[Avida-SVN] r3401 - development/source/classification

[brysonda at myxo.css.msu.edu]

Author: brysonda
Date: 2009-09-15 14:54:15 -0400 (Tue, 15 Sep 2009)
New Revision: 3401

Modified:
   development/source/classification/cClassificationManager.cc
   development/source/classification/cGenotype.h
Log:
Correct an error in the classification manager such that threshold genotype counts are incorrectly reported when track main lineage is active (the default).  The classification manager now handles and clears a genotype's threshold status prior to track main lineage handling.

THIS WILL BREAK CONSISTENCY
- Column 5 of count.dat reports the number of threshold genotypes.  This value will now report the intended value of currently existing threshold genotypes.

Modified: development/source/classification/cClassificationManager.cc
===================================================================
--- development/source/classification/cClassificationManager.cc	2009-09-11 17:25:15 UTC (rev 3400)
+++ development/source/classification/cClassificationManager.cc	2009-09-15 18:54:15 UTC (rev 3401)
@@ -259,6 +259,29 @@
     }
   }
   
+
+  cSpecies* cur_species = in_genotype.GetSpecies();
+
+  // If this is a threshold genotype we must clean up some threshold stats
+  // right now, since the actual genotype may persist under track main lineage
+  if (in_genotype.GetThreshold()) {
+    m_world->GetStats().RemoveThreshold();
+    in_genotype.ClearThreshold();
+
+    if (cur_species) {
+      cur_species->RemoveThreshold(in_genotype);
+      
+      // If we are out of thresholds, move this species to the inactive
+      // list for now.  Otherwise, just adjust it.
+      if (cur_species->GetNumThreshold() == 0) {
+        m_species_ctl->SetInactive(*cur_species);
+      } else {
+        m_species_ctl->Adjust(*cur_species);
+      }      
+    }
+  }
+  
+  
   // If we are tracking the main lineage, we only want to delete a
   // genotype when all of its decendents have also died out.
   
@@ -318,29 +341,12 @@
   // threshold genotype, then the species will only be effected if this was
   // the last genotype of that species.
   
-  cSpecies * cur_species = in_genotype.GetSpecies();
   if (cur_species) {
     
     // First, re-adjust the species.
     
     cur_species->RemoveGenotype();
     
-    // Then, check to see how this species changes if it is a threshold.
-    
-    if (in_genotype.GetThreshold()) {
-      cur_species->RemoveThreshold(in_genotype);
-      
-      // If we are out of thresholds, move this species to the inactive
-      // list for now.  Otherwise, just adjust it.
-      
-      if (cur_species->GetNumThreshold() == 0) {
-        m_species_ctl->SetInactive(*cur_species);
-      }
-      else {
-        m_species_ctl->Adjust(*cur_species);
-      }
-    }
-    
     // Finally, remove the species completely if it has no genotypes left.
     
     if (!cur_species->GetNumGenotypes()) {

Modified: development/source/classification/cGenotype.h
===================================================================
--- development/source/classification/cGenotype.h	2009-09-11 17:25:15 UTC (rev 3400)
+++ development/source/classification/cGenotype.h	2009-09-15 18:54:15 UTC (rev 3401)
@@ -168,6 +168,7 @@
   void SetSymbol(char in_symbol) { symbol = in_symbol; }
   void SetMapColor(int in_id) { map_color_id = in_id; }
   inline void SetThreshold();
+  inline void ClearThreshold();
   void IncDeferAdjust() { defer_adjust++; }
   void DecDeferAdjust() { defer_adjust--; assert(defer_adjust >= 0); }
   void SetLineageLabel(int in_label) { birth_data.lineage_label = in_label; }
@@ -303,6 +304,14 @@
   if (map_color_id == -2) map_color_id = -1;
 }
 
+inline void cGenotype::ClearThreshold()
+{
+  m_flag_threshold = false;
+  if (symbol == '+') symbol = ',';
+  if (map_color_id == -1) map_color_id = -2;
+}
+
+
 inline void cGenotype::SetBreedStats(cGenotype & daughter)
 {
   birth_data.birth_track.Inc();