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matvec::GNodeList Class Reference

#include <gnodestuff.h>

Inheritance diagram for matvec::GNodeList:

SafeSTLVector< GNode * > vector List of all members.

Detailed Description

This is the "list of graph nodes" class.

GNodeList class includes methods relevant to the list of graph nodes

Definition at line 165 of file gnodestuff.h.

Public Types

typedef size_t size_type

Public Methods

 GNodeList (void)
void inputGNodeSets (char *fname)
 method used in determining peeling order for a pedigree (used only if none of the make....GNodeSets methods is called)

void displayGNodeSets ()
 displays the GNodeSets of each Node (pentrance, founder, transition sets)

void getPeelOrder (char *fname)
 returns the peeling order for a pedigree provided in the file given as an argument

void fill (unsigned n)
 method used in determining peeling order for a pedigree (used only if make....GNodeSets is not called)

void makealleleGNodeSets (char *infile, char *outfile)
 creates the AlleleNodeSets from the pedigree

void makegenotGNodeSets (char *infile, char *outfile)
 creates the GenotypeNodeSets from the pedigree

GNode * peelAndCut (unsigned maxCutSetSize)
GNode * peelAndCutFast (void)
void peelCutAndCompute (unsigned maxCutSetSize, unsigned startBlock, unsigned stopBlock, unsigned sizeBlock)
void peelCutAndSample (unsigned maxCutSetSize, unsigned startBlock, unsigned stopBlock, unsigned sizeBlock)
void peelCutAndSample (unsigned maxCutSetSize)
void peelOrderCutAndSample (unsigned maxCutSetSize, unsigned startBlock, unsigned stopBlock, unsigned sizeBlock)
void peelOrderCutAndSample (unsigned maxCutSetSize)
void clearGNodeListForNextLocus (void)
void reinitGNodeList (void)
void releaseGNsts (void)
void releaseCutSets (void)
void resetGNodeList (void)
void setGNodeSampleFlags (unsigned startBlock, unsigned stopBlock, unsigned sizeBlock)
void setGNodeSampleFlags (void)
void findLoopAndCut ()
GNodeList::iterator getMinWeightGNode (void)
set< GNodeSet * >::iterator getCutGNodeSet (GNodeList::iterator cutGNode)
void propagateFlags (unsigned lowFlag, unsigned highFlag)
void resetConnectFlags (void)
GNodeList isolatePureLoop (GNodeList::iterator loopCloser)
void cutLoop (GNodeList::iterator cutGNode, set< GNodeSet * >::iterator cutGNodeSet)
void checkSample (void)
void calculateTargetProb (void)
void makeDistanceMatrix (void)
 fills in distanceMatrix for all pairs of nodes

void calcDistancefrom (GNode *refGNode)
GNode * findSampleGNode (void)
 returns pointer to GNode with largest sum of distances to the "cuts"

GNode *& operator[] (const size_type i)

Public Attributes

float sum
unsigned lastmember
Matrix< int > distanceMat
bool distanceMatDone
SafeSTLVector< GNode * > cutGNodesVector
set< GNode * > loopSetGNodes
unsigned maxDist
GNode * sampleGNodePtr
GNode * containerGNode
set< GNodeSet * > completeSetofGNsts
set< CutSet * > completeSetofCutSets
GNodeList::iterator searchStart
GNodeList::iterator cutGNode
GNode_info choosenGNodeInfo
string howToSample
string name

Static Public Attributes

double logTarget = 0.0
double logProposal = 0.0
double logOldProposal = 0.0
Population * popPtr

Member Typedef Documentation

typedef size_t SafeSTLVector< GNode * >::size_type [inherited]
 

Definition at line 33 of file safe_vectors.h.

Constructor & Destructor Documentation

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

Definition at line 178 of file gnodestuff.h.

References distanceMatDone. 

00178 {distanceMatDone = false;};

Member Function Documentation

void matvec::GNodeList::calcDistancefrom (  GNode *    refGNode ) 
 

Definition at line 456 of file gnodestuff.cpp.

References matvec::GNode::connectFlag, distanceMat, matvec::GNode::id, and matvec::GNode::SetofGNsts.

Referenced by makeDistanceMatrix(). 

