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matvec::Pedigree Class Reference

#include <pedigree.h>

List of all members.

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Detailed Description

a pedigree

See also:

Population

Definition at line 53 of file pedigree.h.

Public Types
enum	ped_type { raw, standard }
Public Methods
	Pedigree (char pedtype[]="")
	Pedigree (Pedigree &P)
	~Pedigree (void)
const Pedigree &	operator= (Pedigree &P)
int	inbcoef_done (void) const
int	in_memory (void) const
void	copyfrom (Pedigree &P)
void	save_pedsheet (const int relse=1)
void	input_pedsheet (void)
void	release_pedsheet (void)
void	resize (const unsigned na)
unsigned	input (const std::string &pfname, const std::string &fmt="individual mother father", const std::string &pedtype="raw")
unsigned	input_standard (std::istream &pedfile, unsigned ind, unsigned mother, unsigned father)
unsigned	ngroup (void) const
unsigned	size (void) const
unsigned	nbase (void) const
Vector< double > *	inbcoef_quaas (int keepinmem=0)
Vector< double > *	inbcoef_meuwissen (int keepinmem=0)
Vector< double > *	inbcoef (int keepinmem=0)
doubleMatrix	mat (void)
double	logdet (int keepinmem=0)
doubleMatrix	rela (int keepinmem=0)
doubleMatrix	ainv (int keepinmem=0)
doubleMatrix	reld (int keepinmem=0)
Pedigree &	sample (const unsigned maxsize, const unsigned maxg, const unsigned sire0=1, const unsigned dam0=1, const double imrate=0.1, const unsigned parent=1, const int no_po=1, const int no_fsib=1, const double sexratio=0.5)
void	out_to_stream (std::ostream &stream, const int style=0, const int ic=0)
void	save (const std::string &fname, const int style=0, const int io_mode=std::ios::out)
void	display (const std::string msg="", const int style=0, const int ic=0)
void	release (void)
const std::string	diskfname (void) const
Public Attributes
PedNode **	pedmember
unsigned	maxnamelen
unsigned	sex_confirmed
Static Public Attributes
Pedigree::ped_type	type
Protected Methods
void	renum (void)
Protected Attributes
std::string	binfname
unsigned	totalna
unsigned	basesize
unsigned	numgroup
unsigned	nang
Vector< double >	fvec
int	fdone
int	ped_on_disk
int	ped_in_memory
int	groupingped
PedNode *	ped_storage
Friends
std::ostream &	operator<< (std::ostream &stream, Pedigree &A)

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Member Enumeration Documentation

enum matvec::Pedigree::ped_type

Enumeration values: raw  standard  Definition at line 63 of file pedigree.h. {raw, standard}; //default = raw pedigree

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Constructor & Destructor Documentation

matvec::Pedigree::Pedigree (  char    pedtype[] = "" )

Definition at line 68 of file pedigree.cpp. References basesize, binfname, fdone, groupingped, maxnamelen, matvec::Session::mktemp(), numgroup, ped_in_memory, ped_on_disk, ped_storage, pedmember, matvec::SESSION, sex_confirmed, totalna, and type. { ///////////////////////////////////////////////// // type = "group" -> group // = "standard" // = anything else -> nongrouop // ///////////////////////////////////////////////// nang = 0; fdone = 0; totalna = 0; numgroup = 0; basesize = 0; maxnamelen = 0; pedmember = 0; ped_storage = 0; sex_confirmed = 0; groupingped = 0; type = Pedigree::raw; if (strcmp(pedtype,"group") == 0) groupingped = 1; if (strcmp(pedtype,"standard") == 0) type = Pedigree::standard; ped_on_disk = 0; ped_in_memory = 1; binfname = SESSION.mktemp(); }

matvec::Pedigree::Pedigree (  Pedigree &    P )

Definition at line 95 of file pedigree.cpp. References copyfrom(), groupingped, ped_storage, pedmember, and totalna. { totalna = 0; pedmember = 0; ped_storage = 0; groupingped = 0; copyfrom(P); }

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

Definition at line 72 of file pedigree.h. References release(). {release();}

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Member Function Documentation

doubleMatrix matvec::Pedigree::ainv (  int    keepinmem = 0 )

Definition at line 1155 of file pedigree.cpp. References matvec::Matrix< T >::begin(), matvec::PedNode::father_id, fdone, fvec, matvec::getlambda(), inbcoef(), input_pedsheet(), matvec::PedNode::mother_id, matvec::PedNode::myid, ped_in_memory, pedmember, release_pedsheet(), and totalna. { doubleMatrix ainvmat(totalna,totalna); if (totalna == 0) return ainvmat; if (!fdone) inbcoef(1); if (!ped_in_memory) input_pedsheet(); Matrix<double> lambda(3,3); getlambda(lambda.begin(),3); double f,x; Vector<unsigned> ids(3); unsigned i,j,k,ii,jj; PedNode *I; for (k=0; k<totalna; k++) memset(ainvmat[k],'\0',sizeof(double)*totalna); for (k=0; k<totalna; k++) { I = pedmember[k]; ids[0] = I->myid; ids[1] = I->mother_id; ids[2] = I->father_id; for (i=1; i<3; i++) if (ids[i]>totalna) ids[i] = 0; f = 2.0; if (ids[1] == 0) {f -= -1.0; } else {f -= fvec[ids[1]-1]; } if (ids[2] == 0) {f -= -1.0; } else {f -= fvec[ids[2]-1]; } f = 4.0/f; for (i=0; i<3; i++) { ii = ids[i]; if (ii) { ii--; for (j=0; j<3; j++) { jj = ids[j]; if (jj) { jj--; x = lambda[i][j]*f; ainvmat[ii][jj] += x; } } } } } if (!keepinmem) release_pedsheet(); return ainvmat; }

void matvec::Pedigree::copyfrom (  Pedigree &    P )

Definition at line 104 of file pedigree.cpp. References basesize, binfname, fdone, fvec, groupingped, input_pedsheet(), maxnamelen, matvec::Session::mktemp(), nang, numgroup, ped_in_memory, ped_on_disk, release_pedsheet(), resize(), save_pedsheet(), matvec::SESSION, sex_confirmed, totalna, and type. Referenced by operator=(), and Pedigree(). { if (this == &P) return; if (P.ped_in_memory) P.release_pedsheet(); resize(P.nang); fvec = P.fvec; fdone = P.fdone; numgroup = P.numgroup; basesize = P.basesize; totalna = P.totalna; // totalna is necessary for save_pedsheet() maxnamelen = P.maxnamelen; groupingped = P.groupingped; type = P.type; sex_confirmed = P.sex_confirmed; if (P.ped_on_disk) { binfname = P.binfname; if (P.ped_in_memory) P.release_pedsheet(); ped_in_memory = 0; ped_on_disk = 1; input_pedsheet(); } else { if (totalna != 0) throw exception("Pedigree::copyfrom(): you have probably found a bug!"); ped_on_disk = 0; } binfname = SESSION.mktemp(); // each ped object must have its own binfname if (totalna != 0) save_pedsheet(0); // save changes without memory-release ped_in_memory = 1; }

const std::string matvec::Pedigree::diskfname (  void    )  const [inline]

