[Avida-cvs] [avida-svn] r815 - development/source/analyze
brysonda@myxo.css.msu.edu
brysonda at myxo.css.msu.edu
Fri Jul 7 07:26:32 PDT 2006
Author: brysonda
Date: 2006-07-07 10:26:32 -0400 (Fri, 07 Jul 2006)
New Revision: 815
Modified:
development/source/analyze/cMutationalNeighborhood.cc
development/source/analyze/cMutationalNeighborhood.h
development/source/analyze/cMutationalNeighborhoodResults.h
Log:
Update terminology and ordering of Beneficial,Deleterious,Neutral,Lethal within MutationalNeighborhood for consistency.
Modified: development/source/analyze/cMutationalNeighborhood.cc
===================================================================
--- development/source/analyze/cMutationalNeighborhood.cc 2006-07-07 14:11:46 UTC (rev 814)
+++ development/source/analyze/cMutationalNeighborhood.cc 2006-07-07 14:26:32 UTC (rev 815)
@@ -243,10 +243,10 @@
// Initialize values
m_o_total = 0;
m_o_total_sqr_fitness = 0.0;
- m_o_dead = 0;
+ m_o_pos = 0;
m_o_neg = 0;
m_o_neut = 0;
- m_o_pos = 0;
+ m_o_dead = 0;
m_o_size_pos = 0.0;
m_o_size_neg = 0.0;
m_o_peak_fitness = m_base_fitness;
@@ -262,10 +262,10 @@
m_o_total += odata.total;
m_o_total_fitness += odata.total_fitness;
m_o_total_sqr_fitness += odata.total_sqr_fitness;
- m_o_dead += odata.dead;
+ m_o_pos += odata.pos;
m_o_neg += odata.neg;
m_o_neut += odata.neut;
- m_o_pos += odata.pos;
+ m_o_dead += odata.dead;
m_o_size_pos += odata.size_pos;
m_o_size_neg += odata.size_neg;
@@ -296,10 +296,10 @@
// Initialize values
m_t_total = 0;
m_t_total_sqr_fitness = 0.0;
- m_t_dead = 0;
+ m_t_pos = 0;
m_t_neg = 0;
m_t_neut = 0;
- m_t_pos = 0;
+ m_t_dead = 0;
m_t_size_pos = 0.0;
m_t_size_neg = 0.0;
m_t_peak_fitness = m_base_fitness;
@@ -319,10 +319,10 @@
m_t_total += tdata.total;
m_t_total_fitness += tdata.total_fitness;
m_t_total_sqr_fitness += tdata.total_sqr_fitness;
- m_t_dead += tdata.dead;
+ m_t_pos += tdata.pos;
m_t_neg += tdata.neg;
m_t_neut += tdata.neut;
- m_t_pos += tdata.pos;
+ m_t_dead += tdata.dead;
m_t_size_pos += tdata.size_pos;
m_t_size_neg += tdata.size_neg;
@@ -382,12 +382,12 @@
df.Write(GetBaseTargetTask(), "Base Performs Target Task");
df.Write(GetSingleTotal(), "Total One Step Mutants");
- df.Write(GetSingleProbPos(), "One Step Probability Positive");
- df.Write(GetSingleProbNeg(), "One Step Probability Deleterious");
- df.Write(GetSingleProbNeut(), "One Step Probability Neutral");
+ df.Write(GetSingleProbBeneficial(), "One Step Probability Beneficial");
+ df.Write(GetSingleProbDeleterious(), "One Step Probability Deleterious");
+ df.Write(GetSingleProbNeutral(), "One Step Probability Neutral");
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(GetSingleAverageSizeBeneficial(), "One Step Average Beneficial Size");
+ df.Write(GetSingleAverageSizeDeleterious(), "One Step Average Deleterious Size");
df.Write(GetSinglePeakFitness(), "One Step Peak Fitness");
df.Write(GetSingleAverageFitness(), "One Step Average Fitness");
df.Write(GetSingleAverageSqrFitness(), "One Step Average Square Fitness");
@@ -401,12 +401,12 @@
df.Write(GetSingleProbKnockout(), "One Step Probability Knockout Task");
df.Write(GetDoubleTotal(), "Total Two Step Mutants");
- df.Write(GetDoubleProbPos(), "Two Step Probability Positive");
- df.Write(GetDoubleProbNeg(), "Two Step Probability Deleterious");
- df.Write(GetDoubleProbNeut(), "Two Step Probability Neutral");
+ df.Write(GetDoubleProbBeneficial(), "Two Step Probability Beneficial");
