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matvec::ChromStruct Class Reference

#include <geneticdist.h>

List of all members.

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Detailed Description

chromosome structure

See also:

Chromosome

Definition at line 90 of file geneticdist.h.

Public Methods
	ChromStruct (void)
	ChromStruct (const unsigned nl)
	~ChromStruct (void)
const ChromStruct &	operator= (const ChromStruct &A)
void	resize (const unsigned nl)
unsigned	nloci (void) const
void	release (void)
Public Attributes
SafeSTLVector< LocusStruct >	locus
doubleMatrix	recomb_rate_mat
SafeSTLVector< int >	peelOrder
Protected Methods
void	copyfrom (const ChromStruct &A)
Protected Attributes
unsigned	numloci

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Constructor & Destructor Documentation

matvec::ChromStruct::ChromStruct (  void    )  [inline]

Definition at line 99 of file geneticdist.h. References numloci. {numloci=0;}

matvec::ChromStruct::ChromStruct (  const unsigned    nl )  [inline]

Definition at line 100 of file geneticdist.h. References numloci, and resize(). {numloci=0; resize(nl);}

matvec::ChromStruct::~ChromStruct (  void    )  [inline]

Definition at line 101 of file geneticdist.h. References release(). {release();}

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Member Function Documentation

void matvec::ChromStruct::copyfrom (  const ChromStruct &    A )  [protected]

Definition at line 49 of file geneticdist.cpp. References numloci, recomb_rate_mat, and resize(). Referenced by operator=(). { if (this == &A) return; resize(A.numloci); recomb_rate_mat = A.recomb_rate_mat; }

unsigned matvec::ChromStruct::nloci (  void    )  const [inline]

Definition at line 107 of file geneticdist.h. References numloci. Referenced by matvec::Population::build_pop_gamete(), matvec::Population::build_trans_mat(), matvec::GeneticDist::display(), matvec::GeneticDist::genotypic_val(), matvec::GeneticDist::get_distance(), matvec::Population::getGNodeListSample(), matvec::Population::getInitialGNodeListSample(), matvec::Population::getOldGNodeListProbability(), matvec::GeneticDist::locus(), matvec::GeneticDist::nloci_chrom(), matvec::GeneticDist::put_distance(), matvec::GeneticDist::putColmNames(), matvec::GeneticDist::recomb_rate(), and matvec::Population::setupRSampler(). {return numloci;}

const ChromStruct& matvec::ChromStruct::operator= (  const ChromStruct &    A )  [inline]

Definition at line 103 of file geneticdist.h. References copyfrom(), and numloci. {numloci=0; copyfrom(A); return *this;}

void matvec::ChromStruct::release (  void    )

Definition at line 64 of file geneticdist.cpp. References locus, and numloci. Referenced by ~ChromStruct(). {locus.resize(0);numloci = 0;}

void matvec::ChromStruct::resize (  const unsigned    nl )

Definition at line 56 of file geneticdist.cpp. References locus, numloci, recomb_rate_mat, and matvec::Matrix< double >::resize(). Referenced by ChromStruct(), copyfrom(), matvec::GeneticDist::GeneticDist(), matvec::GeneticDist::multi_loci(), and matvec::GeneticDist::nloci(). { if (numloci == nl) return; numloci = nl; locus.resize(numloci); recomb_rate_mat.resize(numloci,numloci,0.5); }

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Member Data Documentation

SafeSTLVector<LocusStruct> matvec::ChromStruct::locus

Definition at line 96 of file geneticdist.h. Referenced by matvec::Population::build_pop_gamete(), matvec::Population::CalcFreqHaploFounders(), matvec::Population::compute_pdm(), matvec::Population::countGenotypes(), matvec::Population::descent_graph_init_parm(), matvec::Population::descent_graph_log_lhood(), matvec::Population::DisplayFreqHaploFounders(), matvec::Population::displayGenotypeFrequencies(), matvec::Model::estimate_peeling(), matvec::GeneticDist::genotypic_val(), matvec::GeneticDist::get_distance(), matvec::Individual::getAllelePenetrance(), matvec::Individual::getGenoPenetrance(), matvec::Population::getInitialGNodeListSample(), matvec::RAlleleFounderSet::getValue(), matvec::GenoFounderSet::getValue(), matvec::AlleleFounderSet::getValue(), matvec::Population::initAlleleNodeList(), matvec::Population::initGenotypeFreq(), matvec::Population::initGenotypeNodeList(), matvec::Population::initJointAlleleNodeList(), matvec::Population::input_data(), matvec::Population::input_markerData(), matvec::Population::LGGenotypeElimination(), matvec::Population::ListAlleleFounders(), matvec::GeneticDist::locus(), matvec::Model::minfun_multipoint(), matvec::Model::multipoint_estimate_Qfreq(), matvec::Population::multipoint_init_parm(), matvec::GeneticDist::nallele(), matvec::GNodeList::peelAndCut(), matvec::GNodeList::peelCutAndCompute(), matvec::GNodeList::peelCutAndSample(), matvec::GNodeList::peelOrderCutAndSample(), matvec::GeneticDist::put_distance(), matvec::GeneticDist::putColmNames(), release(), resize(), matvec::Population::SetFreqHaploFounders(), matvec::Population::SetPossibleHaplotypes(), matvec::Population::setupRSampler(), matvec::Population::SimpleGenotypeElimination(), matvec::Population::sum_genotype_freq1(), matvec::Population::sum_genotype_freq2(), matvec::Population::sum_genotype_freq3(), and matvec::Population::UpdateFreqHaploFounders().

unsigned matvec::ChromStruct::numloci [protected]

Definition at line 92 of file geneticdist.h. Referenced by ChromStruct(), copyfrom(), nloci(), operator=(), release(), and resize().

SafeSTLVector<int> matvec::ChromStruct::peelOrder

Definition at line 111 of file geneticdist.h. Referenced by matvec::Population::getInitialGNodeListSample(), and matvec::GNodeList::peelAndCut().

doubleMatrix matvec::ChromStruct::recomb_rate_mat

Definition at line 97 of file geneticdist.h. Referenced by copyfrom(), matvec::GeneticDist::recomb_rate(), and resize().

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The documentation for this class was generated from the following files:

• geneticdist.h
• geneticdist.cpp

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