Added var_lib_genenet_bnw

59 files changed, 14544 insertions, 0 deletions

diff --git a/var_lib_genenet_bnw/build.sh b/var_lib_genenet_bnw/build.sh
new file mode 100644
index 00000000..7f63840d
--- /dev/null
+++ b/var_lib_genenet_bnw/build.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+gcc ./localscore/network_score.c ./localscore/libRmath.so -lm -o network_score
+gcc ./print_structure/structure.c -lm -o structure
+
+cd ./k-best/src/
+sh buildk_poster.sh
+
+
+
diff --git a/var_lib_genenet_bnw/k-best/src/Arguments.h b/var_lib_genenet_bnw/k-best/src/Arguments.h
new file mode 100644
index 00000000..574b2bf7
--- /dev/null
+++ b/var_lib_genenet_bnw/k-best/src/Arguments.h
@@ -0,0 +1,195 @@
+#ifndef ARGUMENTS_H
+#define ARGUMENTS_H
+
+#include<stdio.h>
+#include<stdlib.h>
+
+using namespace std;
+
+class Arguments {
+public:
+	static char* datafile;
+	static char* layeringfile;
+	static char* maxindegree;
+	static char* model;
+	static char* task;
+	static char* maxnumrecords;
+	
+	//HR: Add for in_out features
+	static char* inFeasFileName;
+	static char* outFeasFileName;
+	//
+	
+	//HR: Add for in_out features
+	static int option;
+	//
+	
+	//HR: Add for ADtree option
+	static int ADtree;
+	//
+	
+	//HR: Add for Topk dir option
+	static char* directoryName;
+	//
+
+
+
+	static void init(int argc, char **args){
+		for(int i = 1; i < argc; i ++){
+			
+			if(args[i][0]=='-' && args[i][1]=='d' && args[i][2]=='\0'){
+				int j = i + 1;
+				while (j < argc && args[j][0]!='-') {
+					Arguments::datafile = args[j];
+					j ++;
+				} 
+			}
+			else if(args[i][0]=='-' && args[i][1]=='l' && args[i][2]=='\0'){
+				int j = i + 1;
+				while (j < argc && args[j][0]!='-') {
+					Arguments::layeringfile = args[j]; 
+					j ++;
+				}
+			}
+			else if(args[i][0]=='-' && args[i][1]=='m' && args[i][2]=='\0'){
+				int j = i + 1;
+				while (j < argc && args[j][0]!='-') {
+					Arguments::maxindegree = args[j]; 
+					j ++;
+				}
+			}
+			else if(args[i][0]=='-' && args[i][1]=='u' && args[i][2]=='\0'){
+				int j = i + 1;
+				while (j < argc && args[j][0]!='-') {
+					Arguments::maxnumrecords = args[j]; 
+					j ++;
+				}
+			}
+			else if(args[i][0]=='-' && args[i][1]=='M' && args[i][2]=='\0'){
+				int j = i + 1;
+				while (j < argc && args[j][0]!='-') {
+					Arguments::model = args[j]; 
+					j ++;
+				}
+			}
+			else if(args[i][0]=='-' && args[i][1]=='T' && args[i][2]=='\0'){
+				int j = i + 1;
+				while (j < argc && args[j][0]!='-') {
+					Arguments::task = args[j]; 
+					j ++;
+				}
+			}
+			//HR: Add for in_out feature
+			else if(args[i][0]=='-' && args[i][1]=='i' && args[i][2]=='n' && args[i][3]=='\0'){
+				int j = i + 1;
+				while (j < argc && args[j][0]!='-') {
+					Arguments::inFeasFileName = args[j]; 
+					j ++;
+				}
+			}
+			else if(args[i][0]=='-' && args[i][1]=='o' && args[i][2]=='u' && args[i][3]=='t' && args[i][4]=='\0'){
+				int j = i + 1;
+				while (j < argc && args[j][0]!='-') {
+					Arguments::outFeasFileName = args[j]; 
+					j ++;
+				}
+			}
+			//
+			//HR: Add for in_out feature
+			else if(args[i][0]=='-' && args[i][1]=='o' && args[i][2]=='p' && args[i][3]=='t' && args[i][4]=='\0'){
+				int j = i + 1;
+				while (j < argc && args[j][0]!='-') {
+					Arguments::option = atoi(args[j]); 
+					j ++;
+				}
+			}
+			//
+			//HR: Add for ADtree feature
+			else if(args[i][0]=='-' && args[i][1]=='a' && args[i][2]=='d' && args[i][3]=='\0'){
+				int j = i + 1;
+				while (j < argc && args[j][0]!='-') {
+					Arguments::ADtree = atoi(args[j]); 
+					j ++;
+				}
+			}
+			//
+			//HR: Add for Topk dir
+			else if(args[i][0]=='-' && args[i][1]=='d' && args[i][2]=='i' && args[i][3]=='r' && args[i][4]=='\0'){
+				int j = i + 1;
+				while (j < argc && args[j][0]!='-') {
+					Arguments::directoryName = args[j];
+					j++;
+				}
+			}
+			//
+		}
+	
+		print_arguments(stderr);
+		
+	}
+	static void print_arguments(FILE *f){
+		fprintf(f, " -d Data file:\n");
+		fprintf(f, "   %62s\n", Arguments::datafile);	
+		//fprintf(f, " -l Layering file:\n");
+		//fprintf(f, "   %62s\n", Arguments::layeringfile);
+		fprintf(f, " -m Maximum indegree:\n");
+		fprintf(f, "   %62s\n", Arguments::maxindegree);
+		fprintf(f, " -u Maximum number of data records read:\n");
+		fprintf(f, "   %62s\n", Arguments::maxnumrecords);
+		//fprintf(f, " -M Model:\n");
+		//fprintf(f, "   %62s\n", Arguments::model);
+		//fprintf(f, " -T Task (Infer=I, Generate=G):\n");
+		//fprintf(f, "   %62s\n", Arguments::task);
+		
+		//HR: Add for in_out
+		fprintf(f, " -opt Option:\n");
+		fprintf(f, "   %62d\n", Arguments::option);
+		if(Arguments::option == 5){
+			fprintf(f, " -in In_Feature File:\n");
+			fprintf(f, "   %62s\n", Arguments::inFeasFileName);
+			fprintf(f, " -out Out_Feature File:\n");
+			fprintf(f, "   %62s\n", Arguments::outFeasFileName);
+		}
+		//
+		//HR: Add for ADtree
+		fprintf(f, " -ad ADtree:\n");
+		fprintf(f, "   %62d\n", Arguments::ADtree);
+		//
+		//HR: Add for Topk dir
+		fprintf(f, " -dir directory name:\n");
+		fprintf(f, "   %62s\n", Arguments::directoryName);
+		//
+	}
+};
+
+char* Arguments::datafile = "testdata.dat";
+char* Arguments::layeringfile = "%";
+char* Arguments::maxindegree = "3";
+char* Arguments::model = "M";
+char* Arguments::task = "I";
+char* Arguments::maxnumrecords = "999999";
+
+
+//HR: For test
+//char* Arguments::datafile = "cases/iris.idt";
+//char* Arguments::layeringfile = "%";
+//char* Arguments::maxindegree = "4";
+//char* Arguments::model = "M";
+//char* Arguments::task = "I";
+//char* Arguments::maxnumrecords = "150";
+
+
+//HR: Add for in_out
+char* Arguments::inFeasFileName = "inFeature.txt";
+char* Arguments::outFeasFileName = "outFeature.txt";
+int Arguments::option = 5;
+
+//HR: Add for ADtree
+int Arguments::ADtree = 0;
+
+
+//HR: Add for Topk dir option
+char* Arguments::directoryName = "./";
+//
+
+#endif
diff --git a/var_lib_genenet_bnw/k-best/src/Engine.h b/var_lib_genenet_bnw/k-best/src/Engine.h
new file mode 100644
index 00000000..2e16a701
--- /dev/null
+++ b/var_lib_genenet_bnw/k-best/src/Engine.h
@@ -0,0 +1,2278 @@
+#ifndef ENGINE_H
+#define ENGINE_H
+
+#include<stdio.h>
+#include<stdlib.h>
+
+#include"Arguments.h"
+#include"Model.h"
+
+#include <sys/time.h>
+#include <time.h> 
+
+#define MARK 9.0e99
+
+// Substitutes la += log(1+exp(lb-la)) <=> a = a + b.
+#define LOGADD(la,lb) if(la>8e99||lb-la>100) la=lb;else la+=log(1+exp(lb-la));
+
+#define LOG_ZERO -1.0e101
+
+using namespace std;
+
+#include"UpdateHR.h"
+
+
+
+//----------------
+// Fast Möbius transform routines.
+void sub_fumt(int j, int d, int S, int overlap, double *t, double *s, int n, int k){
+	if (d < n && overlap < k){
+		sub_fumt(j, d+1, S, overlap, t, s, n, k);
+		
+		
+		S |= (1 << d);
+		overlap += (d >= j+1);
+		sub_fumt(j, d+1, S, overlap, t, s, n, k); 
+	}
+	
+	else{
+		//base case: 
+		//since s[S] = MARK initially,  and the following 3 cases, s[S] must be assigned some score (neither MARK nor undecided)
+		s[S] = MARK;
+		
+		//jinS: j is in S
+		int jinS = ((S >> j) & 1);
+		if (overlap + jinS <= k) s[S] = t[S];
+		//if (jinS) LOGADD(s[S], t[S - (1 << j)]);
+		if (jinS) logAdd_New(s[S], t[S - (1 << j)]);
+	}
+}
+
+// Fast upward Möbius transform:
+// s(S) := \sum_{T \subseteq S : |T| \leq k} t(T).
+void fumt(double *t, double *s, int n, int k){
+	double *tmp, *sprev = new double[1 << n];
+	for (int T = 0; T < (1<<n); T ++) 
+		sprev[T] = t[T];
+	for (int j = 0; j < n; j ++){
+		//for each j
+		sub_fumt(j, 0, 0, 0, sprev, s, n, k);
+		//recyclely use sprev, s
+		tmp = sprev; 
+		sprev = s; 
+		s = tmp;
+	}
+	if (n % 2 == 0){ 
+		for (int S = 0; S < (1<<n); S ++){ 
+			s[S] = sprev[S];
+		}
+	}
+	else{ 
+		tmp = sprev; 
+		sprev = s; 
+		s = tmp;
+	}
+	delete [] sprev;
+}
+void test_fumt(){
+	int n = 4;
+	double t[16], s[16];
+	for (int S = 0; S < 16; S ++){
+		t[S] = log(S+1);
+	}
+	fumt(t, s, n, 2);
+	for (int S = 0; S < 16; S ++){
+		cerr<<" s["<<S<<"] = "<<exp(s[S])<<endl;
+	}
+}
+
+
+void sub_fdmt(int j, int d, int T, int overlap, double *s, double *t, int n, int k){
+	//cerr<<" T = "<<T<<":"; print_set(cerr, T); 
+	//cerr<<" overlap = "<<overlap<<endl; 
+	if (d < n && overlap <= k){
+		sub_fdmt(j, d+1, T, overlap, s, t, n, k);
+		T |= (1 << d);
+		overlap += (d <= j);
+		sub_fdmt(j, d+1, T, overlap, s, t, n, k); 
+	}
+	else if (d == n){
+		t[T] = s[T];
+		int jinT = ((T >> j) & 1);
+		//if (jinT == 0) LOGADD(t[T], s[T + (1 << j)]);
+		if (jinT == 0) logAdd_New(t[T], s[T + (1 << j)]);
+		if (overlap > k) t[T] = MARK;
+	}
+}
+// Fast downward Möbius transform:
+// t(T) := \sum_{T \subseteq S} s(S).
+void fdmt(double *s, double *t, int n, int k){
+	double *tmp, *tprev = new double[1 << n];
+	for (int S = 0; S < (1<<n); S ++) tprev[S] = s[S];
+	for (int j = 0; j < n; j ++){
+		
+		sub_fdmt(j, 0, 0, 0, tprev, t, n, k);	
+		tmp = t; t = tprev; tprev = tmp;
+	}
+	if (n % 2 == 0){ for (int T = 0; T < (1<<n); T ++) t[T] = tprev[T];}
+	else{ tmp = t; t = tprev; tprev = tmp;}
+	delete [] tprev;
+}
+
+
+void sub_fdmtLogAddComp(int j, int d, int T, int overlap, double *s, double *t, int n, int k){
+	//cerr<<" T = "<<T<<":"; print_set(cerr, T); 
+	//cerr<<" overlap = "<<overlap<<endl; 
+	if (d < n && overlap <= k){
+		sub_fdmtLogAddComp(j, d+1, T, overlap, s, t, n, k);
+		T |= (1 << d);
+		overlap += (d <= j);
+		sub_fdmtLogAddComp(j, d+1, T, overlap, s, t, n, k); 
+	}
+	else if (d == n){
+		t[T] = s[T];
+		int jinT = ((T >> j) & 1);
+		if (jinT == 0) logAddComp(t[T], s[T + (1 << j)]);
+		if (overlap > k) t[T] = MARK;
+	}
+}
+// Fast downward Möbius transform:
+// t(T) := \sum_{T \subseteq S} s(S).
+void fdmtLogAddComp(double *s, double *t, int n, int k){
+	double *tmp, *tprev = new double[1 << n];
+	for (int S = 0; S < (1<<n); S ++) tprev[S] = s[S];
+	for (int j = 0; j < n; j ++){
+		
+		sub_fdmtLogAddComp(j, 0, 0, 0, tprev, t, n, k);	
+		tmp = t; t = tprev; tprev = tmp;
+	}
+	if (n % 2 == 0){ for (int T = 0; T < (1<<n); T ++) t[T] = tprev[T];}
+	else{ tmp = t; t = tprev; tprev = tmp;}
+	delete [] tprev;
+}
+
+
+void sub_fdmtNoLog(int j, int d, int T, int overlap, double *s, double *t, int n, int k){
+	//cerr<<" T = "<<T<<":"; print_set(cerr, T); 
+	//cerr<<" overlap = "<<overlap<<endl; 
+	if (d < n && overlap <= k){
+		sub_fdmtNoLog(j, d+1, T, overlap, s, t, n, k);
+		T |= (1 << d);
+		overlap += (d <= j);
+		sub_fdmtNoLog(j, d+1, T, overlap, s, t, n, k); 
+	}
+	else if (d == n){
+		t[T] = s[T];
+		int jinT = ((T >> j) & 1);
+		//if (jinT == 0) LOGADD(t[T], s[T + (1 << j)]);
+		//if (jinT == 0) logAdd_New(t[T], s[T + (1 << j)]);
+		if (jinT == 0) t[T] += s[T + (1 << j)];
+		if (overlap > k) t[T] = MARK;
+	}
+}
+
+// Fast downward Möbius transform:
+// t(T) := \sum_{T \subseteq S} s(S).
+void fdmtNoLog(double *s, double *t, int n, int k){
+	double *tmp, *tprev = new double[1 << n];
+	for (int S = 0; S < (1<<n); S ++) tprev[S] = s[S];
+	for (int j = 0; j < n; j ++){
+		
+		sub_fdmtNoLog(j, 0, 0, 0, tprev, t, n, k);	
+		tmp = t; t = tprev; tprev = tmp;
+	}
+	if (n % 2 == 0){ for (int T = 0; T < (1<<n); T ++) t[T] = tprev[T];}
+	else{ tmp = t; t = tprev; tprev = tmp;}
+	delete [] tprev;
+}
+
+
+void test_fdmt(){
+	int n = 4;
+	double t[16], s[16];
+	for (int S = 0; S < 16; S ++){
+		s[S] = log(S+1);
+	}
+	fdmt(s, t, n, 3);
+	for (int T = 0; T < 16; T ++){
+		cerr<<" t["<<T<<"] = "<<exp(t[T])<<endl;
+	}
+}
+
+//----------------
+
+
+
+
+
+
+// NOTE: Engine only calls a veru limited set of interface functions
+// implemented in Model.
+class Engine {
+public:
+	Engine(){}
+	~Engine(){}	
+	
+	void init(Model *m){
+		model = m;
+		//test();
+	
+	}
+	void test(){
+		vector<int> T;
+		T.push_back(1); T.push_back(2);
+		
+		cerr<<" log p(x_0 | x_1,2): "<<model->log_lcp(0, T)<<endl;
+	
+		for (int h = 0; h < model->num_layers(); h ++){
+			int *Vh, *Vu, *Vl;
+			int nh, nu, nl;
+			model->layer(h, &Vh, &nh);	
+			model->upper_layers(h, &Vu, &nu);	
+			model->lower_layers(h, &Vl, &nl);
+			cerr<<"Layer "<<h<<":";
+			cerr<<endl<<" layer: ";
+			print_nodes(cerr, Vh, nh);
+			cerr<<endl<<" upper: ";
+			print_nodes(cerr, Vu, nu);
+			cerr<<endl<<" lower: ";
+			print_nodes(cerr, Vl, nl);
+			cerr<<endl;	
+		}
+		
+		//test_fumt();
+		test_fdmt(); 
+		exit(1);
+
+	}
+	// Computes all edge probabilities.
+	void compute_edge_probabilities(){
+//		int l = model->num_layers();
+	
+		//Arguments::option == 0 means the rebel method with new Dirichlet hyper-param (see sub_beta)
+		if(Arguments::option == 0){
+			compute_edge_probabilities(0);
+		}
+		//Arguments::option == 1 means the forward method
+		else if(Arguments::option == 1){
+			compute_edge_probabilities_forward(0);
+		}
+		//Arguments::option == 2 means the backward method
+		else if(Arguments::option == 2){
+			compute_edge_probabilities_backward(0);
+		}
+		//Arguments::option == 3 means the mix method in the UAI paper
+		else if(Arguments::option == 3){
+			compute_edge_probabilities_mixIndegree(0);
+		 	//compute_edge_probabilities_mixIndegreeNoLog(0);
+		}
+		//Arguments::option == 4 means the computation used in top-k
+		else if(Arguments::option == 4){
+			compute_edge_probabilities_top_k(0);
+		}
+		//Arguments::option == 5 means the computation required for in and out features
+		else if(Arguments::option == 5){
+			//For In_Out features
+			compute_edge_probabilities_in_out_features(0);
+		}
+		
+		
+	}
+	// Computes probabilities for edges pointing to the h-th layer.
+	void compute_edge_probabilities(int h){
+		cerr<<"\nREBEL Method:" << endl;
+		cerr<<" Compute edge probabilities for Layer "<<h<<":"<<endl;
+		
+		// Step 1: Compute beta[][];
+		// Step 2: Compute alpha[][];
+		int *Vh, *Vu; int nh, nu;
+		model->layer(h, &Vh, &nh);
+		model->upper_layers(h-1, &Vu, &nu);
+
+		
+		beta = new double*[nh];
+		alpha = new double*[nh];
+		
+		k = model->max_indegree();
+		
+		cerr<<" . "<<nh<<" nodes"<<endl;
+		
+		struct timeval startTime;
+		struct timeval endTime;
+		struct timezone myTimeZone;
+
+		
+		double betaTime;
+		double alphaTime;
+		double forwardTime;
+		double backwardTime;
+		double gammaTime;
+		
+		double step2BTime;
+	
+		gettimeofday(&startTime, &myTimeZone);		
+
+		//If Arguments::ADtree == 1, user wants to use ADtree, then make the whole tree first
+		if(Arguments::ADtree == 1){
+			model->makeADTree();
+		}
+		
+		for (int j = 0; j < nh; j ++){
+
+			beta[j] = new double[1 << nh];
+			//int i = Vh[j];
+			compute_beta(j, Vh, nh, Vu, nu);
+		
+		}
+		
+		//If Arguments::ADtree == 1, then delete the whole tree
+		if(Arguments::ADtree == 1){
+			model->freeADTree();
+		}
+		
+		gettimeofday(&endTime, &myTimeZone);		
+		betaTime = (endTime.tv_sec - startTime.tv_sec) + 
+		           (endTime.tv_usec - startTime.tv_usec) / 1000000.0 ;
+		           
+		cerr<<" . Tables beta are now ready."<<endl;
+		
+		gettimeofday(&startTime, &myTimeZone);
+		for (int j = 0; j < nh; j ++){
+
+			alpha[j] = new double[1 << nh];	
+			compute_alpha(j, Vh, nh);
+		
+			//cerr<<" . Tables beta and alpha computed for node "<<j<<"."<<endl; 
+		
+		}
+		gettimeofday(&endTime, &myTimeZone);		
+		alphaTime = (endTime.tv_sec - startTime.tv_sec) + 
+		           (endTime.tv_usec - startTime.tv_usec) / 1000000.0 ;
+		
+		cerr<<" . Tables alpha are now ready."<<endl;
+
+			
+		// Step 3: Compute g_forward[];
+		gf = new double[1 << nh];
+		
+		gettimeofday(&startTime, &myTimeZone);
+		
+		compute_g_forward(nh);
+		
+		gettimeofday(&endTime, &myTimeZone);		
+		forwardTime = (endTime.tv_sec - startTime.tv_sec) + 
+		           (endTime.tv_usec - startTime.tv_usec) / 1000000.0 ;
+		
+		//cerr<<" . gf[all] = "<<gf[(1<<nh)-1]<<endl;
+		
+		// Step 4: Compute g_backward[];
+		
+		gb = new double[1 << nh];
+		
+		gettimeofday(&startTime, &myTimeZone);
+		
+		compute_g_backward(nh);
+		
+		gettimeofday(&endTime, &myTimeZone);		
+		backwardTime = (endTime.tv_sec - startTime.tv_sec) + 
+		           (endTime.tv_usec - startTime.tv_usec) / 1000000.0 ;
+		
+		//cerr<<" . gb[all] = "<<gb[(1<<nh)-1]<<endl;
+	
+		// Step 5: Loop over end-point nodes j.
+		
+		gammaTime = 0.0;
+		step2BTime = 0.0;
+		
+		double *gamma = new double[1 << nh];
+		double *gfb = new double[1 << nh];
+		for (int j = 0; j < nh; j ++){
+			// Compute gfb[]. 
+			
+			//start counting gammaTime for each j
+			gettimeofday(&startTime, &myTimeZone);
+			
+			for (int S = 0; S < (1<<nh); S ++){
+				
+				//if j \in the binary repre of S
+				if ((S>>j) & 1){
+					gfb[S] = -MARK;
+				}
+				else{
+					int cS = (1 << nh) - 1 - S - (1 << j);
+					gfb[S] = gf[S] + gb[cS];
+					//cerr<<" j = "<<j<<": ";
+					//print_set(cerr, S);
+					//cerr<<"; ";
+					//print_set(cerr, cS);
+					//cerr<<": "<<gfb[S];
+					//cerr<<endl;
+				}
+			}
+			// Compute gamma_j() := gamma[].
+			fdmt(gfb, gamma, nh, k);
+			
+			gettimeofday(&endTime, &myTimeZone);		
+			gammaTime += (endTime.tv_sec - startTime.tv_sec) + 
+		           (endTime.tv_usec - startTime.tv_usec) / 1000000.0 ;
+			//end counting gammaTime for each j
+			
+			//cerr<<" gamma[0]: "<<gamma[0]<<endl;
+			//cerr<<" gfb[0]: "<<gfb[0]<<endl;
+			
+			cerr<<" . Incoming edges for node "<<j<<":";
+			// Loop over start-point nodes i.
+			
+			//start counting step2BTime for each j
+			gettimeofday(&startTime, &myTimeZone);
+			
+			for (int i = 0; i < nh; i ++){
+				if (i == j) continue;
+				cerr<<" "<<i;		
+				double log_prob = eval_edge(i,  j, gamma, beta[j], nh, k);
+		
+				model->print_edge_prob(
+					cout, Vh[i], Vh[j], exp(log_prob - gb[(1<<nh)-1])); //HR: - gb[(1<<nh)-1] mean /L(v)
+			
+			}
+			gettimeofday(&endTime, &myTimeZone);		
+			step2BTime += (endTime.tv_sec - startTime.tv_sec) + 
+		           (endTime.tv_usec - startTime.tv_usec) / 1000000.0 ;
+			//end counting step2BTime for each j
+			
+			
+			
+			cerr<<endl;
+			
+		} 
+		
+		
+		cout << "\n\n\nTime Statistics" << endl;
+		cout << "betaTime = " << betaTime <<  endl;				
+		cout << "alphaTime = " << alphaTime <<  endl;
+		cout << "forwardTime = " << forwardTime <<  endl;
+		cout << "backwardTime = " << backwardTime <<  endl;				
+		cout << "gammaTime = " << gammaTime <<  endl;
+		
+		cout << "step2BTime = " << step2BTime <<  endl;
+		
+		double totalTime = betaTime + alphaTime + forwardTime 
+						+ backwardTime + gammaTime + step2BTime;
+		cout << "totalTime = " << totalTime <<  endl;
+		
+		/*
+		ofResult << "\n\n\nTime Statistics" << endl;
+		ofResult << "betaTime = " << betaTime <<  endl;				
+		ofResult << "alphaTime = " << alphaTime <<  endl;
+		ofResult << "RRFuncTime = " << RRFuncTime <<  endl;
+		ofResult << "HFuncTime = " << HFuncTime <<  endl;
+		ofResult << "KFuncTime = " << KFuncTime <<  endl;		
+				
+		ofResult << "GammaTime = " << GammaTime <<  endl;
+		ofResult << "step2Time = " << step2Time <<  endl;
+		double totalTime = betaTime + alphaTime + RRFuncTime 
+						+ HFuncTime + KFuncTime + GammaTime + step2Time;
+		ofResult << "totalTime = " << totalTime <<  endl;
+		*/
+		
+		
+		delete [] gamma;
+		delete [] gfb;
+	
+		delete [] gf; delete [] gb;
+		for (int j = 0; j < nh; j ++){
+			delete [] beta[j]; delete [] alpha[j];
+		}
+		delete [] beta; delete [] alpha;
+		cerr<<" Edge probabilities now computed."<<endl; 
+	}
+	
+	
+	void compute_edge_probabilities_ind(int h){
+		cerr<<"\nREBEL Method with each individual edge:" << endl;
+		cerr<<" Compute edge probabilities for Layer "<<h<<":"<<endl;
+				
+		// Step 1: Compute beta[][];
+		// Step 2: Compute alpha[][];
+		int *Vh, *Vu; int nh, nu;
+		model->layer(h, &Vh, &nh);
+		model->upper_layers(h-1, &Vu, &nu);
+				
+		beta = new double*[nh];
+		alpha = new double*[nh];
+		
+		betaNume = new double*[nh];
+		alphaNume = new double*[nh];
+		
+		k = model->max_indegree();
+		
+		cerr<<" . "<<nh<<" nodes"<<endl;
+		
+		for (int j = 0; j < nh; j ++){
+
+			beta[j] = new double[1 << nh];
+
+			//int i = Vh[j];
+			compute_beta(j, Vh, nh, Vu, nu);
+			
+			alpha[j] = new double[1 << nh];	
+			compute_alpha(j, Vh, nh);
+			
+			//alphaNume[j] = new double[1 << nh];	
+			//compute_alphaNume(j, Vh, nh);
+		
+			cerr<<" . Tables beta and alpha computed for node "<<j<<"."<<endl; 
+		
+		}
+	
+	  for(int uu = 0; uu < nh; uu++){
+	   for(int vv = 0; vv < nh; vv++){
+	  	if(vv != uu){
+
+		cerr<<" Compute edge ("<< uu <<"<-" << vv <<")" <<endl;
+
+		for (int j = 0; j < nh; j ++){
+			betaNume[j] = new double[1 << nh];
+			compute_betaNume(j, Vh, nh, Vu, nu, uu, vv);
+			
+			alphaNume[j] = new double[1 << nh];	
+			compute_alphaNume(j, Vh, nh);
+		
+			cerr<<" . Tables betaNume and alphaNume computed for node "<<j<<"."<<endl; 
+		
+		}
+	
+		cerr<<" . Tables beta/betaNume and alpha/alphaNume are now ready."<<endl;
+
+			
+		// Step 3: Compute g_forward[];
+		gf = new double[1 << nh];
+
+		compute_g_forward(nh);
+
+		gfNume = new double[1 << nh];
+		compute_gNume_forward(nh);
+		
+		cerr << "\nalpha" << endl;
+		for (int j = 0; j < nh; j ++){		
+			for(int index=0; index < (1 << nh); index++){
+				cerr<< "alpha[" << j << "][" << index << "] =" <<  alpha[j][index] << endl;
+			}
+		}
+		
+		cerr << "\nalphaNume" << endl;
+		for (int j = 0; j < nh; j ++){		
+			for(int index=0; index < (1 << nh); index++){
+				cerr<< "alphaNume[" << j << "][" << index << "] =" <<  alphaNume[j][index] << endl;
+			}
+		}
+		
+		cerr << "\ngf:" << endl;
+		for(int index = 0; index < (1 << nh); index++){
+			cerr << "gf[" << index << "] = " << gf[index] << endl;
+		}
+		
+		cerr << "\ngfNume:" << endl;
+		for(int index = 0; index < (1 << nh); index++){
+			cerr << "gfNume[" << index << "] = " << gfNume[index] << endl;
+		}
+
+		cerr<<"gf[all] = "<<gf[(1<<nh)-1]<<endl;
+		cerr<<"gfNume[all] = "<<gfNume[(1<<nh)-1]<<endl;
+		
+		//For checking: Compute g_backward[];
+		
+		gb = new double[1 << nh];
+		compute_g_backward(nh);	
+		cerr<<" gb[all] = "<<gb[(1<<nh)-1]<<endl;
+				
+		cerr<<" . Incoming edges from node " << vv << " to node " << uu <<" :";
+		model->print_edge_prob(cout, Vh[vv], Vh[uu], exp(gfNume[(1<<nh)-1] - gf[(1<<nh)-1])); //HR: - gb[(1<<nh)-1] mean /L(v)		
+		cerr<<endl;
+		
+	  	}
+	   }
+	  }
+		
+		delete [] gf; 
+		delete [] gfNume; 
+		for (int j = 0; j < nh; j ++){
+			delete [] beta[j]; 
+			delete [] betaNume[j];
+			delete [] alpha[j];
+			delete [] alphaNume[j];
+		}
+		delete [] beta; 
+		delete [] betaNume; 
+		delete [] alpha;
+		delete [] alphaNume;
+		
+		cerr<<" Edge probabilities now computed."<<endl; 
+		
+		return;
+		
+		
+
+	}
+	
+		
+	//HR: new forward method, compute for each individual edge
+	void compute_edge_probabilities_forward(int h){
+		cerr<<"Forward method: " << endl;
+		cerr<<" Compute edge probabilities for Layer "<<h<<":"<<endl;
+				
+		// Step 1: Compute beta[][];
+		// Step 2: Compute alpha[][];
+		int *Vh, *Vu; int nh, nu;
+		model->layer(h, &Vh, &nh);
+		model->upper_layers(h-1, &Vu, &nu);
+				
+		//If Arguments::ADtree == 1, user wants to use ADtree, then make the whole tree first
+		if(Arguments::ADtree == 1){
+			model->makeADTree();
+		}
+
+	
+		beta = new double*[nh];
+		alpha = new double*[nh];
+		
+		betaNume = new double*[nh];
+		alphaNume = new double*[nh];
+		
+		k = model->max_indegree();
+		
+		cerr<<" . "<<nh<<" nodes"<<endl;
+		
+		for (int j = 0; j < nh; j ++){
+
+			beta[j] = new double[1 << nh];
+					
+			//int i = Vh[j];
+			compute_beta(j, Vh, nh, Vu, nu);
+
+			alpha[j] = new double[1 << nh];	
+			compute_alpha(j, Vh, nh);
+				
+			cerr<<" . Tables beta and alpha computed for node "<<j<<"."<<endl; 
+		
+		}
+		
+		hFunc = new double[1 << nh];
+		compute_h_Fast(nh, hFunc, alpha);
+		cerr<<"hFunc[all] = "<<hFunc[(1<<nh)-1]<<endl;
+
+		
+	    for(int uu = 0; uu < nh; uu++){
+	    	for(int vv = 0; vv < nh; vv++){
+	  			if(vv != uu){
+	  		
+					cerr<<"Compute edge ("<< uu <<"<-" << vv <<")" <<endl;
+	
+					for (int j = 0; j < nh; j ++){
+						betaNume[j] = new double[1 << nh];
+
+						compute_betaNume(j, Vh, nh, Vu, nu, uu, vv);
+			
+						alphaNume[j] = new double[1 << nh];	
+						compute_alphaNume(j, Vh, nh);
+		
+						//cerr<<" . Tables betaNume and alphaNume computed for node "<<j<<"."<<endl; 
+		
+					}
+		
+		
+					cerr<<" . Tables beta/betaNume and alpha/alphaNume are now ready."<<endl;
+
+		
+					hFuncNume = new double[1 << nh];
+					compute_h_Fast(nh, hFuncNume, alphaNume);
+
+					cerr<<"hFunc[all] = "<<hFunc[(1<<nh)-1]<<endl;
+					cerr<<"hFuncNume[all] = "<<hFuncNume[(1<<nh)-1]<<endl;
+				
+					cerr<<" . Incoming edges from node " << vv << " to node " << uu <<" :";
+					model->print_edge_prob(cout, Vh[vv], Vh[uu], exp(hFuncNume[(1<<nh)-1] - hFunc[(1<<nh)-1])); //HR: - gb[(1<<nh)-1] mean /L(v)		
+					cerr<<endl;
+		
+	  			}
+	   		}
+	  	}
+		
+		
+		//If Arguments::ADtree == 1, then delete the whole tree
+		if(Arguments::ADtree == 1){
+			model->freeADTree();
+		}
+		
+		delete [] hFunc; 
+		
+		//it better to move the following line inside the double for loop
+		delete [] hFuncNume; 
+		
+		for (int j = 0; j < nh; j ++){
+			delete [] beta[j]; 
+			delete [] betaNume[j];
+			delete [] alpha[j];
+			delete [] alphaNume[j];
+		}
+		delete [] beta; 
+		delete [] betaNume; 
+		delete [] alpha;
+		delete [] alphaNume;
+		cerr<<" Edge probabilities now computed."<<endl; 
+		
+		return;
+		
+		
+
+	}
+	
+	
+	//HR: new backward method, compute for each individual edge
+	void compute_edge_probabilities_backward(int h){
+		cerr<<"Backward method: " << endl;
+		cerr<<" Compute edge probabilities for Layer "<<h<<":"<<endl;
+				
+		// Step 1: Compute beta[][];
+		// Step 2: Compute alpha[][];
+		int *Vh, *Vu; int nh, nu;
+		model->layer(h, &Vh, &nh);
+		model->upper_layers(h-1, &Vu, &nu);
+		
+		//If Arguments::ADtree == 1, user wants to use ADtree, then make the whole tree first
+		if(Arguments::ADtree == 1){
+			model->makeADTree();
+		}
+	
+		beta = new double*[nh];
+		alpha = new double*[nh];
+		
+		betaNume = new double*[nh];
+		alphaNume = new double*[nh];
+		
+		k = model->max_indegree();
+		
+		cerr<<" . "<<nh<<" nodes"<<endl;
+		
+		for (int j = 0; j < nh; j ++){
+
+			beta[j] = new double[1 << nh];
+
+			compute_beta(j, Vh, nh, Vu, nu);
+
+			alpha[j] = new double[1 << nh];	
+			compute_alpha(j, Vh, nh);
+			
+			cerr<<" . Tables beta and alpha computed for node "<<j<<"."<<endl; 
+		
+		}
+		
+		RRFunc = new double[1 << nh];
+		compute_RR_Fast(nh, RRFunc, alpha);
+		cerr<<"RRFunc[all] = "<<RRFunc[(1<<nh)-1]<<endl;
+		
+					
+		//int uu;
+		//int vv;
+	    //uu = 2;
+		//vv = 1;	
+	    for(int uu = 0; uu < nh; uu++){
+	    	for(int vv = 0; vv < nh; vv++){
+	  			if(vv != uu){
+	  		
+					cerr<<"Compute edge ("<< uu <<"<-" << vv <<")" <<endl;
+	
+					for (int j = 0; j < nh; j ++){
+
+						betaNume[j] = new double[1 << nh];
+						compute_betaNume(j, Vh, nh, Vu, nu, uu, vv);
+			
+						alphaNume[j] = new double[1 << nh];	
+						compute_alphaNume(j, Vh, nh);
+		
+						cerr<<" . Tables betaNume and alphaNume computed for node "<<j<<"."<<endl; 
+		
+					}
+				
+					cerr<<" . Tables beta/betaNume and alpha/alphaNume are now ready."<<endl;
+		
+					RRFuncNume = new double[1 << nh];
+					compute_RR_Fast(nh, RRFuncNume, alphaNume);
+
+					cerr<<"RRFunc[all] = "<<RRFunc[(1<<nh)-1]<<endl;
+					cerr<<"RRFuncNume[all] = "<<RRFuncNume[(1<<nh)-1]<<endl;
+
+					cerr<<" . Incoming edges from node " << vv << " to node " << uu <<" :";
+					model->print_edge_prob(cout, Vh[vv], Vh[uu], exp(RRFuncNume[(1<<nh)-1] - RRFunc[(1<<nh)-1])); //HR: - gb[(1<<nh)-1] mean /L(v)		
+					cerr<<endl;
+		
+	  			}
+	   		}
+	  	}
+		
+		//If Arguments::ADtree == 1, then delete the whole tree
+		if(Arguments::ADtree == 1){
+			model->freeADTree();
+		}
+		
+		delete [] RRFunc;
+		
+		//it better to move the following line inside the double for loop 