+ df.Write(GetDoubleProbDeleterious(), "Two Step Probability Deleterious");
+ df.Write(GetDoubleProbNeutral(), "Two Step Probability Neutral");
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(GetDoubleAverageSizeBeneficial(), "Two Step Average Beneficial Size");
+ df.Write(GetDoubleAverageSizeDeleterious(), "Two Step Average Deleterious Size");
df.Write(GetDoublePeakFitness(), "Two Step Peak Fitness");
df.Write(GetDoubleAverageFitness(), "Two Step Average Fitness");
df.Write(GetDoubleAverageSqrFitness(), "Two Step Average Square Fitness");
@@ -414,12 +414,12 @@
df.Write(GetDoubleComplexity(), "Two Step Total Complexity");
df.Write(GetDoubleTargetTask(), "Two Step Confers Target Task");
df.Write(GetDoubleProbTargetTask(), "Two Step Probability Confers Target Task");
- df.Write(GetDoubleTargetTaskPos(), "Two Step Confers Target - Previous Positive");
- df.Write(GetDoubleProbTargetTaskPos(), "Two Step Prob. Confers Target - Previous Positive");
- df.Write(GetDoubleTargetTaskNeg(), "Two Step Confers Target - Previous Deleterious");
- 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(GetDoubleTargetTaskBeneficial(), "Two Step Confers Target - Previous Beneficial");
+ df.Write(GetDoubleProbTargetTaskBeneficial(), "Two Step Prob. Confers Target - Previous Beneficial");
+ df.Write(GetDoubleTargetTaskDeleterious(), "Two Step Confers Target - Previous Deleterious");
+ df.Write(GetDoubleProbTargetTaskDeleterious(), "Two Step Prob. Confers Target - Previous Deleterious");
+ df.Write(GetDoubleTargetTaskNeutral(), "Two Step Confers Target - Previous Neutral");
+ df.Write(GetDoubleProbTargetTaskNeutral(), "Two Step Prob. Confers Target - Previous Neutral");
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");
Modified: development/source/analyze/cMutationalNeighborhood.h
===================================================================
--- development/source/analyze/cMutationalNeighborhood.h 2006-07-07 14:11:46 UTC (rev 814)
+++ development/source/analyze/cMutationalNeighborhood.h 2006-07-07 14:26:32 UTC (rev 815)
@@ -62,10 +62,10 @@
cGenome peak_genome;
double peak_fitness;
- int dead;
+ int pos;
int neg;
int neut;
- int pos;
+ int dead;
double size_pos;
double size_neg;
@@ -76,7 +76,7 @@
int task_knockout;
- sStep() : total(0), total_fitness(0.0), total_sqr_fitness(0.0), peak_fitness(0.0), dead(0), neg(0), neut(0), pos(0),
+ sStep() : total(0), total_fitness(0.0), total_sqr_fitness(0.0), peak_fitness(0.0), pos(0), neg(0), neut(0), dead(0),
size_pos(0.0), size_neg(0.0), task_target(0), task_total(0), task_knockout(0) { ; }
};
tArray<sStep> m_onestep;
@@ -114,10 +114,10 @@
cGenome m_o_peak_genome;
double m_o_peak_fitness;
- int m_o_dead;
+ int m_o_pos;
int m_o_neg;
int m_o_neut;
- int m_o_pos;
+ int m_o_dead;
double m_o_size_pos;
double m_o_size_neg;
@@ -139,10 +139,10 @@
cGenome m_t_peak_genome;
double m_t_peak_fitness;
- int m_t_dead;
+ int m_t_pos;
int m_t_neg;
int m_t_neut;
- int m_t_pos;
+ int m_t_dead;
double m_t_size_pos;
double m_t_size_neg;
@@ -210,12 +210,12 @@
inline const cGenome& GetSinglePeakGenome() const { return m_o_peak_genome; }
inline double GetSinglePeakFitness() const { return m_o_peak_fitness; }
- 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 GetSingleProbBeneficial() const { return static_cast<double>(m_o_pos) / m_o_total; }
+ inline double GetSingleProbDeleterious() const { return static_cast<double>(m_o_neg) / m_o_total; }