Definition at line 111 of file pedigree.h. References binfname. {return binfname; }

void matvec::Pedigree::display (  const std::string    msg = "", const int    style = 0, const int    ic = 0 )

Definition at line 1404 of file pedigree.cpp. References out_to_stream(). { if (msg != "") std::cout << "\n" << msg << "\n" << std::endl; out_to_stream(std::cout,style,ic); }

int matvec::Pedigree::in_memory (  void    )  const [inline]

Definition at line 78 of file pedigree.h. References ped_in_memory. {return ped_in_memory;}

Vector<double>* matvec::Pedigree::inbcoef (  int    keepinmem = 0 )  [inline]

Definition at line 94 of file pedigree.h. References inbcoef_meuwissen(). Referenced by ainv(). {return inbcoef_meuwissen(keepinmem);}

int matvec::Pedigree::inbcoef_done (  void    )  const [inline]

Definition at line 77 of file pedigree.h. References fdone. {return fdone;}

Vector< double > * matvec::Pedigree::inbcoef_meuwissen (  int    keepinmem = 0 )

Definition at line 1009 of file pedigree.cpp. References matvec::Vector< double >::begin(), matvec::PedNode::father_id, fdone, fvec, input_pedsheet(), matvec::PedNode::mother_id, ped_in_memory, pedmember, release_pedsheet(), and totalna. Referenced by inbcoef(), and logdet(). { if (totalna == 0) return &fvec; if (fdone) return &fvec; if (!ped_in_memory) input_pedsheet(); double *L; if(totalna>0){ L = new double [totalna]; } else { L = 0; } double *D; if(totalna>0){ D = new double [totalna]; } else { D = 0; } unsigned *point; if(totalna>0){ point = new unsigned [totalna]; } else { point = 0; } memset(L,'\0',sizeof(double)*totalna); memset(D,'\0',sizeof(double)*totalna); memset(point,'\0',sizeof(unsigned)*totalna); L--; D--; point--; double *F = fvec.begin()-1; // now F starting from 1, no F[0] at all unsigned i,j,k,d,s,kd,ks,kk,previous_d,previous_s; double r,fi; PedNode *I; previous_s = 0; previous_d = 0; for (i=1; i<=totalna; i++) { I = pedmember[i-1]; d = I->mother_id; if (d > totalna) d = 0; s = I->father_id; if (s > totalna) s = 0; if (s == 0 || d == 0) { if (d+s == 0) { D[i] = 1.0; } else { D[i] = 0.75; } F[i] = 0.0; } else if ((d == previous_d) && (s == previous_s)) { F[i] = F[i-1]; D[i] = D[i-1]; } else { D[i] = 0.5 - 0.25*(F[d] + F[s]); fi = -1.0; L[i] = 1.0; j = i; while (j != 0) { k = j; r = 0.5*L[k]; I = pedmember[k-1]; kd = I->mother_id; ks = I->father_id; if (kd > ks) {kk = ks; ks = kd; kd = kk;} if (ks > 0 && ks <= totalna) { while (point[k] > ks) k = point[k]; L[ks] += r; if (ks != point[k]) { point[ks] = point[k]; point[k] = ks; } if (kd > 0 && kd <=totalna) { while (point[k] > kd) k = point[k]; L[kd] += r; if (kd != point[k]) { point[kd] = point[k]; point[k] = kd; } } } fi += L[j]*L[j]*D[j]; L[j] = 0.0; k = j; j = point[j]; point[k] = 0; } F[i] = fi; } previous_d = d; previous_s = s; } L++; if(L){ delete [] L; L=0; } D++; if(D){ delete [] D; D=0; } point++; if(point){ delete [] point; point=0; } fdone = 1; if (!keepinmem) release_pedsheet(); return &fvec; }

Vector< double > * matvec::Pedigree::inbcoef_quaas (  int    keepinmem = 0 )

Definition at line 973 of file pedigree.cpp. References matvec::Vector< double >::begin(), matvec::PedNode::father_id, fdone, fvec, input_pedsheet(), matvec::PedNode::mother_id, ped_in_memory, pedmember, release_pedsheet(), and totalna. { if (totalna == 0) return &fvec; if (fdone) return &fvec; if (!ped_in_memory) input_pedsheet(); unsigned i,j,s,d; PedNode *I,*J; double t; Vector<double> work(totalna); // working space double *inbc = fvec.begin(); for (j=0; j<totalna; j++) { t = 0.0; J = pedmember[j]; d = J->mother_id; s = J->father_id; if (d> 0 && d <= totalna) t += inbc[d-1]; if (s> 0 && s <= totalna) t += inbc[s-1]; t = 1.0 - 0.25*t; inbc[j] += t; work[j] = std::sqrt(t); for (i=j+1; i<totalna; i++) { t = 0.0; I = pedmember[i]; d = I->mother_id; s = I->father_id; if (d > j && j<=totalna) t += .5*work[d-1]; if (s > j && j<=totalna) t += .5*work[s-1]; work[i] = t; inbc[i] += t*t; } } for (i=0; i<totalna; i++) *inbc++ -= 1.0; fdone = 1; if (!keepinmem) release_pedsheet(); return &fvec; }

unsigned matvec::Pedigree::input (  const std::string &    pfname, const std::string &    fmt = "individual mother father", const std::string &    pedtype = "raw" )