+		delete [] RRFuncNume; 
+		
+		for (int j = 0; j < nh; j ++){
+			delete [] beta[j]; 
+			delete [] betaNume[j];
+			delete [] alpha[j];
+			delete [] alphaNume[j];
+		}
+		delete [] beta; 
+		delete [] betaNume; 
+		delete [] alpha;
+		delete [] alphaNume;
+		cerr<<" Edge probabilities now computed."<<endl; 
+		
+		return;
+		
+		
+
+	}
+	
+
+	void compute_edge_probabilities_in_out_features(int h){
+		cerr<<"Backward method for in and out features: " << endl;
+		//cerr<<" Compute poster probabilities for Layer "<<h<<":"<<endl;
+				
+		// Step 1: Compute beta[][];
+		// Step 2: Compute alpha[][];
+		int *Vh, *Vu; int nh, nu;
+		model->layer(h, &Vh, &nh);
+		model->upper_layers(h-1, &Vu, &nu);
+		
+		beta = new double*[nh];
+		alpha = new double*[nh];
+		
+		betaInOut = new double*[nh];
+		alphaInOut = new double*[nh];
+		
+		k = model->max_indegree();
+		
+		cerr<<" . "<<nh<<" nodes"<<endl;
+
+		//If Arguments::ADtree == 1, user wants to use ADtree, then make the whole tree first
+		if(Arguments::ADtree == 1){
+			model->makeADTree();
+		}
+
+		for (int j = 0; j < nh; j ++){
+
+			beta[j] = new double[1 << nh];
+			compute_beta(j, Vh, nh, Vu, nu);			
+
+			alpha[j] = new double[1 << nh];	
+			compute_alpha(j, Vh, nh);
+				
+			cerr<<" . Tables beta and alpha computed for node "<<j<<"."<<endl; 
+		
+		}
+		
+	
+		inFeatureEdges = new int[nh];
+		outFeatureEdges = new int[nh];	
+		//cerr << "call: getInOutFeatures(" << nh << ")" << endl;	
+		getInOutFeatures(nh);		
+		//cerr << "return: getInOutFeatures()"  << endl;
+		
+//		for(int i = 0; i < nh; i++){
+//			cerr << "inFeatureEdges[" << i << "] = " << inFeatureEdges[i] << endl;
+//		}
+//		for(int i = 0; i < nh; i++){
+//			cerr << "outFeatureEdges[" << i << "] = " << outFeatureEdges[i] << endl;
+//		}
+		
+		for (int j = 0; j < nh; j ++){
+			//cerr<<"\nj = " << j << endl;
+			betaInOut[j] = new double[1 << nh];
+			compute_betaInOut(j, Vh, nh, Vu, nu);
+
+			alphaInOut[j] = new double[1 << nh];			
+			compute_alphaInOut(j, Vh, nh);
+
+			cerr<<" . Tables betaInOut and alphaInOut computed for node "<<j<<"."<<endl; 
+
+		}
+				
+		cerr<<" Tables beta/betaInOut and alpha/alphaInOut are now ready."<<endl;
+
+		cerr << " Compute the postier probability for the specified In-Out features:" << endl;
+		RRFunc = new double[1 << nh];
+		compute_RR_Fast(nh, RRFunc, alpha);
+		//compute_h_Fast(nh, RRFunc, alpha); //To confirm that the result is the same for forward and backward
+
+		RRFuncInOut = new double[1 << nh];
+		compute_RR_Fast(nh, RRFuncInOut, alphaInOut);
+		//compute_h_Fast(nh, RRFuncInOut, alphaInOut); //To confirm that the result is the same for forward and backward
+
+		cerr<<"RRFunc[all] = "<<RRFunc[(1<<nh)-1]<<endl;
+		cerr<<"RRFuncInOut[all] = "<<RRFuncInOut[(1<<nh)-1]<<endl;
+
+		//cerr<<" . Incoming edges from node " << vv << " to node " << uu <<" :";
+		//model->print_edge_prob(cout, Vh[vv], Vh[uu], exp(RRFuncNume[(1<<nh)-1] - RRFunc[(1<<nh)-1])); //HR: - gb[(1<<nh)-1] mean /L(v)
+		cerr << "\nThe postier probability for the specified In-Out features: " <<  exp(RRFuncInOut[(1<<nh)-1] - RRFunc[(1<<nh)-1]);		
+		cerr<<endl;
+		
+		cout << "The postier probability for the specified In-Out features: " <<  exp(RRFuncInOut[(1<<nh)-1] - RRFunc[(1<<nh)-1]);		
+		cout<<endl;
+		
+		//If Arguments::ADtree == 1, then delete the whole tree
+		if(Arguments::ADtree == 1){
+			model->freeADTree();
+		}
+		
+		delete [] RRFunc; 
+		delete [] RRFuncInOut; 
+	
+		
+		delete [] inFeatureEdges;
+		delete [] outFeatureEdges;	
+		
+		for (int j = 0; j < nh; j ++){
+			delete [] beta[j]; 
+			delete [] betaInOut[j];
+			delete [] alpha[j];
+			delete [] alphaInOut[j];
+		}
+		delete [] beta; 
+		delete [] betaInOut; 
+		delete [] alpha;
+		delete [] alphaInOut;
+		cerr<<" Poster probabilities now computed."<<endl; 
+		
+		return;
+		
+		
+	}
+
+
+	void compute_edge_probabilities_top_k(int h){
+		cerr<<"For top-k: compute p(D): " << endl;
+		cerr<<" Compute edge probabilities for Layer "<<h<<":"<<endl;		
+		
+		// Step 1: Compute beta[][];
+		// Step 2: Compute alpha[][];
+		int *Vh, *Vu; int nh, nu;
+		model->layer(h, &Vh, &nh);
+		model->upper_layers(h-1, &Vu, &nu);
+		
+		
+		beta = new double*[nh];
+		alpha = new double*[nh];
+		
+		//betaNume = new double*[nh];
+		//alphaNume = new double*[nh];
+		
+		k = model->max_indegree();
+		
+		cerr<<" . "<<nh<<" nodes"<<endl;
+		
+		//If Arguments::ADtree == 1, user wants to use ADtree, then make the whole tree first
+		if(Arguments::ADtree == 1){
+			model->makeADTree();
+		}
+
+		for (int j = 0; j < nh; j ++){
+
+			beta[j] = new double[1 << nh];
+		
+			//cerr<<" Start compute_beta for node "<<j<<"."<<endl;
+			compute_beta(j, Vh, nh, Vu, nu);
+			//cerr<<" Tables beta computed for node "<<j<<"."<<endl;
+
+			alpha[j] = new double[1 << nh];	
+			compute_alpha(j, Vh, nh);
+				
+			cerr<<" . Tables beta and alpha computed for node "<<j<<"."<<endl; 
+		
+		}
+
+		//If Arguments::ADtree == 1, then delete the whole tree
+		if(Arguments::ADtree == 1){
+			model->freeADTree();
+		}
+			
+		RRFunc = new double[1 << nh];
+		
+		cerr<<"\n Compute_RR_Fast(): "<<endl;		
+		compute_RR_Fast(nh, RRFunc, alpha);
+		cerr<<"\n RRFunc[all] = "<<RRFunc[(1<<nh)-1]<<endl <<endl;
+		cout<<"\n RRFunc[all] = "<<RRFunc[(1<<nh)-1]<<endl <<endl;
+
+		fprintf(stderr, "RRFunc[all] = %18.8f\n", RRFunc[(1<<nh)-1]);
+		
+		//write to 
+		FILE * fp_PD = fopen("exactPD.txt", "a");
+		if(fp_PD){
+			fprintf(fp_PD, "%18.8f\n", RRFunc[(1<<nh)-1]);
+			fclose(fp_PD);
+			
+		}
+		else{
+			cerr <<"fopen exactPD.txt fails" << endl;
+			
+		}
+		
+	
+		delete [] RRFunc; 
+		//delete [] RRFuncNume; 
+		
+		for (int j = 0; j < nh; j ++){
+			delete [] beta[j]; 
+			//delete [] betaNume[j];
+			delete [] alpha[j];
+			//delete [] alphaNume[j];
+		}
+		delete [] beta; 
+		//delete [] betaNume; 
+		delete [] alpha;
+		//delete [] alphaNume;
+		//cerr<<" Edge probabilities now computed."<<endl; 
+		
+		return;
+
+	}
+
+		
+	//HR: new mix with max in-degree method, 
+	void compute_edge_probabilities_mixIndegree(int h){
+		cerr<<" Mix with max in-degree method: " << endl;
+		//cerr<<" Compute edge probabilities for Layer "<<h<<":"<<endl;
+				
+		// Step 1: Compute beta[][];
+		// Step 2: Compute alpha[][];
+		int *Vh, *Vu; int nh, nu;
+		model->layer(h, &Vh, &nh);
+		model->upper_layers(h-1, &Vu, &nu);
+		
+		//Step 1(a) (b)
+		
+		beta = new double*[nh];
+		alpha = new double*[nh];
+		
+		k = model->max_indegree();
+		
+		cerr<<" . "<<nh<<" nodes"<<endl;
+		
+		struct timeval startTime;
+		struct timeval endTime;
+		struct timezone myTimeZone;
+		
+		double betaTime;
+		double alphaTime;
+		double RRFuncTime;
+		double HFuncTime;
+		double KFuncTime;
+		double GammaTime;
+		
+		double step2Time;
+		
+		
+		//Step 1(a)
+
+		gettimeofday(&startTime, &myTimeZone);
+		
+		//If Arguments::ADtree == 1, user wants to use ADtree, then make the whole tree first
+		if(Arguments::ADtree == 1){
+			//cout << "Arguments::ADtree == 1"  << endl;
+			model->makeADTree();
+		}
+		else{
+			//cout << "Arguments::ADtree == 0"  << endl;
+		}
+
+		for (int j = 0; j < nh; j ++){
+			beta[j] = new double[1 << nh];
+					
+			//int i = Vh[j];
+			compute_beta(j, Vh, nh, Vu, nu);
+
+			//cerr<<" . Tables beta and alpha computed for node "<<j<<"."<<endl; 
+		
+		}
+		
+		//If Arguments::ADtree == 1, then delete the whole tree
+		if(Arguments::ADtree == 1){
+			model->freeADTree();
+		}
+		
+		gettimeofday(&endTime, &myTimeZone);		
+		betaTime = (endTime.tv_sec - startTime.tv_sec) + 
+		           (endTime.tv_usec - startTime.tv_usec) / 1000000.0 ;
+				
+		cerr<<" . Tables beta have been computed" << endl;
+
+
+		//HR: Add for Top-k inside void compute_edge_probabilities_mixIndegree(int h)
+		//HR: Use the Poster tool to compute the local scores for all the families of each variable (without max-indegree
+		//	restriction). So for each of n variables, there are 2^(n-1) family scores.
+		write_family_scores_to_files(nh);
+		
+
+		//step 1(b)
+		gettimeofday(&startTime, &myTimeZone);
+		for (int j = 0; j < nh; j ++){
+
+			alpha[j] = new double[1 << nh];	
+			compute_alpha(j, Vh, nh);
+			
+			//cerr<<" . Tables beta and alpha computed for node "<<j<<"."<<endl; 
+		
+		}
+		gettimeofday(&endTime, &myTimeZone);
+		alphaTime = (endTime.tv_sec - startTime.tv_sec) + 
+		           (endTime.tv_usec - startTime.tv_usec) / 1000000.0 ;
+		
+		
+		cerr<<" . Tables alpha has been computed" << endl;
+		
+
+		//Step 1(c)
+		//HR: backward method to compute: for all S \subset V RR(S)
+		RRFunc = new double[1 << nh];
+		
+		cerr<<" . To compute Table RR" << endl;
+		
+		gettimeofday(&startTime, &myTimeZone);
+		
+		compute_RR_Fast(nh, RRFunc, alpha);
+		//compute_RR_Iter(nh, RRFunc, alpha);
+		
+		gettimeofday(&endTime, &myTimeZone);		
+		RRFuncTime = (endTime.tv_sec - startTime.tv_sec) + 
+		           (endTime.tv_usec - startTime.tv_usec) / 1000000.0 ;
+		
+		//cerr<<"RRFunc[all] = "<<RRFunc[(1<<nh)-1]<<endl;
+		//fprintf(stderr, "RRFunc[all] = %18.8f\n", RRFunc[(1<<nh)-1]);
+		cerr<<" . Table RR computed." <<endl;
+
+
+		//HR: merge the function of opt 4 into here.
+		//write to exactPD.txt
+		//string directory_name = "./family_scores";
+		string str;
+		str.assign(Arguments::directoryName);
+		str.append("/");
+		str.append("exactPD.txt");
+
+		//FILE * fp_PD = fopen(str.c_str(), "a");
+		FILE * fp_PD = fopen(str.c_str(), "w");
+		if(fp_PD){
+			fprintf(fp_PD, "%18.8f\n", RRFunc[(1<<nh)-1]);
+			fclose(fp_PD);
+
+		}
+		else{
+			cerr <<"fopen exactPD.txt fails" << endl;
+
+		}
+		
+
+		//Step 1(d)
+		//HR: forward method to compute: for all S \subset V H(S)
+		
+		hFunc = new double[1 << nh];
+		
+		cerr<<" . To compute Table H" << endl;
+		
+		gettimeofday(&startTime, &myTimeZone);
+
+		compute_h_Fast(nh, hFunc, alpha);	
+		//compute_h_Iter(nh, hFunc, alpha);	
+		
+		gettimeofday(&endTime, &myTimeZone);
+		HFuncTime = (endTime.tv_sec - startTime.tv_sec) + 
+		           (endTime.tv_usec - startTime.tv_usec) / 1000000.0 ;
+		
+		
+		//cerr<<"hFunc[all] = "<<hFunc[(1<<nh)-1]<<endl;
+		//fprintf(stderr, "hFunc[all] = %18.8f\n", hFunc[(1<<nh)-1]);
+		cerr<<" . Table H computed" <<endl;
+
+			
+		//Step 1 (e)
+		KFunc = new double*[nh]; 
+		cerr<<" . To compute Table K" << endl; 
+		
+		gettimeofday(&startTime, &myTimeZone);
+		for(int i = 0; i < nh; i++){
+			//cerr<<" For v = " << i << endl;
+			KFunc[i] = new double [1<<nh];
+			compute_all_K_v(nh, KFunc[i], i, alpha);
+			
+		}
+		
+		gettimeofday(&endTime, &myTimeZone);	
+		KFuncTime = (endTime.tv_sec - startTime.tv_sec) + 
+		           (endTime.tv_usec - startTime.tv_usec) / 1000000.0 ;
+		
+		           
+		cerr<<" . Table K computed" <<endl;
+		
+	
+		// Step 1 (f): For all i \in V, for all Pa_i \subset V - {i} with |Pa_i| <= k, compute Gamma_i(Pa_i)
+		
+		double * Gamma = new double[1 << nh];
+		double * Gfb = new double[1 << nh];
+
+		GammaTime = 0.0;
+		step2Time = 0.0;
+
+		for (int v = 0; v < nh; v++){
+			//cerr<<" For v = " << v <<": " << endl;
+			
+			//start counting the GammaTime for each v
+			gettimeofday(&startTime, &myTimeZone);
+			
+			// Compute Gfb[]. 
+			for (int U = 0; U < (1<<nh); U++){				
+				//if v \in the binary repre of U
+				if ((U>>v) & 1){
+					Gfb[U] = LOG_ZERO;
+				}
+				else{
+
+					//Gfb[U] = hFunc[U] + KFunc[v][U];
+					if(KFunc[v][U] == LOG_ZERO){
+						Gfb[U] = LOG_ZERO;
+					}
+					//note that KFunc[v][U] == 0 is possible
+					else if(KFunc[v][U] <= 0){
+						Gfb[U] = hFunc[U] + KFunc[v][U];
+					}
+					else{
+						//Now if Gfb[U] > 0, then Gfb[U]
+				
+						Gfb[U] = -(hFunc[U] - KFunc[v][U]);
+					}
+				
+					//cerr<<" j = "<<j<<": ";
+					//print_set(cerr, S);
+					//cerr<<"; ";
+					//print_set(cerr, cS);
+					//cerr<<": "<<gfb[S];
+					//cerr<<endl;
+				}
+			}
+						
+			//cerr<< "Table Gfb has been computed" << endl;
+					
+			// Compute gamma_j() := gamma[].
+						
+			fdmtLogAddComp(Gfb, Gamma, nh, k);
+			
+			gettimeofday(&endTime, &myTimeZone);
+			 //end counting GammaTime for each v
+			GammaTime += (endTime.tv_sec - startTime.tv_sec) + 
+		           (endTime.tv_usec - startTime.tv_usec) / 1000000.0 ;
+		           
+			
+			//cerr<< "Table Gamma has been computed" << endl;
+						
+			//cerr<< " Gfb[0]: " <<Gfb[0]<<endl;
+			//cerr<< " Gamma[0]: " << Gamma[0]<<endl;
+			
+			
+			//Step 2
+			//cerr<<" . Incoming edges for node "<< v <<":";
+			// Loop over start-point nodes i.
+			
+			//start counting step2Time for each v
+			gettimeofday(&startTime, &myTimeZone);
+
+			for (int i = 0; i < nh; i++){
+				if (i == v) continue;
+				//cerr<<" "<< i;		
+				double log_prob_nume = eval_edge_mixIndegree(i,  v, Gamma, beta[v], nh, k);
+		
+				model->print_edge_prob(
+					cout, Vh[i], Vh[v], exp(log_prob_nume - RRFunc[(1<<nh)-1])); //HR: - gb[(1<<nh)-1] mean /L(v)
+							
+			}
+			
+
+			gettimeofday(&endTime, &myTimeZone);
+			//end counting step2Time for each v	
+			step2Time += (endTime.tv_sec - startTime.tv_sec) + 
+		           (endTime.tv_usec - startTime.tv_usec) / 1000000.0 ;
+		    	
+			//cerr<<endl;
+			
+		} 
+		
+		
+//		cout << "\n\n\nTime Statistics" << endl;
+//		cout << "betaTime = " << betaTime <<  endl;				
+//		cout << "alphaTime = " << alphaTime <<  endl;
+//		cout << "RRFuncTime = " << RRFuncTime <<  endl;
+//		cout << "HFuncTime = " << HFuncTime <<  endl;
+//		cout << "KFuncTime = " << KFuncTime <<  endl;		
+//				
+//		cout << "GammaTime = " << GammaTime <<  endl;
+//		cout << "step2Time = " << step2Time <<  endl;
+//		double totalTime = betaTime + alphaTime + RRFuncTime 
+//						+ HFuncTime + KFuncTime + GammaTime + step2Time;
+//		cout << "totalTime = " << totalTime <<  endl;
+				
+		
+		delete [] Gamma;
+		delete [] Gfb;
+
+		delete [] hFunc;
+		
+		delete [] RRFunc; 
+		
+		delete [] Eta_U;
+		
+		for (int j = 0; j < nh; j ++){
+			delete [] beta[j]; 
+			delete [] alpha[j];
+
+			delete [] KFunc[j]; 
+		
+		}
+		delete [] beta; 
+		delete [] alpha;
+
+		delete [] KFunc;
+		
+		
+		cerr<<" Edge probabilities now computed."<<endl; 
+		
+		return;
+
+	}
+	//HR: end mixIndegree
+	
+	
+	void compute_edge_probabilities_mixIndegreeNoLog(int h){
+		cerr<<"Mix with max in-degree method: " << endl;
+		cerr<<" Compute edge probabilities for Layer "<<h<<":"<<endl;
+		
+		
+		// Step 1: Compute beta[][];
+		// Step 2: Compute alpha[][];
+		int *Vh, *Vu; int nh, nu;
+		model->layer(h, &Vh, &nh);
+		model->upper_layers(h-1, &Vu, &nu);
+		
+		//Step 1(a) (b)
+		
+		beta = new double*[nh];
+		alpha = new double*[nh];
+		
+		k = model->max_indegree();
+		
+		cerr<<" . "<<nh<<" nodes"<<endl;
+
+		for (int j = 0; j < nh; j ++){
+
+			beta[j] = new double[1 << nh];
+					
+			//int i = Vh[j];
+			compute_beta(j, Vh, nh, Vu, nu);
+
+			alpha[j] = new double[1 << nh];	
+			compute_alpha(j, Vh, nh);
+				
+			cerr<<" . Tables beta and alpha computed for node "<<j<<"."<<endl; 
+		
+		}
+		
+		
+		//Step 1(c)
+		//HR: backward method to compute: for all S \subset V RR(S)
+		RRFunc = new double[1 << nh];
+		
+		cerr<<" . To compute Table RR" << endl;
+		
+		compute_RR_Fast(nh, RRFunc, alpha);
+		
+		cerr<<" . Table RR computed." <<endl;
+		
+		
+		//Step 1(d)
+		//HR: forward method to compute: for all S \subset V H(S)
+		
+		hFunc = new double[1 << nh];
+		
+		cerr<<" . To compute Table H" << endl;
+		
+		compute_h_Fast(nh, hFunc, alpha);	
+		
+		cerr<<" . Table H computed" <<endl;
+
+			
+		//Step 1 (e)
+		KFunc = new double*[nh]; 
+		cerr<<" . To compute Table K" << endl; 
+		for(int i = 0; i < nh; i++){
+			cerr<<" For v = " << i << endl;
+			KFunc[i] = new double [1<<nh];
+			compute_all_K_v(nh, KFunc[i], i, alpha);
+			
+		}
+		cerr<<" . Table K computed" <<endl;		
+		
+		// Step 2: Loop over end-point nodes v \in V
+		
+		//No Log transformation
+		double * Gamma = new double[1 << nh];
+		double * Gfb = new double[1 << nh];
+		ofstream ofNoLog("debugEngineNoLog.txt");
+		
+		for (int v = 0; v < nh; v++){
+			cerr<<" For v = " << v <<": " << endl;
+			// Compute Gfb[]. 
+			for (int U = 0; U < (1<<nh); U++){				
+				//if v \in the binary repre of U
+				if ((U>>v) & 1){
+					//Gfb[U] = LOG_ZERO;
+					//Gfb[U] = 0;
+					Gfb[U] = LOG_ZERO;//
+				}
+				else{
+					//Gfb[U] = hFunc[U] + KFunc[v][U];
+					
+					if(KFunc[v][U] == LOG_ZERO){
+						Gfb[U] = exp(hFunc[U]);
+					}
+					else if (KFunc[v][U] > 0){
+						Gfb[U] = - exp(hFunc[U] - KFunc[v][U]);
+						
+					}
+					else{
+						Gfb[U] = exp(hFunc[U] + KFunc[v][U]);
+					}
+					//
+					if(Gfb[U] == 0){
+						Gfb[U] = LOG_ZERO;
+					}
+					else{
+						Gfb[U] = log(Gfb[U]);
+					}
+					//
+										
+					//cerr<<" j = "<<j<<": ";
+					//print_set(cerr, S);
+					//cerr<<"; ";
+					//print_set(cerr, cS);
+					//cerr<<": "<<gfb[S];
+					//cerr<<endl;
+				}
+			}
+			cerr<< "Table Gfb has been computed" << endl;
+					
+			ofNoLog <<"For v = " << v <<": " << endl;
+			ofNoLog << "\nGfb: " << endl;
+			for(int index = 0; index < (1 << nh); index++){
+				ofNoLog << "Gfb[" << index << " ] =" << Gfb[index] << endl;
+			}
+			ofNoLog << endl;
+			
+			
+			// Compute gamma_j() := gamma[].
+			//fdmtNoLog(Gfb, Gamma, nh, k);
+			fdmt(Gfb, Gamma, nh, k);
+			
+			cerr<< "Table Gamma has been computed" << endl;
+			
+			cerr<< " Gamma[0]: " << Gamma[0]<<endl;
+			cerr<< " Gfb[0]: " <<Gfb[0]<<endl;
+			
+			cerr<<" . Incoming edges for node "<< v <<":";
+			// Loop over start-point nodes i.
+			for (int i = 0; i < nh; i++){
+				if (i == v) continue;
+				cerr<<" "<< i;		
+				double log_prob_nume = eval_edge_mixIndegree(i,  v, Gamma, beta[v], nh, k);
+		
+				model->print_edge_prob(
+					cout, Vh[i], Vh[v], exp(log_prob_nume - RRFunc[(1<<nh)-1])); //HR: - gb[(1<<nh)-1] mean /L(v)
+			
+			}
+			cerr<<endl;
+			
+		} 
+	
+		delete [] Gamma;
+		delete [] Gfb;
+
+		delete [] hFunc;
+		
+		delete [] RRFunc; 
+		
+		delete [] Eta_U;
+		
+		for (int j = 0; j < nh; j ++){
+			delete [] beta[j]; 
+			delete [] alpha[j];
+
+			delete [] KFunc[j]; 
+		
+		}
+		delete [] beta; 
+		delete [] alpha;
+
+		delete [] KFunc;
+				
+		cerr<<" Edge probabilities now computed."<<endl; 
+		
+		return;
+
+	}
+	
+	//HR: end mixIndegreeNoLog
+	
+	
+	// beta[j][T] := sum_W gamma[j][T \cup W] .
+	void compute_beta(int j, int *Vh, int nh, int *Vu, int nu){
+		//cerr<<"Compute beta, j = "<<j<<", i = "<< Vh[j];
+		//cerr<<", k = "<<k<<", nh = "<<nh<<":"<<endl;
+		
+		sub_init(0, 0, beta[j], MARK, 0, nh);
+
+		//cerr<<" Initialization done."<<endl;
+		
+		int *S = new int[k];		
+		sub_beta(-1, nh, beta[j], 0, S, Vh[j], Vu, nu, 0);
+		delete [] S;
+				
+	}// end void compute_beta()
+	
+	
+	// beta[j][T] := sum_W gamma[j][T \cup W] .
+	void compute_betaNume(int j, int *Vh, int nh, int *Vu, int nu, int uu, int vv){
+		//cerr<<"Compute betaNume, j = "<<j<<", i = "<< Vh[j];
+		
+		sub_init(0, 0, betaNume[j], MARK, 0, nh);
+		
+		//cerr<<" Initialization done."<<endl;
+
+		int *S = new int[k];
+		
+		//check whether uu == j
+		if(uu != j){
+			sub_beta(-1, nh, betaNume[j], 0, S, Vh[j], Vu, nu, 0);
+		}
+		else{
+			//cerr << "uu == j == " << uu << ": so call sub_betaNume()" << endl;
+			sub_betaNume(-1, nh, betaNume[j], 0, S, Vh[j], Vu, nu, 0, uu, vv);
+		}
+		
+		
+		
+		delete [] S;
+	}
+	
+	
+	void compute_betaInOut(int j, int *Vh, int nh, int *Vu, int nu){
+
+		//cerr << "call: sub_init(0, 0, betaInOut[j], MARK, 0, nh)" << endl;
+		sub_init(0, 0, betaInOut[j], MARK, 0, nh);
+		//cerr << "return: sub_init(0, 0, betaInOut[j], MARK, 0, nh)" << endl;
+
+		//cerr<<" Initialization done."<<endl;
+
+		int *S = new int[k];
+		
+		//cerr << "call: sub_betaInOut()" << endl;
+		
+		sub_betaInOut(-1, nh, betaInOut[j], 0, S, Vh[j], Vu, nu, 0);
+		//sub_beta(-1, nh, betaInOut[j], 0, S, Vh[j], Vu, nu, 0);
+		
+		//cerr << "return: sub_betaInOut()" << endl;
+
+		delete [] S;
+	
+	}//end of compute_betaInOut()
+	
+	
+
+	void sub_beta(int jprev, int nh, double *b, int d, int *S, int i, int *Vu, int nu, int T){
+		//cerr<<" S:"; print_nodes(cerr, S, d); 
+		//cerr<<"; T:"; print_nodes(cerr, T, Vu, nu); cerr<<endl;
+		
+		
+		double lb;	
+		if(Arguments::option < 1){
+		
+			//HR: for old prior for q(G_i)and new Dirichlet hyper-param
+			//used to compare rebel and out method		
+
+			//lb = model->log_prior(i, S, d) + model->log_lcpHR(i, S, d);
+			if(Arguments::ADtree == 0){
+				lb = model->log_prior(i, S, d) + model->log_lcpHR(i, S, d);
+			}
+			else{
+				lb = model->log_prior(i, S, d) + model->log_lcpHR_ADtree(i, S, d);
+			}
+		}
+		else if(Arguments::option >= 1) {					
+
+			//lb = 0 + model->log_lcpHR(i, S, d);
+			if(Arguments::ADtree == 0){
+				lb = 0 + model->log_lcpHR(i, S, d);
+			}
+			else{
+				lb = 0 + model->log_lcpHR_ADtree(i, S, d);
+			}
+		}
+
+		//LOGADD(b[T], lb);
+		logAdd_New(b[T], lb);
+		//
+		
+		if (d < k){
+			for (int j = jprev + 1; j < nu; j ++){	
+				if (Vu[j] != i){
+					S[d] = Vu[j];
+					
+					if (j < nh) {
+						sub_beta(j, nh, b, d+1, S, i, Vu, nu, T | (1 << j));
+					}
+					
+					else{
+						sub_beta(j, nh, b, d+1, S, i, Vu, nu, T);
+					}
+				}
+			}
+		}	
+	}
+	
+	                
+	void sub_betaNume(int jprev, int nh, double *b, int d, int *S, int i, int *Vu, int nu, int T, int uu, int vv){
+		//cerr<<" S:"; print_nodes(cerr, S, d); 
+		//cerr<<"; T:"; print_nodes(cerr, T, Vu, nu); cerr<<endl;
+		int vvInS = 0;
+	
+		for(int ind = 0; ind < d; ind++){
+			if(vv == S[ind]){
+				vvInS = 1;
+				break;
+			}
+		}
+		
+		if(vvInS == 1){
+			double lb;
+			if(Arguments::option < 1){
+				
+				//HR: for old prior for q(G_i)and new Dirichlet hyper-param
+				//used to compare rebel and out method
+
+				//lb = model->log_prior(i, S, d) + model->log_lcpHR(i, S, d);
+				if(Arguments::ADtree == 0){
+					lb = model->log_prior(i, S, d) + model->log_lcpHR(i, S, d);
+				}
+				else{
+					lb = model->log_prior(i, S, d) + model->log_lcpHR_ADtree(i, S, d);
+				}
+			}
+			else if(Arguments::option >= 1) {					
+				//HR: for 1 prior for q(G_i) and new Dirichlet hyper-param
+				//lb = 0 + model->log_lcpHR(i, S, d);
+				if(Arguments::ADtree == 0){
+					lb = 0 + model->log_lcpHR(i, S, d);
+				}
+				else{
+					lb = 0 + model->log_lcpHR_ADtree(i, S, d);
+				}
+				
+			}
+		
+			//double lb = model->log_prior(i, S, d) + model->log_lcp(i, S, d);
+			//double lb = 0 + model->log_lcpHR(i, S, d);
+
+			//LOGADD(b[T], lb);
+			logAdd_New(b[T], lb);
+		}
+		else{
+			//how to set? 0-no, MARK-no; log(0) = -inf = LOG_ZERO
+			//LOGADD(b[T], LOG_ZERO);
+			double tempLogB = LOG_ZERO;
+			logAdd_New(b[T], tempLogB);
+		}
+		
+
+		
+		if (d < k){
+			for (int j = jprev + 1; j < nu; j ++){	
+				if (Vu[j] != i){
+					S[d] = Vu[j];
+					
+					if (j < nh) {
+						sub_betaNume(j, nh, b, d+1, S, i, Vu, nu, T | (1 << j), uu, vv);
+					}
+					
+					else{
+						sub_betaNume(j, nh, b, d+1, S, i, Vu, nu, T, uu, vv);
+					}
+				}
+			}
+		}		
+	}
+	
+	
+
+	void getInOutFeatures(int no_vars){
+	
+		for(int i = 0; i < no_vars; i++){
+			inFeatureEdges[i] = 0;
+		}
+		for(int i = 0; i < no_vars; i++){
+			outFeatureEdges[i] = 0;
+		}
+			
+		FILE * fpIn = fopen(Arguments::inFeasFileName, "r");
+	
+		int fromNode;
+		int toNode;
+		//char c;
+		//int i=0;
+		while(!feof(fpIn)){
+			
+			fromNode = -1;
+			toNode = -1;
+			//c = -1;
+			
+			fscanf(fpIn,"%d->%d\n",&fromNode, &toNode);
+			
+			//cout << "fromNode = "<< fromNode << endl;
+			//cout << "toNode = "<< toNode << endl;
+	
+			//To guard against toNode == -1
+			if(toNode == -1){
+				break;
+			}
+			else{
+				inFeatureEdges[toNode] += (1 << fromNode);
+			}
+
+		}
+		
+		fclose(fpIn);
+		
+//		for(int i = 0; i < no_vars; i++){
+//			cout << "inFeatureEdges[" << i << "] " << inFeatureEdges[i] << endl; 
+//		}
+
+		
+		FILE *fp2 = fopen(Arguments::outFeasFileName, "r");
+
+		while(!feof(fp2)){
+
+			fromNode = -1;
+			toNode = -1;
+			
+			fscanf(fp2,"%d->%d\n",&fromNode, &toNode);
+			
+			//cout << "fromNode = "<< fromNode << endl;
+			//cout << "toNode = "<< toNode << endl;
+	
+			if(toNode == -1){
+				break;
+			}
+			else{
+				outFeatureEdges[toNode] += (1 << fromNode);
+			}
+			
+		
+		}
+		fclose(fp2);
+	
+//		for(int i = 0; i < no_vars; i++){
+//			cout << "outFeatureEdges[" << i << "] " << outFeatureEdges[i] << endl; 
+//		}
+
+	} //end of getInOutFeatures
+	
+	
+	void sub_betaInOut(int jprev, int nh, double *b, int d, int *S, int i, int *Vu, int nu, int T){
+//		cerr<< "Start sub_betaInOut()" << endl;
+//		cerr<<" S:"; print_nodes(cerr, S, d); 
+//		cerr<<" T: " << T << endl;
+//		cerr<<" d: " << d << endl;
+		//cerr<<"; T:"; print_nodes(cerr, T, Vu, nu); cerr<<endl;
+				
+		int compBetaNeeded = 0;
+		
+		//cerr << "inFeatureEdges[" << i << "] = " << inFeatureEdges[i] << endl;
+		//cerr << "outFeatureEdges[" << i << "] = " << outFeatureEdges[i] << endl;
+		
+		//if (each of inFeatureEdges[i] is in T ) && (none of outFeatureEdges[i] is in T )
+		if(((inFeatureEdges[i] & T) == inFeatureEdges[i]) && ((outFeatureEdges[i] & T) == 0) ){
+			compBetaNeeded = 1;		
+			//cerr << "inFeatureEdges[" << i << "] = " << inFeatureEdges[i] << endl;
+			//cerr << "outFeatureEdges[" << i << "] = " << outFeatureEdges[i] << endl;
+			//cerr << "T = " << T << endl;
+			//cerr<<" compBetaNeeded = 1;" << endl;
+			
+		}
+		
+		if(compBetaNeeded == 1){
+			double lb;
+			//Arguments::option must be 5
+			if(Arguments::option < 1){
+				
+				//HR: for old prior for q(G_i)and new Dirichlet hyper-param
+				//used to compare rebel and out method
+				//lb = model->log_prior(i, S, d) + model->log_lcpHR(i, S, d);
+				if(Arguments::ADtree == 0){
+					lb = model->log_prior(i, S, d) + model->log_lcpHR(i, S, d);
+				}
+				else{
+					lb = model->log_prior(i, S, d) + model->log_lcpHR_ADtree(i, S, d);
+				}
+			}
+			else if(Arguments::option >= 1) {					
+				//HR: for 1 prior for q(G_i) and new Dirichlet hyper-param
+				//cerr << "start: double lb = 0 + model->log_lcpHR(i, S, d)" << endl;
+				//lb = 0 + model->log_lcpHR(i, S, d);
+				if(Arguments::ADtree == 0){
+					lb = 0 + model->log_lcpHR(i, S, d);
+				}
+				else{
+					lb = 0 + model->log_lcpHR_ADtree(i, S, d);
+				}
+				//cerr << "end: double lb = 0 + model->log_lcpHR(i, S, d)" << endl;
+			}
+			
+		
+			//LOGADD(b[T], lb);
+			logAdd_New(b[T], lb);
+		}
+		else{
+			//LOGADD(b[T], LOG_ZERO);
+			double tempLogB = LOG_ZERO;
+			logAdd_New(b[T], tempLogB);
+		}
+
+		if (d < k){
+			for (int j = jprev + 1; j < nu; j ++){	
+				if (Vu[j] != i){
+					S[d] = Vu[j];
+					
+					if (j < nh) {						
+						sub_betaInOut(j, nh, b, d+1, S, i, Vu, nu, T | (1 << j));
+					}
+					
+					else{
+						sub_betaInOut(j, nh, b, d+1, S, i, Vu, nu, T);
+					}
+				}
+			}
+		}		
+	} //end of sub_betaInOut
+	
+	
+	void sub_init(int d, int S, double *a, double value, int ones, int nh){
+		//cerr<<" d: "<<d<<endl; 
+		a[S] = value;
+		
+		if (d < nh){
+			sub_init(d+1, S, a, value, ones, nh);
+
+			if (ones < k) sub_init(d+1, S | (1 << d), a, value, ones+1, nh);
+		}
+	}
+
+	//HR: From get_kbest_nets.cc in Top-k
+	//HR: add v itself into the binary repres, v posi should be 0
+	//Convert the parent set to the appropriate variable set
+	unsigned int parset2varset(int v, unsigned int set) {
+		unsigned int sinkleton = 1U << v;
+		unsigned int mask = sinkleton - 1;
+		unsigned int low = set & mask;
+		unsigned int high = set & ~mask;
+		return (high << 1) | low;
+	}
+
+
+	//HR: Add for Top-k inside void compute_edge_probabilities_mixIndegree(int h)
+	//HR: Use the Poster tool to compute the local scores for all the families of each variable (without max-indegree
+	//	restriction). So for each of n variables, there are 2^(n-1) family scores.