00456                                                {
00457         // Authors: Joseph Abraham and Rohan L. Fernando 
00458         // (October, 2004) 
00459         // Contributors: 
00460         
00461         vector<unsigned> dist;
00462         unsigned UHUGE = 2*ULONG_MAX;
00463         GNode *gnodePtr;
00464         GNodeList::iterator GNodeListiter;
00465         set<GNodeSet*>::iterator GNodeSetiter;
00466         set<GNode*>::iterator GNodeiter;
00467         vector<GNode*>::iterator GreyListiter;
00468         vector<GNode*> GreyList;
00469         
00470         GreyList.clear();
00471         unsigned rowId = refGNode->id;
00472         for(GNodeListiter = begin(); GNodeListiter != end(); GNodeListiter++){
00473                 (*GNodeListiter)->connectFlag =  ULONG_MAX; // every one gets white color
00474         }
00475     refGNode->connectFlag = 0; // this is colored gray
00476         GreyList.push_back(refGNode);
00477         distanceMat(rowId,rowId) = 0;
00478         while (GreyList.size() > 0){
00479                 gnodePtr = GreyList.back();
00480                 GreyList.pop_back();
00481                 unsigned uId = gnodePtr->id;
00482                 for(GNodeSetiter= gnodePtr->SetofGNsts.begin();GNodeSetiter !=gnodePtr->SetofGNsts.end();GNodeSetiter++){      
00483                         for(GNodeiter = (*GNodeSetiter)->begin(); GNodeiter!= (*GNodeSetiter)->end(); GNodeiter++){ 
00484                                 if ( (*GNodeiter)->connectFlag == ULONG_MAX) { // if color white
00485                                         (*GNodeiter)->connectFlag = 0;             // make it gray
00486                                         unsigned colId = (*GNodeiter)->id;
00487                                         distanceMat(rowId,colId) = distanceMat(rowId,uId) + 1;
00488                                         GreyList.push_back(*GNodeiter);  
00489                                 }
00490                         }
00491                 }
00492                 gnodePtr->connectFlag = UHUGE;
00493         }
00494 }

void matvec::GNodeList::calculateTargetProb (  void    ) 
 

Referenced by peelCutAndSample(), and peelOrderCutAndSample().

void matvec::GNodeList::checkSample (  void    ) 
 

Referenced by peelCutAndCompute(), peelCutAndSample(), and peelOrderCutAndSample().

void matvec::GNodeList::clearGNodeListForNextLocus (  void    ) 
 

Referenced by peelCutAndCompute(), peelCutAndSample(), and peelOrderCutAndSample().

void matvec::GNodeList::cutLoop (  GNodeList::iterator    cutGNode,
set< GNodeSet * >::iterator    cutGNodeSet
) 
 

void matvec::GNodeList::displayGNodeSets (    ) 
 

displays the GNodeSets of each Node (pentrance, founder, transition sets)

Definition at line 138 of file gnodestuff.cpp.

Referenced by matvec::Population::getInitialGNodeListSample(), and peelAndCut(). 

00138                                 {
00139         // Authors: L. Radu Totir and Rohan L. Fernando 
00140         // (June, 2003) 
00141         // Contributors:
00142         GNodeList::iterator it;
00143         set< GNodeSet*>::iterator GNodeSetit;
00144         GNodeSet::iterator setit;
00145         for (it=begin();it!=end();it++){
00146                 std::cout << (*it)->id << "   ";
00147                 for (GNodeSetit=(*it)->SetofGNsts.begin();GNodeSetit!=(*it)->SetofGNsts.end();GNodeSetit++){
00148                         (*GNodeSetit)->display();
00149                 }
00150                 std::cout << endl;
00151         }
00152         std::cout << "=========== " << endl;
00153 }

void matvec::GNodeList::fill (  unsigned    n ) 
 

method used in determining peeling order for a pedigree (used only if make....GNodeSets is not called)

Definition at line 88 of file gnodestuff.cpp.

References matvec::GNode::peelorder, and matvec::GNode::weight.

Referenced by inputGNodeSets(). 

00088                               {
00089   // Authors: L. Radu Totir and Rohan L. Fernando 
00090   // (June, 2003) 
00091   // Contributors:
00092   resize(n);
00093   for (unsigned i=0;i<n;i++){
00094     GNode* elm_ptr = new GNode;
00095     elm_ptr->peelorder = i+1;
00096     elm_ptr->weight = 1;
00097     (*this)[i] = elm_ptr;
00098   }
00099 }

void matvec::GNodeList::findLoopAndCut (    ) 
 

Referenced by peelAndCut().