Definition at line 239 of file pedigree.cpp. References basesize, matvec::Vector< T >::begin(), binfname, matvec::check_ptr(), matvec::PedNode::father_id, fdone, fvec, matvec::HashTable::get_id(), groupingped, INPUT_LINE_WIDTH, input_standard(), matvec::HashTable::insert(), maxnamelen, matvec::Session::mktemp(), matvec::PedNode::mother_id, matvec::PedNode::myid, matvec::PedNode::myname, matvec::PedNode::mysex, matvec::PedNode::namelen, nang, numgroup, ped_storage, matvec::pedcp1(), pedmember, release(), matvec::HashTable::release(), renum(), matvec::Vector< double >::resize(), resize(), save_pedsheet(), matvec::SESSION, sex_confirmed, totalna, type, matvec::validline(), and matvec::warning(). { std::string fmt(recfmt); // fmt.replace_all('$',' '); std::string::size_type begidx,endidx; begidx = fmt.find("$"); while (begidx != std::string::npos) { fmt[begidx] = ' '; begidx = fmt.find("$",begidx+1); } std::string tempstr,sep(" ,"); unsigned i,j,numrec,k; PedNode *I; int ncol,ind=-1,mother=-1,father=-1,sex=-1; ncol = 0; begidx = fmt.find_first_not_of(sep); while(begidx != std::string::npos) { endidx = fmt.find_first_of(sep,begidx); if (endidx == std::string::npos) endidx = fmt.length(); tempstr = fmt.substr(begidx,endidx - begidx); if (tempstr == "individual") { ind = ncol; } else if (tempstr == "father") { father = ncol; } else if (tempstr == "mother") { mother = ncol; } else if (tempstr == "sex") { sex = ncol; } ncol++; begidx = fmt.find_first_not_of(sep,endidx); } if (ncol < 3) throw exception("Pedigree::input(fmt): fmt must contain at least three columns"); if (ind < 0) throw exception("Pedigree::input(fmt): no individual column in fmt"); if (mother < 0) throw exception("Pedigree::input(fmt): no mother column in fmt"); if (father < 0) throw exception("Pedigree::input(fmt): no father column in fmt"); if (sex >= 0) sex_confirmed = 1; // std::string tmpfname; // tmpfname = SESSION.mktemp(); std::ifstream pedfile(pfname.c_str(),std::ios::in); if (!pedfile) throw exception("Pedigree::input(): can't open pedigree file"); if (pedtype != "") { if (pedtype == "raw") { type = Pedigree::raw; } else if (pedtype == "standard") { type = Pedigree::standard; numrec = input_standard(pedfile,ind,mother,father); pedfile.close(); return numrec; } else if (pedtype == "group") { groupingped = 1; } else { warning("Pedigree::input(): unknown pedigree type: arg3 is ignored"); } } size_t linewidth = INPUT_LINE_WIDTH; char *line; if(linewidth>0){ line = new char [linewidth]; } else { line = 0; } numrec = 0; while (pedfile.getline(line,linewidth)) if (validline(line)) numrec++; if (numrec == 0) { if(line){ delete [] line; line=0; } pedfile.close(); nang = totalna = numrec; throw exception("Pedigree::input(): pedigree is empty"); } pedfile.clear(); pedfile.seekg(0L,std::ios::beg); size_t isdwidth = sizeof(unsigned)*3; char *wd; if(linewidth>0){ wd = new char [linewidth]; } else { wd = 0; } char *sireid; if(linewidth>0){ sireid= new char [linewidth]; } else { sireid = 0; } char *damid; if(linewidth>0){ damid = new char [linewidth]; } else { damid = 0; } char sexid; sexid = '.'; Vector<unsigned> stdrec(3); std::string tmpfname; tmpfname = SESSION.mktemp(); std::fstream tpedfile(tmpfname.c_str(),std::ios::out); if (!tpedfile) throw exception("can't open internal pedigree file " + tmpfname); resize(numrec); HashTable pedigreeTable(numrec,"str"); char *temp; maxnamelen = 0; numrec = 0; unsigned lineNum = 0; while (pedfile.getline(line,linewidth)) { lineNum++; if (!validline(line)) continue; temp = strtok(line,", "); i = 0; while (temp) { if (i == ind) { strcpy(wd, temp); } else if (i == mother) { strcpy(damid,temp); } else if (i == father) { strcpy(sireid,temp); } else if (i == sex) { sexid = temp[0]; } i++; temp = strtok('\0',", "); } if (i < ncol) { std::cerr << "pedigree " << pfname << ", line " << lineNum << ": invalid\n"; throw exception("invalid line"); } if (!groupingped && strcmp(damid,sireid) == 0) { if (strcmp(sireid,".") && strcmp(sireid,"0")) { warning("pedigree %s, line %d, identical parents: %s. It's ignored", pfname.c_str(),lineNum,sireid); continue; } } if (pedigreeTable.get_id(wd)) { warning("pedigree %s, line %d, duplicated id: %s. It's ignored", pfname.c_str(),lineNum,wd); continue; } else { pedigreeTable.insert(wd); } stdrec[0] = strlen(wd)+1; stdrec[1] = strlen(damid)+1; stdrec[2] = strlen(sireid)+1; I = pedmember[numrec]; I->myname = new char [stdrec[0]]; strcpy(I->myname,wd); I->namelen = stdrec[0]; if (stdrec[0] > maxnamelen) maxnamelen = stdrec[0]; numrec++; tpedfile.write((char*)stdrec.begin(),isdwidth); tpedfile.write(wd,(size_t)stdrec[0]); tpedfile.write(damid,(size_t)stdrec[1]); tpedfile.write(sireid,(size_t)stdrec[2]); tpedfile.write((char*)&sexid,1); } if (maxnamelen > 0) maxnamelen--; pedigreeTable.release(); if(line){ delete [] line; line=0; } pedfile.close(); tpedfile.close(); qsort((char *)pedmember,numrec,sizeof(PedNode*),pedcp1); /* for (i=1; i<numrec; i++) { if (strcmp(pedmember[i]->myname,pedmember[i-1]->myname) == 0) { cout << " in pedigree " << pfname <<"\n"; cout << " duplicated id: " << pedmember[i]->myname << "\n"; delete [] wd; delete [] damid; delete [] sireid; delete [] stdrec; release(); return 0; } } */ tpedfile.open(tmpfname.c_str(),std::ios::in); std::set<std::string> table; // binary tree PedNode **d,**s; d = new PedNode*[1]; s = new PedNode*[1]; d[0] = new PedNode[1]; s[0] = new PedNode[1]; d[0]->myname = damid; s[0]->myname = sireid; char *c; for (i=0; i<numrec; i++) { tpedfile.read((char*)stdrec.begin(),isdwidth); tpedfile.read(wd,(size_t)stdrec[0]); tpedfile.read(damid,(size_t)stdrec[1]); tpedfile.read(sireid,(size_t)stdrec[2]); tpedfile.read((char*)&sexid,1); if (groupingped) { c =(char *)bsearch((char *)d,(char *)pedmember,numrec,sizeof(PedNode*), pedcp1); if (!c) table.insert(damid); c =(char *)bsearch((char *)s,(char *)pedmember,numrec,sizeof(PedNode*), pedcp1); if (!c) table.insert(sireid); } else { if (strcmp(damid,"0") && strcmp(damid,".")) { c = (char *)bsearch((char *)d,(char *)pedmember,numrec, sizeof(PedNode*),pedcp1); if (!c) table.insert(damid); } if (strcmp(sireid,"0") && strcmp(sireid,".")) { c =(char *)bsearch((char *)s,(char *)pedmember,numrec, sizeof(PedNode*),pedcp1); if (!c) table.insert(sireid); } } } basesize = table.size(); /////////////////////////////////////////////////////////////////// // it is not really # of base animals, it is # of animals which // are not listed in the individual column. However, it is # of // unknown parents groups for genetic group model. // Real basesize will be calculated in renum(). /////////////////////////////////////////////////////////////////// if (groupingped) { totalna = numrec; numgroup = basesize; } else { totalna = basesize + numrec; numgroup = 0; } fvec.resize(totalna,0.0); fdone = 0; if (basesize ) { // now hash sire and dam which are not in the id list std::fstream bpedfile(binfname.c_str(),std::ios::out); if (!bpedfile) { release(); throw exception("Pedigree.input(): can't open internal file"); } for (i=0; i<numrec; i++) { I = pedmember[i]; j = I->namelen; bpedfile.write((char*)&j,sizeof(unsigned)); bpedfile.write(I->myname,j); } bpedfile.close(); bpedfile.open(binfname.c_str(),std::ios::in); for (i=0; i<numrec; i++) { if(ped_storage[i].myname){ delete [] ped_storage[i].myname; ped_storage[i].myname=0; } } if(ped_storage){ delete [] ped_storage; ped_storage=0; } if(pedmember){ delete [] pedmember; pedmember=0; } nang = basesize + numrec; if(nang>0){ ped_storage = new PedNode[nang]; } else { ped_storage = 0; } check_ptr(ped_storage); pedmember = new PedNode*[nang]; check_ptr(pedmember); for (i=0; i<nang; i++) { I = &(ped_storage[i]); I->mysex = '.'; I->myname = 0; I->namelen = 0; pedmember[i] = I; } for (i=0; i<numrec; i++) { I = pedmember[i]; bpedfile.read((char*)&j,sizeof(unsigned)); I->namelen = j; if(j>0){ I->myname = new char [j]; } else { I->myname = 0; } check_ptr(I->myname); bpedfile.read(I->myname,(size_t)j); } bpedfile.close(); qsort((char *)pedmember,numrec,sizeof(PedNode*),pedcp1); std::set<std::string>::iterator pos; for (i=0,pos=table.begin(); pos != table.end(); ++pos,++i) { j = numrec+i; I = pedmember[j]; k = I->namelen = pos->length()+1; if(k>0){ I->myname = new char [k]; } else { I->myname = 0; } strcpy(I->myname, pos->c_str()); } } for (i=0; i<nang; i++) { I = pedmember[i]; I->myid = i+1; I->father_id = 0; I->mother_id = 0; } tpedfile.close(); tpedfile.open(tmpfname.c_str(),std::ios::in); PedNode **w,**pm; w = new PedNode*[1]; w[0] = new PedNode[1]; w[0]->myname = wd; for (i=0; i<numrec; i++) { tpedfile.read((char*)stdrec.begin(),isdwidth); tpedfile.read(wd,(size_t)stdrec[0]); tpedfile.read(damid,(size_t)stdrec[1]); tpedfile.read(sireid,(size_t)stdrec[2]); tpedfile.read((char*)&sexid,1); pm = (PedNode **)bsearch((char *)w,(char *)pedmember,numrec, sizeof(PedNode*),pedcp1); I = pedmember[pm[0]->myid - 1]; if (groupingped) { pm = (PedNode **)bsearch((char *)d,(char *)pedmember,numrec, sizeof(PedNode*),pedcp1); if (!pm) { pm = (PedNode **)bsearch((char *)d,(char *)&(pedmember[numrec]), basesize, sizeof(PedNode*),pedcp1); if (!pm) throw exception("Pedigree::input(): you have probably found a bug!"); } I->mother_id = pm[0]->myid; pm = (PedNode **)bsearch((char *)s,(char *)pedmember,numrec, sizeof(PedNode*),pedcp1); if (!pm) { pm = (PedNode **)bsearch((char *)s,(char *)&(pedmember[numrec]), basesize, sizeof(PedNode*),pedcp1); if (!pm) throw exception("Pedigree::input(): you have probably found a bug!"); } I->father_id = pm[0]->myid; } else { if (strcmp(damid,"0") && strcmp(damid,".")) { pm = (PedNode **)bsearch((char *)d,(char *)pedmember,numrec, sizeof(PedNode*),pedcp1); if (!pm) { pm =(PedNode **)bsearch((char *)d,(char *)&(pedmember[numrec]), basesize, sizeof(PedNode*),pedcp1); if (!pm) throw exception("Pedigree::input(): you have probably found a bug!"); } I->mother_id = pm[0]->myid; } if (strcmp(sireid,"0") && strcmp(sireid,".") ) { pm = (PedNode **)bsearch((char *)s,(char *)pedmember,numrec, sizeof(PedNode*),pedcp1); if (!pm) { pm =(PedNode **)bsearch((char *)s,(char *)&(pedmember[numrec]), basesize, sizeof(PedNode*),pedcp1); if (!pm) throw exception("Pedigree::input(): you have probably found a bug!"); } I->father_id = pm[0]->myid; } } I->mysex = sexid; } tpedfile.close(); if(wd){ delete [] wd; wd=0; } if(damid){ delete [] damid; damid=0; } if(sireid){ delete [] sireid; sireid=0; } if(w[0]){ delete [] w[0]; w[0]=0; } if(w){ delete [] w; w=0; } if(d[0]){ delete [] d[0]; d[0]=0; } if(d){ delete [] d; d=0; } if(s[0]){ delete [] s[0]; s[0]=0; } if(s){ delete [] s; s=0; } renum(); save_pedsheet(); remove(tmpfname.c_str()); return numrec; }

