree() 745 vector<LocusCell> locuscells = m_loci[locus].GetTipCells(); in CreateTree() 751 vector<vector<LocusCell> > movingtipcells(ntips); in CreateTree() 754 vector<LocusCell> movinglocuscells = m_movingloci[mlocus].GetTipCells(); in CreateTree()
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H A D | locus.cpp | 123 vector<LocusCell> cellsbymarkers; in Setup() 131 … vector<LocusCell> cells = individuals[ind].GetLocusCellsFor(GetName(), marker); in Setup() 138 LocusCell onecell(cellsbymarkers); in Setup()
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H A D | dlcalc.cpp | 433 const vector<LocusCell>& tipcells = locus.GetTipCells(); in SetupAliases()
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/dports/biology/lamarc/lamarc-2.1.8/src/tree/ |
H A D | tree.h | 68 vector<LocusCell> m_protoCells; // cache of locuscells for all loci 97 const vector<LocusCell> & CollectCells(); // Get locuscells for all loci. 110 virtual TBranch_ptr CreateTip(const TipData & tipdata, const vector<LocusCell> & cells, 111 … const vector<LocusCell> & movingcells, const rangeset & diseasesites); 112 virtual TBranch_ptr CreateTip(const TipData & tipdata, const vector<LocusCell> & cells, 113 … const vector<LocusCell> & movingcells, const rangeset & diseasesites, 267 vector<LocusCell> m_protoMovingCells; 270 const vector<LocusCell> & CollectMovingCells(); 297 virtual TBranch_ptr CreateTip(const TipData & tipdata, const vector<LocusCell> & cells, 300 virtual TBranch_ptr CreateTip(const TipData & tipdata, const vector<LocusCell> & cells, [all …]
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H A D | timelist.h | 98 void FillTipsWithDataFrom(const vector<vector<LocusCell> > & tcells); 99 void SetupBodyDLCellsWith(const vector<LocusCell> & loccell); 149 TBranch_ptr CreateTip(const TipData & tipdata, const vector<LocusCell> & cells, 150 … const vector<LocusCell> & movingcells, long nsites, rangeset diseasesites); 151 TBranch_ptr CreateTip(const TipData & tipdata, const vector<LocusCell> & cells, 152 … const vector<LocusCell> & movingcells, long nsites, rangeset diseasesites,
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H A D | individual.cpp | 191 vector<LocusCell> Individual::GetLocusCellsFor(string lname, long marker) const in GetLocusCellsFor() 193 map<pair<string, long>, vector<LocusCell> >::const_iterator hap; in GetLocusCellsFor() 253 vector<LocusCell> cells = hap->second.ChooseNewHaplotypes(); in ChooseNewHaplotypesFor() 254 map<pair<string, long>, vector<LocusCell> >::iterator oldhap; in ChooseNewHaplotypesFor() 281 vector<LocusCell> cells = hap->second.ChooseRandomHaplotypes(); in ChooseRandomHaplotypesFor() 282 map<pair<string, long>, vector<LocusCell> >::iterator oldhap; in ChooseRandomHaplotypesFor() 317 vector<LocusCell> cells = hap->second.ChooseFirstHaplotypes(); in ChooseFirstHaplotypeFor() 333 vector<LocusCell> cells = hap->second.ChooseNextHaplotypes(); in ChooseNextHaplotypeFor()
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H A D | individual.h | 38 std::map<std::pair<string, long>, vector<LocusCell> > m_currentHapsMap; 70 vector<LocusCell> GetLocusCellsFor(string lname, long marker) const; //phase 2
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H A D | rectree.cpp | 138 const vector<LocusCell> & RecTree::CollectMovingCells() in CollectMovingCells() 380 vector<LocusCell> cells = m_individuals[ind].GetLocusCellsFor(lname, marker); in ReassignDLsFor() 632 TBranch_ptr RecTree::CreateTip(const TipData & tipdata, const vector<LocusCell> & cells, in CreateTip() 633 const vector<LocusCell> & movingcells, const rangeset & diseasesites) in CreateTip() 641 TBranch_ptr RecTree::CreateTip(const TipData & tipdata, const vector<LocusCell> & cells, in CreateTip() 642 const vector<LocusCell> & movingcells, const rangeset & diseasesites, in CreateTip()
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H A D | branch.h | 95 vector<LocusCell> m_DLcells; 96 vector<LocusCell> m_movingDLcells; 195 void SetDLCells(const std::vector<LocusCell> & src) { m_DLcells = src; }; in SetDLCells() 197 void SetMovingDLCells(const std::vector<LocusCell> & src) { m_movingDLcells = src; }; in SetMovingDLCells()
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H A D | timelist.cpp | 190 TBranch_ptr TimeList::CreateTip(const TipData & tipdata, const vector<LocusCell> & cells, in CreateTip() 191 … const vector<LocusCell> & movingcells, long nsites, rangeset diseasesites) in CreateTip() 208 TBranch_ptr TimeList::CreateTip(const TipData & tipdata, const vector<LocusCell> & cells, in CreateTip() 209 … const vector<LocusCell> & movingcells, long nsites, rangeset diseasesites, in CreateTip() 427 void TimeList::FillTipsWithDataFrom(const vector<vector<LocusCell> > & tcells) 432 vector<vector<LocusCell> >::const_iterator tcell; 450 void TimeList::SetupBodyDLCellsWith(const vector<LocusCell> & loccell)
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H A D | tree.cpp | 101 const vector<LocusCell> & Tree::CollectCells() in CollectCells() 179 TBranch_ptr Tree::CreateTip(const TipData & tipdata, const vector<LocusCell> & cells, in CreateTip() 180 const vector<LocusCell> & movingcells, const rangeset & diseasesites) in CreateTip() 189 TBranch_ptr Tree::CreateTip(const TipData & tipdata, const vector<LocusCell> & cells, in CreateTip() 190 const vector<LocusCell> & movingcells, const rangeset & diseasesites, in CreateTip() 866 vector<LocusCell> cells = m_individuals[ind].GetLocusCellsFor(lname, marker); in ReassignDLsFor()
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