GNode * matvec::GNodeList::findSampleGNode (  void    ) 
 

returns pointer to GNode with largest sum of distances to the "cuts"

Definition at line 407 of file gnodestuff.cpp.

References cutGNodesVector, distanceMat, matvec::GNode::id, and loopSetGNodes.

Referenced by peelAndCut(). 

00407                                      {
00408         // Authors: Joseph Abraham and Rohan L. Fernando 
00409         // (October, 2004) 
00410         // Contributors: 
00411         unsigned maxDistance = 0;
00412         
00413         GNode* sampleGuy = 0;
00414         set<GNode*>::iterator it;
00415         SafeSTLVector<GNode*>::iterator cutListIter;
00416         for(it=loopSetGNodes.begin();it!=loopSetGNodes.end();it++){
00417                 if((*it)->sampled) continue;
00418                 unsigned rowId = (*it)->id;
00419                 unsigned sumDist = 0;
00420                 for(cutListIter=cutGNodesVector.begin();cutListIter!=cutGNodesVector.end();cutListIter++){
00421                         unsigned colId = (*cutListIter)->id;
00422                         sumDist += distanceMat(rowId,colId);
00423                 }
00424                 cout << "distance " << sumDist << endl;
00425                 if (sumDist>maxDistance){
00426                         maxDistance = sumDist;
00427                         sampleGuy = (*it);
00428                 }
00429         }
00430         if (sampleGuy){
00431                 return sampleGuy;
00432         }
00433         else {
00434                 throw exception("GNodeList::findSampleGNode: Error- possible bug in code\n");
00435         }
00436 }

set< GNodeSet*>::iterator matvec::GNodeList::getCutGNodeSet (  GNodeList::iterator    cutGNode ) 
 

GNodeList::iterator matvec::GNodeList::getMinWeightGNode (  void    ) 
 

void matvec::GNodeList::getPeelOrder (  char *    fname ) 
 

returns the peeling order for a pedigree provided in the file given as an argument

Definition at line 159 of file gnodestuff.cpp.

References min, and sum. 

00159                                        {
00160   // Authors: L. Radu Totir and Rohan L. Fernando 
00161   // (June, 2003) 
00162   // Contributors:
00163   ofstream ordfile(fname);
00164   GNodeList::iterator it1,it2,peel_me;
00165   GNode* temp;
00166   float mag, min;
00167   sum =0.0;
00168   for (it1=begin();it1!=end();it1++){ 
00169     min = 1e+100;
00170     for (it2=it1;it2!=end();it2++){
00171       mag = (*it2)->getCutsetMagnitude();
00172       if (mag<min){
00173         peel_me = it2;
00174         min=mag;
00175       }
00176     }    
00177     sum+=pow(double(4.0),double(min));
00178     ordfile << (*peel_me)->peelorder <<"     "<< min << endl;
00179     //(*peel_me)->peelord = ++ord;
00180     (*peel_me)->updateMysets();
00181     temp = *it1;
00182     *it1 = *peel_me;
00183     *peel_me = temp;  
00184   }
00185   ordfile << "Network size = " << sum << endl; 
00186   std::cout << sum << endl; 
00187 }

void matvec::GNodeList::inputGNodeSets (  char *    fname ) 
 

method used in determining peeling order for a pedigree (used only if none of the make....GNodeSets methods is called)

Definition at line 105 of file gnodestuff.cpp.

References fill(), lastmember, and matvec::GNode::SetofGNsts. 

00105                                          {
00106   // Authors: L. Radu Totir and Rohan L. Fernando 
00107   // (June, 2003) 
00108   // Contributors:  
00109   ifstream setfile(fname);
00110   unsigned n,member;
00111   lastmember = 0;
00112   while (setfile >> n ) {
00113     for (unsigned i=0;i<n;i++){
00114       setfile >> member;
00115       if (member>lastmember){
00116         lastmember=member;
00117       }
00118     }
00119   }
00120   setfile.close();
00121   ifstream setfile1(fname);
00122   fill(lastmember);
00123   while (setfile1 >> n ) {
00124     GNodeSet* myset = new GNodeSet;
00125     for (unsigned i=0;i<n;i++){
00126       setfile1 >> member;
00127       GNode* elm_ptr = (*this)[member-1];
00128       myset->insert(elm_ptr);
00129       elm_ptr->SetofGNsts.insert(myset);
00130     }
00131   }
00132 }

GNodeList matvec::GNodeList::isolatePureLoop (  GNodeList::iterator    loopCloser ) 
 

void matvec::GNodeList::makealleleGNodeSets (  char *    infilename,
char *    outfilename
) 
 

creates the AlleleNodeSets from the pedigree

Definition at line 52 of file gnodestuff.cpp. 