void matvec::Pedigree::input_pedsheet (  void    )

Definition at line 834 of file pedigree.cpp. References binfname, matvec::check_ptr(), matvec::PedNode::father_id, maxnamelen, matvec::PedNode::mother_id, matvec::PedNode::myid, matvec::PedNode::myname, matvec::PedNode::mysex, matvec::PedNode::namelen, nang, ped_in_memory, ped_on_disk, ped_storage, pedmember, and totalna. Referenced by ainv(), copyfrom(), inbcoef_meuwissen(), inbcoef_quaas(), mat(), out_to_stream(), and rela(). { if (ped_in_memory) return; if (!ped_on_disk) throw exception("Pedigree::input_pedsheet(): Pedigre is not on disk"); std::ifstream pedfile(binfname.c_str(),std::ios::in); if (!pedfile) throw exception("(1) most likely, pedigree has not been inputed\n" " (2) or probably, it can't open internal file"); unsigned i,len; PedNode *I; if(nang>0){ ped_storage = new PedNode[nang]; } else { ped_storage = 0; } check_ptr(ped_storage); pedmember = new PedNode*[nang]; check_ptr(pedmember); for (i=0; i<nang; i++) { I = &(ped_storage[i]); I->mysex = '.'; I->myname = 0; I->namelen = 0; pedmember[i] = I; } unsigned idssex[4]; size_t idswidth = 4*sizeof(unsigned); for (i=0; i<totalna; i++) { pedfile.read((char *)idssex,idswidth); I = pedmember[i]; I->myid = idssex[0]; I->mother_id = idssex[1]; I->father_id = idssex[2]; I->mysex = (char)idssex[3]; //cout << "input_pedsheet "<< I << I->myid << " " << I->father_id << " " << I->mother_id <<"\n"; } if (maxnamelen > 0) { for (i=0; i<nang; i++) { I = pedmember[i]; pedfile.read((char *)&len,sizeof(unsigned)); if(len>0){ I->myname = new char [len]; } else { I->myname = 0; } pedfile.read(I->myname,(size_t)len); } } pedfile.close(); ped_in_memory = 1; // pedigree data now is in memorry }

unsigned matvec::Pedigree::input_standard (  std::istream &    pedfile, unsigned    ind, unsigned    mother, unsigned    father )

Definition at line 152 of file pedigree.cpp. References basesize, matvec::PedNode::father_id, fdone, fvec, INPUT_LINE_WIDTH, matvec::PedNode::mother_id, matvec::PedNode::myid, nang, pedmember, matvec::Vector< double >::resize(), resize(), save_pedsheet(), totalna, and matvec::validline(). Referenced by input(). { size_t linewidth = INPUT_LINE_WIDTH; char *line; if(linewidth>0){ line = new char [linewidth]; } else { line = 0; } size_t isdwidth = sizeof(unsigned)*4; pedfile.clear(); pedfile.seekg(0L,std::ios::beg); unsigned i,numrec = 0; while (pedfile.getline(line,linewidth)) if (validline(line)) numrec++; if (numrec == 0) { if(line){ delete [] line; line=0; } nang = totalna = numrec; throw exception("Pedigree::input_standard(): pedigree is empty"); } pedfile.clear(); pedfile.seekg(0L,std::ios::beg); resize(numrec); PedNode *I; char *temp; numrec = 0; basesize = 0; unsigned numsameid = 0; while (pedfile.getline(line,linewidth)) { if (!validline(line)) continue; I = pedmember[numrec++]; temp = strtok(line,", "); i = 0; while (temp) { if (i==individual) { if (!sscanf(temp,"%d",&(I->myid))) { numrec--; throw exception("Pedigree::input_standard(): non-numerical character" " in your standard pedigree"); } } else if (i==father) { if (strcmp(temp,".") == 0) { I->father_id = 0; } else { if (!sscanf(temp,"%d",&(I->father_id))) { numrec--; throw exception("Pedigree::input_standard(): non-numerical character" " in your standard pedigree"); } } } else if (i==mother) { if (strcmp(temp,".") == 0) { I->mother_id = 0; } else { if (!sscanf(temp,"%d",&(I->mother_id))) { numrec--; throw exception("Pedigree::input_standard(): non-numerical character" " in your standard pedigree"); } } } i++; temp = strtok('\0',", "); } if (I->father_id==0 && I->mother_id==0) basesize++; } nang = totalna = numrec; if(line){ delete [] line; line=0; } fvec.resize(totalna,0.0); fdone = 0; save_pedsheet(0); return totalna; }

double matvec::Pedigree::logdet (  int    keepinmem = 0 )

Definition at line 1125 of file pedigree.cpp. References matvec::Vector< double >::begin(), matvec::PedNode::father_id, fdone, fvec, inbcoef_meuwissen(), matvec::PedNode::mother_id, pedmember, release_pedsheet(), and totalna. { //////////////////////////////////////////////////////// // ln of determinant of additive relationship matrix A //////////////////////////////////////////////////////// double retval = 0.0; if (totalna==0) throw exception("Pedigree::logdet(): empty pedigree"); if (!fdone) inbcoef_meuwissen(1); double *F = fvec.begin()-1; // now F starting from 1, no F[0] at all PedNode *I; unsigned father,mother; for (unsigned i=0; i<totalna; i++) { I = pedmember[i]; mother = I->mother_id; father = I->father_id; if (mother && father) { retval += std::log((2.0-F[mother]-F[father])/4.0); } else if (mother && !father) { retval += std::log((3.0-F[mother])/4.0); } else if (!mother && father) { retval += std::log((3.0-F[father])/4.0); } } if (!keepinmem) release_pedsheet(); return retval; }

doubleMatrix matvec::Pedigree::mat (  void    )

Definition at line 1277 of file pedigree.cpp. References matvec::PedNode::father_id, input_pedsheet(), matvec::PedNode::mother_id, matvec::PedNode::myid, ped_in_memory, pedmember, release_pedsheet(), and totalna. { doubleMatrix retval(totalna,3); if (totalna == 0) throw exception("Pedigree::mat(): empty pedigree objec"); if (!ped_in_memory) input_pedsheet(); double *dpt; PedNode *I; for (unsigned i=0; i<totalna; i++) { I = pedmember[i]; dpt = retval[i]; *dpt++ = static_cast<double>(I->myid); *dpt++ = static_cast<double>(I->mother_id); *dpt++ = static_cast<double>(I->father_id); } release_pedsheet(); return retval; }

unsigned matvec::Pedigree::nbase (  void    )  const [inline]

Definition at line 91 of file pedigree.h. References basesize. {return basesize;}

unsigned matvec::Pedigree::ngroup (  void    )  const [inline]

Definition at line 89 of file pedigree.h. References numgroup. Referenced by matvec::Model::RSamplerPrior_dist(). {return numgroup;}

const Pedigree& matvec::Pedigree::operator= (  Pedigree &    P )  [inline]

Definition at line 74 of file pedigree.h. References copyfrom(). {copyfrom(P); return *this;}

void matvec::Pedigree::out_to_stream (  std::ostream &    stream, const int    style = 0, const int    ic = 0 )

