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matvec::UnknownDist Class Reference

#include <geneticdist.h>

Inheritance diagram for matvec::UnknownDist:

matvec::GeneticDist List of all members.

Detailed Description

a dummy genetic distribution

Definition at line 224 of file geneticdist.h.

Public Methods

 UnknownDist (void)
 UnknownDist (const UnknownDist &u)
 UnknownDist (const Vector< double > mu, const doubleMatrix sigma)
 UnknownDist (const double mu, const double sigma)
 ~UnknownDist (void)
void copyfrom (const UnknownDist &A)
void resize (const unsigned n)
unsigned ntrait (void) const
Vector< double > * mean_vector (void)
doubleMatrix * var_matrix (void)
const char * name (void) const
ChromStruct * chrom (void)
double recomb_rate (const unsigned c, const unsigned li, const unsigned lj)
void recomb_rate (const unsigned c, const unsigned li, const unsigned lj, const double r)
unsigned nchrom (void) const
void nchrom (const unsigned nc)
unsigned nloci_chrom (const unsigned c) const
unsigned nallele (const unsigned c, const unsigned l) const
int display (void)
void copyfrom (const GeneticDist &A)
void nloci (const unsigned nl0,...)
void release (void)
void locus (const unsigned c, const unsigned l, const char qm[], const unsigned na,...)
void locus (const unsigned c, const unsigned l, const char qm[], const unsigned na, Vector< double > allele_freq)
void putColmNames (const unsigned c, const unsigned l, char nm1[], char nm2[])
void genotypic_val (const unsigned c, const unsigned l, const double *v)
void genotypic_val (const unsigned c, const unsigned l, const double v0,...)
const double ** genotypic_val (const unsigned c, const unsigned l) const
double sample (void) const
void multi_loci (int num_loci)
void put_distance (const unsigned c, const unsigned l, double distance)
double get_distance (const unsigned c, const unsigned l)

Public Attributes

ChromStruct * chromosome
unsigned numMarkerLoci
SafeSTLVector< MaternalPaternalRQTLAlleles > rqtlVector

Protected Attributes

unsigned dim
Vector< double > mu_vec
doubleMatrix var_mat
char distname [25]
unsigned numchrom
unsigned numtrait

Constructor & Destructor Documentation

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

Definition at line 231 of file geneticdist.h.

References dim, and matvec::GeneticDist::distname. 

00231 {strcpy(distname,"UnknownDist"); dim=0;}

matvec::UnknownDist::UnknownDist (  const UnknownDist &    u )  [inline]
 

Definition at line 232 of file geneticdist.h.

References copyfrom(). 

00232 :GeneticDist() {copyfrom(u);}

matvec::UnknownDist::UnknownDist (  const Vector< double >    mu,
const doubleMatrix    sigma
) 
 

Definition at line 231 of file geneticdist.cpp.

References dim, matvec::GeneticDist::distname, mu_vec, matvec::Matrix< double >::num_rows(), matvec::doubleMatrix::psd(), matvec::Vector< double >::size(), var_mat, and matvec::warning(). 

00232 {
00233    mu_vec = mu;
00234    dim = mu_vec.size();
00235    if (sigma.psd()) {
00236       if (dim == sigma.num_rows()) {
00237          var_mat = sigma;
00238       } else {
00239           warning(" UnknownDist(u,V): u and V incompatible");
00240       }
00241    } else {
00242       warning(" UnknownDist(u,V): V must be psd ");
00243    }
00244    strcpy(distname,"Unknown");
00245 }

matvec::UnknownDist::UnknownDist (  const double    mu,
const double    sigma
) 
 

Definition at line 246 of file geneticdist.cpp.

References matvec::GeneticDist::distname, mu_vec, resize(), and var_mat. 

00247 {
00248    resize(1);
00249    mu_vec[0] = mu;
00250    var_mat[0][0] = sigma;
00251    strcpy(distname,"Unknown");
00252 }

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

Definition at line 235 of file geneticdist.h. 

00235 {;}

Member Function Documentation

ChromStruct* matvec::GeneticDist::chrom (  void    )  [inline, inherited]
 

Definition at line 158 of file geneticdist.h.

