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Searched refs:LocusCell (Results 1 – 18 of 18) sorted by relevance

/dports/biology/lamarc/lamarc-2.1.8/src/datalike/
H A Dlocuscell.cpp18 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()
H A Dlocuscell.h28 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;
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H A Dhaplotypes.h20 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();
H A Ddatatype.h97 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,
H A Dhaplotypes.cpp65 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()
H A Ddatatype.cpp365 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()
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H A Dlocus.h73 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()
H A Dregion.cpp742 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()
H A Dlocus.cpp123 vector<LocusCell> cellsbymarkers; in Setup()
131 … vector<LocusCell> cells = individuals[ind].GetLocusCellsFor(GetName(), marker); in Setup()
138 LocusCell onecell(cellsbymarkers); in Setup()
H A Ddlcalc.cpp433 const vector<LocusCell>& tipcells = locus.GetTipCells(); in SetupAliases()
/dports/biology/lamarc/lamarc-2.1.8/src/tree/
H A Dtree.h68 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,
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H A Dtimelist.h98 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,
H A Dindividual.cpp191 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()
H A Dindividual.h38 std::map<std::pair<string, long>, vector<LocusCell> > m_currentHapsMap;
70 vector<LocusCell> GetLocusCellsFor(string lname, long marker) const; //phase 2
H A Drectree.cpp138 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()
H A Dbranch.h95 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()
H A Dtimelist.cpp190 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)
H A Dtree.cpp101 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()