+	//	Then store them as file 0, 1, 2, ..., n-1 for variable 0, 1, ..., n-1.
+	void write_family_scores_to_files(int nh){
+		FILE* fout;
+		//nh is the number of variables
+		int num_of_vars = nh;
+		unsigned int num_of_parsets = 1U << (num_of_vars - 1);
+		//HR: for each variable
+		for (int v = 0; v < num_of_vars; v++) {
+			char str1[40];
+			sprintf(str1, "%d", v);
+			string str;
+			//string dirname = "./family_scores";
+			string dirname = Arguments::directoryName;
+			str.append(dirname);
+			str.append("/");
+			str.append(str1);
+
+			fout = fopen(str.c_str(), "wb");
+			unsigned int new_par_set;
+			for (unsigned int par_set = 0; par_set < num_of_parsets; par_set++) {
+				//HR: add v itself into the binary repres, v posi should be 0
+				new_par_set = parset2varset(v, par_set);
+				//This is fine.
+				//fwrite(beta[v] + new_par_set, sizeof(double), 1, fout);
+				//This is also fine.
+				fwrite(&(beta[v][new_par_set]), sizeof(double), 1, fout);
+
+			}
+			fclose(fout);
+
+		}
+//		//test
+//		//HR: for each variable
+//		FILE* fin;
+//		for (int v = 0; v < num_of_vars; v++) {
+//			char str1[40];
+//			sprintf(str1, "%d", v);
+//			string str;
+//			//string dirname = "./family_scores";
+//			string dirname = Arguments::directoryName;
+//			str.append(dirname);
+//			str.append("/");
+//			str.append(str1);
+//
+//			fin = fopen(str.c_str(), "rb");
+//			unsigned int new_par_set;
+//			for (unsigned int par_set = 0; par_set < num_of_parsets; par_set++) {
+//				//HR: add v itself into the binary repres, v posi should be 0
+//				new_par_set = parset2varset(v, par_set);
+//				double temp_family_score;
+//				fread(&temp_family_score, sizeof(double), 1, fin);
+//				if(temp_family_score != beta[v][new_par_set]){
+//					cerr << "temp_family_score = " << temp_family_score << endl;
+//					cerr << "beta[" << v << "][" << new_par_set << "] = " << beta[v][new_par_set] << endl;
+//					cerr << "Error: temp_family_score != beta["
+//							<< v << "][" << new_par_set << "]" << endl;
+//					exit(1);
+//				}
+//			}
+//			fclose(fin);
+//
+//		}
+//		//
+
+	}//write_family_scores_to_files(int nh)
+
+	
+	// alpha[j][S] = sum_T beta[j][T]  (...times the prior).
+	void compute_alpha(int j, int *Vh, int nh){
+		// Use fast truncated upward Möbius transform.
+		fumt(beta[j], alpha[j], nh, k); 
+	}
+	
+
+	void compute_alphaNume(int j, int *Vh, int nh){
+		// Use fast truncated upward Möbius transform.
+		fumt(betaNume[j], alphaNume[j], nh, k); 
+	}
+	
+
+	void compute_alphaInOut(int j, int *Vh, int nh){
+		// Use fast truncated upward Möbius transform.
+		fumt(betaInOut[j], alphaInOut[j], nh, k); 
+	}
+	
+	
+	void compute_g_forward(int nh){	
+		sub_gf(0, nh, 0);
+	
+	}
+	
+	
+	void compute_gNume_forward(int nh){	
+		sub_gfNume(0, nh, 0);
+	
+	}
+	
+
+	void sub_gf(int d, int nh, int S){
+		
+		if (d < nh){
+			sub_gf(d+1, nh, S);
+			sub_gf(d+1, nh, S | (1 << d)); 
+		}
+		else {
+			double sum = MARK; 
+			int T = S, J = 1;
+			
+			for (int j = 0; j < nh; j ++){
+				if (T & 1){
+					// Now S - J is a subset of S.
+					
+					double w = alpha[j][S - J] + gf[S - J];
+					//LOGADD(sum, w);
+					logAdd_New(sum, w);
+				} 
+					
+				T >>= 1; J <<= 1;
+			}
+			if (S == 0) 
+				gf[0] = 0; 
+			else 
+				gf[S] = sum;
+		}
+	}
+	
+	
+		void sub_gfNume(int d, int nh, int S){
+		
+		if (d < nh){
+			sub_gfNume(d+1, nh, S);
+			sub_gfNume(d+1, nh, S | (1 << d)); 
+		}
+		else {
+			double sum = MARK; 
+			int T = S, J = 1;
+			
+			for (int j = 0; j < nh; j ++){				
+				if (T & 1){
+					// Now S - J is a subset of S.
+					
+					double w = alphaNume[j][S - J] + gfNume[S - J];
+					//LOGADD(sum, w);
+					logAdd_New(sum, w);
+				} 
+	
+				T >>= 1; J <<= 1;
+			}
+			if (S == 0) 
+				gfNume[0] = 0; 
+			else 
+				gfNume[S] = sum;
+		}
+	}
+	
+	
+	
+	void compute_g_backward(int nh){
+		sub_gb(0, nh, 0);
+	
+	}
+	
+	
+	void sub_gb(int d, int nh, int S){
+		if (d < nh){
+			sub_gb(d+1, nh, S);
+			sub_gb(d+1, nh, S | (1 << d)); 
+		}
+		else {
+			double sum = MARK; 
+			int T = S, J = 1, complS = (1 << nh) - 1 - S;
+			for (int j = 0; j < nh; j ++){
+				if (T & 1){
+					// Now S - J is a subset of S.
+					double w = alpha[j][complS] + gb[S - J];
+					//LOGADD(sum, w);
+					logAdd_New(sum, w);
+				} 		
+				T >>= 1; J <<= 1;
+			}
+			if (S == 0) gb[0] = 0; else gb[S] = sum;
+		}
+	}
+	
+
+	double eval_edge(int i, int j, double *a, double *b, int nh, int k){
+		int T = 1 << i;  
+		return sub_eval_edge(-1, 1, T, i, j, a, b, nh, k);
+	}
+	
+
+	double sub_eval_edge(
+		int tprev, int d, int T, int i, int j, double *a, double *b, int nh, int k){
+		
+		//cerr<<" T:"; print_set(cerr, T); 
+		//cerr<<": "<<a[T]<<"; "<<b[T]<<endl;
+		
+		//if T, d = |G_v| = k	
+		if (d == k){
+			return a[T] + b[T];
+		}
+		
+		//if  T < k, can add more
+		double sum = a[T] + b[T];
+		for (int t = tprev + 1; t < nh; t ++){
+			if (t == i || t == j) continue;
+			
+			int Tnext = T | (1 << t);
+			double w = sub_eval_edge(t, d+1, Tnext, i, j, a, b, nh, k);
+			//LOGADD(sum, w);
+			logAdd_New(sum, w);
+		}
+		return sum;
+	}
+	
+	
+	double eval_edge_mixIndegree(int i, int j, double * Gamma, double * Beta_j, int nh, int k){
+		int T = 1 << i;  
+		return sub_eval_edge_mixIndegree(-1, 1, T, i, j, Gamma, Beta_j, nh, k);
+	}
+	
+	
+	double sub_eval_edge_mixIndegree(
+		int tprev, int d, int T, int i, int j, double * Gamma, double * Beta_j, int nh, int k){
+		
+		//cerr<<" T:"; print_set(cerr, T); 
+		//cerr<<": "<<a[T]<<"; "<<b[T]<<endl;
+		
+		//if T, d = |G_v| = k	
+		if (d == k){
+			double sumRes;
+			if(Beta_j[T] == MARK){
+				cerr<<"\n**** Beta_j[T] == MARK ";
+		   	}
+			
+			//return (Gamma[T] + Beta_j[T]);
+			if(Gamma[T] == LOG_ZERO){
+				sumRes = LOG_ZERO;
+			}
+					
+			else if(Gamma[T] <= 0){
+				sumRes = Beta_j[T] + Gamma[T];
+			}
+			else{
+				cerr<<"\n**** Gamma[T] > 0 ";
+				sumRes = - ( Beta_j[T] - Gamma[T] );
+
+			}
+			return sumRes;
+	
+		}
+		
+		//if  T < k, can add more
+		//double sum = Gamma[T] + Beta_j[T];
+		double sum;
+		if(Beta_j[T] == MARK){
+			cerr<<"\n**** Beta_j[T] == MARK ";
+		}
+		if(Gamma[T] == LOG_ZERO){
+				sum = LOG_ZERO;
+		}
+					
+		else if(Gamma[T] <= 0){
+			sum = Beta_j[T] + Gamma[T];
+		}
+		else{
+			cerr<<"\n**** Gamma[T] > 0 ";
+			sum = - ( Beta_j[T] - Gamma[T] );
+
+		}
+		
+	
+		for (int t = tprev + 1; t < nh; t ++){
+			if (t == i || t == j) continue;
+
+			int Tnext = T | (1 << t);
+			double w = sub_eval_edge_mixIndegree(t, d+1, Tnext, i, j, Gamma, Beta_j, nh, k);
+			logAddComp(sum, w);
+		}
+		return sum;
+	}
+	
+	
+	double eval_edge_mixIndegreeNoLog(int i, int j, double * Gamma, double * Beta_j, int nh, int k){
+		int T = 1 << i;  
+		return sub_eval_edge_mixIndegreeNoLog(-1, 1, T, i, j, Gamma, Beta_j, nh, k);
+	}
+	
+
+	double sub_eval_edge_mixIndegreeNoLog(
+		int tprev, int d, int T, int i, int j, double * Gamma, double * Beta_j, int nh, int k){		
+		//cerr<<" T:"; print_set(cerr, T); 
+		//cerr<<": "<<a[T]<<"; "<<b[T]<<endl;
+		
+		//if T, d = |G_v| = k	
+		if (d == k){
+			//Lose precision
+			//return (Gamma[T] * exp(Beta_j[T]));
+			double product_res;
+			//if Beta_j[T]  has not been initialized
+			if(Beta_j[T] == MARK){
+				cerr<<"***Beta_j[T]  has not been initialized" << endl;
+				product_res = 0;		
+			}
+			else{
+				if(Gamma[T] == 0){
+				 	product_res = exp(Beta_j[T]);
+				}
+				else if(Gamma[T] > 0){
+					product_res = exp(Beta_j[T] + log(Gamma[T]));
+				}
+				else{
+					product_res = - exp(Beta_j[T] + log(-Gamma[T]));
+				}
+				
+			}
+
+			return product_res;
+			
+		}
+		
+		//if  T < k, can add more
+		//double sum = Gamma[T] * exp(Beta_j[T]);
+		double sum;
+		double product_res;
+		
+			//if Beta_j[T]  has not been initialized
+			if(Beta_j[T] == MARK){
+				cerr<<"***Beta_j[T]  has not been initialized" << endl;
+				product_res = 0;		
+			}
+			else{
+				if(Gamma[T] == 0){
+				 	product_res = exp(Beta_j[T]);
+				}
+				else if(Gamma[T] > 0){
+					product_res = exp(Beta_j[T] + log(Gamma[T]));
+				}
+				else{
+					product_res = - exp(Beta_j[T] + log(-Gamma[T]));
+				}
+				
+			}
+			
+		sum = product_res;
+		for (int t = tprev + 1; t < nh; t ++){
+			if (t == i || t == j) continue;
+
+			int Tnext = T | (1 << t);
+			double w = sub_eval_edge_mixIndegreeNoLog(t, d+1, Tnext, i, j, Gamma, Beta_j, nh, k);
+			//LOGADD(sum, w);
+			sum += w;
+		}
+		return sum;
+	}
+	
+	
+	Model *model;
+	
+	double **alpha, **beta;
+	double **alphaNume, **betaNume;
+	
+	double *gf, *gb;
+	
+	double *gfNume;
+	int k;
+	
+	double **alphaInOut, **betaInOut;
+	int * inFeatureEdges; 
+	int * outFeatureEdges; 
+	
+	
+};
+
+
+
+#endif
diff --git a/var_lib_genenet_bnw/k-best/src/buildk_poster.sh b/var_lib_genenet_bnw/k-best/src/buildk_poster.sh
new file mode 100644
index 00000000..a7c11183
--- /dev/null
+++ b/var_lib_genenet_bnw/k-best/src/buildk_poster.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+D=g++
+
+$D -o get_kbest_parents get_kbest_parents.cc 
+$D -o get_kbest_nets get_kbest_nets.cc 
+
diff --git a/var_lib_genenet_bnw/k-best/src/cfg.h b/var_lib_genenet_bnw/k-best/src/cfg.h
new file mode 100644
index 00000000..15e3fe89
--- /dev/null
+++ b/var_lib_genenet_bnw/k-best/src/cfg.h
@@ -0,0 +1,9 @@
+#ifndef __CFG_H_
+#define __CFG_H_
+
+#define MAX_NOF_VARS (32)
+#define LARGEST_SET(NOF_VARS) ((NOF_VARS)==MAX_NOF_VARS?(varset_t)~0:(1U<<(NOF_VARS))-1)
+typedef unsigned int varset_t;
+typedef double score_t;
+
+#endif
diff --git a/var_lib_genenet_bnw/k-best/src/data2netk_poster.sh b/var_lib_genenet_bnw/k-best/src/data2netk_poster.sh
new file mode 100644
index 00000000..19d8f7cd
--- /dev/null
+++ b/var_lib_genenet_bnw/k-best/src/data2netk_poster.sh
@@ -0,0 +1,56 @@
+#!/bin/bash
+
+binpath=`dirname $0`
+
+if [ $# -ne 4 ]; then
+    echo Usage: data2net.sh datafile resultdir k 1>&2
+    exit 1
+fi
+
+datafile=$1;  shift
+#score=$1;     shift
+rdir=$1;      shift
+k=$1;shift
+n=$1;shift
+
+nof_vars=`head -1 $datafile|wc -w`
+#echo "The number of variables is $nof_vars."
+
+#HR:
+if [ "$n" -eq 0 ]
+then
+    maxindegree=`expr $nof_vars - 1`
+else
+    maxindegree=$n
+fi
+
+#maxindegree=`expr $nof_vars - 1`
+#echo "maxindegree is $maxindegree."
+
+#HR:
+nof_instances=`cat $datafile | wc -l`
+#delete the header and type
+nof_instances=`expr $nof_instances - 2`
+#echo "The number of instances is $nof_instances."
+
+
+START=$(date +%s%N)
+$binpath/get_kbest_parents $nof_vars ${rdir} $k
+#HR
+END=$(date +%s%N)
+#DIFF=$(( $END - $START ))
+DIFF2=$(( $END - $START ))
+#echo "get_kbest_parents is done."
+#echo "get_kbest_parents took $DIFF2 n-seconds."
+
+START=$(date +%s%N)
+$binpath/get_kbest_nets $nof_vars ${rdir} $k
+#HR
+END=$(date +%s%N)
+#DIFF=$(( $END - $START ))
+DIFF3=$(( $END - $START ))
+#echo "get_kbest_nets is done."
+#echo "get_kbest_nets took $DIFF3 n-seconds."
+
+DIFF=`expr $DIFF1 + $DIFF2 + $DIFF3`
+#echo "The total process took $DIFF n-seconds."
diff --git a/var_lib_genenet_bnw/k-best/src/files.h b/var_lib_genenet_bnw/k-best/src/files.h
new file mode 100644
index 00000000..f11dd09e
--- /dev/null
+++ b/var_lib_genenet_bnw/k-best/src/files.h
@@ -0,0 +1,12 @@
+#ifndef __FILES_H__
+#define __FILES_H__
+
+#include <stdio.h>
+
+int    nof_lines(char* filename);
+char*  create_fn(char* dirname, int i, char* ext);
+FILE*  open_file(char* dirname, int i, char* ext, char* mode);
+FILE** open_files(int nof_vars, char* dirname, char* ext, char* mode);
+void   free_files(int nof_vars, FILE** files);
+
+#endif
diff --git a/var_lib_genenet_bnw/k-best/src/files.o b/var_lib_genenet_bnw/k-best/src/files.o
new file mode 100644
index 00000000..33f376d3
--- /dev/null
+++ b/var_lib_genenet_bnw/k-best/src/files.o
Binary files differdiff --git a/var_lib_genenet_bnw/k-best/src/get_kbest_nets b/var_lib_genenet_bnw/k-best/src/get_kbest_nets
new file mode 100644
index 00000000..1c4a6041
--- /dev/null
+++ b/var_lib_genenet_bnw/k-best/src/get_kbest_nets
Binary files differdiff --git a/var_lib_genenet_bnw/k-best/src/get_kbest_nets.cc b/var_lib_genenet_bnw/k-best/src/get_kbest_nets.cc
new file mode 100644
index 00000000..2ee35265
--- /dev/null
+++ b/var_lib_genenet_bnw/k-best/src/get_kbest_nets.cc
@@ -0,0 +1,1552 @@
+#include <iostream>
+#include <fstream>
+#include <iomanip>
+//#include "varpar.h"
+#include <stdlib.h>
+#include <math.h>
+#include <list>
+#include <stdio.h>
+#include <vector>
+#include "cfg.h"
+#include <string.h>
+#include <cmath>
+//HR
+//#define EPSILON 0.001
+#define EPSILON 0.00001
+
+
+//HR: Add for hash_set
+#if __GNUC__ < 3 && __GNUC__ >= 2 && __GNUC_MINOR__ >= 95
+# include <hash_set>
+# include <functional>
+# define gnu_namespace std
+#elif __GNUC__ >= 3
+# include <ext/hash_set>
+# if __GNUC_MINOR__ == 0
+# include <functional>
+# define gnu_namespace std
+# else
+# include <ext/functional>
+# define gnu_namespace __gnu_cxx
+# endif
+#else
+# include <hash_set.h>
+# include <functional.h>
+# define gnu_namespace std
+#endif
+using namespace gnu_namespace;
+#include <set>
+//
+
+
+using namespace std;
+
+
+#define MARK 9e99
+#define LOG_ZERO -1e101
+
+//HR: add from UpdateHR.h to deal with the problem in sum = 0 in comp_post()
+//call by reference to the original value
+//the log sum result is stored in logA
+
+#define epsilon 1.0e5
+
+bool logSpecValEquals(double logX, double logSpecVal){
+	return (logX >= logSpecVal - epsilon && logX <= logSpecVal + epsilon);
+}
+
+void logAddComp(double & logA, double & logB){
+
+    	//if(logA == MARK){
+	    if(logSpecValEquals(logA, MARK)){
+    		logA = logB;
+    	}
+    	//else if (logA == LOG_ZERO){
+    	else if (logSpecValEquals(logA, LOG_ZERO)){
+    		logA = logB;
+    	}
+    	//else if(logB == MARK){
+    	else if(logSpecValEquals(logB, MARK)){
+    		logA = logA;
+    	}
+    	//else if(logB == LOG_ZERO){
+    	else if(logSpecValEquals(logB, LOG_ZERO)){
+    		logA = logA;
+    	}
+    	
+    	
+    	//Neither logA nor logB is MARK/LOG_ZERO
+    	else{
+    		//1
+    		if(logA < 0 && logB < 0 ){
+    			//1.1
+				//Gaurd logB-logA <= 100 to avoid that exp(logB-logA) go to inf
+	    		if(logB - logA <= 100 ){
+	    			logA = logA + log( 1 + exp(logB-logA) );
+	
+	    		} 
+	    		//1.2		
+	    		//if logB - logA > 100, then logB > 100 + logA so that B is much bigger than A (B > e^100 * A)
+	    		//    So (A + B) almost = B 
+	    		else{
+	    			//logA = logB; 
+		    		//The following is the real formula,; but it is almost same as //logA = logB; 
+		    		logA = logB + log( exp(logA - logB) + 1);
+	    		}
+    		}
+    		
+    		//2
+    		else if(logA > 0 && logB > 0){
+    			//always make exp(.): . > 0
+    			if(-logB + logA <= 100){
+    				//2.1
+    				logA = -( -logA + log( 1 + exp(-logB+logA) ) );
+    			} 			
+    			else{
+    				//2.2
+    				logA = -( -logB + log( 1 + exp(-logA+logB) ) );
+    			}
+    			
+    		}
+    		//3
+    		else if(logA < 0 && logB > 0){
+    			//3.1
+    			if(logA + logB > 0){   	
+    				if(logA + logB <= 100){
+    					//3.1.2
+    					logA = -logB + log( exp(logA + logB) - 1 );
+    				}	
+    				else{
+    					//3.1.1
+    					logA = logA + log( 1 - exp(-logB-logA) );
+    				}	
+	
+    			}
+    			//3.2
+    			else if(logA + logB < 0){
+    				if(-logA - logB <= 100){
+    					//3.2.2
+    					logA = -( logA + log( exp(-logB-logA)  - 1) );
+    				}
+    				else{
+    					//3.2.1
+    					logA = - ( -logB + log(1 - exp(logA+logB) ) );
+    				}
+
+    			}
+    			//3.3
+    			else{
+    				logA = LOG_ZERO;
+    			}
+    		}
+    		//4
+    		else if(logA > 0 && logB < 0){
+    			//4.1
+    			if(logA + logB > 0){
+    				if(logA + logB <= 100){
+    					//4.1.2
+    					logA = -logA + log( exp(logB+logA) - 1);
+    				}
+    				else{
+    					//4.1.1
+    					logA = logB + log( 1 - exp(-logA-logB) );
+    				}
+    				
+    			}
+    			//4.2
+    			else if(logA + logB < 0){
+    				if(-logA-logB <= 100){
+    					//4.2.2
+    					logA = -( logB + log( exp(-logA-logB) - 1) );
+    				}
+    				else{
+    					//4.2.1
+    					logA = -( -logA + log(1 - exp(logB+logA)) );
+    				}
+	
+    			}
+    			//4.3
+    			else{
+    				logA = LOG_ZERO;
+    			}			
+    		}
+		
+    	}
+	
+} // end of void logAddComp(double & logA, double & logB)c
+
+
+
+//HR: Note: The whole program supposes that max no. of vars = 32 and hardcord 32
+
+
+//Convert the parent set to the appropriate variable set
+//HR:F
+varset_t parset2varset(int v, varset_t set){
+  	varset_t sinkleton = 1U<<v;
+  	varset_t mask      = sinkleton - 1;
+  	varset_t low       = set &  mask;
+  	varset_t high      = set & ~mask;
+  	return (high<<1) | low;
+}
+
+
+
+/*================================================================*/
+//class for bnets 
+//HR:F
+//for (net, score) pair
+//  each net[j] (0 <= j <= 32-1) is the binary repres of the parents
+class net_set{
+	public:
+		score_t score;
+		varset_t net[32];
+
+		net_set(){
+			score=0.0000;
+			for(int j=0;j<32;j++){
+				net[j]=0;
+			}
+		}
+
+		friend int operator<(net_set s1,net_set s2);
+		friend int operator==(net_set s1,net_set s2);
+		friend int operator>(net_set s1,net_set s2);
+		friend bool same_obj(net_set s1, net_set s2, int nof_vars);
+
+};
+
+//HR:F
+/*================================================================*/
+
+int operator<(net_set s1,net_set s2){
+	if(fabs(s1.score-s2.score)<EPSILON){
+		return false;
+	}
+    return(s1.score<s2.score);
+}
+
+int operator>(net_set s1,net_set s2){
+	if(fabs(s1.score-s2.score)<EPSILON){
+		return false;
+	}
+    return(s1.score>s2.score);
+}
+
+int operator==(net_set s1,net_set s2){
+    return(fabs(s1.score-s2.score)<EPSILON);
+}
+
+//HR: check whether s1 and s2 are the same
+bool same_obj(net_set s1, net_set s2, int nof_vars){
+
+    bool flag=true;
+
+    for(int j=0;j<nof_vars;j++){
+        if(s1.net[j]!=s2.net[j]){
+			//cout<<"************************";
+            flag=false;
+            break;
+        }
+    }
+	//cout<<"Flag "<<flag;
+	//		if(flag==true)
+	//	{
+		//	if(fabs(s1.score-s2.score)<0.1)
+			//	flag=true;
+		//	else flag=false;
+	//	}
+			
+    return(flag);
+}
+
+//HR: check whether s1 and s2 are the same
+bool same_obj(net_set s1, net_set s2){
+
+    bool flag=true;
+
+    for(int j=0;j<MAX_NOF_VARS;j++){
+        if(s1.net[j]!=s2.net[j]){
+			//cout<<"************************";
+            flag=false;
+            break;
+        }
+    }
+	//cout<<"Flag "<<flag;
+	//		if(flag==true)
+	//	{
+		//	if(fabs(s1.score-s2.score)<0.1)
+			//	flag=true;
+		//	else flag=false;
+	//	}
+			
+    return(flag);
+}
+//
+
+/*================================================================*/
+//HR:F
+//HR: Refined
+void insert_vec(list<net_set>* v,net_set s, int k, int nof_vars){
+    list<net_set>::iterator it;
+    //HR: can improve its time
+    //first check whether v->size() > 0 && s < v->back()
+    //see Lav's comment
+    
+    
+	bool flag=false;
+
+     
+     //HR: Refined
+     //
+     if( (v->size() > 0) && (s < v->back()) ){
+     	v->push_back(s);
+     	flag=true;
+     }
+     else{
+     //
+     
+        for(it=v->begin();it!=v->end();it++){
+        	if(same_obj(s,*it,nof_vars)){
+//				cout<<"Same object so not inserted!!!!!!!!!!!!!"<<endl;
+				flag=true;
+                break;
+            }
+            else if(s>(*it)){
+	//			cout<<"score of s:"<<s.score<<"Score of kbnet element "<<(*it).score<<endl;
+                v->insert(it,s);
+				flag=true;
+                break;
+            }
+						
+        }
+        
+     }
+
+		if(flag==false){
+			v->push_back(s);
+		}
+    	if(v->size()>k){
+        	v->pop_back();
+      	}
+      	
+		//v->unique();
+}
+
+/*================================================================*/
+//class for bparents
+//HR:F
+//HR: (variable set, score) pair
+class score_network{
+	public:
+		score_t scores;
+		varset_t vset;
+
+	friend int operator<(score_network s1,score_network s2);
+    friend int operator==(score_network s1,score_network s2);
+    friend int operator>(score_network s1,score_network s2);
+    friend bool same_obj(score_network s1, score_network s2);
+
+};
+
+
+//HR:F
+int operator<(score_network s1,score_network s2){
+    if(fabs(s1.scores-s2.scores)<EPSILON){
+        return false;
+    }
+    return(s1.scores<s2.scores);
+
+}
+
+int operator>(score_network s1,score_network s2){
+ 	if(fabs(s1.scores-s2.scores)<EPSILON){
+        return false;
+    }
+    return(s1.scores>s2.scores);
+
+}
+
+int operator==(score_network s1,score_network s2){
+	return(fabs(s1.scores-s2.scores)<EPSILON);
+}
+
+
+bool same_obj(score_network s1, score_network s2){
+    return((s1==s2)&&(s1.vset==s2.vset));
+}
+
+
+
+
+void insert_vec(list<score_network>* v,score_network s, int k)
+  {
+    list<score_network>::iterator it;
+
+    if( s < v->back())
+      {
+        v->push_back(s);
+      }
+    else
+      {
+        for(it=v->begin();it!=v->end();it++)
+          {
+    //        if(same_obj(s,*it))
+      //        {
+        //        break;
+          //    }
+//            else
+ if(s>(*it))
+              {
+                v->insert(it,s);
+                break;
+              }
+
+          }
+      }
+
+    if(v->size()>k)
+      {
+        v->pop_back();
+      }
+
+  }
+
+/*================================================================*/
+//class for node
+//HR:F
+class node{
+	public:
+		int ip;
+		int in;
+		score_t score;
+
+		node(int x, int y, score_t z){
+        	ip=x;
+          	in=y;
+			score=z;
+        }
+
+		friend int operator<(node s1,node s2);
+		friend int operator==(node s1,node s2);
+		friend int operator>(node s1,node s2);
+		friend bool same_obj(node s1, node s2);
+};
+
+/*================================================================*/
+
+int operator<(node s1,node s2){
+ 	if(fabs(s1.score-s2.score)<EPSILON){
+     	return false;
+    }
+    return(s1.score<s2.score);
+}
+
+
+int operator>(node s1,node s2){
+
+	if(fabs(s1.score-s2.score)<EPSILON){
+        return false;
+   	}
+    return(s1.score>s2.score);
+}
+
+
+int operator==(node s1,node s2){
+	return(fabs(s1.score-s2.score)<EPSILON);
+}
+
+
+bool same_obj(node s1, node s2){
+	return((s1==s2)&&(s1.ip==s2.ip)&&(s1.in==s2.in));
+}
+
+/*================================================================*/
+
+//HR: F
+void print_queue(list<net_set> v[],int size,int nof_vars){
+
+    list<net_set>::iterator iter;
+
+	for(int j=0;j<size;j++){
+    	for(iter=v[j].begin();iter!=v[j].end();iter++){
+      		//HR:
+      		//kbnetscore[j] can have at most k (net, score) pairs
+        	cout<<"kbnetscore "<<j<<"    Score:"<<(*iter).score<<"   net   ";
+			for(int p=0;p<nof_vars;p++){
+				cout<<(*iter).net[p];
+			}
+			cout<<endl;
+    	}
+	}
+}
+
+//HR: Add
+void print_netscore(net_set ns,int nof_vars){
+
+
+        cout<<"netscore "<<"    Score:"<<ns.score<<" \tnet   "; //<<endl;
+      	for(int p=0;p<nof_vars;p++){
+         	cout<<ns.net[p] << " ";
+        }
+        cout<<endl;
+        cout<<endl;
+
+}
+//
+
+void print_queue(vector<score_network>* v){
+
+    vector<score_network>::iterator iter;
+
+    for(iter=v->begin();iter!=v->end();iter++){
+        cout<<"bparents    "<<(*iter).vset<<","<<(*iter).scores<<"  ,,  ";
+    }
+
+}
+
+void print_queue(list<node>* v){
+
+   	list<node>::iterator iter;
+	cout<<"fringe"<<endl;
+    for(iter=v->begin();iter!=v->end();iter++){
+      	cout<<"   ip "<<(*iter).ip<<", in "<<(*iter).in<<" score "<<(*iter).score;
+    }
+
+}
+
+void print_queue(vector<net_set>* v,int nof_vars){
+
+    vector<net_set>::iterator iter;
+
+    for(iter=v->begin();iter!=v->end();iter++){
+//      cout<<"    "<<(*iter).bsps<<","<<(*iter).scores;
+		cout<<"bnets "<<"    Score:"<<(*iter).score<<"   net   "<<endl;
+        for(int p=0;p<nof_vars;p++){
+            cout<<(*iter).net[p];
+        }
+
+    }
+}
+
+void print_queue(list<net_set>* v,int nof_vars){
+
+    list<net_set>::iterator iter;
+
+    for(iter=v->begin();iter!=v->end();iter++){
+//    	cout<<"    "<<(*iter).bsps<<","<<(*iter).scores;
+        cout<<"kbnet "<<"    Score:"<<(*iter).score<<"   net   "<<endl;
+      	for(int p=0;p<nof_vars;p++){
+         	cout<<(*iter).net[p];
+        }
+    }
+}
+
+
+
+  
+//HR: call insert_vec(&fringe,n,k);
+//HR: by this way, fringe is in descending order
+//HR: Lav's code is wrong
+//HR: corrected
+void insert_vec(list<node>* v,node s, int k){
+    list<node>::iterator it;
+    
+    //HR: test
+    //bool sameObj = false;
+    //bool inserted = false;
+    //
+
+    //if( s < v->back()){ same
+    if( (v->size() == 0) || (s < v->back())){    	
+        v->push_back(s);
+    }
+    else{
+        for(it=v->begin();it!=v->end();it++){
+        //comment it out will give the different answer. Because Lav's original is wrong, it will still insert the same object. It will eventually pop the correct end > k
+        //
+            if(same_obj(s, *it)){
+                break;                
+//                sameObj = true;
+//                cout << "s: ";
+//                print_node(s);
+//                cout << "*it: ";
+//                print_node(*it);
+//                cout << endl;
+//                print_queue(v);
+             
+            }
+            else{
+         //
+ 				if(s>(*it)){
+                	v->insert(it,s);
+                	//inserted = true;
+                	break;
+            	}
+            }
+            
+      	}
+      	
+      	//HR: test
+//      	if(sameObj == true && inserted == true){
+//      		cout << "Error: sameObj == true && inserted = true" << endl;
+      		
+//      		  cout << "s: ";
+//                print_node(s);
+//                print_queue(v);    		
+//      	}
+  	}
+
+    if(v->size()>k){
+    	//cout << "\n\nv->size()>k happens,  v->pop_back()\n" << endl;
+        v->pop_back();  
+    }
+	//	cout<<"Inserted:"<<endl;
+}
+  
+
+
+
+//===================================================================//
+//HR: Add hash_set to store net_set (i.e. (net, score) pair
+namespace gnu_namespace {
+	
+	template<>
+
+	struct hash<const net_set*> {
+	
+		hash<unsigned> hasher_ns;
+		
+		size_t operator()(const net_set* ns) const {
+			return hasher_ns((unsigned) roundl(- ns->score*10)); // wrong hash function??
