[Avida-cvs] [avida-svn] r814 - development/source/analyze

[brysonda@myxo.css.msu.edu]

Author: brysonda
Date: 2006-07-07 10:11:46 -0400 (Fri, 07 Jul 2006)
New Revision: 814

Modified:
   development/source/analyze/cMutationalNeighborhood.cc
   development/source/analyze/cMutationalNeighborhood.h
   development/source/analyze/cMutationalNeighborhoodResults.h
Log:
Update MutationalNeighborhood terminology, lethal rather than fatal/dead.

Modified: development/source/analyze/cMutationalNeighborhood.cc
===================================================================
--- development/source/analyze/cMutationalNeighborhood.cc	2006-07-07 12:43:32 UTC (rev 813)
+++ development/source/analyze/cMutationalNeighborhood.cc	2006-07-07 14:11:46 UTC (rev 814)
@@ -385,7 +385,7 @@
   df.Write(GetSingleProbPos(), "One Step Probability Positive");
   df.Write(GetSingleProbNeg(), "One Step Probability Deleterious");
   df.Write(GetSingleProbNeut(), "One Step Probability Neutral");
-  df.Write(GetSingleProbDead(), "One Step Probability Fatal");
+  df.Write(GetSingleProbLethal(), "One Step Probability Lethal");
   df.Write(GetSingleAverageSizePos(), "One Step Average Positive Size");
   df.Write(GetSingleAverageSizeNeg(), "One Step Average Negative Size");
   df.Write(GetSinglePeakFitness(), "One Step Peak Fitness");
@@ -404,7 +404,7 @@
   df.Write(GetDoubleProbPos(), "Two Step Probability Positive");
   df.Write(GetDoubleProbNeg(), "Two Step Probability Deleterious");
   df.Write(GetDoubleProbNeut(), "Two Step Probability Neutral");
-  df.Write(GetDoubleProbDead(), "Two Step Probability Fatal");
+  df.Write(GetDoubleProbLethal(), "Two Step Probability Lethal");
   df.Write(GetDoubleAverageSizePos(), "Two Step Average Positive Size");
   df.Write(GetDoubleAverageSizeNeg(), "Two Step Average Negative Size");
   df.Write(GetDoublePeakFitness(), "Two Step Peak Fitness");
@@ -420,8 +420,8 @@
   df.Write(GetDoubleProbTargetTaskNeg(), "Two Step Prob. Confers Target - Previous Deleterious");
   df.Write(GetDoubleTargetTaskNeut(), "Two Step Confers Target - Previous Neutral");
   df.Write(GetDoubleProbTargetTaskNeut(), "Two Step Prob. Confers Target - Previous Neutral");
-  df.Write(GetDoubleTargetTaskDead(), "Two Step Confers Target - Previous Fatal");
-  df.Write(GetDoubleProbTargetTaskDead(), "Two Step Prob. Confers Target - Previous Fatal");
+  df.Write(GetDoubleTargetTaskLethal(), "Two Step Confers Target - Previous Lethal");
+  df.Write(GetDoubleProbTargetTaskLethal(), "Two Step Prob. Confers Target - Previous Lethal");
   df.Write(GetDoubleTask(), "Two Step Confers Any Task");
   df.Write(GetDoubleProbTask(), "Two Step Probability Confers Any Task");
   df.Write(GetDoubleKnockout(), "Two Step Knockout Task");

Modified: development/source/analyze/cMutationalNeighborhood.h
===================================================================
--- development/source/analyze/cMutationalNeighborhood.h	2006-07-07 12:43:32 UTC (rev 813)
+++ development/source/analyze/cMutationalNeighborhood.h	2006-07-07 14:11:46 UTC (rev 814)
@@ -210,10 +210,10 @@
   inline const cGenome& GetSinglePeakGenome() const { return m_o_peak_genome; }
   inline double GetSinglePeakFitness() const { return m_o_peak_fitness; }
   
-  inline double GetSingleProbDead() const { return static_cast<double>(m_o_dead) / m_o_total; }
+  inline double GetSingleProbPos()  const { return static_cast<double>(m_o_pos) / m_o_total; }
   inline double GetSingleProbNeg()  const { return static_cast<double>(m_o_neg) / m_o_total; }
   inline double GetSingleProbNeut() const { return static_cast<double>(m_o_neut) / m_o_total; }
-  inline double GetSingleProbPos()  const { return static_cast<double>(m_o_pos) / m_o_total; }
+  inline double GetSingleProbLethal() const { return static_cast<double>(m_o_dead) / m_o_total; }
   inline double GetSingleAverageSizePos() const { if (m_o_pos == 0) return 0.0; else return m_o_size_pos / m_o_pos; }
   inline double GetSingleAverageSizeNeg() const { if (m_o_neg == 0) return 0.0; else return m_o_size_neg / m_o_neg; }
   
@@ -235,10 +235,10 @@
   inline const cGenome& GetDoublePeakGenome() const { return m_t_peak_genome; }
   inline double GetDoublePeakFitness() const { return m_t_peak_fitness; }
   
