[Avida-SVN] r1169 - branches/uml/source/main

[hjg at myxo.css.msu.edu]

Author: hjg
Date: 2007-01-06 13:38:39 -0500 (Sat, 06 Jan 2007)
New Revision: 1169

Modified:
   branches/uml/source/main/cOrganism.cc
   branches/uml/source/main/cOrganism.h
   branches/uml/source/main/cTaskLib.cc
   branches/uml/source/main/cTaskLib.h
Log:
Enhanced logging of organisms that generate models that pass the SPIN task. 


Modified: branches/uml/source/main/cOrganism.cc
===================================================================
--- branches/uml/source/main/cOrganism.cc	2007-01-05 16:31:32 UTC (rev 1168)
+++ branches/uml/source/main/cOrganism.cc	2007-01-06 18:38:39 UTC (rev 1169)
@@ -741,8 +741,16 @@
 	Graph::edge_iterator e, eend;
 	int count = 0;
 	int s_start_lab, s_end_lab; //, trans_lab;
+	State* st_start;
+	State* st_end;
+	nsm_it i;
+
 //	Transition t;
 
+	if ((pos < 0) || (pos > NumTrans())) {
+		return;
+	}
+
 	for (tie(e, eend) = edges(uml_state_diagram); e != eend; ++e) { 
 		if (count == pos) {
 //			remove_edge(e, uml_state_diagram);
@@ -757,6 +765,24 @@
 		count ++;
 	}
 	
+	for (i=states.begin(); i!=states.end(); ++i)
+	{
+		if (i->first == s_start_lab) {
+			st_start = &(i->second);
+		}
+		if (i->first == s_end_lab) {
+			st_end = &(i->second);
+		}
+	}
+	
+	if ((out_degree(*st_start, uml_state_diagram) == 0) && (in_degree(*st_start, uml_state_diagram) == 0)) {
+		remove_vertex(*st_start, uml_state_diagram);
+	}
+
+	if ((out_degree(*st_end, uml_state_diagram) == 0) && (in_degree(*st_end, uml_state_diagram) == 0)) {
+		remove_vertex(*st_end, uml_state_diagram);
+	}	
+	
 	return;
 }
 
@@ -1098,16 +1124,11 @@
 }
 
 
+
+
 // if you ask for something greater than the number of states then you get the highest numbered state.
 int cOrganism::getStateLabelInPosition (int num)
 {
-	/*std::pair<vertex_iterator, vertex_iterator>
-vertices(const adjacency_list& g)*/
-//	Graph::vertex_iterator vi, vi_end;
-//	tie(vi,vi_end) = vertices(uml_state_diagram);
-//	vi+=num;
-	//graph_traits<Graph>::vertex_descriptor b = *vi;
-//	return *vi;
 
 	int count = 0;
 	// This code uses a value ordering on the states (lowest number = position 0)
@@ -1120,12 +1141,7 @@
 		count++;
 	}
 	return i->first;
-	
 
-/*
-	int x = PosToStateLabel[num];
-	return (states[x]);
-*/	
 }
 
 
@@ -1141,7 +1157,6 @@
 		}
 		count++;
 	}
-	int test = i->first;
 
 	return i->first;
 	

Modified: branches/uml/source/main/cOrganism.h
===================================================================
--- branches/uml/source/main/cOrganism.h	2007-01-05 16:31:32 UTC (rev 1168)
+++ branches/uml/source/main/cOrganism.h	2007-01-06 18:38:39 UTC (rev 1169)
@@ -104,7 +104,9 @@
 
 //!Types of the UML types for states and transitions
 // define graph -- multisetS - allows for the sorting of out edges by target vertex
-typedef adjacency_list<multisetS, vecS, directedS, state_info, edge_info> Graph;
+//bidirectionalS
+//typedef adjacency_list<multisetS, vecS, directedS, state_info, edge_info> Graph;
+typedef adjacency_list<multisetS, vecS, bidirectionalS, state_info, edge_info> Graph;
 // map the graph's vertex's to their descriptors
 typedef graph_traits<Graph>::vertex_descriptor State;
 typedef std::map<int, State> NameStateMap;

Modified: branches/uml/source/main/cTaskLib.cc
===================================================================
--- branches/uml/source/main/cTaskLib.cc	2007-01-05 16:31:32 UTC (rev 1168)
+++ branches/uml/source/main/cTaskLib.cc	2007-01-06 18:38:39 UTC (rev 1169)
@@ -9,6 +9,8 @@
  */
 
 #include "cTaskLib.h"
+#include "cGenotype.h"
+#include <iostream>
 #include <unistd.h>
 #include <math.h>
 #include <sys/types.h>
@@ -2215,7 +2217,8 @@
 	}
 }
 
-double cTaskLib::SpinCoprocess(const std::string& neverclaimFile) const {
+double cTaskLib::SpinCoprocess(cTaskContext* ctx, const std::string& neverclaimFile) const {
+	cOrganism* organism = ctx->organism;
 	m_world->GetStats().SpinAttempt();
 	int status=0;
 	std::string cmd = "cat " + neverclaimFile + " >> tmp.pr && ./spin -a tmp.pr &> /dev/null";
@@ -2228,13 +2231,18 @@
 	if(system("/usr/bin/gcc pan.c -o pan &> /dev/null")!=0) return 0.0;
 	if(system("./pan -a &> ./pan.out")!=0) return 0.0;
 	if(system("cat pan.out | perl -e 'while(<STDIN>) { if(/errors:\\s(\\d+)/) {exit($1);}}'")!=0) return 0.0;
+	//cmd = "cp tmp.xmi " + organism->GetGenotype()->GetID() + ".xml"; 
+	std::ostringstream strstrm;
+	strstrm << "cp tmp.xmi " << m_world->GetStats().GetUpdate() 
+		<< "." + organism->GetID() << "." << organism->GetGenotype()->GetID() << ".xml";
+	if(system(strstrm.str().c_str())!=0) return 0.0;
 	m_world->GetStats().PanPassed();
 	return 1.0;
 }
 
 double cTaskLib::Task_SpinN1(cTaskContext* ctx) const {
 	if (ctx->task_failed) {
-		return SpinCoprocess("N1");
+		return SpinCoprocess(ctx, "N1");
 	} 
 	return 0.0;
 }

Modified: branches/uml/source/main/cTaskLib.h
===================================================================
--- branches/uml/source/main/cTaskLib.h	2007-01-05 16:31:32 UTC (rev 1168)
+++ branches/uml/source/main/cTaskLib.h	2007-01-06 18:38:39 UTC (rev 1169)
@@ -32,6 +32,7 @@
 
 
 class cOrganism;
+class cGenotype;
 class cString;
 class cWorld;
 
@@ -254,7 +255,7 @@
 	double Task_Transition_bs9(cTaskContext* ctx) const;
 	double Task_Transition_bs10(cTaskContext* ctx) const;
 
-	double SpinCoprocess(const std::string& neverclaimFile) const;
+	double SpinCoprocess(cTaskContext* ctx, const std::string& neverclaimFile) const;
 	double Task_SpinN1(cTaskContext* ctx) const;
 };