+ inline double GetSingleProbNeutral() const { return static_cast<double>(m_o_neut) / 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; }
+ inline double GetSingleAverageSizeBeneficial() const { if (m_o_pos == 0) return 0.0; else return m_o_size_pos / m_o_pos; }
+ inline double GetSingleAverageSizeDeleterious() const { if (m_o_neg == 0) return 0.0; else return m_o_size_neg / m_o_neg; }
inline double GetSingleTotalEntropy() const { return m_o_total_entropy; }
inline double GetSingleComplexity() const { return m_o_complexity; }
@@ -235,30 +235,30 @@
inline const cGenome& GetDoublePeakGenome() const { return m_t_peak_genome; }
inline double GetDoublePeakFitness() const { return m_t_peak_fitness; }
- 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 GetDoubleProbBeneficial() const { return static_cast<double>(m_t_pos) / m_t_total; }
+ inline double GetDoubleProbDeleterious() const { return static_cast<double>(m_t_neg) / m_t_total; }
+ inline double GetDoubleProbNeutral() const { return static_cast<double>(m_t_neut) / 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; }
+ inline double GetDoubleAverageSizeBeneficial() const { if (m_t_pos == 0) return 0.0; else return m_t_size_pos / m_t_pos; }
+ inline double GetDoubleAverageSizeDeleterious() const { if (m_t_neg == 0) return 0.0; else return m_t_size_neg / m_t_neg; }
inline double GetDoubleTotalEntropy() const { return m_t_total_entropy; }
inline double GetDoubleComplexity() const { return m_t_complexity; }
inline int GetDoubleTargetTask() const { return m_t_task_target; }
inline double GetDoubleProbTargetTask() const { return static_cast<double>(m_t_task_target) / m_t_total; }
- inline int GetDoubleTargetTaskPos() const { return m_t_task_target_pos; }
- inline double GetDoubleProbTargetTaskPos() const
+ inline int GetDoubleTargetTaskBeneficial() const { return m_t_task_target_pos; }
+ inline double GetDoubleProbTargetTaskBeneficial() const
{
if (m_t_task_target == 0) return 0.0; else return static_cast<double>(m_t_task_target_pos) / (2 * m_t_task_target);
}
- inline int GetDoubleTargetTaskNeg() const { return m_t_task_target_neg; }
- inline double GetDoubleProbTargetTaskNeg() const
+ inline int GetDoubleTargetTaskDeleterious() const { return m_t_task_target_neg; }
+ inline double GetDoubleProbTargetTaskDeleterious() const
{
if (m_t_task_target == 0) return 0.0; else return static_cast<double>(m_t_task_target_neg) / (2 * m_t_task_target);
}
- inline int GetDoubleTargetTaskNeut() const { return m_t_task_target_neut; }
- inline double GetDoubleProbTargetTaskNeut() const
+ inline int GetDoubleTargetTaskNeutral() const { return m_t_task_target_neut; }
+ inline double GetDoubleProbTargetTaskNeutral() const
{
if (m_t_task_target == 0) return 0.0; else return static_cast<double>(m_t_task_target_neut) / (2 * m_t_task_target);
}
Modified: development/source/analyze/cMutationalNeighborhoodResults.h
===================================================================
--- development/source/analyze/cMutationalNeighborhoodResults.h 2006-07-07 14:11:46 UTC (rev 814)
+++ development/source/analyze/cMutationalNeighborhoodResults.h 2006-07-07 14:26:32 UTC (rev 815)
@@ -55,12 +55,12 @@
inline const cGenome& GetSinglePeakGenome() const { return m_src.GetSinglePeakGenome(); }
inline double GetSinglePeakFitness() const { return m_src.GetSinglePeakFitness(); }
- 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 GetSingleProbBeneficial() const { return m_src.GetSingleProbBeneficial(); }