Referenced by matvec::Population::build_pop_gamete(), matvec::Population::build_trans_mat(), matvec::Population::CalcFreqHaploFounders(), matvec::Population::compute_pdm(), matvec::Population::descent_graph_init_parm(), matvec::Population::descent_graph_log_lhood(), matvec::Population::DisplayFreqHaploFounders(), matvec::Individual::getAllelePenetrance(), matvec::Individual::getGenoPenetrance(), matvec::Population::getGNodeListSample(), matvec::Population::getInitialGNodeListSample(), matvec::Population::getOldGNodeListProbability(), matvec::RAlleleFounderSet::getValue(), matvec::GenoFounderSet::getValue(), matvec::AlleleFounderSet::getValue(), matvec::Population::initAlleleNodeList(), matvec::Population::initGenotypeNodeList(), matvec::Population::initJointAlleleNodeList(), matvec::Population::input_data(), matvec::Population::input_markerData(), matvec::Population::LGGenotypeElimination(), matvec::Population::ListAlleleFounders(), matvec::Model::minfun_multipoint(), matvec::Model::multipoint_estimate_Qfreq(), matvec::Population::multipoint_init_parm(), matvec::GNodeList::peelAndCut(), matvec::GNodeList::peelCutAndCompute(), matvec::GNodeList::peelCutAndSample(), matvec::GNodeList::peelOrderCutAndSample(), matvec::Genome::remodel(), 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(). 

00158 {return chromosome;}

void matvec::GeneticDist::copyfrom (  const GeneticDist &    A )  [inherited]
 

Definition at line 87 of file geneticdist.cpp.

References matvec::GeneticDist::chromosome, matvec::GeneticDist::distname, matvec::GeneticDist::numchrom, matvec::GeneticDist::numMarkerLoci, matvec::GeneticDist::numtrait, and matvec::GeneticDist::resize().

Referenced by matvec::GeneticDist::GeneticDist(), and matvec::GeneticDist::operator=(). 

00088 {
00089    if (this == &A) return;
00090    resize(A.numchrom);
00091    for (unsigned i=0; i<numchrom; i++) chromosome[i] = A.chromosome[i];
00092    strcpy(distname,A.distname);
00093 
00094    numtrait = A.numtrait;  // Occurs in old version
00095    numMarkerLoci = A.numMarkerLoci;  //LRT
00096 }

void matvec::UnknownDist::copyfrom (  const UnknownDist &    A ) 
 

Definition at line 254 of file geneticdist.cpp.

References dim, matvec::GeneticDist::distname, mu_vec, and var_mat.

Referenced by matvec::Model::copyfrom(), and UnknownDist(). 

00255 {
00256    if (this == &A) return;
00257    dim = A.dim;
00258    mu_vec = A.mu_vec;
00259    var_mat = A.var_mat;
00260    strcpy(distname,A.distname);
00261 }

int matvec::GeneticDist::display (  void    )  [inherited]
 

Definition at line 293 of file geneticdist.cpp.

References matvec::GeneticDist::chromosome, matvec::ChromStruct::nloci(), and matvec::GeneticDist::numtrait. 

00293                              {
00294   if (chromosome) {
00295     std::cout << "GeneticDist Object: nloci = " << chromosome[0].nloci() << std::endl;
00296              std::cout << "numtrait = " << numtrait <<  std::endl;
00297   }
00298   else {
00299     std::cout << "GeneticDist Object: nloci not initialized yet " << std::endl;
00300     std::cout << "numtrait = " << numtrait <<  std::endl;
00301   }
00302   return 1;
00303 }

const double ** matvec::GeneticDist::genotypic_val (  const unsigned    c,
const unsigned    l
)  const [inline, inherited]
 

Definition at line 194 of file geneticdist.h.

References matvec::GeneticDist::chromosome, and matvec::ChromStruct::locus. 

00196 {
00197    return (const double**)chromosome[c].locus[l].genotypic_val_mat.begin();
00198 }

void matvec::GeneticDist::genotypic_val (  const unsigned    c,
const unsigned    l,
const double    v0,
...   
)  [inherited]
 

Definition at line 187 of file geneticdist.cpp.

References matvec::GeneticDist::chromosome, matvec::ChromStruct::locus, matvec::ChromStruct::nloci(), and matvec::GeneticDist::numchrom. 