+		}
+
+	}; //end of struct
+
+} //end of namespace
+
+
+
+struct eqNetScore{
+	bool operator()(const net_set* ns1, const net_set* ns2) const{
+		return same_obj(*ns1, *ns2);
+	}
+};
+
+
+
+typedef hash_set<const net_set *, hash<const net_set *>, eqNetScore> NetScoreHashSet;
+
+NetScoreHashSet knets;
+
+
+//HR: Add
+void print_nsHashSet(NetScoreHashSet nsHSet, int nof_vars){
+	for(NetScoreHashSet::iterator it = nsHSet.begin(); it != nsHSet.end(); it++){
+		print_netscore(**it, nof_vars);
+	}
+}
+//
+
+
+
+//=====================================================================================//
+
+/*================================================================*/
+
+//HR:F
+//HR: call gettopk(&bnets,&bparents,&kbnetscore[varset],k,sink,nof_vars);
+void gettopk(vector<net_set>* bnets, vector<score_network>* bparents, list<net_set>* kbnet, int k, varset_t sink,int nof_vars){
+	int h;
+	int ipmax=bparents->size();
+//		cout<<"ipmax: "<<ipmax;
+		
+	int inmax=bnets->size();
+	//	cout<<"inmax: "<<inmax;
+	
+	//HR: Add hash_set generated here
+	
+	//
+	
+	int ip,in;
+
+	net_set * netwP;
+	
+	score_t score;
+	
+	list<node> fringe;
+	
+	//HR: different from Algo4, here start from 0 vs. 1
+	node n(0,0,(bparents->at(0)).scores + (bnets->at(0)).score);
+	insert_vec(&fringe,n,k);
+	//	print_queue(&fringe);
+		// scanf("%d",&h);
+		
+	NetScoreHashSet::iterator iter1;
+
+	while(!fringe.empty()){
+		//	cout<<"Fringe not empty"<<endl;		
+		n = fringe.front();
+		fringe.pop_front();
+		//	cout<<"Fringe After popping"<<endl;
+		//	print_queue(&fringe);
+		ip=n.ip;
+		in=n.in;
+		score=n.score;				
+		//	cout<<"Popped node"<<endl;
+		//	cout<<"ip "<<ip<<"in "<<in<<"score "<<score<<endl;
+			
+		if((kbnet->size())<k){
+			//		cout<<"Size < k"<<endl;
+			//HR: Add
+			//net_set netw;
+			//
+			netwP = new net_set();
+			for(int j=0;j<nof_vars;j++){
+				(*netwP).net[j]=(bnets->at(in)).net[j];
+				//			cout<<"Net w j"<<netw.net[j]<<endl;
+			}						
+			(*netwP).net[sink]=((bparents->at(ip)).vset);
+			//cout<<"net w sinkleton"<<netw.net[sinkleton]<<endl;
+			(*netwP).score=score;
+			//cout<<"net score "<<netw.score<<endl;
+			//cout<<"Before inserting:"<<endl;
+			//	print_queue(kbnet,nof_vars);
+			
+			//HR: Add hash_set knets check here
+			//if not find netw
+			if((iter1 = knets.find(netwP)) == knets.end()){
+				//Lav
+			 	//every time call by value of netw
+
+				insert_vec(kbnet, *netwP, k, nof_vars);
+				//cout<<"After inserting"<<endl;
+				//print_queue(kbnet,nof_vars);
+				//scanf("%d",&h);
+				//cout<<"Inserted into kbnetscore"<<endl;
+				//
+				//HR: Add to knets
+				knets.insert(netwP);
+
+		   	}
+		   	
+		   	else{
+		   		if( same_obj(*netwP, **iter1, nof_vars) == false ){
+		   			cout<<"Error: same_obj(*netwP, **iter1, nof_vars) == false"<<endl;
+		   			return;
+		   		}
+
+		   		//delete the memory
+		   		delete netwP;
+
+		   	}
+		   	
+			//
+			
+		}
+				
+		else if((fabs(score-(kbnet->back()).score)>EPSILON)&&(score>(kbnet->back().score))){
+					//	cout<<"score>kbnetback's score"<<endl;
+				
+			//HR: Add
+			//net_set netw;
+			//	
+			netwP = new net_set();
+			for(int j=0;j<nof_vars;j++){
+                (*netwP).net[j]=(bnets->at(in)).net[j];
+				//		cout<<"Net w j"<<netw.net[j]<<endl;
+             }
+            (*netwP).net[sink]=(bparents->at(ip)).vset;				
+			//cout<<"net w sinkleton"<<netw.net[sinkleton]<<endl;
+			(*netwP).score=score;
+			//cout<<"net score"<<netw.score<<endl;
+			//cout<<"Before inserting:"<<endl;
+			//	print_queue(kbnet,nof_vars);
+
+			
+			//HR: Add hash_set knets check here
+			//if not find
+			if((iter1 = knets.find(netwP)) == knets.end()){
+				
+				net_set lastNs = kbnet->back();
+				
+				//Lav
+				insert_vec(kbnet,*netwP,k,nof_vars);           
+				//cout<<"After inserting"<<endl;
+				//print_queue(kbnet,nof_vars);
+				//scanf("%d",&h);
+				//
+				//HR: Add to knets
+				knets.insert(netwP);
+
+				iter1 = knets.find(&lastNs);
+				
+				if(iter1  == knets.end()){
+					cout << "Error: iter1 should != knets.end() since lastNs should be found in kents" << endl;
+					return;
+				}
+				const net_set * nsTempP = * iter1;
+				
+				knets.erase(&lastNs);  //do not remove 
+				delete nsTempP;
+
+				//HR: remove from kbnet has been done inside knets.insert(netwP);
+			}
+			
+			else{
+		   		if( same_obj(*netwP, **iter1, nof_vars) == false ){
+		   			cout<<"Error: same_obj(*netwP, **iter1, nof_vars) == false"<<endl;
+		   			return;
+		   		}
+				
+				//delete the memory
+				delete netwP;
+				
+
+		   	}
+		   	
+
+
+		}
+		else{
+			return;
+		}
+		
+		//HR: since start from 0 not 1; so use ip<ipmax-1
+		if(ip<ipmax-1){
+			//cout<<"before child:"<<endl;
+			node child(ip+1,in,(bparents->at(ip+1)).scores + (bnets->at(in)).score);
+			//cout<<"after child"<<endl;
+			//cout<<"Fringe before inserting:"<<endl;
+			//print_queue(&fringe);
+	
+			//may add hash_set generated check here
+			
+			insert_vec(&fringe,child,k);
+			//cout<<"Fringe after inserting"<<endl;
+			//print_queue(&fringe);
+			//scanf("%d",&h);
+
+		}
+		if(in<inmax-1){
+			//	cout<<"Fringe before inserting:"<<endl;
+           	// print_queue(&fringe);
+
+			node child(ip,in+1,(bparents->at(ip)).scores + (bnets->at(in+1)).score);
+			
+			//may add hash_set generated check here
+			
+			insert_vec(&fringe,child,k);
+			//cout<<"Fringe after inserting"<<endl;
+
+			//	print_queue(&fringe);
+			// scanf("%d",&h);
+
+		}
+	}//end of while		
+	//	scanf("%d",&h);
+}
+
+/*================================================================*/
+//converts from the best parent sets obtained to actual variable set
+//HR: call conv_net(&kbnetscore[nof_combs-1],k,nof_vars);
+//HR:F
+void conv_net(list<net_set>* kbnet, int k,int nof_vars){	
+	list<net_set>::iterator it;
+ 	//int j=0;
+ 	//each it is one of k best 
+	for(it=kbnet->begin();it!=kbnet->end();it++){
+		for(int p=0;p<nof_vars;p++){
+
+			(*it).net[p]=parset2varset(p,((*it).net[p]));
+	//		j++;
+		}
+	}
+}
+
+/*================================================================*/
+//To convert net string into arc set
+//HR: call net2arc(dirname,k,nof_vars);
+//HR:F
+void net2arc(char* dirname,int k,int nof_vars){
+	score_t s;
+	string str;
+	unsigned int vset;
+	char str1[32];
+	//HR: for each j'th best network
+	for(int j=0;j<k;j++){
+		str.assign(dirname);
+	  	str.append("/");
+    	sprintf(str1,"%d",j);
+    	str.append(str1);
+		str.append("net");
+		FILE* netf=fopen(str.c_str(),"r");
+		if(netf==NULL)
+			break;
+		str.assign(dirname);
+      	str.append("/");
+		str.append("arc");
+      	sprintf(str1,"%d",j);
+      	str.append(str1);
+
+		FILE* arcf=fopen(str.c_str(),"w");
+		fscanf(netf,"%f",&s);
+		//	printf("\n ===network %d",j);
+		for(int p=0;p<nof_vars;p++){
+			//		printf("\n\nVar %d's parents:\n\n",p);
+			fscanf(netf,"%u",&vset);
+			const int SHIFT = 8 * sizeof( unsigned ) - 1;
+   			const unsigned MASK = 1 << SHIFT;
+			for ( int i = 1; i <= SHIFT + 1; i++ ) {
+      			//		cout << ( vset & MASK ? '1' : '0' );
+				if(vset&MASK){
+					fprintf(arcf,"%u %d",SHIFT+1-i,p);
+					fprintf(arcf,"\n");
+				}
+				vset <<= 1;
+      	 	 }
+			//	printf("\n\n");
+		}
+		fclose(netf);			
+		fclose(arcf);
+	}
+}
+
+/*================================================================*/
+//Write net file
+//HR: call write_net(kbnetscore,dirname,k,nof_vars);
+//HR: get files: 0net, 1net, ..., (k-1)net
+void write_net(list<net_set> kbnetscore[],char* dirname,int k,int nof_vars)
+{
+	string str;
+	list<net_set>::iterator it;
+	char str1[10];
+	int j=0;
+	//HR: each it is the one of the k best
+	for(it=kbnetscore[(1U<<(nof_vars))-1].begin();it!=kbnetscore[(1U<<(nof_vars))-1].end();it++){
+    	str.assign(dirname);
+      	str.append("/");
+      	sprintf(str1,"%d",j++);
+      	str.append(str1);
+      	str.append("net");
+      	FILE* netf=fopen(str.c_str(),"w");
+      	fprintf(netf,"%f \n",(*it).score);
+		//	cout<<(*it).score<<endl;
+      	for(int p=0;p<nof_vars;p++){
+			//					(*it).net[p]=parset2varset(
+      		fprintf(netf,"%u \n",(*it).net[p]);
+        }
+      	fclose(netf);
+	}
+
+}
+
+/*================================================================*/
+
+void print_scores(list<net_set> kbnetscore[],char* dirname,int k,int nof_vars){
+//	string str;
+	list<net_set>::iterator it;
+		
+	int j=0;
+	for(j=0;j<((1U<<nof_vars)-1);j++) 
+	for(it=kbnetscore[j].begin();it!=kbnetscore[j].end();it++){
+     	cout<<(*it).score<<endl;
+  	}
+	
+}
+
+/*================================================================*/
+
+
+//HR: Add
+//HR: Update from comp_post_compl, now compute the exact post. prob. using
+//    denominator P(D) instead of \hat{P}(D) = \sum{G \in the set of k best G's} P(G,D)
+//    require exactPD.txt (computed by POSTER) is stored under the directory
+//Compute each edge out of nof_vars * nof_vars, instead of just the best network
+
+void comp_postExact_compl(list<net_set>* kbnet, int k, char* dirname, int nof_vars){
+	
+	//cout << "Start comp_postExact_compl()" << endl;
+	//long double Sum=0.0;
+	//double logSum = LOG_ZERO;
+	
+	list<net_set>::iterator it;
+	
+	//HR: assume k < 5000
+	long double postExact[5000];
+
+	string str;
+	char str1[32];
+	
+	//cout << "dirname = " << dirname << endl;
+	str.assign(dirname);
+    str.append("/");
+    str.append("exactPD.txt");
+    //str.assign("exactPD.txt");
+    
+    FILE *fp;
+	fp=fopen(str.c_str(),"r");
+	double exactPD = 0.0;
+
+	if(!feof(fp)){
+		char c;
+		fscanf(fp, "%lf", &exactPD);
+		fscanf(fp,"%c",&c);	
+	}
+	fclose(fp);
+	//printf("exactPD = %18.8f\n", exactPD);
+
+	
+	str.assign(dirname);
+	str.append("/netpostExact");
+	fp=fopen(str.c_str(),"w");
+
+	//for each it of k best networks
+//	for(it=kbnet->begin();it!=kbnet->end();it++){
+//		//HR: change it
+//		//sum+=exp((*it).score);
+//		logAddComp(logSum, (*it).score); //HR
+//	}	
+//	cout << "logSum: " << logSum << endl; //HR
+//	printf("logSum = %18.6f\n", logSum);
+//	//
+//	long double Sum = exp(logSum); //HR
+//	cout << "Sum: " << exp(logSum) << endl; //HR
+	//
+	
+	int i=0;
+	//for each it of k best networks,  compute equation (4)
+	//each post[i] ( 0 <= i <= k - 1). repre post prob for i'th best network  
+	for(it=kbnet->begin();it!=kbnet->end();it++){
+		//post[i]=(exp((*it).score))/sum;
+		//double logScore = (*it).score;
+		//LOGMINUS_NEW(logScore, logSum)
+		postExact[i]=exp( (*it).score - exactPD ); //
+		fprintf(fp,"%Lg\n",postExact[i]);				
+		i++;
+	}
+	fclose(fp);
+	
+	
+	//Start the update
+	
+	//define and init
+	long double postProbExact[nof_vars][nof_vars];
+	for(int i = 0; i < nof_vars; i++){
+		for (int j = 0; j < nof_vars; j++){
+			postProbExact[i][j] = 0.0;
+		}
+	}
+
+	int listSize = kbnet->size();
+	int num1 = -1;
+	int num2 = -1;
+	
+	
+	//HR: for each j of k best networks, j >=1
+	for(int j=0; j<listSize; j++){
+		str.assign(dirname);
+    	str.append("/");
+    	str.append("arc");
+    	sprintf(str1,"%d",j);
+		str.append(str1);
+		fp=fopen(str.c_str(),"r");
+		//				fp=fopen(str.c_str(),"r");
+		
+		//HR: for each edge in j'th best network
+		while(!feof(fp)){
+			char c;
+			fscanf(fp,"%d",&num1);
+			fscanf(fp,"%d",&num2);
+			fscanf(fp,"%c",&c);	
+			postProbExact[num1][num2] += postExact[j];
+			//HR: needed! why? Otherwise there is error. fscanf() could not exactly overwrite the content of &num1/&num2
+			num1 = -1;
+			num2 = -1;
+
+		}//HR: end of while(!feof(fp));
+		fclose(fp);
+	}//HR: end of for
+	
+	str.assign(dirname);
+	str.append("/postProbExactEachEdge.txt");
+	ofstream totalOf1(str.c_str());
+
+	for(int i = 0; i < nof_vars; i++){
+		for (int j = 0; j < nof_vars; j++){
+			totalOf1 << "" << j << " -> " << i << " \t" << postProbExact[j][i] << endl;
+		}
+	}
+			
+} //end void comp_postExact_compl()
+
+
+
+
+//HR: Add
+//HR: Update from comp_post
+//Compute each edge out of nof_vars * nof_vars, instead of just the best network
+void comp_post_compl(list<net_set>* kbnet, int k, char* dirname, int nof_vars){
+	//long double Sum=0.0;
+	double logSum = LOG_ZERO;
+	list<net_set>::iterator it;
+	//HR: assume k < 5000
+	long double post[5000];
+
+	string str;
+	char str1[32];
+	str.assign(dirname);
+	str.append("/netpost");
+	FILE *fp=fopen(str.c_str(),"w");
+
+	//for each it of k best networks
+	for(it=kbnet->begin();it!=kbnet->end();it++){
+		//HR: change it
+		//sum+=exp((*it).score);
+		logAddComp(logSum, (*it).score); //HR
+	}	
+	//cout << "logSum: " << logSum << endl; //HR
+	//printf("logSum = %18.6f\n", logSum);
+	//
+	long double Sum = exp(logSum); //HR
+	//cout << "Sum: " << exp(logSum) << endl; //HR
+	//
+	
+	int i=0;
+	//for each it of k best networks,  compute equation (4)
+	//each post[i] ( 0 <= i <= k - 1). repre post prob for i'th best network  
+	for(it=kbnet->begin();it!=kbnet->end();it++){
+		//post[i]=(exp((*it).score))/sum;
+		//double logScore = (*it).score;
+		//LOGMINUS_NEW(logScore, logSum)
+		post[i]=exp( (*it).score - logSum ); //
+		fprintf(fp,"%Lg\n",post[i]);				
+		i++;
+	}
+	fclose(fp);
+	
+	
+	//Start the update
+	
+	//define and init
+	long double postProb[nof_vars][nof_vars];
+	for(int i = 0; i < nof_vars; i++){
+		for (int j = 0; j < nof_vars; j++){
+			postProb[i][j] = 0.0;
+		}
+	}
+
+	int listSize = kbnet->size();
+	int num1 = -1;
+	int num2 = -1;
+	
+	
+	//HR: for each j of k best networks, j >=1
+	for(int j=0; j<listSize; j++){
+		str.assign(dirname);
+    	str.append("/");
+    	str.append("arc");
+    	sprintf(str1,"%d",j);
+		str.append(str1);
+		fp=fopen(str.c_str(),"r");
+		//				fp=fopen(str.c_str(),"r");
+		
+		//HR: for each edge in j'th best network
+		while(!feof(fp)){
+			char c;
+			fscanf(fp,"%d",&num1);
+			fscanf(fp,"%d",&num2);
+			fscanf(fp,"%c",&c);	
+			postProb[num1][num2] += post[j];
+			//HR: needed! why? Otherwise there is error. fscanf() could not exactly overwrite the content of &num1/&num2
+			num1 = -1;
+			num2 = -1;
+
+		}//HR: end of while(!feof(fp));
+		fclose(fp);
+	}//HR: end of for
+	
+	str.assign(dirname);
+	str.append("/postProbEachEdge.txt");
+	ofstream totalOf1(str.c_str());
+
+	for(int i = 0; i < nof_vars; i++){
+		for (int j = 0; j < nof_vars; j++){
+			totalOf1 << "" << j << " -> " << i << " \t" << postProb[j][i] << endl;
+		}
+	}
+			
+}
+
+
+
+//Computation of posterior probabilities - This function's call has been commented. Remove the commenting slashes if the posterior probability needs to be computed.
+//HR: call comp_post(&kbnetscore[nof_combs-1],k,dirname);
+
+void comp_post(list<net_set>* kbnet, int k, char* dirname){
+	//long double Sum=0.0;
+	double logSum = LOG_ZERO;
+	list<net_set>::iterator it;
+	long double post[5000];
+
+	string str;
+	char str1[32];
+	str.assign(dirname);
+	str.append("/netpost");
+	FILE *fp=fopen(str.c_str(),"w");
+
+	//for each it of k best networks
+	for(it=kbnet->begin();it!=kbnet->end();it++){
+		//HR: change it
+		//sum+=exp((*it).score);
+		logAddComp(logSum, (*it).score); //HR
+	}	
+	cout << "logSum: " << logSum << endl; //HR
+	//
+	long double Sum = exp(logSum); //HR
+	cout << "Sum: " << exp(logSum) << endl; //HR
+	//
+	
+	int i=0;
+	//for each it of k best networks,  compute equation (4)
+	//each post[i] ( 0 <= i <= k - 1). repre post prob for i'th best network  
+	for(it=kbnet->begin();it!=kbnet->end();it++){
+		//post[i]=(exp((*it).score))/sum;
+		//double logScore = (*it).score;
+		//LOGMINUS_NEW(logScore, logSum)
+		post[i]=exp( (*it).score - logSum ); //
+		fprintf(fp,"%Lg\n",post[i]);				
+		i++;
+	}
+	fclose(fp);
+	
+	
+	ifstream indata;
+	int n=0;
+	int num[50][2];
+	int num1,num2;
+	//		char f[50][20];
+	long double postf[50];
+	str.assign(dirname);
+    str.append("/");
+    str.append("arc0");
+	fp=fopen(str.c_str(),"r");
+	//   	fp=fopen(str.c_str(),"r");
+	i=0;
+	while(!feof(fp)){
+		char c;
+		//HR: for parent
+		fscanf(fp,"%d",&num[i][0]);
+		//HR: for var
+		fscanf(fp,"%d",&num[i][1]);
+		fscanf(fp,"%c",&c);
+
+		//indata>>num[i][1];
+		//HR:
+		//				cout<<"HIIIII"<<num[i][0]<<"'"<<num[i][1]<<endl;
+
+		//				indata.getline(f[i],100);
+		i++;
+	}
+	//HR:
+	//i: the no. of lines in the arc0; so only for the edges in the best network
+	n=i-1;
+	cout<<n<<endl;
+	
+	//HR: postf vs. post
+	//HR: due to equality (5)
+	for(i=0;i<n;i++){
+		postf[i]=post[0];
+	}
+		
+	//indata.close();
+	fclose(fp);
+	int j;
+	
+	//HR: for each j of k best networks, j >=1
+	for(j=1;j<k;j++){
+		str.assign(dirname);
+    	str.append("/");
+    	str.append("arc");
+    	sprintf(str1,"%d",j);
+		str.append(str1);
+		fp=fopen(str.c_str(),"r");
+		//				fp=fopen(str.c_str(),"r");
+		
+		//HR: for each edge in j'th best network
+		while(!feof(fp)){
+			char c;
+			fscanf(fp,"%d",&num1);
+			fscanf(fp,"%d",&num2);
+			fscanf(fp,"%c",&c);
+			//						indata>>num1;
+			//					indata>>num2;
+	
+			//HR:
+			//						cout<<endl<<endl<<endl<<num1<<",,,"<<num2<<endl;
+			//HR: check whether such edge is one of the edeges in the best network 0net
+			for(i=0;i<n;i++){
+//				if(!strcmp(str1,f[i]))
+				//HR: if such edge is one of the edeges in the best network 0net
+				if(num1==num[i][0]&&num2==num[i][1]){
+					postf[i]+=post[j];
+					//HR: can add break; since each edge out of n edges in the best net is different
+				}	
+			}
+			num1=num2=-1;
+		}//HR: end of while(!feof(fp));
+		fclose(fp);
+	}//HR: end of for
+
+	//HR: print out the posterior prob. for each edge in the best network
+	for(j=0;j<n;j++)
+		cout<<postf[j]<<endl;
+			
+}
+
+
+/*================================================================*/
+//inside it: get_top_k for the features
+//HR:F
+void get_kbest_nets(int nof_vars, FILE** fp,int k, char* dirname){
+    int h;
+    //HR: 2^nof_vars
+	varset_t nof_combs = 1U<<(nof_vars);
+	//HR:
+	//cout<<"No of combs:  "<<nof_combs<<endl;
+    //cout<<"Get k best nets"<<endl;
+    //
+	
+	//cout << "before list<net_set> kbnetscore[nof_combs]" << endl;
+	//cerr << "before list<net_set> kbnetscore[nof_combs]" << endl;
+	//HR: net_set is the (net, score) pair
+	//HR: have not yet set each list kbnetscore[W] the size k
+	list<net_set> kbnetscore[nof_combs];
+	//cerr << "after list<net_set> kbnetscore[nof_combs]" << endl;
+	//cout << "after list<net_set> kbnetscore[nof_combs]" << endl;
+    list<net_set>::iterator it;
+    
+	vector<net_set> bnets;
+	
+	//HR: score_network is (variable set, score) pair
+	score_network s;
+	
+	vector<score_network> bparents;
+	
+	//HR: Add hash_set knets here; global may be better so that gettopk can access
+	//NetScoreHashSet knets;
+	//
+	//cout << "before net_set netw" << endl;
+	
+	net_set netw;
+	netw.score=0;
+	for(int j=0;j<nof_vars;j++)
+		netw.net[j]=0;
+	kbnetscore[0].push_back(netw);
+	
+	//cout << "before insert_vec(&kbnetscore[0],netw,k,nof_vars)" << endl;
+		
+	//HR
+	insert_vec(&kbnetscore[0],netw,k,nof_vars);
+		
+	//HR: call void print_queue(list<net_set> v[],int size,int nof_vars)
+	//cout << "print_queue(kbnetscore)" << endl;
+	//print_queue(kbnetscore,(1U<<nof_vars),nof_vars);
+//	scanf("%d",&h);
+//	cout<<"Pushed!!!"<<endl;
+	//
+	
+	varset_t varset;
+	int sink;
+	
+	//HR: W \subset V except empty set; 	
+	//HR: varset is the binary repre of W
+	for(varset=1;varset<nof_combs;varset++){
+		//HR
+//		if(varset % 10000 == 1){
+//			cout<<"====Varset==="<<varset<<endl; //
+//		}
+		//
+		
+		
+		//HR: Add for hash_set knets
+		//totally clean
+		//cout << "knets.clear() begins:" << endl;		
+		int knetsSize = knets.size() ;
+		const net_set * nsPtrA[knetsSize];
+		int j = 0;
+		for(NetScoreHashSet::iterator it = knets.begin(); it != knets.end(); it++){
+			nsPtrA[j++] = *it;
+		}
+		knets.clear();
+
+		//really delete each object
+		for(j = 0; j < knetsSize; j++){
+			delete nsPtrA[j];  //delete (*nsPtrA[j]) is wrong 
+		}		
+		//cout << "knets.clear() ends." << endl;
+		//
+		
+
+ 		//HR: for each sink
+		for(sink = 0; sink<nof_vars;sink++){
+			//		cout<<"Sink "<<sink<<endl;
+			varset_t sinkleton = 1U<<sink;
+			//			cout<<"sinkleton"<<sinkleton<<endl;
+			varset_t upvars;
+			
+			//HR: if sink is the subset of W
+			if (varset & sinkleton){
+				//				cout<<"inside if loop";
+				upvars = varset& ~sinkleton;
+				//			cout<<"Upvars:"<<upvars<<endl;
+				
+				//HR: construct array bnets from kbnetscore[upvars]
+				bnets.clear();
+				bnets.resize(kbnetscore[upvars].size());
+				copy(kbnetscore[upvars].begin(), kbnetscore[upvars].end(), bnets.begin());
+				//	print_queue(&bnets,nof_vars);
+				//	scanf("%d",&h);
+				//cout<<"Copied"<<endl;
+				
+				//HR: construct array bparents from kbps[s][upvars]
+				bparents.clear();
+				while(1){
+					fread(&s.scores,sizeof(score_t),1,fp[sink]);
+					//cout<<"read score"<<endl;
+					if(s.scores==1000.0)
+						break;
+
+					fread(&s.vset,sizeof(varset_t),1,fp[sink]);	
+					//	cout<<"read varset"<<endl;
+					//int num =k;
+					//insert_vec(&bparents,s,num);
+										
+					bparents.push_back(s);
+					//	print_queue(&bparents);
+					//scanf("%d",&h);
+				}
+				
+				//scanf("%d",&h);
+				//printf("\n\n\nB PARENTS ============\n\n");
+				//print_queue(&bparents);
+				//scanf("%d",&h);
+
+				//printf("\n\n\nB nets =================\n\n");
+				//print_queue(&bnets,nof_vars);
+				//scanf("%d",&h);
+
+				//printf("\n\n\nKBNETSCORE %u =================\n\n",varset);
+				//print_queue(&kbnetscore[varset],nof_vars);
+				//scanf("%d",&h);
+
+				////printf("K = %d",k);
+
+				//printf("Sink = %d",sink);
+
+
+
+				//cout<<"Goin to call gettopk"<<endl;
+            	gettopk(&bnets,&bparents,&kbnetscore[varset],k,sink,nof_vars); //new function: for each combination from n: totally 2^n
+				//printf("\n\n\nAfter topkKBNETSCORE %u =================\n\n",varset);
+				//print_queue(&kbnetscore[varset],nof_vars);
+				
+			}//end of if
+
+
+		}//end of for each sink
+		//scanf("%d",&h);
+		
+	}//end of for each W
+	//HR: last clear
+	//cout << "knets.clear() at the end of V begins: " << endl;
+		int knetsSize = knets.size() ;
+		const net_set * nsPtrA[knetsSize];
+		int j = 0;
+		for(NetScoreHashSet::iterator it = knets.begin(); it != knets.end(); it++){
+			nsPtrA[j++] = *it;
+		}
+		knets.clear();
+
+		//really delete each object
+		for(j = 0; j < knetsSize; j++){
+			delete nsPtrA[j];  //delete (*nsPtrA[j]) is wrong 
+		}
+	//cout << "knets.clear() at the end of V ends. " << endl;
+	
+
+	
+	//HR
+	//print_queue(kbnetscore,32,5); //32 = 2^5
+
+	//cout << "main part of get__kbest_nets() is done." << endl;
+	
+	//HR: only consider V, the bianary repre is nof_combs-1
+	conv_net(&kbnetscore[nof_combs-1],k,nof_vars);
+	//cout << "conv_net(&kbnetscore[nof_combs-1],k,nof_vars) is done." << endl;
+		
+	//HR: get files: 0net, 1net, ..., (k-1)net	
+	write_net(kbnetscore,dirname,k,nof_vars);
+	//cout << "write_net(kbnetscore,dirname,k,nof_vars) is done." << endl;
+	
+	net2arc(dirname,k,nof_vars);
+	//cout << "net2arc(dirname,k,nof_vars) is done." << endl;
+	
+	//HR:
+	//cout << endl;
+	//cout << "kbnetscore[nof_combs-1].size() = " << kbnetscore[nof_combs-1].size() << endl;
+	//cout << "1st network score: " << kbnetscore[nof_combs-1].front().score << endl;
+	//cout << "last network score: " << kbnetscore[nof_combs-1].back().score << endl;
+	//cout << "The difference of the scores = " << ( kbnetscore[nof_combs-1].front().score - kbnetscore[nof_combs-1].back().score ) << endl;
+	//cout << endl;
+	//
+
+	//comp_post(&kbnetscore[nof_combs-1],k,dirname);  //new function: compute the posterior prob.
+	comp_post_compl(&kbnetscore[nof_combs-1],k,dirname, nof_vars);	
+	//cout << "comp_post_compl(&kbnetscore[nof_combs-1],k,dirname) is done." << endl;
+	
+	//comp_postExact_compl(&kbnetscore[nof_combs-1],k,dirname, nof_vars);
+	//cout << "comp_postExact_compl(&kbnetscore[nof_combs-1],k,dirname, nof_vars) is not done. we will change it if requires" << endl;
+	
+	//HR:
+	//	print_scores(kbnetscore,dirname,k,nof_vars);	
+	
+}//end of get_kbest_nets
+
+/*================================================================*/
+
+//HR:F
+int main(int argc, char* argv[]){
+	FILE* fp[32];
+	string str;
+	char str1[10];
+	//	printf("argc : %d \n\n",argc);
+	if(argc!=4){
+		fprintf(stderr, "Usage: get_kbest_nets nof_vars dirname k\n");
+        return 1;
+	}
+		
+	int nof_vars = atoi(argv[1]);
+	int k = atoi(argv[3]);
+	//	printf("No of vars: %d   K: %d\n\n",nof_vars,k);
+	for(int j=0;j<nof_vars;j++){
+		str.assign(argv[2]);
+		str.append("/");
+		sprintf(str1,"%d",j);
+		str.append(str1);
+		str.append(".kbps");
+		//		cout<<str<<endl;
+		//HR:   In order to open a file as a binary file, a "b" character has to be included in the mode string
+		fp[j]=fopen(str.c_str(),"rb");
+	}
+	//HR:
+	//cout<<"Calling function getkbestnets\n";
+	//
+	get_kbest_nets(nof_vars, fp, k,argv[2]);
+	//cout<<"Success!"<<endl;
+	return 0;
+		
+}
+	
+
+
diff --git a/var_lib_genenet_bnw/k-best/src/get_kbest_parents b/var_lib_genenet_bnw/k-best/src/get_kbest_parents
new file mode 100644
index 00000000..c31a73ee
--- /dev/null
+++ b/var_lib_genenet_bnw/k-best/src/get_kbest_parents
Binary files differdiff --git a/var_lib_genenet_bnw/k-best/src/get_kbest_parents.cc b/var_lib_genenet_bnw/k-best/src/get_kbest_parents.cc
new file mode 100644
index 00000000..9377d11e
--- /dev/null
+++ b/var_lib_genenet_bnw/k-best/src/get_kbest_parents.cc
@@ -0,0 +1,249 @@
+//HR: formetted only, no code change
+
+#include <string>
+#include <cmath>
+#include <iostream>
+#include "cfg.h"
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <list>
+#define EPSILON 0.001
+
+
+#include "files.h"
+
+using namespace std;
+
+int h;
+
+//class for bparents
+//HR:F
+//HR: (variable set, score) pair
+//This class is to store the best parent set and the corresponding score
+class score_network{
+   	public:
+    	score_t scores;
+		varset_t bsps;
+
+       	score_network(score_t a,varset_t b){ 
+        	scores=a;
+          	bsps=b;
+      	}
+
+        score_network(){
+          	scores=bsps=0;
+       	}
+     
+      	friend int operator<(score_network s1,score_network s2);
+      	friend int operator==(score_network s1,score_network s2);
+      	friend int operator>(score_network s1,score_network s2);
+      	friend bool same_obj(score_network s1, score_network s2);
+         
+
+};
+
+//HR:F
+/*================================================================*/
+
+void print_queue(list<score_network>* v){
+
+	list<score_network>::iterator iter;
+
+	for(iter=v->begin();iter!=v->end();iter++){
+		cout<<"    "<<(*iter).bsps<<","<<(*iter).scores;
+	}
+    
+}
+	
+//HR:F
+/*================================================================*/
+
+int operator<(score_network s1,score_network s2){
+ 	if(fabs(s1.scores-s2.scores)<EPSILON){
+     	return false;
+   	}
+    return(s1.scores<s2.scores);
+
+}
+
+
+int operator>(score_network s1,score_network s2){
+
+	if(fabs(s1.scores-s2.scores)<EPSILON){
+    	return false;
+    }
+    return(s1.scores>s2.scores);
+
+}
+
+int operator==(score_network s1,score_network s2){
+	return(fabs(s1.scores-s2.scores)<EPSILON);
+
+}
+
+
+bool same_obj(score_network s1, score_network s2){
+    return((s1==s2)&&(s1.bsps==s2.bsps));
+    
+}
+
+/*================================================================*/
+//HR:F
+//To insert into the best parent set list
+void insert_vec(list<score_network>* v,score_network s, int k){
+  	list<score_network>::iterator it;
+
+	if( s < v->back()){
+		v->push_back(s);
+   	}
+    else{
+      	for(it=v->begin();it!=v->end();it++){
+			if(same_obj(s,*it)){
+				break;
+	        }
+            else if(s>(*it)){
+              	v->insert(it,s);
+				break;
+			}
+
+		}
+	}
+     
+	if(v->size()>k){
+		v->pop_back();
+  	}   
+
+}
+
+/*================================================================*/
+
+void get_best_parents(int nof_vars, char* dirname, int k){
+	varset_t nof_parsets = 1U<<(nof_vars-1);
+	int i;
+//		cout<<endl<<"Inside fn";
+	list<score_network> v[nof_parsets];
+    list<score_network>::iterator it;
+	score_network s;
+   	string str;
+    char str1[40];
+    
+    //HR: For each var
+  	for(i=0;i<nof_vars; ++i){
+		/* READ SCORES FOR i */
+		str.assign(dirname);
+        str.append("/");
+        sprintf(str1,"%d",i); 
+        str.append(str1);
+		//	cout<<str;
+		FILE* fin = fopen(str.c_str(),"rb");
+
+		//	cout<<fin;
+		//	scanf("%d",&h);
+		
+		//HR: for all the possible parents 
+		//Read local score and add it to the queue
+		for(int j=0;j<nof_parsets;j++){
+			fread(&s.scores, sizeof(score_t), 1, fin);
+			//	cout<<s.scores;
+			//	scanf("%d",&h);
+			s.bsps = j;
+			
+			//HR: At this time, every queue has only one element s
+			v[j].push_back(s);
+
+
+		}
+		fclose(fin);
+
+
+		/* FIND BEST PARENTS AND THEIR SCORES IN EACH SET FOR i */
+
+		varset_t ps;
+		
+		//HR: for each possible parent set cs 
+		//For each possible parent set compare and  add to the list if it is within best k parent sets
+		for(ps=0; ps<nof_parsets; ++ps){
+			varset_t psel = 1U;
+
+			//HR: psel represents the number equals the single element which is not in the ps
+			//
+			for(psel=1; psel<nof_parsets; psel <<= 1){
+				if (ps & psel){
+					
+					//HR: use xor to get the subset whose size is 1 smaller
+					varset_t subset = ps^psel;                                        
+					for(it=v[subset].begin();it!=v[subset].end();it++){
+						if(v[ps].size()<k){
+							insert_vec(&v[ps],*it, k);
+
+						}
+						else if(v[ps].size()==k){
+							if(((*it)<v[ps].back())||(*it)==v[ps].back()){
+								break;
+							}
+							else{
+								insert_vec(&v[ps], *it, k);
+
+
+							}
+						}
+					}
+				}
+			}
+		}
+
+
+
+		/* WRITE BEST PARENTS FOR i */
+		str.append(".kbps");
+		FILE* fout = fopen(str.c_str(),"wb");
+		double sentinel = 1000.0;
+		//printf("nofparset: %u",nof_parsets);				
+		for(int j=0;j<nof_parsets;j++){
+			//	int g=0;
+			//	print_queue(&v[j]);
+			//	printf("\n");
+			for(it=v[j].begin();it!=v[j].end();it++){
+				//	g++;
+				//fwrite(&v[j]
+				fwrite(&(it->scores), sizeof(double), 1, fout);
+				fwrite(&(it->bsps),sizeof(unsigned int),1,fout);
+				//print_queue(&v[j]);
+				//printf("\n");
+				//fprintf(fout,"\n");
+			}
+						
+			fwrite(&sentinel,sizeof(double),1,fout);
+			v[j].clear();
+							
+		}
+		//printf("\n");
+		fclose(fout);
+				
+	}// endfor(i=0;i<nof_vars; ++i)
+	
+}
+
+/*================================================================*/
+
+//HR: F
+int main(int argc, char* argv[]){
+	
+	//    cout<<endl<<"Get K Best Parent sets"<<endl;      
+   	if (argc!=4){
+      	fprintf(stderr, "Usage: best_parents nof_vars dirname k\n");
+       	return 1;
+  	}
+      
+	char str[32];
+	int nof_vars = atoi(argv[1]);
+   	int k = atoi(argv[3]);
+      
+   	//strcpy(str,argv[2]);
+      
+   	get_best_parents(nof_vars, argv[2],k);
+  
+   	return 0;
+}
diff --git a/var_lib_genenet_bnw/k-best/src/varpar.o b/var_lib_genenet_bnw/k-best/src/varpar.o
new file mode 100644
index 00000000..4fa1b165
--- /dev/null
+++ b/var_lib_genenet_bnw/k-best/src/varpar.o
Binary files differdiff --git a/var_lib_genenet_bnw/localscore/Applic.h b/var_lib_genenet_bnw/localscore/Applic.h
new file mode 100644
index 00000000..0ae5e981
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/Applic.h
@@ -0,0 +1,291 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 1998-2012   Robert Gentleman, Ross Ihaka
+ *                             and the R Core Team
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ *
+ *
+ * Application Routines, typically implemented in  ../appl/
+ * ----------------------------------------------  ========
+ */
+
+/* This header file contains routines which are in the R API and ones which
+   are not.