00052                                                                      {
00053   // Authors: L. Radu Totir and Rohan L. Fernando 
00054   // (June, 2003) 
00055   // Contributors:
00056   ifstream infile(infilename);
00057   ofstream outfile(outfilename);
00058   unsigned ind,mom,dad;
00059   while (infile >> ind >> dad >> mom) {
00060     outfile << "2   " << (ind-1)*2 +1 << setw(5) << (ind-1)*2 +2 << endl;
00061     if(!dad) continue;
00062     outfile << "3   " << (dad-1)*2 +1 << setw(5) << (dad-1)*2 +2 << setw(5) << (ind-1)*2 +1 << endl;
00063     outfile << "3   " << (mom-1)*2 +1 << setw(5) << (mom-1)*2 +2 << setw(5) << (ind-1)*2 +2 << endl;
00064   }
00065 }

void matvec::GNodeList::makeDistanceMatrix (  void    ) 
 

fills in distanceMatrix for all pairs of nodes

Definition at line 440 of file gnodestuff.cpp.

References calcDistancefrom(), distanceMat, distanceMatDone, and matvec::Matrix< int >::resize().

Referenced by peelAndCut(). 

00440                                       {
00441         // Authors: Joseph Abraham and Rohan L. Fernando 
00442         // (October, 2004) 
00443         // Contributors: 
00444         unsigned numGnodes = size();
00445         distanceMat.resize(numGnodes,numGnodes);
00446         GNodeList::iterator it;
00447         for (it=begin();it!=end();it++){
00448                 calcDistancefrom(*it);
00449         }
00450         distanceMatDone = true;
00451         //cout << distanceMat;
00452 }

void matvec::GNodeList::makegenotGNodeSets (  char *    infilename,
char *    outfilename
) 
 

creates the GenotypeNodeSets from the pedigree

Definition at line 71 of file gnodestuff.cpp. 

00071                                                                     {
00072   // Authors: L. Radu Totir and Rohan L. Fernando 
00073   // (June, 2003) 
00074   // Contributors:
00075   ifstream infile(infilename);
00076   ofstream outfile(outfilename);
00077   unsigned ind,mom,dad;
00078   while (infile >> ind >> dad >> mom) {
00079     if(!dad) continue;
00080     outfile << "3   " << dad << setw(5) << mom << setw(5) << ind << endl;
00081   }
00082 }

GNode *& SafeSTLVector< GNode * >::operator[] (  const size_type    i )  [inline, inherited]
 

Definition at line 39 of file safe_vectors.h. 

00039                                            {
00040                 if (i >= vector<T>::size()) {
00041                         cout << "out of range error in SafeSTLVector: " << name << endl;
00042                         cout << "i = " << i << endl;
00043                         cout << "size of vector = " << vector<T>::size() << endl;
00044                         throw matvec::exception("SafeSTLVector: out of range error");
00045                         exit(1);
00046                 }
00047                 return *(vector<T>::begin() + i) ;
00048         }

GNode * matvec::GNodeList::peelAndCut (  unsigned    maxCutSetSize ) 
 

Definition at line 342 of file gnodestuff.cpp.

References matvec::GeneticDist::chrom(), cutGNodesVector, displayGNodeSets(), distanceMatDone, findLoopAndCut(), findSampleGNode(), howToSample, matvec::ChromStruct::locus, loopSetGNodes, makeDistanceMatrix(), maxDist, min, matvec::Population::model, matvec::Model::myRSamplerParms, matvec::ChromStruct::peelOrder, popPtr, matvec::RSamplerParms::printFlag, resetConnectFlags(), sampleGNodePtr, searchStart, matvec::sort(), and sum.

Referenced by peelCutAndCompute(), peelCutAndSample(), and peelOrderCutAndSample(). 

