C++ (Cpp) evaluateParsimonyIterativeFast Beispiele

Beispiel #1

Datei: fastDNAparsimony.c Projekt: KhaosResearch/MORPHY

static unsigned int evaluateParsimony(tree *tr, nodeptr p, boolean full)
{
  volatile unsigned int result;
  nodeptr q = p->back;
  int
    *ti = tr->ti,
    counter = 4;
  
  ti[1] = p->number;
  ti[2] = q->number;

  if(full)
    {
      if(p->number > tr->mxtips)
	computeTraversalInfoParsimony(p, ti, &counter, tr->mxtips, full);
      if(q->number > tr->mxtips)
	computeTraversalInfoParsimony(q, ti, &counter, tr->mxtips, full); 
    }
  else
    {
      if(p->number > tr->mxtips && !p->xPars)
	computeTraversalInfoParsimony(p, ti, &counter, tr->mxtips, full);
      if(q->number > tr->mxtips && !q->xPars)
	computeTraversalInfoParsimony(q, ti, &counter, tr->mxtips, full); 
    }

  ti[0] = counter;

  result = evaluateParsimonyIterativeFast(tr);

  return result;
}

Beispiel #2

Datei: parsimony.c Projekt: ajnebro/MO-Phylogenetics

unsigned int pllEvaluateParsimony(pllInstance *tr, partitionList *pr, nodeptr p, boolean full, boolean perSiteScores)
{

  
  volatile unsigned int result;
  nodeptr q = p->back;
  int
    *ti = tr->ti,
    counter = 4;
  
  ti[1] = p->number;
  ti[2] = q->number;

  if(full)
    {
      if(p->number > tr->mxtips)
        computeTraversalInfoParsimony(p, ti, &counter, tr->mxtips, full);
      if(q->number > tr->mxtips)
        computeTraversalInfoParsimony(q, ti, &counter, tr->mxtips, full); 
    }
  else
    {
      if(p->number > tr->mxtips && !p->xPars)
        computeTraversalInfoParsimony(p, ti, &counter, tr->mxtips, full);
      if(q->number > tr->mxtips && !q->xPars)
        computeTraversalInfoParsimony(q, ti, &counter, tr->mxtips, full); 
    }

  ti[0] = counter;

  result = evaluateParsimonyIterativeFast(tr, pr, perSiteScores);

  return result;
}

Beispiel #3

Datei: TreeRandomizer.cpp Projekt: pombredanne/exa-bayes

void TreeRandomizer::stepwiseAddition(pllInstance *tr, partitionList *pr, nodeptr p, nodeptr q, ParallelSetup& pl)
{            
  nodeptr 
    r = q->back;

  unsigned int 
    mp;
  
  int 
    counter = 4;
  
  p->next->back = q;
  q->back = p->next;

  p->next->next->back = r;
  r->back = p->next->next;
   
  computeTraversalInfoParsimony(p, tr->ti, &counter, tr->mxtips, PLL_FALSE);              
  tr->ti[0] = counter;
  tr->ti[1] = p->number;
  tr->ti[2] = p->back->number;
    
  mp = evaluateParsimonyIterativeFast(tr, pr);

  auto result = std::vector<nat>{mp}; 
  // std::cout <<  "my score was " << mp << std::endl; 
  result = pl.getChainComm().allReduce(result);
  mp = result.at(0); 
  // std::cout << "after allreduce "<< mp << std::endl; 
  
  
  if(mp < tr->bestParsimony)
    {    
      tr->bestParsimony = mp;
      tr->insertNode = q;     
    }
 
  q->back = r;
  r->back = q;
   
  if(q->number > tr->mxtips
#if 0 
     && tr->parsimonyScore[q->number] > 0
#endif
     )
    {         
      stepwiseAddition(tr, pr, p, q->next->back, pl);
      stepwiseAddition(tr, pr, p, q->next->next->back, pl);
    }
}

Beispiel #4

Datei: fastDNAparsimony.c Projekt: KhaosResearch/MORPHY

static void stepwiseAddition(tree *tr, nodeptr p, nodeptr q)
{            
  nodeptr 
    r = q->back;

  unsigned int 
    mp;
  
  int 
    counter = 4;
  
  p->next->back = q;
  q->back = p->next;

  p->next->next->back = r;
  r->back = p->next->next;
   
  computeTraversalInfoParsimony(p, tr->ti, &counter, tr->mxtips, FALSE);              
  tr->ti[0] = counter;
  tr->ti[1] = p->number;
  tr->ti[2] = p->back->number;
    
  mp = evaluateParsimonyIterativeFast(tr);
  
  if(mp < tr->bestParsimony)
    {    
      tr->bestParsimony = mp;
      tr->insertNode = q;     
    }
 
  q->back = r;
  r->back = q;
   
  if(q->number > tr->mxtips && tr->parsimonyScore[q->number] > 0)
    {	      
      stepwiseAddition(tr, p, q->next->back);	      
      stepwiseAddition(tr, p, q->next->next->back);              	     
    }
}