+
+   Those which are not can be used only at the user's risk and may change
+   or disappear in a future release of R.
+*/
+
+
+#ifndef R_APPLIC_H_
+#define R_APPLIC_H_
+
+#include <R_ext/Boolean.h>
+#include <R_ext/RS.h>		/* F77_... */
+#include <R_ext/BLAS.h>
+
+#ifdef  __cplusplus
+extern "C" {
+#endif
+
+/* Entry points in the R API */
+
+/* appl/integrate.c */
+typedef void integr_fn(double *x, int n, void *ex);
+/* vectorizing function   f(x[1:n], ...) -> x[]  {overwriting x[]}. */
+
+void Rdqags(integr_fn f, void *ex, double *a, double *b,
+	    double *epsabs, double *epsrel,
+	    double *result, double *abserr, int *neval, int *ier,
+	    int *limit, int *lenw, int *last, int *iwork, double *work);
+
+void Rdqagi(integr_fn f, void *ex, double *bound, int *inf,
+	    double *epsabs, double *epsrel,
+	    double *result, double *abserr, int *neval, int *ier,
+	    int *limit, int *lenw, int *last,
+	    int *iwork, double *work);
+
+/* main/optim.c */
+typedef double optimfn(int, double *, void *);
+typedef void optimgr(int, double *, double *, void *);
+
+void vmmin(int n, double *b, double *Fmin,
+	   optimfn fn, optimgr gr, int maxit, int trace,
+	   int *mask, double abstol, double reltol, int nREPORT,
+	   void *ex, int *fncount, int *grcount, int *fail);
+void nmmin(int n, double *Bvec, double *X, double *Fmin, optimfn fn,
+	   int *fail, double abstol, double intol, void *ex,
+	   double alpha, double bet, double gamm, int trace,
+	   int *fncount, int maxit);
+void cgmin(int n, double *Bvec, double *X, double *Fmin,
+	   optimfn fn, optimgr gr,
+	   int *fail, double abstol, double intol, void *ex,
+	   int type, int trace, int *fncount, int *grcount, int maxit);
+void lbfgsb(int n, int m, double *x, double *l, double *u, int *nbd,
+	    double *Fmin, optimfn fn, optimgr gr, int *fail, void *ex,
+	    double factr, double pgtol, int *fncount, int *grcount,
+	    int maxit, char *msg, int trace, int nREPORT);
+void samin(int n, double *pb, double *yb, optimfn fn, int maxit,
+	   int tmax, double ti, int trace, void *ex);
+
+
+
+/* Entry points NOT in the R API */
+
+/* appl/bakslv.c : hidden */
+void bakslv(double *, int *, int *,
+	    double *, int *, int *,
+	    double *, int *, int *);
+
+/* appl/binning.c : hidden */
+void bincode (double *x, int *n, double *breaks, int *nb,
+	      int *code, int *right, int *include_border, int *naok);
+void bincount(double *x, int *n, double *breaks, int *nb, int *count,
+	      int *right, int *include_border, int *naok);
+
+/* appl/ch2inv.f */
+void F77_NAME(ch2inv)(double *x, int *ldx, int *n, double *v, int *info);
+
+/* appl/chol.f Used in nlme */
+void F77_NAME(chol)(double *a, int *lda, int *n, double *v, int *info);
+
+/* appl/cpoly.c : hidden */
+void R_cpolyroot(double *opr, double *opi, int *degree,
+		 double *zeror, double *zeroi, Rboolean *fail);
+/* More `Complex Polynomial Utilities' could be exported:
+
+   polyev(...)
+   errev(...)
+   cpoly_cauchy(...)
+   cpoly_scale(...)
+   cdivid(...)
+*/
+
+
+/* appl/cumsum.c : non-API, used in package DCluster */
+void R_cumsum(double *, int *, double *, double *);
+
+/* appl/eigen.f */
+int F77_NAME(cg)(int *nm, int *n, double *ar, double *ai,
+		 double *wr, double *wi, int *matz, double *zr, double *zi,
+		 double *fv1, double *fv2, double *fv3, int *ierr);
+int F77_NAME(ch)(int *nm, int *n, double *ar, double *ai,
+		 double *w, int *matz, double *zr, double *zi,
+		 double *fv1, double *fv2, double *fm1, int *ierr);
+int F77_NAME(rg)(int *nm, int *n, double *a, double *wr, double *wi,
+		 int *matz, double *z, int *iv1, double *fv1, int *ierr);
+/* used in nlme */
+int F77_NAME(rs)(int *nm, int *n, double *a, double *w,
+		 int *matz, double *z, double *fv1, double *fv2, int *ierr);
+
+/* appl/fft.c */
+/* NOTE:  The following functions use GLOBAL (static) variables !!
+ * ----   some of R-core think that this should be changed,
+ *        which will INEVITABLY extend the argument lists ...!
+ */
+/* non-API, but used by package RandomFields */
+void fft_factor(int n, int *pmaxf, int *pmaxp);
+Rboolean fft_work(double *a, double *b, int nseg, int n, int nspn,
+/* TRUE: success */ int isn, double *work, int *iwork);
+
+/* appl/fmin.c : */
+double Brent_fmin(double ax, double bx, double (*f)(double, void *),
+		  void *info, double tol);
+
+/* appl/interv.c: also in Utils.h */
+/* used in packages gam and mda */
+int F77_SUB(interv)(double *xt, int *n, double *x,
+		    Rboolean *rightmost_closed, Rboolean *all_inside,
+		    int *ilo, int *mflag);
+/* Non-API No longer used */
+void find_interv_vec(double *xt, int *n, double *x, int *nx,
+		     int *rightmost_closed, int *all_inside, int *indx);
+/* API, used in package eco */
+int findInterval(double *xt, int n, double x,
+		 Rboolean rightmost_closed,  Rboolean all_inside, int ilo,
+		 int *mflag);
+
+/* appl/lbfgsb.c */
+void setulb(int n, int m, double *x, double *l, double *u, int *nbd,
+	    double *f, double *g, double factr, double *pgtol,
+	    double *wa, int * iwa, char *task, int iprint,
+	    int *lsave, int *isave, double *dsave);
+
+/* appl/machar.c */
+void machar(int *ibeta, int *it, int *irnd, int *ngrd, int *machep,
+	    int *negep, int *iexp, int *minexp, int *maxexp,
+	    double *eps, double *epsneg, double *xmin, double *xmax);
+
+/* appl/maxcol.c: also in Utils.h  Used in package MNP */
+void R_max_col(double *matrix, int *nr, int *nc, int *maxes, int *ties_meth);
+
+
+/* appl/pretty.c */
+double R_pretty0(double *lo, double *up, int *ndiv, int min_n,
+		 double shrink_sml, double high_u_fact[],
+		 int eps_correction, int return_bounds);
+void R_pretty(double *lo, double *up, int *ndiv, int *min_n,
+	      double *shrink_sml, double *high_u_fact,
+	      int *eps_correction);
+
+/* appl/rcont.c: API prior to R 2.15.2 */
+void rcont2(int *nrow, int *ncol, int *nrowt, int *ncolt, int *ntotal,
+	    double *fact, int *jwork, int *matrix);
+
+/* appl/rowsum.c */
+void R_rowsum(int *dim, double *na_x, double *x, double *group);
+
+/* appl/stem.c */
+Rboolean stemleaf(double *x, int *n, double *scale, int *width, double *atom);
+
+/* appl/strsignif.c */
+void str_signif(char *x, int *n, const char **type, int *width, int *digits,
+		const char **format, const char **flag, char **result);
+
+/* appl/tabulate.c : non-API, used in package ape, phangorn, pcaPA */
+void R_tabulate(int *x, int *n, int *nbin, int *ans);
+
+/* appl/uncmin.c : */
+
+/* type of pointer to the target and gradient functions */
+typedef void (*fcn_p)(int, double *, double *, void *);
+
+/* type of pointer to the hessian functions */
+typedef void (*d2fcn_p)(int, int, double *, double *, void *);
+
+void fdhess(int n, double *x, double fval, fcn_p fun, void *state,
+	    double *h, int nfd, double *step, double *f, int ndigit,
+	    double *typx);
+
+/* used in nlme */
+void optif9(int nr, int n, double *x,
+	    fcn_p fcn, fcn_p d1fcn, d2fcn_p d2fcn,
+	    void *state, double *typsiz, double fscale, int method,
+	    int iexp, int *msg, int ndigit, int itnlim, int iagflg,
+	    int iahflg, double dlt, double gradtl, double stepmx,
+	    double steptl, double *xpls, double *fpls, double *gpls,
+	    int *itrmcd, double *a, double *wrk, int *itncnt);
+
+void optif0(int nr, int n, double *x, fcn_p fcn, void *state,
+	    double *xpls, double *fpls, double *gpls, int *itrmcd,
+	    double *a, double *wrk);
+
+/* appl/zeroin.c : non API, but used in package qtl */
+double R_zeroin(double ax, double bx, double (*f)(double, void *), void *info,
+		double *Tol, int *Maxit);
+/* R_zeroin2() is faster for "expensive" f(), in those typical cases where
+ *             f(ax) and f(bx) are available anyway : */
+double R_zeroin2(double ax, double bx, double fa, double fb,
+		 double (*f)(double, void *), void *info, double *Tol, int *Maxit);
+
+
+/* ALL appl/<foobar>.f	[semi-automatically by
+ *				 f2c -A -P *.f; cat *.P > all.h	 and editing]
+ */
+
+/* This is not in the applications but in the BLAS, and defined in Lapack.h
+extern int F77_NAME(lsame)(const char *, const char *);
+*/
+
+/* LINPACK routines also declared in Linpack.h
+void F77_NAME(dpoco)(double *a, int *lda, int *n, double *rcond,
+		     double *z__, int *info);
+void F77_NAME(dpodi)(double *a, int *lda, int *n, double *det, int *job);
+void F77_NAME(dpofa)(double *a, int *lda, int *n, int *info);
+void F77_NAME(dposl)(double *a, int *lda, int *n, double *b);
+void F77_NAME(dqrdc)(double *x, int *ldx, int *n, int *p,
+		     double *qraux, int *jpvt, double *work, int *job);
+void F77_NAME(dqrsl)(double *x, int *ldx, int *n, int *k,
+		     double *qraux, double *y,
+		     double *qy, double *qty, double *b,
+		     double *rsd, double *xb, int *job, int *info);
+void F77_NAME(dsvdc)(double *x, int *ldx, int *n, int *p,
+		     double *s, double *e,
+		     double *u, int *ldu, double *v, int *ldv,
+		     double *work, int *job, int *info);
+void F77_NAME(dtrco)(double *t, int *ldt, int *n, double *rcond,
+		     double *z__, int *job);
+void F77_NAME(dtrsl)(double *t, int *ldt, int *n, double *b, int *job,
+		     int *info);
+*/
+
+/* find qr decomposition, dqrdc2() is basis of R's qr(), also used by nlme */
+void F77_NAME(dqrdc2)(double *x, int *ldx, int *n, int *p,
+		      double *tol, int *rank,
+		      double *qraux, int *pivot, double *work);
+void F77_NAME(dqrls)(double *x, int *n, int *p, double *y, int *ny,
+		     double *tol, double *b, double *rsd,
+		     double *qty, int *k,
+		     int *jpvt, double *qraux, double *work);
+
+/* appl/dqrutl.f: interfaces to dqrsl */
+void F77_NAME(dqrqty)(double *x, int *n, int *k, double *qraux,
+		      double *y, int *ny, double *qty);
+void F77_NAME(dqrqy)(double *x, int *n, int *k, double *qraux,
+		     double *y, int *ny, double *qy);
+void F77_NAME(dqrcf)(double *x, int *n, int *k, double *qraux,
+		     double *y, int *ny, double *b, int *info);
+void F77_NAME(dqrrsd)(double *x, int *n, int *k, double *qraux,
+		     double *y, int *ny, double *rsd);
+void F77_NAME(dqrxb)(double *x, int *n, int *k, double *qraux,
+		     double *y, int *ny, double *xb);
+
+
+#ifdef  __cplusplus
+}
+#endif
+
+#endif /* R_APPLIC_H_ */
diff --git a/var_lib_genenet_bnw/localscore/Arith.h b/var_lib_genenet_bnw/localscore/Arith.h
new file mode 100644
index 00000000..4a0030f1
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/Arith.h
@@ -0,0 +1,87 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 1995, 1996  Robert Gentleman and Ross Ihaka
+ *  Copyright (C) 1998--2007  The R Core Team.
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/* Included by R.h: API */
+
+#ifndef R_ARITH_H_
+#define R_ARITH_H_
+
+/* Only for use where config.h has not already been included */
+#if defined(HAVE_GLIBC2) && !defined(_BSD_SOURCE)
+/* ensure that finite and isnan are declared */
+# define _BSD_SOURCE 1
+#endif
+
+#include "libextern.h"
+#ifdef  __cplusplus
+extern "C" {
+#elif !defined(NO_C_HEADERS)
+/* needed for isnan and isfinite, neither of which are used under C++ */
+# include <math.h>
+#endif
+
+/* implementation of these : ../../main/arithmetic.c */
+LibExtern double R_NaN;		/* IEEE NaN */
+LibExtern double R_PosInf;	/* IEEE Inf */
+LibExtern double R_NegInf;	/* IEEE -Inf */
+LibExtern double R_NaReal;	/* NA_REAL: IEEE */
+LibExtern int	 R_NaInt;	/* NA_INTEGER:= INT_MIN currently */
+#ifdef __MAIN__
+#undef extern
+#undef LibExtern
+#endif
+
+#define NA_LOGICAL	R_NaInt
+#define NA_INTEGER	R_NaInt
+/* #define NA_FACTOR	R_NaInt  unused */
+#define NA_REAL		R_NaReal
+/* NA_STRING is a SEXP, so defined in Rinternals.h */
+
+int R_IsNA(double);		/* True for R's NA only */
+int R_IsNaN(double);		/* True for special NaN, *not* for NA */
+int R_finite(double);		/* True if none of NA, NaN, +/-Inf */
+#define ISNA(x)	       R_IsNA(x)
+
+/* ISNAN(): True for *both* NA and NaN.
+   NOTE: some systems do not return 1 for TRUE.
+   Also note that C++ math headers specifically undefine
+   isnan if it is a macro (it is on OS X and in C99),
+   hence the workaround.  This code also appears in Rmath.h
+*/
+#ifdef __cplusplus
+  int R_isnancpp(double); /* in arithmetic.c */
+#  define ISNAN(x)     R_isnancpp(x)
+#else
+#  define ISNAN(x)     (isnan(x)!=0)
+#endif
+
+/* The following is only defined inside R */
+#ifdef HAVE_WORKING_ISFINITE
+/* isfinite is defined in <math.h> according to C99 */
+# define R_FINITE(x)    isfinite(x)
+#else
+# define R_FINITE(x)    R_finite(x)
+#endif
+
+#ifdef  __cplusplus
+}
+#endif
+
+#endif /* R_ARITH_H_ */
diff --git a/var_lib_genenet_bnw/localscore/BLAS.h b/var_lib_genenet_bnw/localscore/BLAS.h
new file mode 100644
index 00000000..98c192e9
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/BLAS.h
@@ -0,0 +1,382 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2003-12 The R Core Team.
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/*
+   C declarations of BLAS Fortran subroutines always available in R.
+
+   Part of the API.
+
+   R packages that use these should have PKG_LIBS in src/Makevars include 
+   $(BLAS_LIBS) $(FLIBS)
+ */
+
+/* Part of the API */
+
+#ifndef R_BLAS_H
+#define R_BLAS_H
+
+#include <R_ext/RS.h>		/* for F77_... */
+#include <R_ext/Complex.h>	/* for Rcomplex */
+
+#ifdef  __cplusplus
+extern "C" {
+#endif
+
+// never defined in R itself.
+#ifndef BLAS_extern
+#define BLAS_extern extern
+#endif
+
+/* Double Precision Level 1 BLAS */
+
+BLAS_extern double /* DASUM - sum of absolute values of a one-dimensional array */
+F77_NAME(dasum)(const int *n, const double *dx, const int *incx);
+BLAS_extern void   /* DAXPY - replace y by alpha*x + y */
+F77_NAME(daxpy)(const int *n, const double *alpha,
+		const double *dx, const int *incx,
+		double *dy, const int *incy);
+BLAS_extern void   /* DCOPY - copy x to y */
+F77_NAME(dcopy)(const int *n, const double *dx, const int *incx,
+		double *dy, const int *incy);
+BLAS_extern double /* DDOT - inner product of x and y */
+F77_NAME(ddot)(const int *n, const double *dx, const int *incx,
+	       const double *dy, const int *incy);
+BLAS_extern double /* DNRM2 - 2-norm of a vector */
+F77_NAME(dnrm2)(const int *n, const double *dx, const int *incx);
+BLAS_extern void   /* DROT - apply a Given's rotation */
+F77_NAME(drot)(const int *n, double *dx, const int *incx,
+	       double *dy, const int *incy, const double *c, const double *s);
+BLAS_extern void   /* DROTG - generate a Given's rotation */
+F77_NAME(drotg)(const double *a, const double *b, double *c, double *s);
+BLAS_extern void   /* DROTM - apply a modified Given's rotation */
+F77_NAME(drotm)(const int *n, double *dx, const int *incx,
+		double *dy, const int *incy, const double *dparam);
+BLAS_extern void   /* DROTMG - generate a modified Given's rotation */
+F77_NAME(drotmg)(const double *dd1, const double *dd2, const double *dx1,
+		 const double *dy1, double *param);
+BLAS_extern void   /* DSCAL - scale a one-dimensional array */
+F77_NAME(dscal)(const int *n, const double *alpha, double *dx, const int *incx);
+BLAS_extern void   /* DSWAP - interchange one-dimensional arrays */
+F77_NAME(dswap)(const int *n, double *dx, const int *incx,
+		double *dy, const int *incy);
+BLAS_extern int    /* IDAMAX - return the index of the element with max abs value */
+F77_NAME(idamax)(const int *n, const double *dx, const int *incx);
+
+/* Double Precision Level 2 BLAS */
+
+/* DGBMV - perform one of the matrix-vector operations */
+/* y := alpha*A*x + beta*y, or y := alpha*A'*x + beta*y, */
+BLAS_extern void
+F77_NAME(dgbmv)(const char *trans, const int *m, const int *n,
+		const int *kl,const int *ku,
+		const double *alpha, const double *a, const int *lda,
+		const double *x, const int *incx,
+		const double *beta, double *y, const int *incy);
+/* DGEMV - perform one of the matrix-vector operations */
+/* y := alpha*A*x + beta*y, or y := alpha*A'*x + beta*y,  */
+BLAS_extern void
+F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
+		const double *alpha, const double *a, const int *lda,
+		const double *x, const int *incx, const double *beta,
+		double *y, const int *incy);
+/* DSBMV - perform the matrix-vector operation */
+/* y := alpha*A*x + beta*y, */
+BLAS_extern void
+F77_NAME(dsbmv)(const char *uplo, const int *n, const int *k,
+		const double *alpha, const double *a, const int *lda,
+		const double *x, const int *incx,
+		const double *beta, double *y, const int *incy);
+/* DSPMV - perform the matrix-vector operation */
+/* y := alpha*A*x + beta*y, */
+BLAS_extern void
+F77_NAME(dspmv)(const char *uplo, const int *n,
+		const double *alpha, const double *ap,
+		const double *x, const int *incx,
+		const double *beta, double *y, const int *incy);
+
+/* DSYMV - perform the matrix-vector operation */
+/*  y := alpha*A*x + beta*y, */
+BLAS_extern void
+F77_NAME(dsymv)(const char *uplo, const int *n, const double *alpha,
+		const double *a, const int *lda,
+		const double *x, const int *incx,
+		const double *beta, double *y, const int *incy);
+/* DTBMV - perform one of the matrix-vector operations */
+/* x := A*x, or x := A'*x, */
+BLAS_extern void
+F77_NAME(dtbmv)(const char *uplo, const char *trans,
+		const char *diag, const int *n, const int *k,
+		const double *a, const int *lda,
+		double *x, const int *incx);
+/* DTPMV - perform one of the matrix-vector operations */
+/* x := A*x, or x := A'*x, */
+BLAS_extern void
+F77_NAME(dtpmv)(const char *uplo, const char *trans, const char *diag,
+		const int *n, const double *ap,
+		double *x, const int *incx);
+/* DTRMV - perform one of the matrix-vector operations  */
+/* x := A*x, or x := A'*x, */
+BLAS_extern void
+F77_NAME(dtrmv)(const char *uplo, const char *trans, const char *diag,
+		const int *n, const double *a, const int *lda,
+		double *x, const int *incx);
+/* DTBSV - solve one of the systems of equations */
+/* A*x = b, or A'*x = b, */
+BLAS_extern void
+F77_NAME(dtbsv)(const char *uplo, const char *trans,
+		const char *diag, const int *n, const int *k,
+		const double *a, const int *lda,
+		double *x, const int *incx);
+/* DTPSV - solve one of the systems of equations */
+/* A*x = b, or A'*x = b, */
+BLAS_extern void
+F77_NAME(dtpsv)(const char *uplo, const char *trans,
+		const char *diag, const int *n,
+		const double *ap, double *x, const int *incx);
+/* DTRSV - solve one of the systems of equations */
+/* A*x = b, or A'*x = b, */
+BLAS_extern void
+F77_NAME(dtrsv)(const char *uplo, const char *trans,
+		const char *diag, const int *n,
+		const double *a, const int *lda,
+		double *x, const int *incx);
+/* DGER - perform the rank 1 operation   A := alpha*x*y' + A */
+BLAS_extern void
+F77_NAME(dger)(const int *m, const int *n, const double *alpha,
+	       const double *x, const int *incx,
+	       const double *y, const int *incy,
+	       double *a, const int *lda);
+/* DSYR - perform the symmetric rank 1 operation A := alpha*x*x' + A */
+BLAS_extern void
+F77_NAME(dsyr)(const char *uplo, const int *n, const double *alpha,
+	       const double *x, const int *incx,
+	       double *a, const int *lda);
+/* DSPR - perform the symmetric rank 1 operation A := alpha*x*x' + A */
+BLAS_extern void
+F77_NAME(dspr)(const char *uplo, const int *n, const double *alpha,
+	       const double *x, const int *incx, double *ap);
+/* DSYR2 - perform the symmetric rank 2 operation */
+/* A := alpha*x*y' + alpha*y*x' + A, */
+BLAS_extern void
+F77_NAME(dsyr2)(const char *uplo, const int *n, const double *alpha,
+		const double *x, const int *incx,
+		const double *y, const int *incy,
+		double *a, const int *lda);
+/* DSPR2 - perform the symmetric rank 2 operation */
+/* A := alpha*x*y' + alpha*y*x' + A,  */
+BLAS_extern void
+F77_NAME(dspr2)(const char *uplo, const int *n, const double *alpha,
+		const double *x, const int *incx,
+		const double *y, const int *incy, double *ap);
+
+/* Double Precision Level 3 BLAS */
+
+/* DGEMM - perform one of the matrix-matrix operations    */
+/* C := alpha*op( A )*op( B ) + beta*C */
+BLAS_extern void
+F77_NAME(dgemm)(const char *transa, const char *transb, const int *m,
+		const int *n, const int *k, const double *alpha,
+		const double *a, const int *lda,
+		const double *b, const int *ldb,
+		const double *beta, double *c, const int *ldc);
+/* DTRSM - solve one of the matrix equations  */
+/* op(A)*X = alpha*B, or  X*op(A) = alpha*B  */
+BLAS_extern void
+F77_NAME(dtrsm)(const char *side, const char *uplo,
+		const char *transa, const char *diag,
+		const int *m, const int *n, const double *alpha,
+		const double *a, const int *lda,
+		double *b, const int *ldb);
+/* DTRMM - perform one of the matrix-matrix operations */
+/* B := alpha*op( A )*B, or B := alpha*B*op( A ) */
+BLAS_extern void
+F77_NAME(dtrmm)(const char *side, const char *uplo, const char *transa,
+		const char *diag, const int *m, const int *n,
+		const double *alpha, const double *a, const int *lda,
+		double *b, const int *ldb);
+/* DSYMM - perform one of the matrix-matrix operations   */
+/*  C := alpha*A*B + beta*C, */
+BLAS_extern void
+F77_NAME(dsymm)(const char *side, const char *uplo, const int *m,
+		const int *n, const double *alpha,
+		const double *a, const int *lda,
+		const double *b, const int *ldb,
+		const double *beta, double *c, const int *ldc);
+/* DSYRK - perform one of the symmetric rank k operations */
+/* C := alpha*A*A' + beta*C or C := alpha*A'*A + beta*C */
+BLAS_extern void
+F77_NAME(dsyrk)(const char *uplo, const char *trans,
+		const int *n, const int *k,
+		const double *alpha, const double *a, const int *lda,
+		const double *beta, double *c, const int *ldc);
+/* DSYR2K - perform one of the symmetric rank 2k operations */
+/* C := alpha*A*B' + alpha*B*A' + beta*C or */
+/* C := alpha*A'*B + alpha*B'*A + beta*C */
+BLAS_extern void
+F77_NAME(dsyr2k)(const char *uplo, const char *trans,
+		 const int *n, const int *k,
+		 const double *alpha, const double *a, const int *lda,
+		 const double *b, const int *ldb,
+		 const double *beta, double *c, const int *ldc);
+/*
+  LSAME is a LAPACK support routine, not part of BLAS
+*/
+
+/* Double complex BLAS routines added for 2.3.0 */
+/* #ifdef HAVE_FORTRAN_DOUBLE_COMPLEX */
+    BLAS_extern double
+    F77_NAME(dcabs1)(double *z);
+    BLAS_extern double
+    F77_NAME(dzasum)(int *n, Rcomplex *zx, int *incx);
+    BLAS_extern double
+    F77_NAME(dznrm2)(int *n, Rcomplex *x, int *incx);
+    BLAS_extern int
+    F77_NAME(izamax)(int *n, Rcomplex *zx, int *incx);
+    BLAS_extern void
+    F77_NAME(zaxpy)(int *n, Rcomplex *za, Rcomplex *zx,
+		    int *incx, Rcomplex *zy, int *incy);
+    BLAS_extern void
+    F77_NAME(zcopy)(int *n, Rcomplex *zx, int *incx,
+		    Rcomplex *zy, int *incy);
+
+    /* WARNING!  The next two return a value that may not be
+       compatible between C and Fortran, and even if it is, this might
+       not be the right translation to C.  Only use after
+       configure-testing with your compilers.
+     */
+    BLAS_extern Rcomplex
+    F77_NAME(zdotc)(int *n,
+		    Rcomplex *zx, int *incx, Rcomplex *zy, int *incy);
+    BLAS_extern Rcomplex
+    F77_NAME(zdotu)(int *n,
+		    Rcomplex *zx, int *incx, Rcomplex *zy, int *incy);
+
+    BLAS_extern void
+    F77_NAME(zdrot)(int *n, Rcomplex *zx, int *incx, Rcomplex *zy,
+		int *incy, double *c, double *s);
+    BLAS_extern void
+    F77_NAME(zdscal)(int *n, double *da, Rcomplex *zx, int *incx);
+    BLAS_extern void
+    F77_NAME(zgbmv)(char *trans, int *m, int *n, int *kl,
+		    int *ku, Rcomplex *alpha, Rcomplex *a, int *lda,
+		    Rcomplex *x, int *incx, Rcomplex *beta, Rcomplex *y,
+		    int *incy);
+    BLAS_extern void
+    F77_NAME(zgemm)(const char *transa, const char *transb, const int *m,
+		    const int *n, const int *k, const Rcomplex *alpha,
+		    const Rcomplex *a, const int *lda,
+		    const Rcomplex *b, const int *ldb,
+		    const Rcomplex *beta, Rcomplex *c, const int *ldc);
+    BLAS_extern void
+    F77_NAME(zgemv)(char *trans, int *m, int *n, Rcomplex *alpha,
+		    Rcomplex *a, int *lda, Rcomplex *x, int *incx,
+		    Rcomplex *beta, Rcomplex *y, int * incy);
+    BLAS_extern void
+    F77_NAME(zgerc)(int *m, int *n, Rcomplex *alpha, Rcomplex *x,
+		    int *incx, Rcomplex *y, int *incy, Rcomplex *a, int *lda);
+    BLAS_extern void
+    F77_NAME(zgeru)(int *m, int *n, Rcomplex *alpha, Rcomplex *x,
+		    int *incx, Rcomplex *y, int *incy, Rcomplex *a, int *lda);
+    BLAS_extern void
+    F77_NAME(zhbmv)(char *uplo, int *n, int *k, Rcomplex *alpha,
+		    Rcomplex *a, int *lda, Rcomplex *x, int *incx,
+		    Rcomplex *beta, Rcomplex *y, int *incy);
+    BLAS_extern void
+    F77_NAME(zhemm)(char *side, char *uplo, int *m, int *n,
+		    Rcomplex *alpha, Rcomplex *a, int *lda, Rcomplex *b,
+		    int *ldb, Rcomplex *beta, Rcomplex *c, int *ldc);
+    BLAS_extern void
+    F77_NAME(zhemv)(char *uplo, int *n, Rcomplex *alpha, Rcomplex *a,
+		    int *lda, Rcomplex *x, int *incx, Rcomplex *beta,
+		    Rcomplex *y, int *incy);
+    BLAS_extern void
+    F77_NAME(zher)(char *uplo, int *n, double *alpha, Rcomplex *x,
+		   int *incx, Rcomplex *a, int *lda);
+    BLAS_extern void
+    F77_NAME(zher2)(char *uplo, int *n, Rcomplex *alpha, Rcomplex *x,
+		    int *incx, Rcomplex *y, int *incy, Rcomplex *a, int *lda);
+    BLAS_extern void
+    F77_NAME(zher2k)(char *uplo, char *trans, int *n, int *k,
+		     Rcomplex *alpha, Rcomplex *a, int *lda, Rcomplex *b,
+		     int *ldb, double *beta, Rcomplex *c, int *ldc);
+    BLAS_extern void
+    F77_NAME(zherk)(char *uplo, char *trans, int *n, int *k,
+		    double *alpha, Rcomplex *a, int *lda, double *beta,
+		    Rcomplex *c, int *ldc);
+    BLAS_extern void
+    F77_NAME(zhpmv)(char *uplo, int *n, Rcomplex *alpha, Rcomplex *ap,
+		    Rcomplex *x, int *incx, Rcomplex * beta, Rcomplex *y,
+		    int *incy);
+    BLAS_extern void
+    F77_NAME(zhpr)(char *uplo, int *n, double *alpha,
+		   Rcomplex *x, int *incx, Rcomplex *ap);
+    BLAS_extern void
+    F77_NAME(zhpr2)(char *uplo, int *n, Rcomplex *alpha, Rcomplex *x,
+		    int *incx, Rcomplex *y, int *incy, Rcomplex *ap);
+    BLAS_extern void
+    F77_NAME(zrotg)(Rcomplex *ca, Rcomplex *cb, double *c, Rcomplex *s);
+    BLAS_extern void
+    F77_NAME(zscal)(int *n, Rcomplex *za, Rcomplex *zx, int *incx);
+    BLAS_extern void
+    F77_NAME(zswap)(int *n, Rcomplex *zx, int *incx, Rcomplex *zy, int *incy);
+    BLAS_extern void
+    F77_NAME(zsymm)(char *side, char *uplo, int *m, int *n,
+		    Rcomplex *alpha, Rcomplex *a, int *lda, Rcomplex *b,
+		    int *ldb, Rcomplex *beta, Rcomplex *c, int *ldc);
+    BLAS_extern void
+    F77_NAME(zsyr2k)(char *uplo, char *trans, int *n, int *k,
+		     Rcomplex *alpha, Rcomplex *a, int *lda, Rcomplex *b,
+		     int *ldb, Rcomplex *beta, Rcomplex *c, int *ldc);
+    BLAS_extern void
+    F77_NAME(zsyrk)(char *uplo, char *trans, int *n, int *k,
+		    Rcomplex *alpha, Rcomplex *a, int *lda,
+		    Rcomplex *beta, Rcomplex *c, int *ldc);
+    BLAS_extern void
+    F77_NAME(ztbmv)(char *uplo, char *trans, char *diag, int *n, int *k,
+		    Rcomplex *a, int *lda, Rcomplex *x, int *incx);
+    BLAS_extern void
+    F77_NAME(ztbsv)(char *uplo, char *trans, char *diag, int *n, int *k,
+		    Rcomplex *a, int *lda, Rcomplex *x, int *incx);
+    BLAS_extern void
+    F77_NAME(ztpmv)(char *uplo, char *trans, char *diag, int *n,
+		    Rcomplex *ap, Rcomplex *x, int *incx);
+    BLAS_extern void
+    F77_NAME(ztpsv)(char *uplo, char *trans, char *diag, int *n,
+		    Rcomplex *ap, Rcomplex *x, int *incx);
+    BLAS_extern void
+    F77_NAME(ztrmm)(char *side, char *uplo, char *transa, char *diag,
+		    int *m, int *n, Rcomplex *alpha, Rcomplex *a,
+		    int *lda, Rcomplex *b, int *ldb);
+    BLAS_extern void
+    F77_NAME(ztrmv)(char *uplo, char *trans, char *diag, int *n,
+		    Rcomplex *a, int *lda, Rcomplex *x, int *incx);
+    BLAS_extern void
+    F77_NAME(ztrsm)(char *side, char *uplo, char *transa, char *diag,
+		    int *m, int *n, Rcomplex *alpha, Rcomplex *a,
+		    int *lda, Rcomplex *b, int *ldb);
+    BLAS_extern void
+    F77_NAME(ztrsv)(char *uplo, char *trans, char *diag, int *n,
+		    Rcomplex *a, int *lda, Rcomplex *x, int *incx);
+/* #endif */
+
+#ifdef  __cplusplus
+}
+#endif
+
+#endif /* R_BLAS_H */
diff --git a/var_lib_genenet_bnw/localscore/Boolean.h b/var_lib_genenet_bnw/localscore/Boolean.h
new file mode 100644
index 00000000..ea855a29
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/Boolean.h
@@ -0,0 +1,37 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2000, 2001 The R Core Team.
