C++ (Cpp) allSmoothed Examples

Example #1

File: searchAlgo.c Project: gtb-togerther/standard-RAxML

boolean regionalSmooth (tree *tr, nodeptr p, int maxtimes, int region)
  {
    nodeptr  q;
    int i;

    if (isTip(p->number, tr->rdta->numsp)) return FALSE;            /* Should be an error */

    for(i = 0; i < tr->numBranches; i++)
      tr->partitionConverged[i] = FALSE;

    while (--maxtimes >= 0) 
      {	
	for(i = 0; i < tr->numBranches; i++)	  
	  tr->partitionSmoothed[i] = TRUE;
	  
	q = p;
	do 
	  {
	    if (! smoothRegion(tr, q, region)) return FALSE;
	    q = q->next;
	  } 
	while (q != p);
	
	if (allSmoothed(tr)) 
	  break;
      }

    for(i = 0; i < tr->numBranches; i++)
      tr->partitionSmoothed[i] = FALSE;
    for(i = 0; i < tr->numBranches; i++)
      tr->partitionConverged[i] = FALSE;
   
    return TRUE;
  } /* localSmooth */

Example #2

File: searchAlgo.c Project: gtb-togerther/standard-RAxML

boolean localSmooth (tree *tr, nodeptr p, int maxtimes)
{ 
  nodeptr  q;
  int i;
  
  if (isTip(p->number, tr->rdta->numsp)) return FALSE;
  
   for(i = 0; i < tr->numBranches; i++)	
     tr->partitionConverged[i] = FALSE;	

  while (--maxtimes >= 0) 
    {     
      for(i = 0; i < tr->numBranches; i++)	
	tr->partitionSmoothed[i] = TRUE;
	 	
      q = p;
      do 
	{
	  if (! update(tr, q)) return FALSE;
	  q = q->next;
        } 
      while (q != p);
      
      if (allSmoothed(tr)) 
	break;
    }

  for(i = 0; i < tr->numBranches; i++)
    {
      tr->partitionSmoothed[i] = FALSE; 
      tr->partitionConverged[i] = FALSE;
    }

  return TRUE;
}

Example #3

File: fastSearch.c Project: gnewton/standard-RAxML

void nniSmooth(tree *tr, nodeptr p, int maxtimes)
{
  int
    i;

  for(i = 0; i < tr->numBranches; i++)	
    tr->partitionConverged[i] = FALSE;	

 

  while (--maxtimes >= 0) 
    {     
      

      for(i = 0; i < tr->numBranches; i++)	
	tr->partitionSmoothed[i] = TRUE;
      
      

      assert(!isTip(p->number, tr->mxtips)); 	

     

      assert(!isTip(p->back->number, tr->mxtips));  
      
      update(tr, p);
     
      update(tr, p->next);
     
      update(tr, p->next->next);
      
      update(tr, p->back->next);
      
      update(tr, p->back->next->next);           
     
      if (allSmoothed(tr)) 
	break;
      
    }

  

  for(i = 0; i < tr->numBranches; i++)
    {
      tr->partitionSmoothed[i] = FALSE; 
      tr->partitionConverged[i] = FALSE;
    }

  
}

Example #4

File: searchAlgo.c Project: gtb-togerther/standard-RAxML

boolean smoothTree (tree *tr, int maxtimes)
{
  nodeptr  p, q;   
  int i, count = 0;
   
  p = tr->start;
  for(i = 0; i < tr->numBranches; i++)
    tr->partitionConverged[i] = FALSE;

  while (--maxtimes >= 0) 
    {    
      for(i = 0; i < tr->numBranches; i++)	
	tr->partitionSmoothed[i] = TRUE;		

      if (! smooth(tr, p->back))       return FALSE;
      if (!isTip(p->number, tr->rdta->numsp)) 
	{
	  q = p->next;
	  while (q != p) 
	    {
	      if (! smooth(tr, q->back))   return FALSE;
	      q = q->next;
	    }
	}
         
      count++;

      if (allSmoothed(tr)) 
	break;      
    }

  for(i = 0; i < tr->numBranches; i++)
    tr->partitionConverged[i] = FALSE;



  return TRUE;
} 

Example #5

File: searchAlgo.c Project: gtb-togerther/standard-RAxML

static void smoothTreeRandom (tree *tr, int maxtimes)
{
  int i, k, *perm;

  tr->branchCounter = 0;
  tr->numberOfBranches = 2 * tr->mxtips - 3;
  
  tr->bInf = (branchInfo*)rax_malloc(tr->numberOfBranches * sizeof(branchInfo)); 

  perm = (int*)rax_malloc(sizeof(int) * tr->numberOfBranches);

  setupBranches(tr, tr->start->back, tr->bInf);



  for(i = 0; i < tr->numBranches; i++)
    tr->partitionConverged[i] = FALSE;

  /*printf("%d \n", maxtimes);*/

  while (--maxtimes >= 0) 
    {    
      for(i = 0; i < tr->numBranches; i++)	
	tr->partitionSmoothed[i] = TRUE;		

      /*printf("%d %d\n", maxtimes, tr->numberOfBranches);*/

      for(k = 0; k < tr->numberOfBranches; k++)
	perm[k] = k;

      makePerm(perm, tr->numberOfBranches);

      for(k = 0; k < tr->numberOfBranches; k++)
	{
	  /*printf("%d Node %d\n", k, tr->bInf[k].oP->number);*/
	  update(tr, tr->bInf[perm[k]].oP);
	  newviewGeneric(tr, tr->bInf[perm[k]].oP);     
	}

      /*if (! smooth(tr, p->back))       return FALSE;
      if (!isTip(p->number, tr->rdta->numsp)) 
	{
	  q = p->next;
	  while (q != p) 
	    {
	      if (! smooth(tr, q->back))   return FALSE;
	      q = q->next;
	    }
	}             
      */

      if (allSmoothed(tr)) 
	break;      
    }

  for(i = 0; i < tr->numBranches; i++)
    tr->partitionConverged[i] = FALSE;

  rax_free(tr->bInf);
  rax_free(perm);
}