00342                                                   {
00343         // Authors: L. Radu Totir and Rohan L. Fernando 
00344         // (August, 2003) 
00345         // Contributors: 
00346         unsigned printFlag = popPtr->model->myRSamplerParms.printFlag;          
00347         if (!distanceMatDone) makeDistanceMatrix(); 
00348         cutGNodesVector.clear();
00349         loopSetGNodes.clear();  
00350         searchStart = begin();
00351         resetConnectFlags();
00352         sampleGNodePtr=NULL;
00353         maxDist = 0;
00354         GNodeList::iterator it1,it2,peel_me;
00355         GNode* temp;
00356         float mag, min;
00357         sum =0.0;
00358         unsigned count=0;
00359         unsigned loopCount=0;
00360         it1=begin();
00361         while (it1!=end()){
00362                 min = 1e+100;
00363                 for (it2=it1;it2!=end();it2++){
00364                         mag = (*it2)->getCutsetMagnitude();
00365                         if (mag<min){
00366                                 peel_me = it2;
00367                                 min=mag;
00368                         }
00369                 } 
00370                 if(min<=maxCutSetSize){
00371                         sum+=min;
00372                         (*peel_me)->peelorder = ++count;
00373                         (*peel_me)->updateMysets();
00374                         if(printFlag>1) cout << "Peeling node " << count << endl;
00375                         (*peel_me)->peel();
00376                         if(howToSample=="joint"){
00377                                 GNodeSet::prior->chrom()[0].peelOrder[count-1] = (*peel_me)->id;
00378                         }
00379                         else{
00380                                 GNodeSet::prior->chrom()[0].locus[Individual::currentLocus].peelOrder[count-1] = (*peel_me)->id;
00381                         }
00382                         temp = *it1;
00383                         *it1 = *peel_me;
00384                         *peel_me = temp;
00385                         it1++;
00386                 }
00387                 else {
00388                         if(printFlag>1) cout << "Peeled " << count << " gNodes, now I need to cut ";
00389                         searchStart = it1;
00390                         sort(searchStart,end(),compareGNodesWeight());
00391                         findLoopAndCut();
00392                         loopCount++;
00393                 }
00394                 if(printFlag>2) {
00395                         displayGNodeSets();
00396                 }
00397         }
00398         if (cutGNodesVector.size()>0){
00399                 sampleGNodePtr = findSampleGNode();
00400         }               
00401         return sampleGNodePtr;
00402 }

GNode* matvec::GNodeList::peelAndCutFast (  void    ) 
 

Referenced by peelCutAndCompute(), and peelCutAndSample().

void matvec::GNodeList::peelCutAndCompute (  unsigned    maxCutSetSize,
unsigned    startBlock,
unsigned    stopBlock,
unsigned    sizeBlock
) 
 

Definition at line 193 of file gnodestuff.cpp.

References checkSample(), matvec::GeneticDist::chrom(), clearGNodeListForNextLocus(), matvec::GNode::id, matvec::ChromStruct::locus, peelAndCut(), peelAndCutFast(), matvec::GNode::reComputeGNode(), reinitGNodeList(), sampleGNodePtr, and setGNodeSampleFlags().

Referenced by matvec::Population::getOldGNodeListProbability(). 

00193                                                                                                                     {
00194   // Authors: L. Radu Totir and Rohan L. Fernando 
00195   // (October, 2003) 
00196   // Contributors: 
00197   unsigned sampledCount = 0;
00198   GNodeList::reverse_iterator it;
00199   setGNodeSampleFlags(startBlock, stopBlock, sizeBlock);        
00200   if (GNodeSet::prior->chrom()[0].locus[Individual::currentLocus].peelOrder.size()==size()){
00201     sampleGNodePtr = peelAndCutFast();
00202   }
00203   else{
00204     // cout << "We determine the peeling order again (inefficient!!)" << endl;
00205     sampleGNodePtr = peelAndCut(maxCutSetSize);
00206   }
00207   // cout << "I am calculating the probability of the previous sample" << endl;
00208   // cout << "Log Old Proposal before processing locus " << Individual::currentLocus+1 << " = " << GNodeList::logOldProposal << endl;
00209   //cout << "Log Target before = " << GNodeList::logTarget << endl;
00210   while (sampleGNodePtr) {
00211     sampledCount++;
00212     //displayGNodeSets();
00213     cout << "GNode sampled after " << sampledCount << " 'th peeling: " << sampleGNodePtr->id << endl;
00214     sampleGNodePtr->reComputeGNode();
00215     reinitGNodeList();
00216     //displayGNodeSets();
00217     sampleGNodePtr = peelAndCut(maxCutSetSize);
00218   }
00219   //cout << "Number of GNodes sampled to break loops = " << sampledCount << endl;
00220   //cout << "GNodeList before sampling all GNodes" << endl;
00221   for (it=rbegin();it!=rend();it++){
00222     if(!(*it)->sampled){
00223       (*it)->reComputeGNode();
00224     }
00225   }
00226   checkSample();
00227   // cout << "Log Old Proposal after processing locus " << Individual::currentLocus+1 << " = " << GNodeList::logOldProposal << endl;
00228   //calculateTargetProb();
00229   //cout << "Log Target after = " << GNodeList::logTarget << endl;
00230   //cout << "Final gNodeList (after peeling, cutting and sampling):" << endl;
00231   //displayGNodeSets();
00232   clearGNodeListForNextLocus();
00233 }