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/* Included by R.h: API */
+
+#ifndef R_EXT_BOOLEAN_H_
+#define R_EXT_BOOLEAN_H_
+
+#undef FALSE
+#undef TRUE
+
+#ifdef  __cplusplus
+extern "C" {
+#endif
+typedef enum { FALSE = 0, TRUE /*, MAYBE */ } Rboolean;
+
+#ifdef  __cplusplus
+}
+#endif
+
+#endif /* R_EXT_BOOLEAN_H_ */
diff --git a/var_lib_genenet_bnw/localscore/Callbacks.h b/var_lib_genenet_bnw/localscore/Callbacks.h
new file mode 100644
index 00000000..cb1d64ca
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/Callbacks.h
@@ -0,0 +1,116 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2001-2 The R Core Team.
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/* 
+   Not part of the API, subject to change at any time.
+*/
+
+#ifndef R_CALLBACKS_H
+#define R_CALLBACKS_H
+
+/**
+  These structures are for C (and R function) top-level task handlers.
+  Such routines are called at the end of every (successful) top-level task
+  in the regular REPL. 
+ */
+
+#include <Rinternals.h>
+/**
+  The signature of the C routine that a callback must implement.
+  expr - the expression for the top-level task that was evaluated.
+  value - the result of the top-level task, i.e. evaluating expr.
+  succeeded - a logical value indicating whether the task completed propertly.
+  visible - a logical value indicating whether the result was printed to the R ``console''/stdout.
+  data - user-level data passed to the registration routine.
+ */
+typedef Rboolean (*R_ToplevelCallback)(SEXP expr, SEXP value, Rboolean succeeded, Rboolean visible, void *);
+
+typedef struct _ToplevelCallback  R_ToplevelCallbackEl;
+/** 
+ Linked list element for storing the top-level task callbacks.
+ */
+struct _ToplevelCallback {
+    R_ToplevelCallback cb; /* the C routine to call. */
+    void *data;            /* the user-level data to pass to the call to cb() */
+    void (*finalizer)(void *data); /* Called when the callback is removed. */
+
+    char *name;  /* a name by which to identify this element. */ 
+
+    R_ToplevelCallbackEl *next; /* the next element in the linked list. */
+};
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+Rboolean Rf_removeTaskCallbackByIndex(int id);
+Rboolean Rf_removeTaskCallbackByName(const char *name);
+SEXP R_removeTaskCallback(SEXP which);
+R_ToplevelCallbackEl* Rf_addTaskCallback(R_ToplevelCallback cb, void *data, void (*finalizer)(void *), const char *name, int *pos);
+
+
+
+/*
+  The following definitions are for callbacks to R functions and
+  methods related to user-level tables.  This was implemented in a
+  separate package on Omegahat and these declarations allow the package
+  to interface to the internal R code.
+  
+  See http://developer.r-project.org/RObjectTables.pdf,
+  http://www.omegahat.org/RObjectTables/
+*/
+
+typedef struct  _R_ObjectTable R_ObjectTable;
+
+/* Do we actually need the exists() since it is never called but R
+   uses get to see if the symbol is bound to anything? */
+typedef Rboolean (*Rdb_exists)(const char * const name, Rboolean *canCache, R_ObjectTable *);
+typedef SEXP     (*Rdb_get)(const char * const name, Rboolean *canCache, R_ObjectTable *);
+typedef int      (*Rdb_remove)(const char * const name, R_ObjectTable *);
+typedef SEXP     (*Rdb_assign)(const char * const name, SEXP value, R_ObjectTable *);
+typedef SEXP     (*Rdb_objects)(R_ObjectTable *);
+typedef Rboolean (*Rdb_canCache)(const char * const name, R_ObjectTable *);
+
+typedef void     (*Rdb_onDetach)(R_ObjectTable *);
+typedef void     (*Rdb_onAttach)(R_ObjectTable *);
+
+struct  _R_ObjectTable{
+  int       type;
+  char    **cachedNames;
+  Rboolean  active;
+
+  Rdb_exists   exists;
+  Rdb_get      get;
+  Rdb_remove   remove;
+  Rdb_assign   assign;
+  Rdb_objects  objects;
+  Rdb_canCache canCache;
+
+  Rdb_onDetach onDetach;
+  Rdb_onAttach onAttach;
+  
+  void     *privateData;
+};
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* R_CALLBACKS_H */
diff --git a/var_lib_genenet_bnw/localscore/Complex.h b/var_lib_genenet_bnw/localscore/Complex.h
new file mode 100644
index 00000000..06417a71
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/Complex.h
@@ -0,0 +1,38 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 1998-2001   The R Core Team
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/* Included by R.h: API */
+
+#ifndef R_COMPLEX_H
+#define R_COMPLEX_H
+
+#ifdef  __cplusplus
+extern "C" {
+#endif
+
+typedef struct {
+	double r;
+	double i;
+} Rcomplex;
+
+#ifdef  __cplusplus
+}
+#endif
+
+#endif /* R_COMPLEX_H */
diff --git a/var_lib_genenet_bnw/localscore/Constants.h b/var_lib_genenet_bnw/localscore/Constants.h
new file mode 100644
index 00000000..08e3d158
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/Constants.h
@@ -0,0 +1,44 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 1995, 1996  Robert Gentleman and Ross Ihaka
+ *  Copyright (C) 1998-2012   The R Core Team.
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/* Included by R.h: API */
+
+#ifndef R_EXT_CONSTANTS_H_
+#define R_EXT_CONSTANTS_H_
+
+/* usually in math.h, but not with strict C99 compliance */
+#ifndef M_PI
+#define M_PI 3.141592653589793238462643383279502884197169399375
+#endif
+
+#ifndef STRICT_R_HEADERS
+#define PI             M_PI
+#include <float.h>  /* Defines the rest, at least in C99 */
+#define SINGLE_EPS     FLT_EPSILON
+#define SINGLE_BASE    FLT_RADIX
+#define SINGLE_XMIN    FLT_MIN
+#define SINGLE_XMAX    FLT_MAX
+#define DOUBLE_DIGITS  DBL_MANT_DIG
+#define DOUBLE_EPS     DBL_EPSILON
+#define DOUBLE_XMAX    DBL_MAX
+#define DOUBLE_XMIN    DBL_MIN
+#endif
+
+#endif /* R_EXT_CONSTANTS_H_ */
diff --git a/var_lib_genenet_bnw/localscore/Error.h b/var_lib_genenet_bnw/localscore/Error.h
new file mode 100644
index 00000000..1a8905c6
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/Error.h
@@ -0,0 +1,46 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 1998-2005   The R Core Team
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/* Included by R.h: API */
+
+#ifndef R_ERROR_H_
+#define R_ERROR_H_
+
+#ifdef  __cplusplus
+extern "C" {
+#endif
+
+void	Rf_error(const char *, ...);
+void	Rf_warning(const char *, ...);
+void	WrongArgCount(const char *);
+void	UNIMPLEMENTED(const char *);
+void 	R_ShowMessage(const char *s);
+    
+
+#ifdef  __cplusplus
+}
+#endif
+
+#ifndef R_NO_REMAP
+#define error Rf_error
+#define warning Rf_warning
+#endif
+
+
+#endif /* R_ERROR_H_ */
diff --git a/var_lib_genenet_bnw/localscore/GetX11Image.h b/var_lib_genenet_bnw/localscore/GetX11Image.h
new file mode 100644
index 00000000..a7181fa3
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/GetX11Image.h
@@ -0,0 +1,36 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2003  R Core Team
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation; either version 2 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+#ifndef GETX11IMAGE_H_
+#define GETX11IMAGE_H_
+
+#ifdef  __cplusplus
+extern "C" {
+#endif
+
+/* used by package tkrplot */
+
+Rboolean R_GetX11Image(int d, void *pximage, int *pwidth, int *pheight);
+/* pximage is really (XImage **) */
+
+#ifdef  __cplusplus
+}
+#endif
+
+#endif
diff --git a/var_lib_genenet_bnw/localscore/GraphicsDevice.h b/var_lib_genenet_bnw/localscore/GraphicsDevice.h
new file mode 100644
index 00000000..10851b26
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/GraphicsDevice.h
@@ -0,0 +1,863 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2001-11 The R Core Team.
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/* Used by third-party graphics devices.
+ *
+ * This defines DevDesc, whereas GraphicsEngine.h defines GEDevDesc.
+ * Also contains entry points from gevents.c
+ */
+
+#ifndef R_GRAPHICSDEVICE_H_
+#define R_GRAPHICSDEVICE_H_
+
+
+/* ideally we would use prototypes in DevDesc.  
+   Some devices have taken to passing pointers to their own structure
+   instead of DevDesc* , defining R_USE_PROTOTYPES 0 allows them to
+   opt out.
+*/
+
+#ifndef  R_USE_PROTOTYPES
+# define R_USE_PROTOTYPES 1
+# ifndef R_GRAPHICSENGINE_H_
+#  error R_ext/GraphicsEngine.h must be included first, and includes this header
+# endif
+#endif
+
+#include <R_ext/Boolean.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* --------- New (in 1.4.0) device driver structure ---------
+ * NOTES:
+ * 1. All locations and dimensions are in device coordinates.
+ * 2. I found this comment in the doc for dev_Open -- looks nasty
+ *    Any known instances of such a thing happening?  Should be
+ *    replaced by a function to query the device for preferred gpars
+ *    settings? (to be called when the device is initialised)
+         *
+         * NOTE that it is perfectly acceptable for this
+         * function to set generic graphics parameters too
+         * (i.e., override the generic parameter settings
+         * which GInit sets up) all at the author's own risk
+         * of course :)
+	 *
+ * 3. Do we really need dev_StrWidth as well as dev_MetricInfo?
+ *    I can see the difference between the two -- its just a
+ *    question of whether dev_MetricInfo should just return
+ *    what dev_StrWidth would give if font metric information is
+ *    not available.  I guess having both allows the developer
+ *    to decide when to ask for which sort of value, and to decide
+ *    what to do when font metric information is not available.
+ *    And why not a dev_StrHeight?
+ * 4. Should "ipr", "asp", and "cra" be in the device description?
+ *    If not, then where?
+ *    I guess they don't need to be if no device makes use of them.
+ *    On the other hand, they would need to be replaced by a device
+ *    call that R base graphics could use to get enough information
+ *    to figure them out.  (e.g., some sort of dpi() function to
+ *    complement the size() function.)
+ */
+
+typedef struct _DevDesc DevDesc;
+typedef DevDesc* pDevDesc;
+
+struct _DevDesc {
+    /********************************************************
+     * Device physical characteristics
+     ********************************************************/
+    double left;	        /* left raster coordinate */
+    double right;	        /* right raster coordinate */
+    double bottom;	        /* bottom raster coordinate */
+    double top;		        /* top raster coordinate */
+    /* R only has the notion of a rectangular clipping region
+     */
+    double clipLeft;
+    double clipRight;
+    double clipBottom;
+    double clipTop;
+    /* I hate these next three -- they seem like a real fudge
+     * BUT I'm not sure what to replace them with so they stay for now.
+     */
+    double xCharOffset;	        /* x character addressing offset - unused */
+    double yCharOffset;	        /* y character addressing offset */
+    double yLineBias;	        /* 1/2 interline space as frac of line height */
+    double ipr[2];	        /* Inches per raster; [0]=x, [1]=y */
+    /* I hate this guy too -- seems to assume that a device can only
+     * have one font size during its lifetime
+     * BUT removing/replacing it would take quite a lot of work
+     * to design and insert a good replacement so it stays for now.
+     */
+    double cra[2];	        /* Character size in rasters; [0]=x, [1]=y */
+    double gamma;	        /* (initial) Device Gamma Correction */
+    /********************************************************
+     * Device capabilities
+     ********************************************************/
+    Rboolean canClip;		/* Device-level clipping */
+    Rboolean canChangeGamma;    /* can the gamma factor be modified? */
+    int canHAdj;	        /* Can do at least some horiz adjust of text
+			           0 = none, 1 = {0,0.5,1}, 2 = [0,1] */
+    /********************************************************
+     * Device initial settings
+     ********************************************************/
+    /* These are things that the device must set up when it is created.
+     * The graphics system can modify them and track current values,
+     */
+    double startps;
+    int startcol;  /* sets par("fg"), par("col") and gpar("col") */
+    int startfill; /* sets par("bg") and gpar("fill") */
+    int startlty;
+    int startfont;
+    double startgamma;
+    /********************************************************
+     * Device specific information
+     ********************************************************/
+    void *deviceSpecific;	/* pointer to device specific parameters */
+    /********************************************************
+     * Device display list
+     ********************************************************/
+    Rboolean displayListOn;     /* toggle for initial display list status */
+
+
+    /********************************************************
+     * Event handling entries
+     ********************************************************/
+
+    /* Used in do_setGraphicsEventEnv */
+
+    Rboolean canGenMouseDown; /* can the device generate mousedown events */
+    Rboolean canGenMouseMove; /* can the device generate mousemove events */
+    Rboolean canGenMouseUp;   /* can the device generate mouseup events */
+    Rboolean canGenKeybd;     /* can the device generate keyboard events */
+
+    Rboolean gettingEvent;    /* This is set while getGraphicsEvent
+				 is actively looking for events */
+    
+    /********************************************************
+     * Device procedures.
+     ********************************************************/
+
+    /*
+     * ---------------------------------------
+     * GENERAL COMMENT ON GRAPHICS PARAMETERS:
+     * ---------------------------------------
+     * Graphical parameters are now passed in a pointer to a 
+     * graphics context structure (pGEcontext) rather than individually.
+     * Each device action should extract the parameters it needs
+     * and ignore the others.  Thought should be given to which
+     * parameters are relevant in each case -- the graphics engine
+     * does not REQUIRE that each parameter is honoured, but if
+     * a parameter is NOT honoured, it might be a good idea to
+     * issue a warning when a parameter is not honoured (or at
+     * the very least document which parameters are not honoured
+     * in the user-level documentation for the device).  [An example
+     * of a parameter that may not be honoured by many devices is
+     * transparency.]
+     */
+
+    /*
+     * device_Activate is called when a device becomes the
+     * active device.  For example, it can be used to change the
+     * title of a window to indicate the active status of
+     * the device to the user.  Not all device types will
+     * do anything.
+     * The only parameter is a device driver structure.
+     * An example is ...
+     *
+     * static void   X11_Activate(pDevDesc dd);
+     *
+     * As from R 2.14.0 this can be omitted or set to NULL.
+     */
+#if R_USE_PROTOTYPES
+    void (*activate)(const pDevDesc );
+#else
+    void (*activate)();
+#endif
+    /*
+     * device_Circle should have the side-effect that a
+     * circle is drawn, centred at the given location, with
+     * the given radius.
+     * (If the device has non-square pixels, 'radius' should
+     * be interpreted in the units of the x direction.)
+     * The border of the circle should be
+     * drawn in the given "col", and the circle should be
+     * filled with the given "fill" colour.
+     * If "col" is NA_INTEGER then no border should be drawn
+     * If "fill" is NA_INTEGER then the circle should not
+     * be filled.
+     * An example is ...
+     *
+     * static void X11_Circle(double x, double y, double r,
+     *                        pGEcontext gc,
+     *                        pDevDesc dd);
+     *
+     * R_GE_gcontext parameters that should be honoured (if possible):
+     *   col, fill, gamma, lty, lwd
+     */
+#if R_USE_PROTOTYPES
+    void (*circle)(double x, double y, double r, const pGEcontext gc, pDevDesc dd);
+#else
+    void (*circle)();
+#endif
+    /*
+     * device_Clip is given the left, right, bottom, and
+     * top of a rectangle (in DEVICE coordinates).
+     * It should have the side-effect that subsequent output
+     * is clipped to the given rectangle.
+     * NOTE that R's graphics engine already clips to the
+     * extent of the device.
+     * NOTE also that this will probably only be called if
+     * the flag canClip is true.
+     * An example is ...
+     *
+     * static void X11_Clip(double x0, double x1, double y0, double y1,
+     *                      pDevDesc dd)
+     */
+#if R_USE_PROTOTYPES
+    void (*clip)(double x0, double x1, double y0, double y1, pDevDesc dd);
+#else
+    void (*clip)();
+#endif
+    /*
+     * device_Close is called when the device is killed.
+     * This function is responsible for destroying any
+     * device-specific resources that were created in
+     * device_Open and for FREEing the device-specific
+     * parameters structure.
+     * An example is ...
+     *
+     * static void X11_Close(pDevDesc dd)
+     *
+     */
+#if R_USE_PROTOTYPES
+    void (*close)(pDevDesc dd);
+#else
+    void (*close)();
+#endif
+    /*
+     * device_Deactivate is called when a device becomes
+     * inactive.
+     * This allows the device to undo anything it did in
+     * dev_Activate.
+     * Not all device types will do anything.
+     * An example is ...
+     *
+     * static void X11_Deactivate(pDevDesc dd)
+     *
+     * As from R 2.14.0 this can be omitted or set to NULL.
+     */
+#if R_USE_PROTOTYPES
+    void (*deactivate)(pDevDesc );
+#else
+    void (*deactivate)();
+#endif
+
+
+    /*
+     * device_Locator should return the location of the next
+     * mouse click (in DEVICE coordinates)
+     * Not all devices will do anything (e.g., postscript)
+     * An example is ...
+     *
+     * static Rboolean X11_Locator(double *x, double *y, pDevDesc dd)
+     *
+     * As from R 2.14.0 this can be omitted or set to NULL.
+     */
+#if R_USE_PROTOTYPES
+    Rboolean (*locator)(double *x, double *y, pDevDesc dd);
+#else
+    Rboolean (*locator)();
+#endif
+    /*
+     * device_Line should have the side-effect that a single
+     * line is drawn (from x1,y1 to x2,y2)
+     * An example is ...
+     *
+     * static void X11_Line(double x1, double y1, double x2, double y2,
+     *                      const pGEcontext gc,
+     *                      pDevDesc dd);
+     *
+     * R_GE_gcontext parameters that should be honoured (if possible):
+     *   col, gamma, lty, lwd
+     */
+#if R_USE_PROTOTYPES
+    void (*line)(double x1, double y1, double x2, double y2,
+		 const pGEcontext gc, pDevDesc dd);
+#else
+    void (*line)();
+#endif
+    /*
+     * device_MetricInfo should return height, depth, and
+     * width information for the given character in DEVICE
+     * units.
+     * Note: in an 8-bit locale, c is 'char'.
+     * In an mbcslocale, it is wchar_t, and at least some
+     * of code assumes that is UCS-2 (Windows, true) or UCS-4.
+     * This is used for formatting mathematical expressions
+     * and for exact centering of text (see GText)
+     * If the device cannot provide metric information then
+     * it MUST return 0.0 for ascent, descent, and width.
+     * An example is ...
+     *
+     * static void X11_MetricInfo(int c,
+     *                            const pGEcontext gc,
+     *                            double* ascent, double* descent,
+     *                            double* width, pDevDesc dd);
+     *
+     * R_GE_gcontext parameters that should be honoured (if possible):
+     *   font, cex, ps
+     */
+#if R_USE_PROTOTYPES
+    void (*metricInfo)(int c, const pGEcontext gc,
+		       double* ascent, double* descent, double* width,
+		       pDevDesc dd);
+#else
+    void (*metricInfo)();
+#endif
+    /*
+     * device_Mode is called whenever the graphics engine
+     * starts drawing (mode=1) or stops drawing (mode=0)
+     * GMode (in graphics.c) also says that 
+     * mode = 2 (graphical input on) exists.
+     * The device is not required to do anything
+     * An example is ...
+     *
+     * static void X11_Mode(int mode, pDevDesc dd);
+     *
+     * As from R 2.14.0 this can be omitted or set to NULL.
+     */
+#if R_USE_PROTOTYPES
+    void (*mode)(int mode, pDevDesc dd);
+#else
+    void (*mode)();
+#endif
+    /*
+     * device_NewPage is called whenever a new plot requires
+     * a new page.
+     * A new page might mean just clearing the
+     * device (e.g., X11) or moving to a new page
+     * (e.g., postscript)
+     * An example is ...
+     *
+     *
+     * static void X11_NewPage(const pGEcontext gc,
+     *                         pDevDesc dd);
+     *
+     */
+#if R_USE_PROTOTYPES
+    void (*newPage)(const pGEcontext gc, pDevDesc dd);
+#else
+    void (*newPage)();
+#endif
+    /*
+     * device_Polygon should have the side-effect that a
+     * polygon is drawn using the given x and y values
+     * the polygon border should be drawn in the "col"
+     * colour and filled with the "fill" colour.
+     * If "col" is NA_INTEGER don't draw the border
+     * If "fill" is NA_INTEGER don't fill the polygon
+     * An example is ...
+     *
+     * static void X11_Polygon(int n, double *x, double *y,
+     *                         const pGEcontext gc,
+     *                         pDevDesc dd);
+     *
+     * R_GE_gcontext parameters that should be honoured (if possible):
+     *   col, fill, gamma, lty, lwd
+     */
+#if R_USE_PROTOTYPES
+    void (*polygon)(int n, double *x, double *y, const pGEcontext gc, pDevDesc dd);
+#else
+    void (*polygon)();
+#endif
+    /*
+     * device_Polyline should have the side-effect that a
+     * series of line segments are drawn using the given x
+     * and y values.
+     * An example is ...
+     *
+     * static void X11_Polyline(int n, double *x, double *y,
+     *                          const pGEcontext gc,
+     *                          pDevDesc dd);
+     *
+     * R_GE_gcontext parameters that should be honoured (if possible):
+     *   col, gamma, lty, lwd
+     */
+#if R_USE_PROTOTYPES
+    void (*polyline)(int n, double *x, double *y, const pGEcontext gc, pDevDesc dd);
+#else
+    void (*polyline)();
+#endif
+    /*
+     * device_Rect should have the side-effect that a
+     * rectangle is drawn with the given locations for its
+     * opposite corners.  The border of the rectangle
+     * should be in the given "col" colour and the rectangle
+     * should be filled with the given "fill" colour.
+     * If "col" is NA_INTEGER then no border should be drawn
+     * If "fill" is NA_INTEGER then the rectangle should not
+     * be filled.
+     * An example is ...
+     *
+     * static void X11_Rect(double x0, double y0, double x1, double y1,
+     *                      const pGEcontext gc,
+     *                      pDevDesc dd);
+     *
+     */
+#if R_USE_PROTOTYPES
+    void (*rect)(double x0, double y0, double x1, double y1,
+		 const pGEcontext gc, pDevDesc dd);
+#else
+    void (*rect)();
+#endif
+    /* 
+     * device_Path should draw one or more sets of points 
+     * as a single path
+     * 
+     * 'x' and 'y' give the points
+     *
+     * 'npoly' gives the number of polygons in the path
+     * MUST be at least 1
+     *
+     * 'nper' gives the number of points in each polygon
+     * each value MUST be at least 2
+     *
+     * 'winding' says whether to fill using the nonzero 
+     * winding rule or the even-odd rule
+     *
+     * Added 2010-06-27
+     *
+     * As from R 2.13.2 this can be left unimplemented as NULL.
+     */
+#if R_USE_PROTOTYPES
+    void (*path)(double *x, double *y, 
+                 int npoly, int *nper,
+                 Rboolean winding,
+                 const pGEcontext gc, pDevDesc dd);
+#else
+    void (*path)();
+#endif
+    /* 
+     * device_Raster should draw a raster image justified 
+     * at the given location,
+     * size, and rotation (not all devices may be able to rotate?)
+     * 
+     * 'raster' gives the image data BY ROW, with every four bytes
+     * giving one R colour (ABGR).
+     *
+     * 'x and 'y' give the bottom-left corner.
+     *
+     * 'rot' is in degrees (as per device_Text), with positive
+     * rotation anticlockwise from the positive x-axis.
+     *
+     * As from R 2.13.2 this can be left unimplemented as NULL.
+     */
+#if R_USE_PROTOTYPES
+    void (*raster)(unsigned int *raster, int w, int h,
+                   double x, double y, 
+                   double width, double height,
+                   double rot, 
+                   Rboolean interpolate,
+                   const pGEcontext gc, pDevDesc dd);
+#else
+    void (*raster)();
+#endif
+    /* 
+     * device_Cap should return an integer matrix (R colors)
+     * representing the current contents of the device display.
+     * 
+     * The result is expected to be ROW FIRST.
+     *
+     * This will only make sense for raster devices and can 
+     * probably only be implemented for screen devices.
+     *
+     * added 2010-06-27
+     *
+     * As from R 2.13.2 this can be left unimplemented as NULL.
+     * For earlier versions of R it should return R_NilValue.
+     */
+#if R_USE_PROTOTYPES
+    SEXP (*cap)(pDevDesc dd);
+#else
+    SEXP (*cap)();
+#endif
+    /*
+     * device_Size is called whenever the device is
+     * resized.
+     * The function returns (left, right, bottom, and top) for the
+     * new device size.
+     * This is not usually called directly by the graphics
+     * engine because the detection of device resizes
+     * (e.g., a window resize) are usually detected by
+     * device-specific code.
+     * An example is ...
+     *
+     * static void X11_Size(double *left, double *right,
+     *                      double *bottom, double *top,
+     *                      pDevDesc dd);
+     *
+     * R_GE_gcontext parameters that should be honoured (if possible):
+     *   col, fill, gamma, lty, lwd
+     *
+     * As from R 2.13.2 this can be left unimplemented as NULL.
+     */
+#if R_USE_PROTOTYPES
+    void (*size)(double *left, double *right, double *bottom, double *top,
+		 pDevDesc dd);
+#else
+    void (*size)();
+#endif
+    /*
+     * device_StrWidth should return the width of the given
+     * string in DEVICE units.
+     * An example is ...
+     *
+     * static double X11_StrWidth(const char *str,
+     *                            const pGEcontext gc,
+     *                            pDevDesc dd)
+     *
+     * R_GE_gcontext parameters that should be honoured (if possible):
+     *   font, cex, ps
+     */
+#if R_USE_PROTOTYPES
+    double (*strWidth)(const char *str, const pGEcontext gc, pDevDesc dd);
+#else
+    double (*strWidth)();
+#endif
+    /*
+     * device_Text should have the side-effect that the
+     * given text is drawn at the given location.
+     * The text should be rotated according to rot (degrees)
+     * An example is ...
+     *
+     * static void X11_Text(double x, double y, const char *str,
+     *                      double rot, double hadj,
+     *                      const pGEcontext gc,
+     * 	                    pDevDesc dd);
+     *
+     * R_GE_gcontext parameters that should be honoured (if possible):
+     *   font, cex, ps, col, gamma
+     */
+#if R_USE_PROTOTYPES
+    void (*text)(double x, double y, const char *str, double rot,
+		 double hadj, const pGEcontext gc, pDevDesc dd);
+#else
+    void (*text)();
+#endif
+    /*
+     * device_onExit is called by GEonExit when the user has aborted
+     * some operation, and so an R_ProcessEvents call may not return normally.
+     * It need not be set to any value; if null, it will not be called.
+     *
+     * An example is ...
+     *
+     * static void GA_onExit(pDevDesc dd);
+    */
+#if R_USE_PROTOTYPES
+    void (*onExit)(pDevDesc dd);
+#else
+    void (*onExit)();
+#endif
+    /*
+     * device_getEvent is no longer used, but the slot is kept for back
+     * compatibility of the structure.
+     */
+    SEXP (*getEvent)(SEXP, const char *);
+
+    /* --------- Optional features introduced in 2.7.0 --------- */
+
+    /* Does the device have a device-specific way to confirm a 
+       new frame (for e.g. par(ask=TRUE))?
+       This should be NULL if it does not.
+       If it does, it returns TRUE if the device handled this, and
+       FALSE if it wants the engine to do so. 
+
+       There is an example in the windows() device.
+
+       Can be left unimplemented as NULL.
+    */
+#if R_USE_PROTOTYPES
+    Rboolean (*newFrameConfirm)(pDevDesc dd);
+#else
+    Rboolean (*newFrameConfirm)();
+#endif
+
+    /* Some devices can plot UTF-8 text directly without converting
+       to the native encoding, e.g. windows(), quartz() ....
+
+       If this flag is true, all text *not in the symbol font* is sent
+       in UTF8 to the textUTF8/strWidthUTF8 entry points.
+
+       If the flag is TRUE, the metricInfo entry point should
+       accept negative values for 'c' and treat them as indicating
+       Unicode points (as well as positive values in a MBCS locale).
+    */
+    Rboolean hasTextUTF8; /* and strWidthUTF8 */
+#if R_USE_PROTOTYPES
+    void (*textUTF8)(double x, double y, const char *str, double rot,
+		     double hadj, const pGEcontext gc, pDevDesc dd);
+    double (*strWidthUTF8)(const char *str, const pGEcontext gc, pDevDesc dd);
+#else
+    void (*textUTF8)();
+    double (*strWidthUTF8)();
+#endif
+    Rboolean wantSymbolUTF8;
+
+    /* Is rotated text good enough to be preferable to Hershey in
+       contour labels?  Old default was FALSE.
+    */
+    Rboolean useRotatedTextInContour;
+
+    /* --------- Post-2.7.0 features --------- */
+
+    /* Added in 2.12.0:  Changed graphics event handling. */
+    
+    SEXP eventEnv;   /* This is an environment holding event handlers. */
+    /*
+     * eventHelper(dd, 1) is called by do_getGraphicsEvent before looking for a 
+     * graphics event.  It will then call R_ProcessEvents() and eventHelper(dd, 2)
+     * until this or another device returns sets a non-null result value in eventEnv,
+     * at which time eventHelper(dd, 0) will be called.
+     * 
+     * An example is ...
+     *
+     * static SEXP GA_eventHelper(pDevDesc dd, int code);
+
+     * Can be left unimplemented as NULL
+     */
+#if R_USE_PROTOTYPES
+    void (*eventHelper)(pDevDesc dd, int code);
+#else
+    void (*eventHelper)();
+#endif
+
+    /* added in 2.14.0, only used by screen devices.
+
+       Allows graphics devices to have multiple levels of suspension: 
+       when this reaches zero output is flushed.
+
+       Can be left unimplemented as NULL.
+     */
+#if R_USE_PROTOTYPES
+    int (*holdflush)(pDevDesc dd, int level);
+#else
+    int (*holdflush)();
+#endif
+
+    /* added in 2.14.0, for dev.capabilities.
+       In all cases 0 means NA (unset).
+    */
+    int haveTransparency; /* 1 = no, 2 = yes */
+    int haveTransparentBg; /* 1 = no, 2 = fully, 3 = semi */
+    int haveRaster; /* 1 = no, 2 = yes, 3 = except for missing values */
+    int haveCapture, haveLocator;  /* 1 = no, 2 = yes */
+
+
+    /* Area for future expansion.
+       By zeroing this, devices are more likely to work if loaded
+       into a later version of R than that they were compiled under.
+    */
+    char reserved[64];
+};
+
+
+	/********************************************************/
+	/* the device-driver entry point is given a device	*/
+	/* description structure that it must set up.  this	*/
+	/* involves several important jobs ...			*/
+	/* (1) it must ALLOCATE a new device-specific parameters*/
+	/* structure and FREE that structure if anything goes	*/
+	/* wrong (i.e., it won't report a successful setup to	*/
+	/* the graphics engine (the graphics engine is NOT	*/
+	/* responsible for allocating or freeing device-specific*/
+	/* resources or parameters)				*/
+	/* (2) it must initialise the device-specific resources */
+	/* and parameters (mostly done by calling device_Open)	*/
+	/* (3) it must initialise the generic graphical		*/
+	/* parameters that are not initialised by GInit (because*/
+	/* only the device knows what values they should have)	*/
+	/* see Graphics.h for the official list of these	*/
+	/* (4) it may reset generic graphics parameters that	*/
+	/* have already been initialised by GInit (although you	*/
+	/* should know what you are doing if you do this)	*/
+	/* (5) it must attach the device-specific parameters	*/
+	/* structure to the device description structure	*/
+	/* e.g., dd->deviceSpecfic = (void *) xd;		*/
+	/* (6) it must FREE the overall device description if	*/
+	/* it wants to bail out to the top-level		*/
+	/* the graphics engine is responsible for allocating	*/
+	/* the device description and freeing it in most cases	*/
+	/* but if the device driver freaks out it needs to do	*/
+	/* the clean-up itself					*/
+	/********************************************************/
+
+/* moved from Rgraphics.h */
+
+/*
+ *	Some Notes on Color
+ *
+ *	R uses a 24-bit color model.  Colors are specified in 32-bit
+ *	integers which are partitioned into 4 bytes as follows.
+ *
+ *		<-- most sig	    least sig -->
+ *		+-------------------------------+
+ *		|   0	| blue	| green |  red	|
+ *		+-------------------------------+
+ *
+ *	The red, green and blue bytes can be extracted as follows.
+ *
+ *		red   = ((color	     ) & 255)
+ *		green = ((color >>  8) & 255)
+ *		blue  = ((color >> 16) & 255)
+ */
+/*
+ *	Changes as from 1.4.0: use top 8 bits as an alpha channel.
+ * 	0 = opaque, 255 = transparent.
+ */
+/*
+ * Changes as from 2.0.0:  use top 8 bits as full alpha channel
+ *      255 = opaque, 0 = transparent
+ *      [to conform with SVG, PDF and others]
+ *      and everything in between is used
+ *      [which means that NA is not stored as an internal colour;
+ *       it is converted to R_RGBA(255, 255, 255, 0)]
+ */
+
+#define R_RGB(r,g,b)	((r)|((g)<<8)|((b)<<16)|0xFF000000)
+#define R_RGBA(r,g,b,a)	((r)|((g)<<8)|((b)<<16)|((a)<<24))
+#define R_RED(col)	(((col)	   )&255)
+#define R_GREEN(col)	(((col)>> 8)&255)
+#define R_BLUE(col)	(((col)>>16)&255)
+#define R_ALPHA(col)	(((col)>>24)&255)
+#define R_OPAQUE(col)	(R_ALPHA(col) == 255)
+#define R_TRANSPARENT(col) (R_ALPHA(col) == 0)
+    /*
+     * A transparent white
+     */
+#define R_TRANWHITE     (R_RGBA(255, 255, 255, 0))
+
+
+/* used in various devices */
+
+#define curDevice		Rf_curDevice
+#define killDevice		Rf_killDevice
+#define ndevNumber		Rf_ndevNumber
+#define NewFrameConfirm		Rf_NewFrameConfirm
+#define nextDevice		Rf_nextDevice
+#define NoDevices		Rf_NoDevices
+#define NumDevices		Rf_NumDevices
+#define prevDevice		Rf_prevDevice
+#define selectDevice		Rf_selectDevice
+#define AdobeSymbol2utf8	Rf_AdobeSymbol2utf8
+
+/* Properly declared version of devNumber */
+int ndevNumber(pDevDesc );
+
+/* Formerly in Rdevices.h */
+
+/* How many devices exist ? (>= 1) */
+int NumDevices(void);
+
+/* Check for an available device slot */
+void R_CheckDeviceAvailable(void);
+Rboolean R_CheckDeviceAvailableBool(void);
+
+/* Return the number of the current device. */
+int curDevice(void);
+
+/* Return the number of the next device. */
+int nextDevice(int);
+
+/* Return the number of the previous device. */
+int prevDevice(int);
+
+/* Make the specified device (specified by number) the current device */
+int selectDevice(int);
+
+/* Kill device which is identified by number. */
+void killDevice(int);
+
+int NoDevices(void); /* used in engine, graphics, plot, grid */
+
+void NewFrameConfirm(pDevDesc); /* used in graphics.c, grid */
+
+
+/* Graphics events: defined in gevents.c */
+
+/* These give the indices of some known keys */
+
+typedef enum {knUNKNOWN = -1,
+              knLEFT = 0, knUP, knRIGHT, knDOWN,
+              knF1, knF2, knF3, knF4, knF5, knF6, knF7, knF8, knF9, knF10,
+              knF11, knF12,
+              knPGUP, knPGDN, knEND, knHOME, knINS, knDEL} R_KeyName;
+
+/* These are the three possible mouse events */
+
+typedef enum {meMouseDown = 0,
+	      meMouseUp,
+	      meMouseMove} R_MouseEvent;
+
+#define leftButton   1
+#define middleButton 2
+#define rightButton  4
+
+#define doKeybd			Rf_doKeybd
+#define doMouseEvent		Rf_doMouseEvent
+
+void doMouseEvent(pDevDesc dd, R_MouseEvent event,
+                  int buttons, double x, double y);
+void doKeybd(pDevDesc dd, R_KeyName rkey,
+	     const char *keyname);
+
+
+/* For use in third-party devices when setting up a device:
+ * duplicates Defn.h which is used internally.