00189 {
00190    if (c < 1 || c>numchrom || l < 1 || l>chromosome[c-1].nloci()) throw exception("GeneticDist::genotypic_val(): bad args");
00191    unsigned i,j,na,cc,ll;
00192    cc = c-1; ll = l-1;
00193    na = chromosome[cc].locus[ll].nallele();
00194    double **me = chromosome[cc].locus[ll].genotypic_val_mat.begin();
00195    me[0][0] = v0;
00196    va_list ppt;
00197    va_start(ppt,v0);
00198    for (j=1; j<na; j++) me[j][0] = me[0][j] = va_arg(ppt,double);
00199    for (i=1;i<na;i++) for (j=i;j<na;j++) me[j][i]=me[i][j]= va_arg(ppt,double);
00200    va_end(ppt);
00201 }

void matvec::GeneticDist::genotypic_val (  const unsigned    c,
const unsigned    l,
const double *    v
)  [inherited]
 

Definition at line 169 of file geneticdist.cpp.

References matvec::GeneticDist::chromosome, and matvec::ChromStruct::locus. 

00171 {
00172    ///////////////////////////////////////////
00173    // requiements
00174    // v must have enough elements
00175    ///////////////////////////////////////////
00176    if (c < 1 || c>numchrom || l < 1 || l>chromosome[c-1].nloci()) throw exception("GeneticDist::genotypic_val(): bad args");
00177    unsigned i,j,k,na,cc,ll;
00178    cc = c-1; ll = l-1;
00179    na = chromosome[cc].locus[ll].nallele();
00180    double **me = chromosome[cc].locus[ll].genotypic_val_mat.begin();
00181    for (k=0,i=0; i<na; i++) for (j=0; j<=i; j++) {
00182       me[i][j] = v[k++];
00183       me[j][i] =  me[i][j];
00184    }
00185 }

double matvec::GeneticDist::get_distance (  const unsigned    c,
const unsigned    l
)  [inherited]
 

Definition at line 278 of file geneticdist.cpp.

References matvec::GeneticDist::chromosome, matvec::LocusStruct::distance, matvec::ChromStruct::locus, matvec::ChromStruct::nloci(), and matvec::GeneticDist::numchrom.

Referenced by matvec::Population::buildRecombinationMatrix(), matvec::Population::descent_graph_setup(), and matvec::Model::multipoint_Rec_table(). 

00279 {
00280    if (c < 1 || c>numchrom || l < 1 || l> chromosome[c-1].nloci()) throw exception(" GeneticDist.get_distance(): bad args");
00281    LocusStruct *L = &(chromosome[c-1].locus[l-1]);
00282    return (L->distance);
00283 }

void matvec::GeneticDist::locus (  const unsigned    c,
const unsigned    l,
const char    qm[],
const unsigned    na,
Vector< double >    allele_freq
)  [inherited]
 

Definition at line 305 of file geneticdist.cpp.

References matvec::LocusStruct::allele_freq, matvec::GeneticDist::chromosome, matvec::LocusStruct::genotypic_val_mat, matvec::ChromStruct::locus, matvec::LocusStruct::nallele(), matvec::ChromStruct::nloci(), matvec::GeneticDist::numchrom, matvec::LocusStruct::qtl_ml, matvec::Vector< double >::resize(), and matvec::Matrix< double >::resize(). 

00307 {
00308         //      std::cout << "V " << c << " " << l << " " << na << std::endl;
00309   if (c < 1 || c>numchrom || l < 1 || l> chromosome[c-1].nloci()) throw exception("GeneticDist::locus(): bad args");
00310   LocusStruct *L = &(chromosome[c-1].locus[l-1]);
00311   
00312   //RLF modified block
00313   if (strcmp(qm,"qtl")==0) {
00314     L->qtl_ml='q';
00315     L->genotypic_val_mat.resize(na,na);
00316   }
00317   // next else if added by LRT
00318   else if(strcmp(qm,"recessiveLocus")==0) { 
00319     L->qtl_ml='r';
00320   }
00321   else  {
00322     L->qtl_ml = 'm';
00323   }
00324   L->nallele(na);
00325   L->allele_freq.resize(na);
00326   //RLF modified block
00327   //   va_list param_pt;
00328   //   va_start(param_pt,na);
00329   double sumf = 0.0, temp=0.0;
00330   for (int i=0;i<na; i++) {
00331     temp=init_freqs[i];
00332     sumf += temp;
00333     L->allele_freq[i] = temp;
00334     //     std::cout << i << " freq " << temp << " Sumf " << sumf << std::endl;
00335   }
00336   //   va_end(param_pt);
00337   if (fabs(sumf-1.0) > 1.0e-10) throw exception("GeneticDist::locus(): allele_freq does not sum to 1.0");
00338 }

void matvec::GeneticDist::locus (  const unsigned    c,
const unsigned    l,
const char    qm[],
const unsigned    na,
...   
)  [inherited]
 

Definition at line 128 of file geneticdist.cpp.