void matvec::GNodeList::peelCutAndSample (  unsigned    maxCutSetSize ) 
 

void matvec::GNodeList::peelCutAndSample (  unsigned    maxCutSetSize,
unsigned    startBlock,
unsigned    stopBlock,
unsigned    sizeBlock
) 
 

Definition at line 238 of file gnodestuff.cpp.

References calculateTargetProb(), checkSample(), matvec::GeneticDist::chrom(), clearGNodeListForNextLocus(), matvec::GNode::id, matvec::Population::LGGenotypeElimination(), matvec::ChromStruct::locus, matvec::Population::model, matvec::Model::myRSamplerParms, peelAndCut(), peelAndCutFast(), popPtr, matvec::RSamplerParms::printFlag, reinitGNodeList(), matvec::GNode::sampleGNode(), sampleGNodePtr, matvec::RSamplerParms::samplerType, matvec::Population::setAlleleStateVectors(), setGNodeSampleFlags(), and matvec::Population::SimpleGenotypeElimination().

Referenced by matvec::Population::getGNodeListSample(). 

00238                                                                                                                    {
00239   // Authors: L. Radu Totir and Rohan L. Fernando 
00240   // (October, 2003) 
00241   // Contributors: 
00242   unsigned printFlag = popPtr->model->myRSamplerParms.printFlag;                
00243   unsigned sampledCount = 0;
00244   Model *modelPtr = popPtr->model;      
00245   GNodeList::reverse_iterator it;
00246   setGNodeSampleFlags(startBlock, stopBlock, sizeBlock);  
00247   bool cutLoops = GNodeSet::prior->chrom()[0].locus[Individual::currentLocus].cutLoops;
00248   if (GNodeSet::prior->chrom()[0].locus[Individual::currentLocus].peelOrder.size()==size() && !cutLoops){
00249     sampleGNodePtr = peelAndCutFast();
00250   }
00251   else{
00252           // cout << "We determine the peeling order again (inefficient!!)" << endl;
00253           popPtr->SimpleGenotypeElimination(Individual::currentLocus);                  
00254           if (sizeBlock == size() && GNodeSet::prior->chrom()[0].locus[Individual::currentLocus].qtl_ml=='m') {
00255                   popPtr->LGGenotypeElimination(Individual::currentLocus); 
00256           }
00257           popPtr->setAlleleStateVectors(Individual::currentLocus);
00258           sampleGNodePtr = peelAndCut(maxCutSetSize);
00259   }
00260   //cout << "I am actually sampling a new sample" << endl;
00261   //cout << "Log Proposal before processing locus " << Individual::currentLocus+1 << " = " << GNodeList::logProposal << endl;
00262   //cout << "Log Target before = " << GNodeList::logTarget << endl;
00263   while (sampleGNodePtr) {
00264     sampledCount++;
00265     //displayGNodeSets();
00266     if(printFlag>0) cout << "GNode sampled after " << sampledCount << " 'th peeling: " << sampleGNodePtr->id << endl;
00267     sampleGNodePtr->sampleGNode();
00268     reinitGNodeList();
00269     //displayGNodeSets();
00270         if (modelPtr->myRSamplerParms.samplerType=="genotypic"){
00271                 popPtr->LGGenotypeElimination(Individual::currentLocus);
00272                 popPtr->setAlleleStateVectors(Individual::currentLocus);
00273         }
00274     sampleGNodePtr = peelAndCut(maxCutSetSize);
00275   }
00276   if(printFlag>0) cout << "Number of GNodes sampled to break loops = " << sampledCount << endl;
00277   //cout << "GNodeList before sampling all GNodes" << endl;
00278   for (it=rbegin();it!=rend();it++){
00279     if(!(*it)->sampled){
00280       (*it)->reverseSampleGNode();
00281     }
00282   }
00283   checkSample();
00284   //cout << "Log Proposal after processing locus " << Individual::currentLocus+1 << " = " << GNodeList::logProposal << endl;
00285   calculateTargetProb();
00286   //cout << "Log Target after = " << GNodeList::logTarget << endl;
00287   //cout << "Final gNodeList (after peeling, cutting and sampling):" << endl;
00288   //displayGNodeSets();
00289   clearGNodeListForNextLocus();
00290 }