+ * (Tested in devNull.c)
+ */
+
+#ifndef BEGIN_SUSPEND_INTERRUPTS
+/* Macros for suspending interrupts */
+#define BEGIN_SUSPEND_INTERRUPTS do { \
+    Rboolean __oldsusp__ = R_interrupts_suspended; \
+    R_interrupts_suspended = TRUE;
+#define END_SUSPEND_INTERRUPTS R_interrupts_suspended = __oldsusp__; \
+    if (R_interrupts_pending && ! R_interrupts_suspended) \
+        Rf_onintr(); \
+} while(0)
+    
+#include <R_ext/libextern.h>
+LibExtern Rboolean R_interrupts_suspended;    
+LibExtern int R_interrupts_pending;
+extern void Rf_onintr(void);
+LibExtern Rboolean mbcslocale;
+#endif
+
+/* Useful for devices: translates Adobe symbol encoding to UTF-8 */
+extern void *AdobeSymbol2utf8(char*out, const char *in, int nwork);
+/* Translates Unicode point to UTF-8 */
+extern size_t Rf_ucstoutf8(char *s, const unsigned int c);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* R_GRAPHICSDEVICE_ */
diff --git a/var_lib_genenet_bnw/localscore/GraphicsEngine.h b/var_lib_genenet_bnw/localscore/GraphicsEngine.h
new file mode 100644
index 00000000..8d4a8748
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/GraphicsEngine.h
@@ -0,0 +1,514 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2001-11 The R Core Team.
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/* Used by graphics.c, grid and by third-party graphics devices */
+
+#ifndef R_GRAPHICSENGINE_H_
+#define R_GRAPHICSENGINE_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * The current graphics engine (including graphics device) API version
+ * MUST be integer
+ *
+ * This number should be bumped whenever there are changes to
+ * GraphicsEngine.h or GraphicsDevice.h so that add-on packages
+ * that compile against these headers (graphics systems such as
+ * graphics and grid;  graphics devices such as gtkDevice, RSvgDevice)
+ * can detect any version mismatch.
+ *
+ * Version 1:  Introduction of the version number.
+ * Version 2:  GEDevDesc *dd dropped from GEcontourLines().
+ * Version 3:  R_GE_str2col() added to API. (r41887)
+ * Version 4:  UTF-8 text hooks, useRotatedTextInContour,
+ *             add newFrameConfirm() to NewDevDesc.
+ *             New API: GEaddDevice[2] GEgetDevice, GEkillDevice,
+ *             ndevNumber. (R 2.7.0)
+ * Version 5:  Clean up 1.4.0/2.0.0 changes!
+ *             Remove newDevStruct from GEDevDesc and NewDevDesc.
+ *             Remove asp, dot(), hold(), open() from NewDevDesc.
+ *             Move displayList, DLlastElt, savedSnapshot from
+ *             NewDevDesc to GEDevDesc.
+ *             Add 'ask' to GEDevDesc. (R 2.8.0)
+ * Version 6:  Add dev_Raster() and dev_Cap()  (R 2.11.0)
+ * Version 7:  Change graphics event handling, adding eventEnv and eventHelper()
+ *	       to DevDesc.  (R 2.12.0)
+ * Version 8:  Add dev_Path() (R 2.12.0)
+ * Version 9:  Add dev_HoldFlush(), haveTrans*, haveRaster,
+ *             haveCapture, haveLocator.  (R 2.14.0)
+ */
+
+#define R_GE_version 9
+
+int R_GE_getVersion(void);
+
+void R_GE_checkVersionOrDie(int version);
+
+/* The graphics engine will only accept locations and dimensions
+ * in native device coordinates, but it provides the following functions
+ * for converting between a couple of simple alternative coordinate
+ * systems and device coordinates:
+ *    DEVICE = native units of the device
+ *    NDC = Normalised device coordinates
+ *    INCHES = inches (!)
+ *    CM = centimetres (!!)
+ */
+
+typedef enum {
+ GE_DEVICE	= 0,	/* native device coordinates (rasters) */
+ GE_NDC	= 1,	/* normalised device coordinates x=(0,1), y=(0,1) */
+ GE_INCHES = 2,
+ GE_CM     = 3
+} GEUnit;
+
+#define MAX_GRAPHICS_SYSTEMS 24
+
+typedef enum {
+    /* In response to this event, the registered graphics system
+     * should allocate and initialise the systemSpecific structure
+     *
+     * Should return R_NilValue on failure so that engine
+     * can tidy up memory allocation
+     */
+    GE_InitState = 0,
+    /* This event gives the registered system a chance to undo
+     * anything done in the initialisation.
+     */
+    GE_FinaliseState = 1,
+    /* This is sent by the graphics engine prior to initialising
+     * the display list.  It give the graphics system the chance
+     * to squirrel away information it will need for redrawing the
+     * the display list
+     */
+    GE_SaveState = 2,
+    /* This is sent by the graphics engine prior to replaying the
+     * display list.  It gives the graphics system the chance to
+     * restore any information it saved on the GE_SaveState event
+     */
+    GE_RestoreState = 6,
+    /* Copy system state information to the current device.
+     * This is used when copying graphics from one device to another
+     * so all the graphics system needs to do is to copy across
+     * the bits required for the display list to draw faithfully
+     * on the new device.
+     */
+    GE_CopyState = 3,
+    /* Create a snapshot of the system state that is sufficient
+     * for the current "image" to be reproduced
+     */
+    GE_SaveSnapshotState = 4,
+    /* Restore the system state that is saved by GE_SaveSnapshotState
+     */
+    GE_RestoreSnapshotState = 5,
+    /* When replaying the display list, the graphics engine
+     * checks, after each replayed action, that the action
+     * produced valid output.  This is the graphics system's
+     * chance to say that the output is crap (in which case the
+     * graphics engine will abort the display list replay).
+     */
+    GE_CheckPlot = 7,
+    /* The device wants to scale the current pointsize
+     * (for scaling an image)
+     * This is not a nice general solution, but a quick fix for
+     * the Windows device.
+     */
+    GE_ScalePS = 8
+} GEevent;
+
+/*
+ *  Some line end/join constants
+ */
+typedef enum {
+  GE_ROUND_CAP  = 1,
+  GE_BUTT_CAP   = 2,
+  GE_SQUARE_CAP = 3
+} R_GE_lineend;
+
+typedef enum {
+  GE_ROUND_JOIN = 1,
+  GE_MITRE_JOIN = 2,
+  GE_BEVEL_JOIN = 3
+} R_GE_linejoin;
+
+/*
+ * A structure containing graphical parameters
+ *
+ * This is how graphical parameters are passed from graphics systems
+ * to the graphics engine AND from the graphics engine to graphics
+ * devices.
+ *
+ * Devices are not *required* to honour graphical parameters
+ * (e.g., alpha transparency is going to be tough for some)
+ */
+typedef struct {
+    /*
+     * Colours
+     *
+     * NOTE:  Alpha transparency included in col & fill
+     */
+    int col;             /* pen colour (lines, text, borders, ...) */
+    int fill;            /* fill colour (for polygons, circles, rects, ...) */
+    double gamma;        /* Gamma correction */
+    /*
+     * Line characteristics
+     */
+    double lwd;          /* Line width (roughly number of pixels) */
+    int lty;             /* Line type (solid, dashed, dotted, ...) */
+    R_GE_lineend lend;   /* Line end */
+    R_GE_linejoin ljoin; /* line join */
+    double lmitre;       /* line mitre */
+    /*
+     * Text characteristics
+     */
+    double cex;          /* Character expansion (font size = fontsize*cex) */
+    double ps;           /* Font size in points */
+    double lineheight;   /* Line height (multiply by font size) */
+    int fontface;        /* Font face (plain, italic, bold, ...) */
+    char fontfamily[201]; /* Font family */
+} R_GE_gcontext;
+
+typedef R_GE_gcontext* pGEcontext;
+
+
+#include <R_ext/GraphicsDevice.h> /* needed for DevDesc */
+
+typedef struct _GEDevDesc GEDevDesc;
+
+typedef SEXP (* GEcallback)(GEevent, GEDevDesc *, SEXP);
+
+typedef struct {
+    /* An array of information about each graphics system that
+     * has registered with the graphics engine.
+     * This is used to store graphics state for each graphics
+     * system on each device.
+     */
+    void *systemSpecific;
+    /*
+     * An array of function pointers, one per graphics system that
+     * has registered with the graphics engine.
+     *
+     * system_Callback is called when the graphics engine wants
+     * to give a graphics system the chance to play with its
+     * device-specific information (stored in systemSpecific)
+     * There are two parameters:  an "event" to tell the graphics
+     * system why the graphics engine has called this function,
+     * and the systemSpecific pointer.  The graphics engine
+     * has to pass the systemSpecific pointer because only
+     * the graphics engine will know what array index to use.
+     */
+    GEcallback callback;
+} GESystemDesc;
+
+struct _GEDevDesc {
+    /*
+     * Stuff that the devices can see (and modify).
+     * All detailed in GraphicsDevice.h
+     */
+    pDevDesc dev;
+    /*
+     * Stuff about the device that only the graphics engine sees
+     * (the devices don't see it).
+     */
+    Rboolean displayListOn;  /* toggle for display list status */
+    SEXP displayList;        /* display list */
+    SEXP DLlastElt;          /* A pointer to the end of the display list
+				to avoid tranversing pairlists */
+    SEXP savedSnapshot;      /* The last element of the display list
+			      * just prior to when the display list
+			      * was last initialised
+			      */
+    Rboolean dirty;          /* Has the device received any output? */
+    Rboolean recordGraphics; /* Should a graphics call be stored
+			      * on the display list?
+			      * Set to FALSE by do_recordGraphics,
+			      * do_dotcallgr, and do_Externalgr
+			      * so that nested calls are not
+			      * recorded on the display list
+			      */
+    /*
+     * Stuff about the device that only graphics systems see.
+     * The graphics engine has no idea what is in here.
+     * Used by graphics systems to store system state per device.
+     */
+    GESystemDesc *gesd[MAX_GRAPHICS_SYSTEMS];
+
+    /* per-device setting for 'ask' (use NewFrameConfirm) */
+    Rboolean ask;
+};
+
+typedef GEDevDesc* pGEDevDesc;
+
+/* functions from devices.c for use by graphics devices */
+
+#define desc2GEDesc		Rf_desc2GEDesc
+/* map DevDesc to enclosing GEDevDesc */
+pGEDevDesc desc2GEDesc(pDevDesc dd);
+int GEdeviceNumber(pGEDevDesc);
+pGEDevDesc GEgetDevice(int);
+void GEaddDevice(pGEDevDesc);
+void GEaddDevice2(pGEDevDesc, const char *);
+void GEkillDevice(pGEDevDesc);
+pGEDevDesc GEcreateDevDesc(pDevDesc dev);
+
+void GEdestroyDevDesc(pGEDevDesc dd);
+void *GEsystemState(pGEDevDesc dd, int index);
+void GEregisterWithDevice(pGEDevDesc dd);
+void GEregisterSystem(GEcallback callback, int *systemRegisterIndex);
+void GEunregisterSystem(int registerIndex);
+SEXP GEhandleEvent(GEevent event, pDevDesc dev, SEXP data);
+
+#define fromDeviceX		GEfromDeviceX
+#define toDeviceX		GEtoDeviceX
+#define fromDeviceY		GEfromDeviceY
+#define toDeviceY		GEtoDeviceY
+#define fromDeviceWidth		GEfromDeviceWidth
+#define toDeviceWidth		GEtoDeviceWidth
+#define fromDeviceHeight	GEfromDeviceHeight
+#define toDeviceHeight		GEtoDeviceHeight
+
+double fromDeviceX(double value, GEUnit to, pGEDevDesc dd);
+double toDeviceX(double value, GEUnit from, pGEDevDesc dd);
+double fromDeviceY(double value, GEUnit to, pGEDevDesc dd);
+double toDeviceY(double value, GEUnit from, pGEDevDesc dd);
+double fromDeviceWidth(double value, GEUnit to, pGEDevDesc dd);
+double toDeviceWidth(double value, GEUnit from, pGEDevDesc dd);
+double fromDeviceHeight(double value, GEUnit to, pGEDevDesc dd);
+double toDeviceHeight(double value, GEUnit from, pGEDevDesc dd);
+
+/*-------------------------------------------------------------------
+ *
+ *  COLOUR CODE is concerned with the internals of R colour representation
+ *
+ *  From colors.c, used in par.c, grid/src/gpar.c
+ */
+
+#define RGBpar			Rf_RGBpar
+#define RGBpar3			Rf_RGBpar3
+#define col2name                Rf_col2name
+#define name2col		Rf_name2col
+
+/* Convert an element of a R colour specification (which might be a
+   number or a string) into an internal colour specification. */
+unsigned int RGBpar(SEXP, int);
+unsigned int RGBpar3(SEXP, int, unsigned int);
+
+/* Convert an internal colour specification to/from a colour name */
+const char *col2name(unsigned int col); /* used in par.c, grid */
+unsigned int name2col(const char *);    /* used by plotmath.c */
+
+/* Convert either a name or a #RRGGBB[AA] string to internal.
+   Because people were using it, it also converts "1", "2" ...
+   to a colour in the palette, and "0" to transparent white.
+*/
+unsigned int R_GE_str2col(const char *s);
+
+
+
+/*
+ *	Some Notes on Line Textures
+ *
+ *	Line textures are stored as an array of 4-bit integers within
+ *	a single 32-bit word.  These integers contain the lengths of
+ *	lines to be drawn with the pen alternately down and then up.
+ *	The device should try to arrange that these values are measured
+ *	in points if possible, although pixels is ok on most displays.
+ *
+ *	If newlty contains a line texture description it is decoded
+ *	as follows:
+ *
+ *		ndash = 0;
+ *		for(i=0 ; i<8 && newlty & 15 ; i++) {
+ *			dashlist[ndash++] = newlty & 15;
+ *			newlty = newlty>>4;
+ *		}
+ *		dashlist[0] = length of pen-down segment
+ *		dashlist[1] = length of pen-up segment
+ *		etc
+ *
+ *	An integer containing a zero terminates the pattern.  Hence
+ *	ndash in this code fragment gives the length of the texture
+ *	description.  If a description contains an odd number of
+ *	elements it is replicated to create a pattern with an
+ *	even number of elements.  (If this is a pain, do something
+ *	different its not crucial).
+ *
+ */
+
+/*--- The basic numbered & names line types; Here device-independent:
+  e.g. "dashed" == "44",  "dotdash" == "1343"
+*/
+
+/* NB: was also in Rgraphics.h in R < 2.7.0 */
+#define LTY_BLANK	-1
+#define LTY_SOLID	0
+#define LTY_DASHED	4 + (4<<4)
+#define LTY_DOTTED	1 + (3<<4)
+#define LTY_DOTDASH	1 + (3<<4) + (4<<8) + (3<<12)
+#define LTY_LONGDASH	7 + (3<<4)
+#define LTY_TWODASH	2 + (2<<4) + (6<<8) + (2<<12)
+
+R_GE_lineend GE_LENDpar(SEXP value, int ind);
+SEXP GE_LENDget(R_GE_lineend lend);
+R_GE_linejoin GE_LJOINpar(SEXP value, int ind);
+SEXP GE_LJOINget(R_GE_linejoin ljoin);
+
+void GESetClip(double x1, double y1, double x2, double y2, pGEDevDesc dd);
+void GENewPage(const pGEcontext gc, pGEDevDesc dd);
+void GELine(double x1, double y1, double x2, double y2,
+	    const pGEcontext gc, pGEDevDesc dd);
+void GEPolyline(int n, double *x, double *y,
+		const pGEcontext gc, pGEDevDesc dd);
+void GEPolygon(int n, double *x, double *y,
+	       const pGEcontext gc, pGEDevDesc dd);
+SEXP GEXspline(int n, double *x, double *y, double *s, Rboolean open,
+	       Rboolean repEnds, Rboolean draw,
+	       const pGEcontext gc, pGEDevDesc dd);
+void GECircle(double x, double y, double radius,
+	      const pGEcontext gc, pGEDevDesc dd);
+void GERect(double x0, double y0, double x1, double y1,
+	    const pGEcontext gc, pGEDevDesc dd);
+void GEPath(double *x, double *y,
+            int npoly, int *nper,
+            Rboolean winding,
+            const pGEcontext gc, pGEDevDesc dd);
+void GERaster(unsigned int *raster, int w, int h,
+              double x, double y, double width, double height,
+              double angle, Rboolean interpolate,
+              const pGEcontext gc, pGEDevDesc dd);
+SEXP GECap(pGEDevDesc dd);
+void GEText(double x, double y, const char * const str, cetype_t enc,
+	    double xc, double yc, double rot,
+	    const pGEcontext gc, pGEDevDesc dd);
+void GEMode(int mode, pGEDevDesc dd);
+void GESymbol(double x, double y, int pch, double size,
+	      const pGEcontext gc, pGEDevDesc dd);
+void GEPretty(double *lo, double *up, int *ndiv);
+void GEMetricInfo(int c, const pGEcontext gc,
+		  double *ascent, double *descent, double *width,
+		  pGEDevDesc dd);
+double GEStrWidth(const char *str, cetype_t enc,
+		  const pGEcontext gc, pGEDevDesc dd);
+double GEStrHeight(const char *str, cetype_t enc,
+		  const pGEcontext gc, pGEDevDesc dd);
+void GEStrMetric(const char *str, cetype_t enc, const pGEcontext gc,
+                 double *ascent, double *descent, double *width,
+                 pGEDevDesc dd);
+int GEstring_to_pch(SEXP pch);
+
+/*-------------------------------------------------------------------
+ *
+ *  LINE TEXTURE CODE is concerned with the internals of R
+ *  line texture representation.
+ */
+unsigned int GE_LTYpar(SEXP, int);
+SEXP GE_LTYget(unsigned int);
+
+/*
+ * Raster operations
+ */
+void R_GE_rasterScale(unsigned int *sraster, int sw, int sh,
+                      unsigned int *draster, int dw, int dh);
+void R_GE_rasterInterpolate(unsigned int *sraster, int sw, int sh,
+                            unsigned int *draster, int dw, int dh);
+void R_GE_rasterRotatedSize(int w, int h, double angle,
+                            int *wnew, int *hnew);
+void R_GE_rasterRotatedOffset(int w, int h, double angle, int botleft,
+                              double *xoff, double *yoff);
+void R_GE_rasterResizeForRotation(unsigned int *sraster,
+                                  int w, int h,
+                                  unsigned int *newRaster,
+                                  int wnew, int hnew,
+                                  const pGEcontext gc);
+void R_GE_rasterRotate(unsigned int *sraster, int w, int h, double angle,
+                       unsigned int *draster, const pGEcontext gc,
+                       Rboolean perPixelAlpha);
+
+
+/*
+ * From plotmath.c
+ */
+double GEExpressionWidth(SEXP expr,
+			 const pGEcontext gc, pGEDevDesc dd);
+double GEExpressionHeight(SEXP expr,
+			  const pGEcontext gc, pGEDevDesc dd);
+void GEExpressionMetric(SEXP expr, const pGEcontext gc,
+                        double *ascent, double *descent, double *width,
+                        pGEDevDesc dd);
+void GEMathText(double x, double y, SEXP expr,
+		double xc, double yc, double rot,
+		const pGEcontext gc, pGEDevDesc dd);
+/*
+ * (End from plotmath.c)
+ */
+
+/*
+ * From plot3d.c : used in package clines
+ */
+SEXP GEcontourLines(double *x, int nx, double *y, int ny,
+		    double *z, double *levels, int nl);
+/*
+ * (End from plot3d.c)
+ */
+
+/*
+ * From vfonts.c
+ */
+double R_GE_VStrWidth(const char *s, cetype_t enc, const pGEcontext gc, pGEDevDesc dd);
+
+double R_GE_VStrHeight(const char *s, cetype_t enc, const pGEcontext gc, pGEDevDesc dd);
+void R_GE_VText(double x, double y, const char * const s, cetype_t enc,
+		double x_justify, double y_justify, double rotation,
+		const pGEcontext gc, pGEDevDesc dd);
+/*
+ * (End from vfonts.c)
+ */
+
+/* Also in Graphics.h */
+#define	DEG2RAD 0.01745329251994329576
+
+pGEDevDesc GEcurrentDevice(void);
+Rboolean GEdeviceDirty(pGEDevDesc dd);
+void GEdirtyDevice(pGEDevDesc dd);
+Rboolean GEcheckState(pGEDevDesc dd);
+Rboolean GErecording(SEXP call, pGEDevDesc dd);
+void GErecordGraphicOperation(SEXP op, SEXP args, pGEDevDesc dd);
+void GEinitDisplayList(pGEDevDesc dd);
+void GEplayDisplayList(pGEDevDesc dd);
+void GEcopyDisplayList(int fromDevice);
+SEXP GEcreateSnapshot(pGEDevDesc dd);
+void GEplaySnapshot(SEXP snapshot, pGEDevDesc dd);
+void GEonExit(void);
+void GEnullDevice(void);
+
+
+/* From ../../main/plot.c, used by ../../library/grid/src/grid.c */
+#define CreateAtVector		Rf_CreateAtVector
+SEXP CreateAtVector(double*, double*, int, Rboolean);
+/* From ../../main/graphics.c, used by ../../library/grDevices/src/axis_scales.c */
+#define GAxisPars 		Rf_GAxisPars
+void GAxisPars(double *min, double *max, int *n, Rboolean log, int axis);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* R_GRAPHICSENGINE_ */
diff --git a/var_lib_genenet_bnw/localscore/Lapack.h b/var_lib_genenet_bnw/localscore/Lapack.h
new file mode 100644
index 00000000..ad044ef7
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/Lapack.h
@@ -0,0 +1,3072 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2003-12 The R Core Team.
+ *  Copyright (C) 2008   The R Foundation
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/* 
+   C declarations of LAPACK Fortran subroutines included in R.
+   Just those used (currently or previously) by C routines in R itself.
+
+   Part of the API.
+
+   R packages that use these should have PKG_LIBS in src/Makevars include 
+   $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+ */
+
+
+#ifndef R_LAPACK_H
+#define R_LAPACK_H
+
+#include <R_ext/RS.h>		/* for F77_... */
+#include <R_ext/Complex.h>	/* for Rcomplex */
+#include <R_ext/BLAS.h>
+
+/*
+  LAPACK function names are [dz]<name>(), where d denotes the real
+  version of the function, z the complex version.  (Only
+  double-precision versions are used in R.)
+*/
+
+#ifdef	__cplusplus
+extern "C" {
+#endif
+
+// Never defined by R itself.
+#ifndef La_extern
+#define La_extern extern
+#endif
+
+/* Utilities for Lapack-using packages : */
+
+/* matrix norms: converting typstr[]  to one of {'M', 'O', 'I', 'F'}
+ * or signal error(): */
+La_extern char La_norm_type(const char *typstr);
+
+/* matrix (reciprocal) condition numbers: convert typstr[]  to 'O'(ne) or 'I'(nf)
+ * or signal error(): */
+La_extern char La_rcond_type(const char *typstr);
+
+
+
+/* Selected Double Precision Lapack Routines
+   ========
+ */
+
+/* Double precision BiDiagonal matrices */
+
+/* DBDSQR - compute the singular value decomposition (SVD) of a real */
+/* N-by-N (upper or lower) bidiagonal matrix B */
+La_extern void
+F77_NAME(dbdsqr)(const char* uplo, const int* n, const int* ncvt,
+		 const int* nru, const int* ncc, double* d, double* e,
+		 double* vt, const int* ldvt, double* u, const int* ldu,
+		 double* c, const int* ldc, double* work, int* info);
+/* DDISNA - compute the reciprocal condition numbers for the */
+/* eigenvectors of a real symmetric or complex Hermitian matrix or */
+/* for the left or right singular vectors of a general m-by-n */
+/* matrix */
+La_extern void
+F77_NAME(ddisna)(const char* job, const int* m, const int* n,
+		 double* d, double* sep, int* info);
+
+/* Double precision General Banded matrices */
+
+/* DGBBRD - reduce a real general m-by-n band matrix A to upper */
+/* bidiagonal form B by an orthogonal transformation  */
+La_extern void
+F77_NAME(dgbbrd)(const char* vect, const int* m, const int* n,
+		 const int* ncc, const int* kl, const int* ku,
+		 double* ab, const int* ldab,
+		 double* d, double* e, double* q,
+		 const int* ldq, double* pt, const int* ldpt,
+		 double* c, const int* ldc,
+		 double* work, int* info);
+/* DGBCON - estimate the reciprocal of the condition number of a */
+/* real general band matrix A, in either the 1-norm or the */
+/* infinity-norm */
+La_extern void
+F77_NAME(dgbcon)(const char* norm, const int* n, const int* kl,
+		 const int* ku, double* ab, const int* ldab,
+		 int* ipiv, const double* anorm, double* rcond,
+		 double* work, int* iwork, int* info);
+/* DGBEQU - compute row and column scalings intended to equilibrate */
+/* an M-by-N band matrix A and reduce its condition number */
+La_extern void
+F77_NAME(dgbequ)(const int* m, const int* n, const int* kl, const int* ku,
+		 double* ab, const int* ldab, double* r, double* c,
+		 double* rowcnd, double* colcnd, double* amax, int* info);
+/* DGBRFS - improve the computed solution to a system of linear */
+/* equations when the coefficient matrix is banded, and provides */
+/* error bounds and backward error estimates for the solution */
+La_extern void
+F77_NAME(dgbrfs)(const char* trans, const int* n, const int* kl,
+		 const int* ku, const int* nrhs, double* ab,
+		 const int* ldab, double* afb, const int* ldafb,
+		 int* ipiv, double* b, const int* ldb,
+		 double* x, const int* ldx, double* ferr, double* berr,
+		 double* work, int* iwork, int* info);
+/* DGBSV - compute the solution to a real system of linear */
+/* equations A * X = B, where A is a band matrix of order N with */
+/* KL subdiagonals and KU superdiagonals, and X and B are */
+/* N-by-NRHS matrices */
+La_extern void
+F77_NAME(dgbsv)(const int* n, const int* kl,const int* ku,
+		const int* nrhs, double* ab, const int* ldab,
+		int* ipiv, double* b, const int* ldb, int* info);
+/* DGBSVX - use the LU factorization to compute the solution to a */
+/* real system of linear equations A * X = B or A**T * X = B */
+La_extern void
+F77_NAME(dgbsvx)(const int* fact, const char* trans,
+		 const int* n, const int* kl,const int* ku,
+		 const int* nrhs, double* ab, const int* ldab,
+		 double* afb, const int* ldafb, int* ipiv,
+		 const char* equed, double* r, double* c,
+		 double* b, const int* ldb,
+		 double* x, const int* ldx,
+		 double* rcond, double* ferr, double* berr,
+		 double* work, int* iwork, int* info);
+/* DGBTF2 - compute an LU factorization of a real m-by-n band */
+/* matrix A using partial pivoting with row interchanges */
+La_extern void
+F77_NAME(dgbtf2)(const int* m, const int* n, const int* kl,const int* ku,
+		 double* ab, const int* ldab, int* ipiv, int* info);
+/* DGBTRF - compute an LU factorization of a real m-by-n band */
+/* matrix A using partial pivoting with row interchanges */
+La_extern void
+F77_NAME(dgbtrf)(const int* m, const int* n, const int* kl,const int* ku,
+		  double* ab, const int* ldab, int* ipiv, int* info);
+/* DGBTRS - solve a system of linear equations	A * X = B or  */
+/* A' * X = B with a general band matrix A using the LU */
+/* factorization computed by DGBTRF */
+La_extern void
+F77_NAME(dgbtrs)(const char* trans, const int* n,
+		 const int* kl, const int* ku, const int* nrhs,
+		 const double* ab, const int* ldab, const int* ipiv,
+		 double* b, const int* ldb, int* info);
+
+/* Double precision GEneral matrices */
+
+/* DGEBAK - form the right or left eigenvectors of a real general */
+/* matrix by backward transformation on the computed eigenvectors */
+/* of the balanced matrix output by DGEBAL  */
+La_extern void
+F77_NAME(dgebak)(const char* job, const char* side, const int* n,
+		 const int* ilo, const int* ihi, double* scale,
+		 const int* m, double* v, const int* ldv, int* info);
+/* DGEBAL - balance a general real matrix A */
+La_extern void
+F77_NAME(dgebal)(const char* job, const int* n, double* a, const int* lda,
+		  int* ilo, int* ihi, double* scale, int* info);
+/* DGEBD2 - reduce a real general m by n matrix A to upper or */
+/* lower bidiagonal form B by an orthogonal transformation */
+La_extern void
+F77_NAME(dgebd2)(const int* m, const int* n, double* a, const int* lda,
+		 double* d, double* e, double* tauq, double* taup,
+		 double* work, int* info);
+/* DGEBRD - reduce a general real M-by-N matrix A to upper or */
+/* lower bidiagonal form B by an orthogonal transformation */
+La_extern void
+F77_NAME(dgebrd)(const int* m, const int* n, double* a, const int* lda,
+		 double* d, double* e, double* tauq, double* taup,
+		 double* work, const int* lwork, int* info);
+/* DGECON - estimate the reciprocal of the condition number of a */
+/* general real matrix A, in either the 1-norm or the */
+/* infinity-norm, using the LU factorization computed by DGETRF */
+La_extern void
+F77_NAME(dgecon)(const char* norm, const int* n,
+		 const double* a, const int* lda,
+		 const double* anorm, double* rcond,
+		 double* work, int* iwork, int* info);
+/* DGEEQU - compute row and column scalings intended to equilibrate */
+/* an M-by-N matrix A and reduce its condition number */
+La_extern void
+F77_NAME(dgeequ)(const int* m, const int* n, double* a, const int* lda,
+		 double* r, double* c, double* rowcnd, double* colcnd,
+		 double* amax, int* info);
+/* DGEES - compute for an N-by-N real nonsymmetric matrix A, the */
+/* eigenvalues, the real Schur form T, and, optionally, the matrix */
+/* of Schur vectors Z */
+La_extern void
+F77_NAME(dgees)(const char* jobvs, const char* sort,
+		int (*select)(const double*, const double*),
+		const int* n, double* a, const int* lda,
+		int* sdim, double* wr, double* wi,
+		double* vs, const int* ldvs,
+		double* work, const int* lwork, int* bwork, int* info);
+/* DGEESX - compute for an N-by-N real nonsymmetric matrix A, the */
+/* eigenvalues, the real Schur form T, and, optionally, the matrix */
+/* of Schur vectors Z */
+La_extern void
+F77_NAME(dgeesx)(const char* jobvs, const char* sort,
+		 int (*select)(const double*, const double*),
+		 const char* sense, const int* n, double* a,
+		 const int* lda, int* sdim, double* wr, double* wi,
+		 double* vs, const int* ldvs, double* rconde,
+		 double* rcondv, double* work, const int* lwork,
+		 int* iwork, const int* liwork, int* bwork, int* info);
+/* DGEEV - compute for an N-by-N real nonsymmetric matrix A, the */
+/* eigenvalues and, optionally, the left and/or right eigenvectors */
+La_extern void
+F77_NAME(dgeev)(const char* jobvl, const char* jobvr,
+		const int* n, double* a, const int* lda,
+		double* wr, double* wi, double* vl, const int* ldvl,
+		double* vr, const int* ldvr,
+		double* work, const int* lwork, int* info);
+/* DGEEVX - compute for an N-by-N real nonsymmetric matrix A, the */
+/* eigenvalues and, optionally, the left and/or right eigenvectors */
+La_extern void
+F77_NAME(dgeevx)(const char* balanc, const char* jobvl, const char* jobvr,
+		 const char* sense, const int* n, double* a, const int* lda,
+		 double* wr, double* wi, double* vl, const int* ldvl,
+		 double* vr, const int* ldvr, int* ilo, int* ihi,
+		 double* scale, double* abnrm, double* rconde, double* rcondv,
+		 double* work, const int* lwork, int* iwork, int* info);
+/* DGEGV - compute for a pair of n-by-n real nonsymmetric */
+/* matrices A and B, the generalized eigenvalues (alphar +/- */
+/* alphai*i, beta);, and optionally, the left and/or right */
+/* generalized eigenvectors (VL and VR); */
+La_extern void
+F77_NAME(dgegv)(const char* jobvl, const char* jobvr,
+		const int* n, double* a, const int* lda,
+		double* b, const int* ldb,
+		double* alphar, double* alphai,
+		const double* beta, double* vl, const int* ldvl,
+		double* vr, const int* ldvr,
+		double* work, const int* lwork, int* info);
+/* DGEHD2 - reduce a real general matrix A to upper Hessenberg */
+/* form H by an orthogonal similarity transformation */
+La_extern void
+F77_NAME(dgehd2)(const int* n, const int* ilo, const int* ihi,
+		 double* a, const int* lda, double* tau,
+		 double* work, int* info);
+/* DGEHRD - reduce a real general matrix A to upper Hessenberg */
+/* form H by an orthogonal similarity transformation */
+La_extern void
+F77_NAME(dgehrd)(const int* n, const int* ilo, const int* ihi,
+		 double* a, const int* lda, double* tau,
+		 double* work, const int* lwork, int* info);
+/* DGELQ2 - compute an LQ factorization of a real m by n matrix A */
+La_extern void
+F77_NAME(dgelq2)(const int* m, const int* n,
+		 double* a, const int* lda, double* tau,
+		 double* work, int* info);
+/* DGELQF - compute an LQ factorization of a real M-by-N matrix A */
+La_extern void
+F77_NAME(dgelqf)(const int* m, const int* n,
+		 double* a, const int* lda, double* tau,
+		 double* work, const int* lwork, int* info);
+/* DGELS - solve overdetermined or underdetermined real linear */
+/* systems involving an M-by-N matrix A, or its transpose, using a */
+/* QR or LQ factorization of A */
+La_extern void
+F77_NAME(dgels)(const char* trans, const int* m, const int* n,
+		const int* nrhs, double* a, const int* lda,
+		double* b, const int* ldb,
+		double* work, const int* lwork, int* info);
+/* DGELSS - compute the minimum norm solution to a real linear */
+/* least squares problem */
+La_extern void
+F77_NAME(dgelss)(const int* m, const int* n, const int* nrhs,
+		 double* a, const int* lda, double* b, const int* ldb,
+		 double* s, double* rcond, int* rank,
+		 double* work, const int* lwork, int* info);
+/* DGELSY - compute the minimum-norm solution to a real linear */
+/* least squares problem */
+La_extern void
+F77_NAME(dgelsy)(const int* m, const int* n, const int* nrhs,
+		 double* a, const int* lda, double* b, const int* ldb,
+		 int* jpvt, const double* rcond, int* rank,
+		 double* work, const int* lwork, int* info);
+/* DGEQL2 - compute a QL factorization of a real m by n matrix A */
+La_extern void
+F77_NAME(dgeql2)(const int* m, const int* n, double* a, const int* lda,
+		 double* tau, double* work, int* info);
+/* DGEQLF - compute a QL factorization of a real M-by-N matrix A */
+La_extern void
+F77_NAME(dgeqlf)(const int* m, const int* n,
+		 double* a, const int* lda, double* tau,
+		 double* work, const int* lwork, int* info);
+/* DGEQP3 - compute a QR factorization with column pivoting of a */
+/* real M-by-N matrix A using level 3 BLAS */
+La_extern void
+F77_NAME(dgeqp3)(const int* m, const int* n, double* a, const int* lda,
+		 int* jpvt, double* tau, double* work, const int* lwork,
+		 int* info);