Definition at line 1296 of file pedigree.cpp. References matvec::PedNode::father_id, fvec, input_pedsheet(), maxnamelen, matvec::PedNode::mother_id, matvec::PedNode::myid, matvec::PedNode::myname, matvec::PedNode::mysex, matvec::Session::output_precision, ped_in_memory, pedmember, release_pedsheet(), matvec::SESSION, totalna, and matvec::warning(). Referenced by display(), matvec::operator<<(), and save(). { if (totalna == 0) { os << "\t empty pedigree object\n" << std::flush; return; } char line[10]; unsigned i,k; int W = SESSION.output_precision+6; // 6 = +.e+00 char S = ' '; // one blank space PedNode *I; if (!ped_in_memory) input_pedsheet(); if (maxnamelen > 0) { if (style==0) { os << " string_ID renumed_ID mother_ID father_ID" << " sex"; if (fdone) os << " inbcoef"; os << "\n"; for (k=23,i=0; i<totalna; i++) { if (ic && i>=k) { k += 23; os << " more ... [q for quit] "; std::cin.getline(line,sizeof(line)); if (line[0]=='q') break; } I = pedmember[i]; os << std::setw(maxnamelen) << I->myname << S << std::setw(W)<< I->myid << S << std::setw(W) << I->mother_id << S << std::setw(W) << I->father_id << S << std::setw(1) << I->mysex; if (fdone) os << S << std::setw(W) << fvec[i]; os << "\n"; } } else if (style==1) { for (k=23,i=0; i<totalna; i++) { if (ic && i>=k) { k += 23; os << " more ... [q for quit] "; std::cin.getline(line,sizeof(line)); if (line[0]=='q') break; } I = pedmember[i]; os << std::setw(maxnamelen) << I->myname; if (I->mother_id) { os << S << std::setw(maxnamelen) << pedmember[I->mother_id-1]->myname; } else { os << S << std::setw(maxnamelen) << "0"; } if (I->father_id) { os << S << std::setw(maxnamelen) << pedmember[I->father_id-1]->myname; } else { os << S << std::setw(maxnamelen) << "0"; } os << S << std::setw(1) << I->mysex; if (fdone) os << S << std::setw(W) << fvec[i]; os << "\n"; } } else { warning("Pedigree::out_to_stream(,style): invalid style"); return; } } else { if (style==0) { os << " renumed_ID mother_ID father_ID sex"; if (fdone) os << " inbcoef"; os << "\n"; } for (k=23,i=0; i<totalna; i++) { if (ic && i>=k) { k += 23; os << " more ... [q for quit] "; std::cin.getline(line,sizeof(line)); if (line[0]=='q') break; } I = pedmember[i]; os << std::setw(W)<< I->myid << S << std::setw(W) << I->mother_id << S << std::setw(W) << I->father_id << S << std::setw(1) << I->mysex; if (fdone) os << S << std::setw(W) << fvec[i]; os << "\n"; } } os << std::flush; release_pedsheet(); }

doubleMatrix matvec::Pedigree::rela (  int    keepinmem = 0 )

Definition at line 1203 of file pedigree.cpp. References matvec::PedNode::father_id, input_pedsheet(), matvec::PedNode::mother_id, matvec::PedNode::myid, ped_in_memory, pedmember, release_pedsheet(), and totalna. Referenced by reld(). { doubleMatrix amat(totalna,totalna); if (totalna == 0) return amat; if (!ped_in_memory) input_pedsheet(); PedNode *I; unsigned i,j,a,d,s; for (i=0; i<totalna; i++) { memset(amat[i],'\0',sizeof(double)*totalna); I = pedmember[i]; a = I->myid-1; d = I->mother_id; s = I->father_id; amat[a][a] = 1.0; if ( d>totalna ) d = 0; if ( s>totalna ) s = 0; if (d && s) { d--; s--; for (j=0; j<a; j++) { amat[j][a] = amat[a][j] = (amat[d][j]+amat[s][j])/2.0; } amat[a][a] += amat[d][s]/2.0; } else if (s && !d) { s--; for (j=0; j<a; j++) amat[j][a] = amat[a][j] = amat[s][j]/2.0; } else if (!s && d) { d--; for (j=0; j<a; j++) amat[j][a] = amat[a][j] = amat[d][j]/2.0; } } if (!keepinmem) release_pedsheet(); return amat; }

doubleMatrix matvec::Pedigree::reld (  int    keepinmem = 0 )

Definition at line 1240 of file pedigree.cpp. References matvec::Matrix< double >::begin(), matvec::PedNode::father_id, matvec::PedNode::mother_id, pedmember, rela(), release_pedsheet(), totalna, and matvec::warning(). { doubleMatrix temp(totalna,totalna); if (totalna == 0) return temp; warning("P.reld() is appropriate only if pedigree is non-inbred"); doubleMatrix A(totalna,totalna); A = rela(1); double **me = A.begin(); PedNode *I,*J; unsigned i,j,di,si,dj,sj; for (i=0; i<totalna; i++) memset(temp[i],'\0',sizeof(double)*totalna); for (i=0; i<totalna-1; i++) { temp[i][i] = 1.0; I = pedmember[i]; di = I->mother_id; si = I->father_id; if (di>0 && di<=totalna && si>0 && si<=totalna) { di--; si--; for (j=i+1; j<totalna; j++) { J = pedmember[j]; dj = J->mother_id; sj = J->father_id; if ( dj>0 && dj<=totalna && sj>0 && sj<=totalna) { dj--; sj--; temp[j][i] = temp[i][j] = .25*(me[di][dj]*me[si][sj]+ me[di][sj]*me[si][dj]); } } } } temp[totalna-1][totalna-1] = 1.0; if (!keepinmem) release_pedsheet(); return temp; }

void matvec::Pedigree::release (  void    )

Definition at line 960 of file pedigree.cpp. References basesize, binfname, fdone, maxnamelen, nang, ped_in_memory, ped_on_disk, release_pedsheet(), and totalna. Referenced by input(), resize(), and ~Pedigree(). { release_pedsheet(); nang = 0; fdone = 0; totalna = 0; basesize = 0; maxnamelen = 0; ped_on_disk = 0; ped_in_memory = 0; remove(binfname.c_str()); }

void matvec::Pedigree::release_pedsheet (  void    )

Definition at line 886 of file pedigree.cpp. References matvec::PedNode::myname, nang, ped_in_memory, ped_storage, and pedmember. Referenced by ainv(), copyfrom(), inbcoef_meuwissen(), inbcoef_quaas(), logdet(), mat(), out_to_stream(), rela(), reld(), release(), and save_pedsheet(). { if (ped_storage) { for (unsigned i=0; i<nang; i++) { if (ped_storage[i].myname) { if(ped_storage[i].myname){ delete [] ped_storage[i].myname; ped_storage[i].myname=0; } } } if(ped_storage){ delete [] ped_storage; ped_storage=0; } ped_storage = 0; } if (pedmember) {delete [] pedmember; pedmember = 0;} ped_in_memory = 0; // pedigree is not in memory, but should on disk; }

void matvec::Pedigree::renum (  void    )  [protected]