void matvec::GNodeList::peelOrderCutAndSample (  unsigned    maxCutSetSize ) 
 

void matvec::GNodeList::peelOrderCutAndSample (  unsigned    maxCutSetSize,
unsigned    startBlock,
unsigned    stopBlock,
unsigned    sizeBlock
) 
 

Definition at line 295 of file gnodestuff.cpp.

References calculateTargetProb(), checkSample(), matvec::GeneticDist::chrom(), clearGNodeListForNextLocus(), matvec::GNode::id, matvec::Population::LGGenotypeElimination(), matvec::ChromStruct::locus, matvec::Population::model, matvec::Model::myRSamplerParms, peelAndCut(), popPtr, matvec::RSamplerParms::printFlag, reinitGNodeList(), matvec::GNode::sampleGNode(), sampleGNodePtr, matvec::RSamplerParms::samplerType, matvec::Population::setAlleleStateVectors(), and setGNodeSampleFlags().

Referenced by matvec::Population::getInitialGNodeListSample(). 

00295                                                                                                                         {
00296   // Authors: L. Radu Totir and Rohan L. Fernando 
00297   // (February, 2004) 
00298   // Contributors: 
00299   unsigned printFlag = popPtr->model->myRSamplerParms.printFlag; 
00300   Model *modelPtr = popPtr->model;
00301   unsigned sampledCount = 0;
00302   GNodeList::reverse_iterator it;
00303   setGNodeSampleFlags(startBlock, stopBlock, sizeBlock); 
00304   sampleGNodePtr = peelAndCut(maxCutSetSize);
00305   GNodeSet::prior->chrom()[0].locus[Individual::currentLocus].cutLoops = false;
00306   //cout << "Log Proposal before = " << GNodeList::logProposal << endl;
00307   //cout << "Log Target before = " << GNodeList::logTarget << endl;
00308   while (sampleGNodePtr) {
00309         GNodeSet::prior->chrom()[0].locus[Individual::currentLocus].cutLoops = true;  
00310     sampledCount++;
00311     //displayGNodeSets();
00312     if(printFlag>0) cout << "GNode sampled after " << sampledCount << " 'th peeling: " << sampleGNodePtr->id << endl;
00313     sampleGNodePtr->sampleGNode();
00314     reinitGNodeList();
00315         if (modelPtr->myRSamplerParms.samplerType=="genotypic"){
00316                 popPtr->LGGenotypeElimination(Individual::currentLocus);
00317                 popPtr->setAlleleStateVectors(Individual::currentLocus);
00318         }
00319     //displayGNodeSets();
00320     sampleGNodePtr = peelAndCut(maxCutSetSize);
00321   }
00322   if(printFlag>0) cout << "Number of GNodes sampled to break loops = " << sampledCount << endl;
00323   //cout << "GNodeList before sampling all GNodes" << endl;
00324   for (it=rbegin();it!=rend();it++){
00325     if(!(*it)->sampled){
00326       (*it)->reverseSampleGNode();
00327     }
00328   }
00329   checkSample();
00330   //cout << "Log Proposal after = " << GNodeList::logProposal << endl;
00331   calculateTargetProb();
00332   //cout << "Log Target after = " << GNodeList::logTarget << endl;
00333   //cout << "Final gNodeList (after peeling, cutting and sampling):" << endl;
00334   //displayGNodeSets();
00335   clearGNodeListForNextLocus();
00336 }

void matvec::GNodeList::propagateFlags (  unsigned    lowFlag,
unsigned    highFlag
) 
 

void matvec::GNodeList::reinitGNodeList (  void    ) 
 

Referenced by matvec::Population::getGNodeListSample(), matvec::Population::getInitialGNodeListSample(), matvec::Population::getOldGNodeListProbability(), peelCutAndCompute(), peelCutAndSample(), and peelOrderCutAndSample().

void matvec::GNodeList::releaseCutSets (  void    ) 
 

void matvec::GNodeList::releaseGNsts (  void    ) 
 

