[avida-cvs] avida CVS commits: /current/source/main analyze.cc

[dule123]

dule123		Tue Nov  4 22:52:48 2003 EDT

  Modified files:              
    /avida/current/source/main	analyze.cc 
  Log:
  Fixed some bugs in ANALYZE_MODULARITY. 
  Also, made sure 'binary' option for this command works. 
  
  
  
Index: avida/current/source/main/analyze.cc
diff -u avida/current/source/main/analyze.cc:1.83 avida/current/source/main/analyze.cc:1.84
--- avida/current/source/main/analyze.cc:1.83	Mon Nov  3 22:51:59 2003
+++ avida/current/source/main/analyze.cc	Tue Nov  4 22:52:48 2003
@@ -2164,6 +2164,7 @@
 
       mod_genome[line_num] = null_inst;
       cAnalyzeGenotype test_genotype(mod_genome, map_inst_set);
+      cAnalyzeGenotype old_genotype(base_genome, map_inst_set);
       test_genotype.Recalculate();
 
       // Print the individual columns...
@@ -2173,6 +2174,11 @@
       while ((data_command = output_it.Next()) != NULL) {
 	data_command->SetTarget(&test_genotype);
 	test_genotype.SetSpecialArgs(data_command->GetArgs());
+	// This is done so that under 'binary' option it marks
+	// the task as being influenced by the mutation iff
+	// it is completely knocked out, not just decreased
+	genotype->SetSpecialArgs(data_command->GetArgs());
+
 	int compare = data_command->Compare(genotype);
 
 	// If knocking out an instruction stops the expression of a
@@ -2180,8 +2186,7 @@
 	// and add it to two counts
 	// Only do the checking if the test_genotype replicate, i.e.
 	// if it's fitness is not zeros
-
-	if (compare == -2 && test_genotype.GetFitness() != 0) { 
+	if (compare < 0  && test_genotype.GetFitness() != 0) { 
 		mod_matrix(cur_col,line_num) = 1;
 		num_inst[cur_col]++;
 		num_task[line_num]++;
@@ -2191,7 +2196,7 @@
       // Reset the mod_genome back to the original sequence.
       mod_genome[line_num].SetOp(cur_inst);
     } // end of genotype-phenotype mapping for a single organism
-    
+
     for (int i = 0; i < num_cols; i++) {if (num_inst[i] != 0) total_task++;}
     for (int i = 0; i < max_line; i++) {if (num_task[i] != 0) total_inst++;}
     for (int i = 0; i < num_cols; i++) {total_all = total_all + num_inst[i];}
@@ -2213,7 +2218,7 @@
     for (int i = 0; i < num_cols; i++) { 
 	if (num_inst[i] > 0) {
 		av_num_inst[i] = av_num_inst[i] + num_inst[i] * num_cpus;
-		org_task[i]++; 	// count how many are actually doing the task
+		org_task[i] = org_task[i] + num_cpus; 	// count how many are actually doing the task
 	}
     }