[Avida-SVN] r3376 - branches/goings/source/main

[goingssh at myxo.css.msu.edu]

Author: goingssh
Date: 2009-08-23 23:17:42 -0400 (Sun, 23 Aug 2009)
New Revision: 3376

Modified:
   branches/goings/source/main/cPopulation.cc
Log:
updated distance calculations in fitness sharing to use more of the information about the parent organism to highly increase the speed at which runs can be done with fitness sharing

Modified: branches/goings/source/main/cPopulation.cc
===================================================================
--- branches/goings/source/main/cPopulation.cc	2009-08-22 15:50:04 UTC (rev 3375)
+++ branches/goings/source/main/cPopulation.cc	2009-08-24 03:17:42 UTC (rev 3376)
@@ -433,8 +433,7 @@
   // Place all of the offspring...
   for (int i = 0; i < child_array.GetSize(); i++) 
   {
-	  int parent_cell = (child_array[i]->GetGenotype() == parent_genotype) ? parent_id : -1;
-	  ActivateOrganism(ctx, child_array[i], GetCell(target_cells[i]), parent_cell);
+	  ActivateOrganism(ctx, child_array[i], GetCell(target_cells[i]), parent_id);
 
     //@JEB - we may want to pass along some state information from parent to child
     if ( (m_world->GetConfig().EPIGENETIC_METHOD.Get() == EPIGENETIC_METHOD_OFFSPRING) 
@@ -935,15 +934,30 @@
 // cell_id is cell we're about to place a new org, gen is its genotype
 void cPopulation::UpdateHDists(int cell_id, int par_id, cGenotype* gen)
 {
+	int par_dist=-1;
+	if (par_id>=0)
+	{
+		const cGenome& par_gen = cell_array[par_id].GetOrganism()->GetGenome();
+		if ( par_gen == gen->GetGenome() )
+			par_dist = 0;
+		else
+			par_dist = cGenomeUtil::FindEditDistance(par_gen, gen->GetGenome());
+	}
 	for (int i=0; i<cell_array.GetSize(); i++)
 	{
 		int dist = m_world->GetConfig().NICHE_RADIUS.Get();
 		if (cell_array[i].GetOrganism())
 		{
-			if (par_id==-1)
+			if ( par_dist != -1 && (par_dist==0 || hdists[i][par_id]-par_dist >= dist) )
+			{
+				dist = hdists[i][par_id]-par_dist;
+				//cout << dist << " ";
+			}
+			else
+			{
 				dist = cGenomeUtil::FindEditDistance(cell_array[i].GetOrganism()->GetGenome(), gen->GetGenome());
-			else
-				dist = hdists[i][par_id];
+				cout << dist << " ";
+			}
 		}
 		hdists[i][cell_id] = dist;
 		hdists[cell_id][i] = dist;