Referenced by matvec::Population::initAlleleNodeList(), matvec::Population::initGenotypeNodeList(), matvec::Population::initJointAlleleNodeList(), and matvec::Population::release().

void matvec::GNodeList::resetConnectFlags (  void    ) 
 

Referenced by peelAndCut().

void matvec::GNodeList::resetGNodeList (  void    ) 
 

void matvec::GNodeList::setGNodeSampleFlags (  void    ) 
 

Referenced by peelCutAndCompute(), peelCutAndSample(), and peelOrderCutAndSample().

void matvec::GNodeList::setGNodeSampleFlags (  unsigned    startBlock,
unsigned    stopBlock,
unsigned    sizeBlock
) 
 

Member Data Documentation

GNode_info matvec::GNodeList::choosenGNodeInfo
 

Definition at line 212 of file gnodestuff.h.

set< CutSet*> matvec::GNodeList::completeSetofCutSets
 

Definition at line 190 of file gnodestuff.h.

set< GNodeSet*> matvec::GNodeList::completeSetofGNsts
 

Definition at line 189 of file gnodestuff.h.

Referenced by matvec::Population::initAlleleNodeList(), matvec::Population::initGenotypeNodeList(), and matvec::Population::initJointAlleleNodeList().

GNode* matvec::GNodeList::containerGNode
 

Definition at line 188 of file gnodestuff.h.

GNodeList::iterator matvec::GNodeList::cutGNode
 

Definition at line 192 of file gnodestuff.h.

SafeSTLVector<GNode*> matvec::GNodeList::cutGNodesVector
 

Definition at line 176 of file gnodestuff.h.

Referenced by findSampleGNode(), and peelAndCut().

Matrix<int> matvec::GNodeList::distanceMat
 

Definition at line 174 of file gnodestuff.h.

Referenced by calcDistancefrom(), findSampleGNode(), and makeDistanceMatrix().

bool matvec::GNodeList::distanceMatDone
 

Definition at line 175 of file gnodestuff.h.

Referenced by GNodeList(), makeDistanceMatrix(), and peelAndCut().

string matvec::GNodeList::howToSample
 

Definition at line 217 of file gnodestuff.h.

Referenced by matvec::Population::initAlleleNodeList(), matvec::Population::initGenotypeNodeList(), matvec::Population::initJointAlleleNodeList(), and peelAndCut().

unsigned matvec::GNodeList::lastmember
 

Definition at line 173 of file gnodestuff.h.

Referenced by inputGNodeSets().

double matvec::GNodeList::logOldProposal = 0.0 [static]
 

Definition at line 46 of file gnodestuff.cpp.

Referenced by matvec::Model::RSamplerGibbsMH(), and matvec::Model::RSamplerMH().

double matvec::GNodeList::logProposal = 0.0 [static]
 

Definition at line 45 of file gnodestuff.cpp.

Referenced by matvec::Model::RSamplerGibbsMH(), and matvec::Model::RSamplerMH().

double matvec::GNodeList::logTarget = 0.0 [static]
 

Definition at line 44 of file gnodestuff.cpp.

Referenced by matvec::Model::RSamplerGibbsMH(), and matvec::Model::RSamplerMH().

set<GNode*> matvec::GNodeList::loopSetGNodes
 

Definition at line 177 of file gnodestuff.h.

Referenced by findSampleGNode(), and peelAndCut().

unsigned matvec::GNodeList::maxDist
 

Definition at line 186 of file gnodestuff.h.

Referenced by peelAndCut().

string SafeSTLVector< GNode * >::name [inherited]
 

Definition at line 32 of file safe_vectors.h.

Population * matvec::GNodeList::popPtr [static]
 

Definition at line 47 of file gnodestuff.cpp.

Referenced by peelAndCut(), peelCutAndSample(), and peelOrderCutAndSample().

GNode* matvec::GNodeList::sampleGNodePtr
 

Definition at line 187 of file gnodestuff.h.

Referenced by peelAndCut(), peelCutAndCompute(), peelCutAndSample(), and peelOrderCutAndSample().

GNodeList::iterator matvec::GNodeList::searchStart
 

Definition at line 191 of file gnodestuff.h.

Referenced by peelAndCut().

float matvec::GNodeList::sum
 

Definition at line 172 of file gnodestuff.h.

Referenced by getPeelOrder(), and peelAndCut().

The documentation for this class was generated from the following files:
Generated on Thu Jun 16 17:14:29 2005 for Matvec by doxygen1.2.16