-  inline double GetDoubleProbDead() const { return static_cast<double>(m_t_dead) / m_t_total; }
+  inline double GetDoubleProbPos()  const { return static_cast<double>(m_t_pos) / m_t_total; }
   inline double GetDoubleProbNeg()  const { return static_cast<double>(m_t_neg) / m_t_total; }
   inline double GetDoubleProbNeut() const { return static_cast<double>(m_t_neut) / m_t_total; }
-  inline double GetDoubleProbPos()  const { return static_cast<double>(m_t_pos) / m_t_total; }
+  inline double GetDoubleProbLethal() const { return static_cast<double>(m_t_dead) / m_t_total; }
   inline double GetDoubleAverageSizePos() const { if (m_t_pos == 0) return 0.0; else return m_t_size_pos / m_t_pos; }
   inline double GetDoubleAverageSizeNeg() const { if (m_t_neg == 0) return 0.0; else return m_t_size_neg / m_t_neg; }
   
@@ -262,8 +262,8 @@
   {
     if (m_t_task_target == 0) return 0.0; else return static_cast<double>(m_t_task_target_neut) / (2 * m_t_task_target);
   }
-  inline int GetDoubleTargetTaskDead() const { return m_t_task_target_dead; }
-  inline double GetDoubleProbTargetTaskDead() const
+  inline int GetDoubleTargetTaskLethal() const { return m_t_task_target_dead; }
+  inline double GetDoubleProbTargetTaskLethal() const
   {
     if (m_t_task_target == 0) return 0.0; else return static_cast<double>(m_t_task_target_dead) / (2 * m_t_task_target);
   }

Modified: development/source/analyze/cMutationalNeighborhoodResults.h
===================================================================
--- development/source/analyze/cMutationalNeighborhoodResults.h	2006-07-07 12:43:32 UTC (rev 813)
+++ development/source/analyze/cMutationalNeighborhoodResults.h	2006-07-07 14:11:46 UTC (rev 814)
@@ -55,10 +55,10 @@
   inline const cGenome& GetSinglePeakGenome() const { return m_src.GetSinglePeakGenome(); }
   inline double GetSinglePeakFitness() const { return m_src.GetSinglePeakFitness(); }
 
-  inline double GetSingleProbDead() const { return m_src.GetSingleProbDead(); }
+  inline double GetSingleProbPos() const { return m_src.GetSingleProbPos(); }
   inline double GetSingleProbNeg() const { return m_src.GetSingleProbNeg(); }
   inline double GetSingleProbNeut() const { return m_src.GetSingleProbNeut(); }
-  inline double GetSingleProbPos() const { return m_src.GetSingleProbPos(); }
+  inline double GetSingleProbLethal() const { return m_src.GetSingleProbLethal(); }
   inline double GetSingleAverageSizePos() const { return m_src.GetSingleAverageSizePos(); }
   inline double GetSingleAverageSizeNeg() const { return m_src.GetSingleAverageSizeNeg(); }
 
@@ -80,10 +80,10 @@
   inline const cGenome& GetDoublePeakGenome() const { return m_src.GetDoublePeakGenome(); }
   inline double GetDoublePeakFitness() const { return m_src.GetDoublePeakFitness(); }
 
-  inline double GetDoubleProbDead() const { return m_src.GetDoubleProbDead(); }
+  inline double GetDoubleProbPos() const { return m_src.GetDoubleProbPos(); }
   inline double GetDoubleProbNeg() const { return m_src.GetDoubleProbNeg(); }
   inline double GetDoubleProbNeut() const { return m_src.GetDoubleProbNeut(); }
-  inline double GetDoubleProbPos() const { return m_src.GetDoubleProbPos(); }
+  inline double GetDoubleProbLethal() const { return m_src.GetDoubleProbLethal(); }
   inline double GetDoubleAverageSizePos() const { return m_src.GetDoubleAverageSizePos(); }
   inline double GetDoubleAverageSizeNeg() const { return m_src.GetDoubleAverageSizeNeg(); }
 
@@ -98,8 +98,8 @@
   inline double GetDoubleProbTargetTaskNeg() const { return m_src.GetDoubleProbTargetTaskNeg(); }
   inline int GetDoubleTargetTaskNeut() const { return m_src.GetDoubleTargetTaskNeut(); }
   inline double GetDoubleProbTargetTaskNeut() const { return m_src.GetDoubleProbTargetTaskNeut(); }
-  inline int GetDoubleTargetTaskDead() const { return m_src.GetDoubleTargetTaskDead(); }
-  inline double GetDoubleProbTargetTaskDead() const { return m_src.GetDoubleProbTargetTaskDead(); }
+  inline int GetDoubleTargetTaskLethal() const { return m_src.GetDoubleTargetTaskLethal(); }
+  inline double GetDoubleProbTargetTaskLethal() const { return m_src.GetDoubleProbTargetTaskLethal(); }
   inline int GetDoubleTask() const { return m_src.GetDoubleProbTask(); }
   inline double GetDoubleProbTask() const { return m_src.GetDoubleProbTask(); }
   inline int GetDoubleKnockout() const { return m_src.GetDoubleKnockout(); }