Definition at line 907 of file pedigree.cpp. References basesize, matvec::PedNode::father_id, groupingped, matvec::Vector< T >::max(), matvec::PedNode::mother_id, matvec::PedNode::myid, matvec::PedNode::myname, nang, matvec::pedcp2(), pedmember, matvec::Vector< T >::reserve(), and totalna. Referenced by input(). { if (totalna == 0) return; unsigned i,j,k,d,s; PedNode *I; Vector<unsigned> agen; agen.reserve(nang+1); agen[0] = 0; for (i=1; i<=totalna; i++) agen[i] = 1; for (i=(totalna+1); i<=nang; i++) agen[i] = 0; // group is assigned 0 int okk = 1; int g = 0; while (okk) { okk = 0; for (i=0; i<totalna; i++) { I = pedmember[i]; d = agen[I->mother_id]; s = agen[I->father_id]; k = std::max(d,s); if (agen[i+1] <= k) { agen[i+1]= k+1; okk = I->myid; } } if (g++ >100) { std::cout << " A B C" << std::endl; std::cout << " B A D" << std::endl; std::cout << "Is it strange ? but it's in your pedigree\n"; std::cout << "check the families with " << pedmember[okk-1]->myname << std::endl; exit(1); } } unsigned mg = agen.max(); k = 0; for (i=1; i<=mg; i++) { for (j=0; j<totalna; j++) { if (agen[j+1] == i) pedmember[j]->myid = ++k; } } basesize = 0; if (!groupingped) { for (i=1; i<=totalna; i++) if (agen[i]==1) basesize++; } for (i=0; i<totalna; i++) { I = pedmember[i]; d = I->mother_id; s = I->father_id; if (d>0 && d<=totalna) I->mother_id = pedmember[d-1]->myid; if (s>0 && s<=totalna) I->father_id = pedmember[s-1]->myid; // std::cout << "renum " << i << " " <<I->father_id <<" " <<I->mother_id<< "\n"; } qsort((char *)pedmember,totalna,sizeof(PedNode*),pedcp2); }

void matvec::Pedigree::resize (  const unsigned    na )

Definition at line 135 of file pedigree.cpp. References matvec::PedNode::myname, matvec::PedNode::mysex, matvec::PedNode::namelen, nang, ped_storage, pedmember, and release(). Referenced by copyfrom(), input(), and input_standard(). { if (nang == na) return; release(); nang = na; if(!(ped_storage = new PedNode[nang])) throw exception("Pedigree.resize(): out of memory"); if (!(pedmember = new PedNode*[nang])) throw exception("Pedigree.resize(): out of memory"); PedNode* I; for (unsigned i=0; i<nang; i++) { I = &(ped_storage[i]); I->mysex = '.'; I->myname = 0; I->namelen = 0; pedmember[i] = I; } }

Pedigree & matvec::Pedigree::sample (  const unsigned    maxsize, const unsigned    maxg, const unsigned    sire0 = 1, const unsigned    dam0 = 1, const double    imrate = 0.1, const unsigned    parent = 1, const int    no_po = 1, const int    no_fsib = 1, const double    sexratio = 0.5 )

Definition at line 684 of file pedigree.cpp. References basesize, matvec::Vector< T >::begin(), binfname, fdone, fvec, matvec::ignbin(), maxnamelen, nang, numgroup, ped_in_memory, ped_on_disk, matvec::ran1(), matvec::Vector< double >::resize(), sex_confirmed, and totalna. { if (maxg < 1) throw exception("Pedigree::sample(maxsize,maxg,...): maxg must >= 1"); size_t isdsexwidth = 4*sizeof(unsigned); unsigned tgsire, tsire = sire0; unsigned tgdam, tdam = dam0; if ((tdam+tsire) > maxsize) throw exception("Pedigree::sample(): out of memory"); unsigned s,d,i,j,max_male,max_female; d = maxsize-tsire-tdam; s = static_cast<unsigned>(d*sexratio); max_female = tdam+d-s+200; max_male = tsire+s+200; // 200 is the buffer for randomness Vector<unsigned> female(max_female--); Vector<unsigned> male(max_male--); for (i=0; i<=tdam; i++) female[i]=i; for (male[0]=0,i=1; i<=tsire; i++) male[i] = tdam + i; totalna = tdam + tsire; unsigned npg = (maxsize-tdam-tsire)/maxg +1; Matrix<unsigned> pedholder(3,maxsize+1); // sexcode: female = 1, male = 2 for (i=1; i<=tdam; i++) pedholder[2][i] = 1; for (i=tdam+1; i<=totalna; i++) pedholder[2][i] = 2; long selecteddam,selectedsire; unsigned ds,dd,ss,sd; int tryagain,ntry; for (tgdam=tdam, tgsire=tsire, i=0; i<maxg; i++) { if (totalna >= maxsize) break; for (j=0; j<npg; j++) { if (totalna >= maxsize) break; if (ran1() > imrate) { ntry = 0; do { selecteddam = ignbin(long(tdam),0.6); selectedsire = ignbin(long(tsire),0.6); if (selecteddam == 0) selecteddam = parent; if (selectedsire == 0) selectedsire = parent; tryagain = 0; d = female[selecteddam]; s = male[selectedsire]; dd = pedholder[0][d]; ds = pedholder[1][d]; sd = pedholder[0][s]; ss = pedholder[1][s]; if (no_po) { if ( d>0 && sd == d) { tryagain = 1; } else if (s > 0 && ds == s) { tryagain = 1; } } if (no_fsib) { if (ss > 0 && sd >0) if (ss == ds && sd == dd) tryagain = 1; } if (tryagain) ntry++; if (ntry >100) { tryagain = 0; selecteddam = 0; selectedsire = 0; } } while (tryagain); } else { selecteddam = 0; selectedsire = 0; } totalna++; pedholder[0][totalna] = female[selecteddam]; pedholder[1][totalna] = male[selectedsire]; if (ran1()<sexratio && tgdam < max_female) { tgdam++; female[tgdam] = totalna; pedholder[2][totalna] = 1; } else { if (tgsire < max_male) { tgsire++; male[tgdam] = totalna; pedholder[2][totalna] = 2; } else { tgdam++; female[tgdam] = totalna; pedholder[2][totalna] = 1; } } } tdam = tgdam; tsire = tgsire; } std::ofstream outfile(binfname.c_str(),std::ios::out); if (!outfile) throw exception("can't open internal file"); Vector<unsigned> stdrec(3); basesize = 0; for (j=1; j<=totalna; j++) { stdrec[0] = j; stdrec[1] = pedholder[0][j]; stdrec[2] = pedholder[1][j]; stdrec[3] = pedholder[2][j]; if (stdrec[1] == 0 && stdrec[2] == 0) basesize++; outfile.write((char *)stdrec.begin(),isdsexwidth); } outfile.close(); ped_in_memory = 0; ped_on_disk = 1; nang = totalna; numgroup = 0; fdone = 0; fvec.resize(totalna,0.0); maxnamelen = 0; sex_confirmed = 1; return *this; }

void matvec::Pedigree::save (  const std::string &    fname, const int    style = 0, const int    io_mode = std::ios::out )