References matvec::LocusStruct::allele_freq, matvec::GeneticDist::chromosome, matvec::LocusStruct::genotypic_val_mat, matvec::ChromStruct::locus, matvec::LocusStruct::nallele(), matvec::ChromStruct::nloci(), matvec::GeneticDist::numchrom, matvec::GeneticDist::numMarkerLoci, matvec::LocusStruct::qtl_ml, matvec::Vector< double >::resize(), and matvec::Matrix< double >::resize(). 

00130 {
00131    if (c < 1 || c>numchrom || l < 1 || l> chromosome[c-1].nloci()) throw exception("GeneticDist::locus(): bad args");
00132    LocusStruct *L = &(chromosome[c-1].locus[l-1]);
00133    
00134    //RLF modified block
00135    if (strcmp(qm,"qtl")==0) {
00136      L->qtl_ml='q';
00137      L->genotypic_val_mat.resize(na,na);
00138    }
00139    // next else if added by LRT
00140    else if(strcmp(qm,"recessiveLocus")==0) { 
00141      L->qtl_ml='r';
00142    }
00143    else {
00144      L->qtl_ml = 'm';
00145      numMarkerLoci++;
00146    }
00147    L->nallele(na);
00148    L->allele_freq.resize(na);
00149 //RLF modified block
00150    va_list param_pt;
00151    va_start(param_pt,na);
00152    double sumf = 0.0;
00153    for (int i=0;i<na; i++) sumf += L->allele_freq[i] = va_arg(param_pt,double);
00154    va_end(param_pt);
00155    if (fabs(sumf-1.0) > 1.0e-10) throw exception("GeneticDist::locus(): allele_freq does not sum to 1.0");
00156 }

Vector<double>* matvec::UnknownDist::mean_vector (  void    )  [inline]
 

Definition at line 241 of file geneticdist.h. 

00241 {return &mu_vec;}

void matvec::GeneticDist::multi_loci (  int    num_loci )  [inherited]
 

Definition at line 285 of file geneticdist.cpp.

References matvec::GeneticDist::chromosome, matvec::ChromStruct::resize(), and matvec::GeneticDist::resize(). 

00286 {
00287 
00288    resize(1);
00289 //   cout << "in GeneticDist::multi_loci: numtrait = " << numtrait<< endl;
00290    chromosome[0].resize(num_loci);
00291 }

unsigned matvec::GeneticDist::nallele (  const unsigned    c,
const unsigned    l
)  const [inline, inherited]
 

Definition at line 162 of file geneticdist.h.

References matvec::ChromStruct::locus. 

00163                            {return chromosome[c].locus[l].nallele();}

const char* matvec::GeneticDist::name (  void    )  const [inline, inherited]
 

Definition at line 157 of file geneticdist.h.

References matvec::GeneticDist::distname.

Referenced by matvec::Model::copyfrom(), matvec::Population::input_data(), matvec::Population::input_ped(), and matvec::Model::RSamplerPrior_dist(). 

00157 {return distname;}

void matvec::GeneticDist::nchrom (  const unsigned    nc )  [inherited]
 

Definition at line 98 of file geneticdist.cpp.

References matvec::check_ptr(), matvec::GeneticDist::chromosome, and matvec::GeneticDist::numchrom. 

00099 {
00100    if (numchrom == nc) return;
00101    numchrom = nc;
00102    if (chromosome) {
00103      delete [] chromosome;
00104      chromosome=0;
00105    }
00106    if(numchrom>0){
00107      chromosome = new ChromStruct[numchrom];
00108    }
00109    else {
00110      chromosome = 0;
00111    }
00112    check_ptr(chromosome);
00113 }

unsigned matvec::GeneticDist::nchrom (  void    )  const [inline, inherited]
 

Definition at line 160 of file geneticdist.h.

References matvec::GeneticDist::numchrom.

Referenced by matvec::Population::build_trans_mat(), matvec::Population::get_genotype_freq(), matvec::Individual::remodel(), matvec::Genome::remodel(), matvec::Population::resize(), and matvec::GeneticDist::resize(). 

00160 {return numchrom;}

void matvec::GeneticDist::nloci (  const unsigned    nl0,
...   
)  [inherited]
 

Definition at line 115 of file geneticdist.cpp.