+ inline double GetSingleProbDeleterious() const { return m_src.GetSingleProbDeleterious(); }
+ inline double GetSingleProbNeutral() const { return m_src.GetSingleProbNeutral(); }
inline double GetSingleProbLethal() const { return m_src.GetSingleProbLethal(); }
- inline double GetSingleAverageSizePos() const { return m_src.GetSingleAverageSizePos(); }
- inline double GetSingleAverageSizeNeg() const { return m_src.GetSingleAverageSizeNeg(); }
+ inline double GetSingleAverageSizeBeneficial() const { return m_src.GetSingleAverageSizeBeneficial(); }
+ inline double GetSingleAverageSizeDeleterious() const { return m_src.GetSingleAverageSizeDeleterious(); }
inline double GetSingleTotalEntropy() const { return m_src.GetSingleTotalEntropy(); }
inline double GetSingleComplexity() const { return m_src.GetSingleComplexity(); }
@@ -80,24 +80,24 @@
inline const cGenome& GetDoublePeakGenome() const { return m_src.GetDoublePeakGenome(); }
inline double GetDoublePeakFitness() const { return m_src.GetDoublePeakFitness(); }
- 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 GetDoubleProbBeneficial() const { return m_src.GetDoubleProbBeneficial(); }
+ inline double GetDoubleProbDeleterious() const { return m_src.GetDoubleProbDeleterious(); }
+ inline double GetDoubleProbNeutral() const { return m_src.GetDoubleProbNeutral(); }
inline double GetDoubleProbLethal() const { return m_src.GetDoubleProbLethal(); }
- inline double GetDoubleAverageSizePos() const { return m_src.GetDoubleAverageSizePos(); }
- inline double GetDoubleAverageSizeNeg() const { return m_src.GetDoubleAverageSizeNeg(); }
+ inline double GetDoubleAverageSizeBeneficial() const { return m_src.GetDoubleAverageSizeBeneficial(); }
+ inline double GetDoubleAverageSizeDeleterious() const { return m_src.GetDoubleAverageSizeDeleterious(); }
inline double GetDoubleTotalEntropy() const { return m_src.GetDoubleTotalEntropy(); }
inline double GetDoubleComplexity() const { return m_src.GetDoubleComplexity(); }
inline int GetDoubleTargetTask() const { return m_src.GetDoubleTargetTask(); }
inline double GetDoubleProbTargetTask() const { return m_src.GetDoubleProbTargetTask(); }
- inline int GetDoubleTargetTaskPos() const { return m_src.GetDoubleTargetTaskPos(); }
- inline double GetDoubleProbTargetTaskPos() const { return m_src.GetDoubleProbTargetTaskPos(); }
- inline int GetDoubleTargetTaskNeg() const { return m_src.GetDoubleTargetTaskNeg(); }
- 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 GetDoubleTargetTaskBeneficial() const { return m_src.GetDoubleTargetTaskBeneficial(); }
+ inline double GetDoubleProbTargetTaskBeneficial() const { return m_src.GetDoubleProbTargetTaskBeneficial(); }
+ inline int GetDoubleTargetTaskDeleterious() const { return m_src.GetDoubleTargetTaskDeleterious(); }
+ inline double GetDoubleProbTargetTaskDeleterious() const { return m_src.GetDoubleProbTargetTaskDeleterious(); }
+ inline int GetDoubleTargetTaskNeutral() const { return m_src.GetDoubleTargetTaskNeutral(); }
+ inline double GetDoubleProbTargetTaskNeutral() const { return m_src.GetDoubleProbTargetTaskNeutral(); }
inline int GetDoubleTargetTaskLethal() const { return m_src.GetDoubleTargetTaskLethal(); }
inline double GetDoubleProbTargetTaskLethal() const { return m_src.GetDoubleProbTargetTaskLethal(); }
inline int GetDoubleTask() const { return m_src.GetDoubleProbTask(); }
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