Definition at line 1389 of file pedigree.cpp. References out_to_stream(). { std::ofstream opedf; opedf.open(fname.c_str(),(OpenModeType)io_mode); if (!opedf) throw exception("Pedigree::save(): cannot open file"); out_to_stream(opedf,style); opedf.close(); }

void matvec::Pedigree::save_pedsheet (  const int    relse = 1 )

Definition at line 807 of file pedigree.cpp. References binfname, matvec::PedNode::father_id, maxnamelen, matvec::PedNode::mother_id, matvec::PedNode::myid, matvec::PedNode::myname, matvec::PedNode::mysex, matvec::PedNode::namelen, nang, ped_on_disk, pedmember, release_pedsheet(), and totalna. Referenced by copyfrom(), input(), and input_standard(). { //cout << "Save pedsheet\n"; std::ofstream pedfile(binfname.c_str(),std::ios::out); if (!pedfile) throw exception("can't open internal file"); PedNode *I; unsigned idssex[4]; size_t idssexwidth = 4*sizeof(unsigned); unsigned i; for (i=0; i<totalna; i++) { I = pedmember[i]; idssex[0] = I->myid; idssex[1] = I->mother_id; idssex[2] = I->father_id; idssex[3] = I->mysex; pedfile.write((char *)idssex,idssexwidth); } if (maxnamelen > 0) { for (i=0; i<nang; i++) { I = pedmember[i]; pedfile.write((char *)&(I->namelen),sizeof(unsigned)); pedfile.write(I->myname,I->namelen); } } pedfile.close(); ped_on_disk = 1; if (relse) release_pedsheet(); }

unsigned matvec::Pedigree::size (  void    )  const [inline]

Definition at line 90 of file pedigree.h. References totalna. {return totalna;}

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Friends And Related Function Documentation

std::ostream& operator<< (  std::ostream &    stream, Pedigree &    A )  [friend]

Definition at line 1398 of file pedigree.cpp. { A.out_to_stream(stream); return stream; }

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Member Data Documentation

unsigned matvec::Pedigree::basesize [protected]

Definition at line 56 of file pedigree.h. Referenced by copyfrom(), input(), input_standard(), nbase(), Pedigree(), release(), renum(), and sample().

std::string matvec::Pedigree::binfname [protected]

Definition at line 55 of file pedigree.h. Referenced by copyfrom(), diskfname(), input(), input_pedsheet(), Pedigree(), release(), sample(), and save_pedsheet().

int matvec::Pedigree::fdone [protected]

Definition at line 58 of file pedigree.h. Referenced by ainv(), copyfrom(), inbcoef_done(), inbcoef_meuwissen(), inbcoef_quaas(), input(), input_standard(), logdet(), Pedigree(), release(), and sample().

Vector<double> matvec::Pedigree::fvec [protected]

Definition at line 57 of file pedigree.h. Referenced by ainv(), copyfrom(), inbcoef_meuwissen(), inbcoef_quaas(), input(), input_standard(), logdet(), out_to_stream(), and sample().

int matvec::Pedigree::groupingped [protected]

Definition at line 58 of file pedigree.h. Referenced by copyfrom(), input(), Pedigree(), and renum().

unsigned matvec::Pedigree::maxnamelen

Definition at line 68 of file pedigree.h. Referenced by copyfrom(), input(), input_pedsheet(), out_to_stream(), Pedigree(), release(), sample(), and save_pedsheet().

unsigned matvec::Pedigree::nang [protected]

Definition at line 56 of file pedigree.h. Referenced by copyfrom(), input(), input_pedsheet(), input_standard(), release(), release_pedsheet(), renum(), resize(), sample(), and save_pedsheet().

unsigned matvec::Pedigree::numgroup [protected]

Definition at line 56 of file pedigree.h. Referenced by copyfrom(), input(), ngroup(), Pedigree(), and sample().

int matvec::Pedigree::ped_in_memory [protected]

Definition at line 58 of file pedigree.h. Referenced by ainv(), copyfrom(), in_memory(), inbcoef_meuwissen(), inbcoef_quaas(), input_pedsheet(), mat(), out_to_stream(), Pedigree(), rela(), release(), release_pedsheet(), and sample().

int matvec::Pedigree::ped_on_disk [protected]

Definition at line 58 of file pedigree.h. Referenced by copyfrom(), input_pedsheet(), Pedigree(), release(), sample(), and save_pedsheet().

PedNode* matvec::Pedigree::ped_storage [protected]

Definition at line 59 of file pedigree.h. Referenced by input(), input_pedsheet(), Pedigree(), release_pedsheet(), and resize().

PedNode** matvec::Pedigree::pedmember

Definition at line 67 of file pedigree.h. Referenced by ainv(), inbcoef_meuwissen(), inbcoef_quaas(), input(), input_pedsheet(), input_standard(), logdet(), mat(), out_to_stream(), Pedigree(), rela(), reld(), release_pedsheet(), renum(), resize(), and save_pedsheet().

unsigned matvec::Pedigree::sex_confirmed

Definition at line 68 of file pedigree.h. Referenced by copyfrom(), input(), matvec::Population::input_ped(), Pedigree(), and sample().

unsigned matvec::Pedigree::totalna [protected]

Definition at line 56 of file pedigree.h. Referenced by ainv(), copyfrom(), inbcoef_meuwissen(), inbcoef_quaas(), input(), input_pedsheet(), input_standard(), logdet(), mat(), out_to_stream(), Pedigree(), rela(), reld(), release(), renum(), sample(), save_pedsheet(), and size().

Pedigree::ped_type matvec::Pedigree::type [static]

Definition at line 35 of file pedigree.cpp. Referenced by copyfrom(), input(), and Pedigree().

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

• pedigree.h
• pedigree.cpp

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