References matvec::GeneticDist::chromosome, matvec::GeneticDist::numchrom, and matvec::ChromStruct::resize(). 

00116 {
00117    chromosome[0].resize(nl0);
00118    va_list param_pt;
00119    va_start(param_pt,nl0);
00120    unsigned nl;
00121    for (int i=1;i<numchrom;i++) {
00122       nl = va_arg(param_pt,unsigned);
00123       chromosome[i].resize(nl);
00124    }
00125    va_end(param_pt);
00126 }

unsigned matvec::GeneticDist::nloci_chrom (  const unsigned    c )  const [inline, inherited]
 

Definition at line 207 of file geneticdist.h.

References matvec::GeneticDist::chromosome, and matvec::ChromStruct::nloci().

Referenced by matvec::Population::input_descentGraph(), matvec::Population::input_markerData(), and matvec::Population::output_descentGraph(). 

00208 {
00209    if (c > 0) {
00210       return chromosome[c-1].nloci();
00211    }
00212    else {
00213       std::cerr << "GeneticDist::nloci(c): arg value out of range";
00214       exit(1);
00215    }
00216 }

unsigned matvec::UnknownDist::ntrait (  void    )  const [inline, virtual]
 

Reimplemented from matvec::GeneticDist.

Definition at line 239 of file geneticdist.h.

References dim. 

00239 {return dim;}

void matvec::GeneticDist::put_distance (  const unsigned    c,
const unsigned    l,
double    distance
)  [inherited]
 

Definition at line 272 of file geneticdist.cpp.

References matvec::GeneticDist::chromosome, matvec::LocusStruct::distance, matvec::ChromStruct::locus, matvec::ChromStruct::nloci(), and matvec::GeneticDist::numchrom. 

00273 {
00274    if (c < 1 || c>numchrom || l < 1 || l> chromosome[c-1].nloci()) throw exception("GeneticDist::put_distance() : bad args");
00275    LocusStruct *L = &(chromosome[c-1].locus[l-1]);
00276    L->distance = dist;
00277 }

void matvec::GeneticDist::putColmNames (  const unsigned    c,
const unsigned    l,
char    nm1[],
char    nm2[]
)  [inherited]
 

Definition at line 159 of file geneticdist.cpp.

References matvec::GeneticDist::chromosome, matvec::ChromStruct::locus, matvec::LocusStruct::nameOfcol1, matvec::LocusStruct::nameOfcol2, matvec::ChromStruct::nloci(), and matvec::GeneticDist::numchrom. 

00161 {
00162    if (c < 1 || c>numchrom || l < 1 || l> chromosome[c-1].nloci()) throw exception("GeneticDist::locus(): bad args");
00163    LocusStruct *L = &(chromosome[c-1].locus[l-1]);
00164    L->nameOfcol1 = nm1;
00165    L->nameOfcol2 = nm2;
00166 }

void matvec::GeneticDist::recomb_rate (  const unsigned    c,
const unsigned    li,
const unsigned    lj,
const double    r
)  [inherited]
 

Definition at line 220 of file geneticdist.cpp.

References matvec::GeneticDist::chromosome, matvec::ChromStruct::nloci(), and matvec::ChromStruct::recomb_rate_mat. 

00222 {
00223    if (c <= 0) throw exception("GeneticDist.recomb_rate(): out of range");
00224    int n = chromosome[c-1].nloci();
00225    if (li<1 || li>n || lj<1 || lj>n) throw exception("GeneticDist::recomb_rate(): out of range");
00226    chromosome[c-1].recomb_rate_mat[li-1][lj-1] = r;
00227 }

double matvec::GeneticDist::recomb_rate (  const unsigned    c,
const unsigned    li,
const unsigned    lj
)  [inherited]
 

Definition at line 210 of file geneticdist.cpp.

References matvec::GeneticDist::chromosome, and matvec::ChromStruct::recomb_rate_mat. 

00212 {
00213    if (c==0 || li==0) throw exception("GeneticDist::recomb_rate(): bad args");
00214    double d=0.0;
00215    unsigned k, ii=li-1;
00216    for (k=li; k<lj; k++) d += chromosome[c-1].recomb_rate_mat[ii][k];
00217    return 0.5*tanh(2.0*d);
00218 }

void matvec::GeneticDist::release (  void    )  [inherited]
 

Definition at line 203 of file geneticdist.cpp.

References matvec::GeneticDist::chromosome, and matvec::GeneticDist::numchrom.

Referenced by matvec::GeneticDist::~GeneticDist(). 

00204 {
00205    if (chromosome) {
00206       delete [] chromosome; chromosome = 0; numchrom = 0;
00207    }
00208 }

void matvec::UnknownDist::resize (  const unsigned    n )  [virtual]
 

Reimplemented from matvec::GeneticDist.

Definition at line 263 of file geneticdist.cpp.

References dim, mu_vec, matvec::Matrix< double >::resize(), matvec::Vector< double >::resize(), and var_mat.

Referenced by UnknownDist(). 

00264 {
00265    if (dim == n) return;
00266    dim = n;
00267    mu_vec.resize(dim);
00268    var_mat.resize(dim,dim);
00269 }

double matvec::GeneticDist::sample (  void    )  const [inline, inherited]
 

Definition at line 183 of file geneticdist.h. 

00183 {return 0.0;}

doubleMatrix* matvec::UnknownDist::var_matrix (  void    )  [inline, virtual]
 

Reimplemented from matvec::GeneticDist.

Definition at line 242 of file geneticdist.h. 

00242 {return &var_mat;}

Member Data Documentation

ChromStruct* matvec::GeneticDist::chromosome [inherited]
 

Definition at line 142 of file geneticdist.h.

Referenced by matvec::GeneticDist::copyfrom(), matvec::Population::countGenotypes(), matvec::GeneticDist::display(), matvec::Population::displayGenotypeFrequencies(), matvec::GeneticDist::GeneticDist(), matvec::GeneticDist::genotypic_val(), matvec::GeneticDist::get_distance(), matvec::Population::initGenotypeFreq(), matvec::GeneticDist::locus(), matvec::GeneticDist::multi_loci(), matvec::GeneticDist::nchrom(), matvec::GeneticDist::nloci(), matvec::GeneticDist::nloci_chrom(), matvec::GeneticDist::put_distance(), matvec::GeneticDist::putColmNames(), matvec::GeneticDist::recomb_rate(), and matvec::GeneticDist::release().

unsigned matvec::UnknownDist::dim [protected]
 

Definition at line 226 of file geneticdist.h.

Referenced by copyfrom(), ntrait(), resize(), and UnknownDist().

char matvec::GeneticDist::distname[25] [protected, inherited]
 

Definition at line 137 of file geneticdist.h.

Referenced by copyfrom(), matvec::GeneticDist::copyfrom(), matvec::GeneticDist::GeneticDist(), matvec::GeneticDist::name(), and UnknownDist().

Vector<double> matvec::UnknownDist::mu_vec [protected]
 

Definition at line 227 of file geneticdist.h.

Referenced by copyfrom(), resize(), and UnknownDist().

unsigned matvec::GeneticDist::numchrom [protected, inherited]
 

Definition at line 138 of file geneticdist.h.

Referenced by matvec::GeneticDist::copyfrom(), matvec::GeneticDist::GeneticDist(), matvec::GeneticDist::genotypic_val(), matvec::GeneticDist::get_distance(), matvec::GeneticDist::locus(), matvec::GeneticDist::nchrom(), matvec::GeneticDist::nloci(), matvec::GeneticDist::operator=(), matvec::GeneticDist::put_distance(), matvec::GeneticDist::putColmNames(), and matvec::GeneticDist::release().

unsigned matvec::GeneticDist::numMarkerLoci [inherited]
 

Definition at line 143 of file geneticdist.h.

Referenced by matvec::GeneticDist::copyfrom(), matvec::GeneticDist::GeneticDist(), matvec::Population::input_markerData(), and matvec::GeneticDist::locus().

unsigned matvec::GeneticDist::numtrait [protected, inherited]
 

Definition at line 138 of file geneticdist.h.

Referenced by matvec::GeneticDist::copyfrom(), matvec::GeneticDist::display(), matvec::GeneticDist::GeneticDist(), and matvec::GeneticDist::ntrait().

SafeSTLVector<MaternalPaternalRQTLAlleles> matvec::GeneticDist::rqtlVector [inherited]
 

Definition at line 191 of file geneticdist.h.

doubleMatrix matvec::UnknownDist::var_mat [protected]
 

Definition at line 228 of file geneticdist.h.

Referenced by copyfrom(), resize(), and UnknownDist().

The documentation for this class was generated from the following files:
Generated on Thu Jun 16 17:14:52 2005 for Matvec by doxygen1.2.16