+/* DGEQPF - compute a QR factorization with column pivoting of a */
+/* real M-by-N matrix A */
+La_extern void
+F77_NAME(dgeqpf)(const int* m, const int* n, double* a, const int* lda,
+		 int* jpvt, double* tau, double* work, int* info);
+/* DGEQR2 - compute a QR factorization of a real m by n matrix A */
+La_extern void
+F77_NAME(dgeqr2)(const int* m, const int* n, double* a, const int* lda,
+		 double* tau, double* work, int* info);
+/* DGEQRF - compute a QR factorization of a real M-by-N matrix A */
+La_extern void
+F77_NAME(dgeqrf)(const int* m, const int* n, double* a, const int* lda,
+		 double* tau, double* work, const int* lwork, int* info);
+/* DGERFS - improve the computed solution to a system of linear */
+/* equations and provides error bounds and backward error */
+/* estimates for the solution */
+La_extern void
+F77_NAME(dgerfs)(const char* trans, const int* n, const int* nrhs,
+		 double* a, const int* lda, double* af, const int* ldaf,
+		 int* ipiv, double* b, const int* ldb,
+		 double* x, const int* ldx, double* ferr, double* berr,
+		 double* work, int* iwork, int* info);
+/* DGERQ2 - compute an RQ factorization of a real m by n matrix A */
+La_extern void
+F77_NAME(dgerq2)(const int* m, const int* n, double* a, const int* lda,
+		 double* tau, double* work, int* info);
+/* DGERQF - compute an RQ factorization of a real M-by-N matrix A */
+La_extern void
+F77_NAME(dgerqf)(const int* m, const int* n, double* a, const int* lda,
+		 double* tau, double* work, const int* lwork, int* info);
+/* DGESV - compute the solution to a real system of linear */
+/* equations  A * X = B, */
+La_extern void
+F77_NAME(dgesv)(const int* n, const int* nrhs, double* a, const int* lda,
+		int* ipiv, double* b, const int* ldb, int* info);
+/* DGESVD - compute the singular value decomposition (SVD); of a */
+/* real M-by-N matrix A, optionally computing the left and/or */
+/* right singular vectors */
+La_extern void
+F77_NAME(dgesvd)(const char* jobu, const char* jobvt, const int* m,
+		 const int* n, double* a, const int* lda, double* s,
+		 double* u, const int* ldu, double* vt, const int* ldvt,
+		 double* work, const int* lwork, int* info);
+/* DGESVX - use the LU factorization to compute the solution to a */
+/* real system of linear equations  A * X = B, */
+La_extern void
+F77_NAME(dgesvx)(const int* fact, const char* trans, const int* n,
+		 const int* nrhs, double* a, const int* lda,
+		 double* af, const int* ldaf, int* ipiv,
+		 char *equed, double* r, double* c,
+		 double* b, const int* ldb,
+		 double* x, const int* ldx,
+		 double* rcond, double* ferr, double* berr,
+		 double* work, int* iwork, int* info);
+/* DGETF2 - compute an LU factorization of a general m-by-n */
+/* matrix A using partial pivoting with row interchanges */
+La_extern void
+F77_NAME(dgetf2)(const int* m, const int* n, double* a, const int* lda,
+		 int* ipiv, int* info);
+/* DGETRF - compute an LU factorization of a general M-by-N */
+/* matrix A using partial pivoting with row interchanges */
+La_extern void
+F77_NAME(dgetrf)(const int* m, const int* n, double* a, const int* lda,
+		 int* ipiv, int* info);
+/* DGETRI - compute the inverse of a matrix using the LU */
+/* factorization computed by DGETRF */
+La_extern void
+F77_NAME(dgetri)(const int* n, double* a, const int* lda,
+		 int* ipiv, double* work, const int* lwork, int* info);
+/* DGETRS - solve a system of linear equations	A * X = B or A' * */
+/* X = B with a general N-by-N matrix A using the LU factorization */
+/* computed by DGETRF */
+La_extern void
+F77_NAME(dgetrs)(const char* trans, const int* n, const int* nrhs,
+		 const double* a, const int* lda, const int* ipiv,
+		 double* b, const int* ldb, int* info);
+
+/* Double precision General matrices Generalized problems */
+
+/* DGGBAK - form the right or left eigenvectors of a real */
+/* generalized eigenvalue problem A*x = lambda*B*x, by backward */
+/* transformation on the computed eigenvectors of the balanced */
+/* pair of matrices output by DGGBAL */
+La_extern void
+F77_NAME(dggbak)(const char* job, const char* side,
+		 const int* n, const int* ilo, const int* ihi,
+		 double* lscale, double* rscale, const int* m,
+		 double* v, const int* ldv, int* info);
+/* DGGBAL - balance a pair of general real matrices (A,B); */
+La_extern void
+F77_NAME(dggbal)(const char* job, const int* n, double* a, const int* lda,
+		 double* b, const int* ldb, int* ilo, int* ihi,
+		 double* lscale, double* rscale, double* work, int* info);
+/* DGGES - compute for a pair of N-by-N real nonsymmetric */
+/* matrices A, B the generalized eigenvalues, the generalized */
+/* real Schur form (S,T), optionally, the left and/or right matrices */
+/* of Schur vectors (VSL and VSR)*/
+La_extern void
+F77_NAME(dgges)(const char* jobvsl, const char* jobvsr, const char* sort,
+		int (*delztg)(double*, double*, double*),
+		const int* n, double* a, const int* lda,
+		double* b, const int* ldb, double* alphar,
+		double* alphai, const double* beta,
+		double* vsl, const int* ldvsl,
+		double* vsr, const int* ldvsr,
+		double* work, const int* lwork, int* bwork, int* info);
+
+/* DGGGLM - solve a general Gauss-Markov linear model (GLM) problem */
+La_extern void
+F77_NAME(dggglm)(const int* n, const int* m, const int* p,
+		 double* a, const int* lda, double* b, const int* ldb,
+		 double* d, double* x, double* y,
+		 double* work, const int* lwork, int* info);
+/* DGGHRD - reduce a pair of real matrices (A,B); to generalized */
+/* upper Hessenberg form using orthogonal transformations, where A */
+/* is a general matrix and B is upper triangular */
+La_extern void
+F77_NAME(dgghrd)(const char* compq, const char* compz, const int* n,
+		 const int* ilo, const int* ihi, double* a, const int* lda,
+		 double* b, const int* ldb, double* q, const int* ldq,
+		 double* z, const int* ldz, int* info);
+/* DGGLSE - solve the linear equality-constrained least squares */
+/* (LSE) problem */
+La_extern void
+F77_NAME(dgglse)(const int* m, const int* n, const int* p,
+		 double* a, const int* lda,
+		 double* b, const int* ldb,
+		 double* c, double* d, double* x,
+		 double* work, const int* lwork, int* info);
+/* DGGQRF - compute a generalized QR factorization of an N-by-M */
+/* matrix A and an N-by-P matrix B */
+La_extern void
+F77_NAME(dggqrf)(const int* n, const int* m, const int* p,
+		 double* a, const int* lda, double* taua,
+		 double* b, const int* ldb, double* taub,
+		 double* work, const int* lwork, int* info);
+/* DGGRQF - compute a generalized RQ factorization of an M-by-N */
+/* matrix A and a P-by-N matrix B */
+La_extern void
+F77_NAME(dggrqf)(const int* m, const int* p, const int* n,
+		 double* a, const int* lda, double* taua,
+		 double* b, const int* ldb, double* taub,
+		 double* work, const int* lwork, int* info);
+/* DGGSVD - compute the generalized singular value decomposition */
+/* (GSVD) of an M-by-N real matrix A and P-by-N real matrix B */
+La_extern void
+F77_NAME(dggsvd)(const char* jobu, const char* jobv, const char* jobq,
+		 const int* m, const int* n, const int* p,
+		 const int* k, const int* l,
+		 double* a, const int* lda,
+		 double* b, const int* ldb,
+		 const double* alpha, const double* beta,
+		 double* u, const int* ldu,
+		 double* v, const int* ldv,
+		 double* q, const int* ldq,
+		 double* work, int* iwork, int* info);
+
+/* Double precision General Tridiagonal matrices */
+
+/* DGTCON - estimate the reciprocal of the condition number of a real */
+/* tridiagonal matrix A using the LU factorization as computed by DGTTRF */
+La_extern void
+F77_NAME(dgtcon)(const char* norm, const int* n, double* dl, double* d,
+		 double* du, double* du2, int* ipiv, const double* anorm,
+		 double* rcond, double* work, int* iwork, int* info);
+/* DGTRFS - improve the computed solution to a system of linear equations */
+/* when the coefficient matrix is tridiagonal, and provides error bounds */
+/* and backward error estimates for the solution */
+La_extern void
+F77_NAME(dgtrfs)(const char* trans, const int* n, const int* nrhs,
+		 double* dl, double* d, double* du, double* dlf,
+		 double* df, double* duf, double* du2,
+		 int* ipiv, double* b, const int* ldb,
+		 double* x, const int* ldx,
+		 double* ferr, double* berr,
+		 double* work, int* iwork, int* info);
+/* DGTSV - solve the equation	A*X = B, */
+La_extern void
+F77_NAME(dgtsv)(const int* n, const int* nrhs,
+		double* dl, double* d, double* du,
+		double* b, const int* ldb, int* info);
+/* DGTSVX - use the LU factorization to compute the solution to a */
+/* real system of linear equations A * X = B or A**T * X = B, */
+La_extern void
+F77_NAME(dgtsvx)(const int* fact, const char* trans,
+		 const int* n, const int* nrhs,
+		 double* dl, double* d, double* du,
+		 double* dlf, double* df, double* duf,
+		 double* du2, int* ipiv,
+		 double* b, const int* ldb,
+		 double* x, const int* ldx,
+		 double* rcond, double* ferr, double* berr,
+		 double* work, int* iwork, int* info);
+/* DGTTRF - compute an LU factorization of a real tridiagonal matrix */
+/* A using elimination with partial pivoting and row interchanges */
+La_extern void
+F77_NAME(dgttrf)(const int* n, double* dl, double* d,
+		 double* du, double* du2, int* ipiv, int* info);
+/* DGTTRS - solve one of the systems of equations  A*X = B or */
+/* A'*X = B, */
+La_extern void
+F77_NAME(dgttrs)(const char* trans, const int* n, const int* nrhs,
+		 double* dl, double* d, double* du, double* du2,
+		 int* ipiv, double* b, const int* ldb, int* info);
+
+/* Double precision Orthogonal matrices */
+
+/* DOPGTR - generate a real orthogonal matrix Q which is defined */
+/* as the product of n-1 elementary reflectors H(i); of order n, */
+/* as returned by DSPTRD using packed storage */
+La_extern void
+F77_NAME(dopgtr)(const char* uplo, const int* n,
+		 const double* ap, const double* tau,
+		 double* q, const int* ldq,
+		 double* work, int* info);
+/* DOPMTR - overwrite the general real M-by-N matrix C with */
+/* SIDE = 'L' SIDE = 'R' TRANS = 'N' */
+La_extern void
+F77_NAME(dopmtr)(const char* side, const char* uplo,
+		 const char* trans, const int* m, const int* n,
+		 const double* ap, const double* tau,
+		 double* c, const int* ldc,
+		 double* work, int* info);
+/* DORG2L - generate an m by n real matrix Q with orthonormal */
+/* columns, */
+La_extern void
+F77_NAME(dorg2l)(const int* m, const int* n, const int* k,
+		 double* a, const int* lda,
+		 const double* tau, double* work, int* info);
+/* DORG2R - generate an m by n real matrix Q with orthonormal */
+/* columns, */
+La_extern void
+F77_NAME(dorg2r)(const int* m, const int* n, const int* k,
+		 double* a, const int* lda,
+		 const double* tau, double* work, int* info);
+/* DORGBR - generate one of the real orthogonal matrices Q or */
+/* P**T determined by DGEBRD when reducing a real matrix A to */
+/* bidiagonal form */
+La_extern void
+F77_NAME(dorgbr)(const char* vect, const int* m,
+		 const int* n, const int* k,
+		 double* a, const int* lda,
+		 const double* tau, double* work,
+		 const int* lwork, int* info);
+/* DORGHR - generate a real orthogonal matrix Q which is defined */
+/* as the product of IHI-ILO elementary reflectors of order N, as */
+/* returned by DGEHRD */
+La_extern void
+F77_NAME(dorghr)(const int* n, const int* ilo, const int* ihi,
+		 double* a, const int* lda, const double* tau,
+		 double* work, const int* lwork, int* info);
+/* DORGL2 - generate an m by n real matrix Q with orthonormal */
+/* rows, */
+La_extern void
+F77_NAME(dorgl2)(const int* m, const int* n, const int* k,
+		 double* a, const int* lda, const double* tau,
+		 double* work, int* info);
+/* DORGLQ - generate an M-by-N real matrix Q with orthonormal */
+/* rows, */
+La_extern void
+F77_NAME(dorglq)(const int* m, const int* n, const int* k,
+		 double* a, const int* lda,
+		 const double* tau, double* work,
+		 const int* lwork, int* info);
+/* DORGQL - generate an M-by-N real matrix Q with orthonormal */
+/* columns, */
+La_extern void
+F77_NAME(dorgql)(const int* m, const int* n, const int* k,
+		 double* a, const int* lda,
+		 const double* tau, double* work,
+		 const int* lwork, int* info);
+/* DORGQR - generate an M-by-N real matrix Q with orthonormal */
+/* columns, */
+La_extern void
+F77_NAME(dorgqr)(const int* m, const int* n, const int* k,
+		 double* a, const int* lda, const double* tau,
+		 double* work, const int* lwork, int* info);
+/* DORGR2 - generate an m by n real matrix Q with orthonormal */
+/* rows, */
+La_extern void
+F77_NAME(dorgr2)(const int* m, const int* n, const int* k,
+		 double* a, const int* lda, const double* tau,
+		 double* work, int* info);
+/* DORGRQ - generate an M-by-N real matrix Q with orthonormal rows */
+La_extern void
+F77_NAME(dorgrq)(const int* m, const int* n, const int* k,
+		 double* a, const int* lda, const double* tau,
+		 double* work, const int* lwork, int* info);
+/* DORGTR - generate a real orthogonal matrix Q which is defined */
+/* as the product of n-1 elementary reflectors of order const int* n, as */
+/* returned by DSYTRD */
+La_extern void
+F77_NAME(dorgtr)(const char* uplo, const int* n,
+		 double* a, const int* lda, const double* tau,
+		 double* work, const int* lwork, int* info);
+/* DORM2L - overwrite the general real m by n matrix C with   Q * */
+/* C if SIDE = 'L' and TRANS = 'N', or	 Q'* C if SIDE = 'L' and */
+/* TRANS = 'T', or   C * Q if SIDE = 'R' and TRANS = 'N', or   C * */
+/* Q' if SIDE = 'R' and TRANS = 'T', */
+La_extern void
+F77_NAME(dorm2l)(const char* side, const char* trans,
+		 const int* m, const int* n, const int* k,
+		 const double* a, const int* lda,
+		 const double* tau, double* c, const int* ldc,
+		 double* work, int* info);
+/* DORM2R - overwrite the general real m by n matrix C with   Q * C */
+/* if SIDE = 'L' and TRANS = 'N', or   Q'* C if SIDE = 'L' and */
+/* TRANS = 'T', or   C * Q if SIDE = 'R' and TRANS = 'N', or   C * */
+/* Q' if SIDE = 'R' and TRANS = 'T', */
+La_extern void
+F77_NAME(dorm2r)(const char* side, const char* trans,
+		 const int* m, const int* n, const int* k,
+		 const double* a, const int* lda, const double* tau,
+		 double* c, const int* ldc, double* work, int* info);
+/* DORMBR - VECT = 'Q', DORMBR overwrites the general real M-by-N */
+/* matrix C with  SIDE = 'L' SIDE = 'R' TRANS = 'N' */
+La_extern void
+F77_NAME(dormbr)(const char* vect, const char* side, const char* trans,
+		 const int* m, const int* n, const int* k,
+		 const double* a, const int* lda, const double* tau,
+		 double* c, const int* ldc,
+		 double* work, const int* lwork, int* info);
+/* DORMHR - overwrite the general real M-by-N matrix C with */
+/* SIDE = 'L' SIDE = 'R' TRANS = 'N' */
+La_extern void
+F77_NAME(dormhr)(const char* side, const char* trans, const int* m,
+		 const int* n, const int* ilo, const int* ihi,
+		 const double* a, const int* lda, const double* tau,
+		 double* c, const int* ldc,
+		 double* work, const int* lwork, int* info);
+/* DORML2 - overwrite the general real m by n matrix C with   Q * */
+/* C if SIDE = 'L' and TRANS = 'N', or	 Q'* C if SIDE = 'L' and */
+/* TRANS = 'T', or   C * Q if SIDE = 'R' and TRANS = 'N', or   C * */
+/* Q' if SIDE = 'R' and TRANS = 'T', */
+La_extern void
+F77_NAME(dorml2)(const char* side, const char* trans,
+		 const int* m, const int* n, const int* k,
+		 const double* a, const int* lda, const double* tau,
+		 double* c, const int* ldc, double* work, int* info);
+/* DORMLQ - overwrite the general real M-by-N matrix C with */
+/* SIDE = 'L' SIDE = 'R' TRANS = 'N'  */
+La_extern void
+F77_NAME(dormlq)(const char* side, const char* trans,
+		 const int* m, const int* n, const int* k,
+		 const double* a, const int* lda,
+		 const double* tau, double* c, const int* ldc,
+		 double* work, const int* lwork, int* info);
+/* DORMQL - overwrite the general real M-by-N matrix C with */
+/* SIDE = 'L' SIDE = 'R' TRANS = 'N' */
+La_extern void
+F77_NAME(dormql)(const char* side, const char* trans,
+		 const int* m, const int* n, const int* k,
+		 const double* a, const int* lda,
+		 const double* tau, double* c, const int* ldc,
+		 double* work, const int* lwork, int* info);
+/* DORMQR - overwrite the general real M-by-N matrix C with   SIDE = */
+/* 'L' SIDE = 'R' TRANS = 'N' */
+La_extern void
+F77_NAME(dormqr)(const char* side, const char* trans,
+		 const int* m, const int* n, const int* k,
+		 const double* a, const int* lda,
+		 const double* tau, double* c, const int* ldc,
+		 double* work, const int* lwork, int* info);
+/* DORMR2 - overwrite the general real m by n matrix C with   Q * */
+/* C if SIDE = 'L' and TRANS = 'N', or	 Q'* C if SIDE = 'L' and */
+/* TRANS = 'T', or   C * Q if SIDE = 'R' and TRANS = 'N', or   C * */
+/* Q' if SIDE = 'R' and TRANS = 'T', */
+La_extern void
+F77_NAME(dormr2)(const char* side, const char* trans,
+		 const int* m, const int* n, const int* k,
+		 const double* a, const int* lda,
+		 const double* tau, double* c, const int* ldc,
+		 double* work, int* info);
+/* DORMRQ - overwrite the general real M-by-N matrix C with */
+/* SIDE = 'L' SIDE = 'R' TRANS = 'N' */
+La_extern void
+F77_NAME(dormrq)(const char* side, const char* trans,
+		 const int* m, const int* n, const int* k,
+		 const double* a, const int* lda,
+		 const double* tau, double* c, const int* ldc,
+		 double* work, const int* lwork, int* info);
+/* DORMTR - overwrite the general real M-by-N matrix C with */
+/* SIDE = 'L' SIDE = 'R' TRANS = 'N' */
+La_extern void
+F77_NAME(dormtr)(const char* side, const char* uplo,
+		 const char* trans, const int* m, const int* n,
+		 const double* a, const int* lda,
+		 const double* tau, double* c, const int* ldc,
+		 double* work, const int* lwork, int* info);
+
+/* Double precision Positive definite Band matrices */
+
+/* DPBCON - estimate the reciprocal of the condition number (in */
+/* the 1-norm); of a real symmetric positive definite band matrix */
+/* using the Cholesky factorization A = U**T*U or A = L*L**T */
+/* computed by DPBTRF */
+La_extern void
+F77_NAME(dpbcon)(const char* uplo, const int* n, const int* kd,
+		 const double* ab, const int* ldab,
+		 const double* anorm, double* rcond,
+		 double* work, int* iwork, int* info);
+/* DPBEQU - compute row and column scalings intended to */
+/* equilibrate a symmetric positive definite band matrix A and */
+/* reduce its condition number (with respect to the two-norm); */
+La_extern void
+F77_NAME(dpbequ)(const char* uplo, const int* n, const int* kd,
+		 const double* ab, const int* ldab,
+		 double* s, double* scond, double* amax, int* info);
+/* DPBRFS - improve the computed solution to a system of linear */
+/* equations when the coefficient matrix is symmetric positive */
+/* definite and banded, and provides error bounds and backward */
+/* error estimates for the solution */
+La_extern void
+F77_NAME(dpbrfs)(const char* uplo, const int* n,
+		 const int* kd, const int* nrhs,
+		 const double* ab, const int* ldab,
+		 const double* afb, const int* ldafb,
+		 const double* b, const int* ldb,
+		 double* x, const int* ldx,
+		 double* ferr, double* berr,
+		 double* work, int* iwork, int* info);
+/* DPBSTF - compute a split Cholesky factorization of a real */
+/* symmetric positive definite band matrix A */
+La_extern void
+F77_NAME(dpbstf)(const char* uplo, const int* n, const int* kd,
+		 double* ab, const int* ldab, int* info);
+/* DPBSV - compute the solution to a real system of linear */
+/* equations  A * X = B, */
+La_extern void
+F77_NAME(dpbsv)(const char* uplo, const int* n,
+		const int* kd, const int* nrhs,
+		double* ab, const int* ldab,
+		double* b, const int* ldb, int* info);
+/* DPBSVX - use the Cholesky factorization A = U**T*U or A = */
+/* L*L**T to compute the solution to a real system of linear */
+/* equations  A * X = B, */
+La_extern void
+F77_NAME(dpbsvx)(const int* fact, const char* uplo, const int* n,
+		 const int* kd, const int* nrhs,
+		 double* ab, const int* ldab,
+		 double* afb, const int* ldafb,
+		 char* equed, double* s,
+		 double* b, const int* ldb,
+		 double* x, const int* ldx, double* rcond,
+		 double* ferr, double* berr,
+		 double* work, int* iwork, int* info);
+/* DPBTF2 - compute the Cholesky factorization of a real */
+/* symmetric positive definite band matrix A */
+La_extern void
+F77_NAME(dpbtf2)(const char* uplo, const int* n, const int* kd,
+		 double* ab, const int* ldab, int* info);
+/* DPBTRF - compute the Cholesky factorization of a real */
+/* symmetric positive definite band matrix A */
+La_extern void
+F77_NAME(dpbtrf)(const char* uplo, const int* n, const int* kd,
+		 double* ab, const int* ldab, int* info);
+/* DPBTRS - solve a system of linear equations A*X = B with a */
+/* symmetric positive definite band matrix A using the Cholesky */
+/* factorization A = U**T*U or A = L*L**T computed by DPBTRF */
+La_extern void
+F77_NAME(dpbtrs)(const char* uplo, const int* n,
+		 const int* kd, const int* nrhs,
+		 const double* ab, const int* ldab,
+		 double* b, const int* ldb, int* info);
+
+/* Double precision Positive definite matrices */
+
+/* DPOCON - estimate the reciprocal of the condition number (in */
+/* the 1-norm); of a real symmetric positive definite matrix using */
+/* the Cholesky factorization A = U**T*U or A = L*L**T computed by */
+/* DPOTRF */
+La_extern void
+F77_NAME(dpocon)(const char* uplo, const int* n,
+		 const double* a, const int* lda,
+		 const double* anorm, double* rcond,
+		 double* work, int* iwork, int* info);
+/* DPOEQU - compute row and column scalings intended to */
+/* equilibrate a symmetric positive definite matrix A and reduce */
+/* its condition number (with respect to the two-norm); */
+La_extern void
+F77_NAME(dpoequ)(const int* n, const double* a, const int* lda,
+		 double* s, double* scond, double* amax, int* info);
+/* DPORFS - improve the computed solution to a system of linear */
+/* equations when the coefficient matrix is symmetric positive */
+/* definite, */
+La_extern void
+F77_NAME(dporfs)(const char* uplo, const int* n, const int* nrhs,
+		 const double* a, const int* lda,
+		 const double* af, const int* ldaf,
+		 const double* b, const int* ldb,
+		 double* x, const int* ldx,
+		 double* ferr, double* berr,
+		 double* work, int* iwork, int* info);
+/* DPOSV - compute the solution to a real system of linear */
+/* equations  A * X = B, */
+La_extern void
+F77_NAME(dposv)(const char* uplo, const int* n, const int* nrhs,
+		double* a, const int* lda,
+		double* b, const int* ldb, int* info);
+/* DPOSVX - use the Cholesky factorization A = U**T*U or A = */
+/* L*L**T to compute the solution to a real system of linear */
+/* equations  A * X = B, */
+La_extern void
+F77_NAME(dposvx)(const int* fact, const char* uplo,
+		 const int* n, const int* nrhs,
+		 double* a, const int* lda,
+		 double* af, const int* ldaf, char* equed,
+		 double* s, double* b, const int* ldb,
+		 double* x, const int* ldx, double* rcond,
+		 double* ferr, double* berr, double* work,
+		 int* iwork, int* info);
+/* DPOTF2 - compute the Cholesky factorization of a real */
+/* symmetric positive definite matrix A */
+La_extern void
+F77_NAME(dpotf2)(const char* uplo, const int* n,
+		 double* a, const int* lda, int* info);
+/* DPOTRF - compute the Cholesky factorization of a real */
+/* symmetric positive definite matrix A */
+La_extern void
+F77_NAME(dpotrf)(const char* uplo, const int* n,
+		 double* a, const int* lda, int* info);
+/* DPOTRI - compute the inverse of a real symmetric positive */
+/* definite matrix A using the Cholesky factorization A = U**T*U */
+/* or A = L*L**T computed by DPOTRF */
+La_extern void
+F77_NAME(dpotri)(const char* uplo, const int* n,
+		 double* a, const int* lda, int* info);
+/* DPOTRS - solve a system of linear equations A*X = B with a */
+/* symmetric positive definite matrix A using the Cholesky */
+/* factorization A = U**T*U or A = L*L**T computed by DPOTRF */
+La_extern void
+F77_NAME(dpotrs)(const char* uplo, const int* n,
+		 const int* nrhs, const double* a, const int* lda,
+		 double* b, const int* ldb, int* info);
+/* DPPCON - estimate the reciprocal of the condition number (in */
+/* the 1-norm); of a real symmetric positive definite packed */
+/* matrix using the Cholesky factorization A = U**T*U or A = */
+/* L*L**T computed by DPPTRF */
+La_extern void
+F77_NAME(dppcon)(const char* uplo, const int* n,
+		 const double* ap, const double* anorm, double* rcond,
+		 double* work, int* iwork, int* info);
+/* DPPEQU - compute row and column scalings intended to */
+/* equilibrate a symmetric positive definite matrix A in packed */
+/* storage and reduce its condition number (with respect to the */
+/* two-norm); */
+La_extern void
+F77_NAME(dppequ)(const char* uplo, const int* n,
+		 const double* ap, double* s, double* scond,
+		 double* amax, int* info);
+
+/* Double precision Positive definite matrices in Packed storage */
+
+/* DPPRFS - improve the computed solution to a system of linear */
+/* equations when the coefficient matrix is symmetric positive */
+/* definite and packed, and provides error bounds and backward */
+/* error estimates for the solution */
+La_extern void
+F77_NAME(dpprfs)(const char* uplo, const int* n, const int* nrhs,
+		 const double* ap, const double* afp,
+		 const double* b, const int* ldb,
+		 double* x, const int* ldx,
+		 double* ferr, double* berr,
+		 double* work, int* iwork, int* info);
+/* DPPSV - compute the solution to a real system of linear */
+/* equations  A * X = B, */
+La_extern void
+F77_NAME(dppsv)(const char* uplo, const int* n,
+		const int* nrhs, const double* ap,
+		double* b, const int* ldb, int* info);
+/* DPPSVX - use the Cholesky factorization A = U**T*U or A = */
+/* L*L**T to compute the solution to a real system of linear */
+/* equations  A * X = B, */
+La_extern void
+F77_NAME(dppsvx)(const int* fact, const char* uplo,
+		 const int* n, const int* nrhs, double* ap,
+		 double* afp, char* equed, double* s,
+		 double* b, const int* ldb,
+		 double* x, const int* ldx,
+		 double* rcond, double* ferr, double* berr,
+		 double* work, int* iwork, int* info);
+/* DPPTRF - compute the Cholesky factorization of a real */
+/* symmetric positive definite matrix A stored in packed format */
+La_extern void
+F77_NAME(dpptrf)(const char* uplo, const int* n, double* ap, int* info);
+/* DPPTRI - compute the inverse of a real symmetric positive */
+/* definite matrix A using the Cholesky factorization A = U**T*U */
+/* or A = L*L**T computed by DPPTRF  */
+La_extern void
+F77_NAME(dpptri)(const char* uplo, const int* n, double* ap, int* info);
+/* DPPTRS - solve a system of linear equations A*X = B with a */
+/* symmetric positive definite matrix A in packed storage using */
+/* the Cholesky factorization A = U**T*U or A = L*L**T computed by */
+/* DPPTRF */
+La_extern void
+F77_NAME(dpptrs)(const char* uplo, const int* n,
+		 const int* nrhs, const double* ap,
+		 double* b, const int* ldb, int* info);
+
+/* Double precision symmetric Positive definite Tridiagonal matrices */
+
+/* DPTCON - compute the reciprocal of the condition number (in */
+/* the 1-norm); of a real symmetric positive definite tridiagonal */
+/* matrix using the factorization A = L*D*L**T or A = U**T*D*U */
+/* computed by DPTTRF */
+La_extern void
+F77_NAME(dptcon)(const int* n,
+		 const double* d, const double* e,
+		 const double* anorm, double* rcond,
+		 double* work, int* info);
+/* DPTEQR - compute all eigenvalues and, optionally, eigenvectors */
+/* of a symmetric positive definite tridiagonal matrix by first */
+/* factoring the matrix using DPTTRF, and then calling DBDSQR to */
+/* compute the singular values of the bidiagonal factor */
+La_extern void
+F77_NAME(dpteqr)(const char* compz, const int* n, double* d,
+		 double* e, double* z, const int* ldz,
+		 double* work, int* info);
+/* DPTRFS - improve the computed solution to a system of linear */
+/* equations when the coefficient matrix is symmetric positive */
+/* definite and tridiagonal, and provides error bounds and */
+/* backward error estimates for the solution */
+La_extern void
+F77_NAME(dptrfs)(const int* n, const int* nrhs,
+		 const double* d, const double* e,
+		 const double* df, const double* ef,
+		 const double* b, const int* ldb,
+		 double* x, const int* ldx,
+		 double* ferr, double* berr,
+		 double* work, int* info);
+/* DPTSV - compute the solution to a real system of linear */
+/* equations A*X = B, where A is an N-by-N symmetric positive */
+/* definite tridiagonal matrix, and X and B are N-by-NRHS matrices */
+La_extern void
+F77_NAME(dptsv)(const int* n, const int* nrhs, double* d,
+		double* e, double* b, const int* ldb, int* info);
+/* DPTSVX - use the factorization A = L*D*L**T to compute the */
+/* solution to a real system of linear equations A*X = B, where A */
+/* is an N-by-N symmetric positive definite tridiagonal matrix and */
+/* X and B are N-by-NRHS matrices */
+La_extern void
+F77_NAME(dptsvx)(const int* fact, const int* n,
+		 const int* nrhs,
+		 const double* d, const double* e,
+		 double* df, double* ef,
+		 const double* b, const int* ldb,
+		 double* x, const int* ldx, double* rcond,
+		 double* ferr, double* berr,
+		 double* work, int* info);
+/* DPTTRF - compute the factorization of a real symmetric */
+/* positive definite tridiagonal matrix A */
+La_extern void
+F77_NAME(dpttrf)(const int* n, double* d, double* e, int* info);
+/* DPTTRS - solve a system of linear equations A * X = B with a */
+/* symmetric positive definite tridiagonal matrix A using the */
+/* factorization A = L*D*L**T or A = U**T*D*U computed by DPTTRF */
+La_extern void
+F77_NAME(dpttrs)(const int* n, const int* nrhs,
+		 const double* d, const double* e,
+		 double* b, const int* ldb, int* info);
+/* DRSCL - multiply an n-element real vector x by the real scalar */
+/* 1/a */
+La_extern void
+F77_NAME(drscl)(const int* n, const double* da,
+		double* x, const int* incx);
+
+/* Double precision Symmetric Band matrices */
+
+/* DSBEV - compute all the eigenvalues and, optionally, */
+/* eigenvectors of a real symmetric band matrix A */
+La_extern void
+F77_NAME(dsbev)(const char* jobz, const char* uplo,
+		const int* n, const int* kd,
+		double* ab, const int* ldab,
+		double* w, double* z, const int* ldz,
+		double* work, int* info);
+/* DSBEVD - compute all the eigenvalues and, optionally, */
+/* eigenvectors of a real symmetric band matrix A */
+La_extern void
+F77_NAME(dsbevd)(const char* jobz, const char* uplo,
+		 const int* n, const int* kd,
+		 double* ab, const int* ldab,
+		 double* w, double* z, const int* ldz,
+		 double* work, const int* lwork,
+		 int* iwork, const int* liwork, int* info);
+/* DSBEVX - compute selected eigenvalues and, optionally, */
+/* eigenvectors of a real symmetric band matrix A */
+La_extern void
+F77_NAME(dsbevx)(const char* jobz, const char* range,
+		 const char* uplo, const int* n, const int* kd,
+		 double* ab, const int* ldab,
+		 double* q, const int* ldq,
+		 const double* vl, const double* vu,
+		 const int* il, const int* iu,
+		 const double* abstol,
+		 int* m, double* w,
+		 double* z, const int* ldz,
+		 double* work, int* iwork,
+		 int* ifail, int* info);
+/* DSBGST - reduce a real symmetric-definite banded generalized */
+/* eigenproblem A*x = lambda*B*x to standard form C*y = lambda*y, */
+La_extern void
+F77_NAME(dsbgst)(const char* vect, const char* uplo,
+		 const int* n, const int* ka, const int* kb,
+		 double* ab, const int* ldab,
+		 double* bb, const int* ldbb,
+		 double* x, const int* ldx,
+		 double* work, int* info);
+/* DSBGV - compute all the eigenvalues, and optionally, the */
+/* eigenvectors of a real generalized symmetric-definite banded */
+/* eigenproblem, of the form A*x=(lambda);*B*x */
+La_extern void
+F77_NAME(dsbgv)(const char* jobz, const char* uplo,
+		const int* n, const int* ka, const int* kb,
+		double* ab, const int* ldab,
+		double* bb, const int* ldbb,
+		double* w, double* z, const int* ldz,
+		double* work, int* info);
+/* DSBTRD - reduce a real symmetric band matrix A to symmetric */
+/* tridiagonal form T by an orthogonal similarity transformation */
+La_extern void
+F77_NAME(dsbtrd)(const char* vect, const char* uplo,
+		 const int* n, const int* kd,
+		 double* ab, const int* ldab,
+		 double* d, double* e,
+		 double* q, const int* ldq,
+		 double* work, int* info);
+
+/* Double precision Symmetric Packed matrices */
+
+/* DSPCON - estimate the reciprocal of the condition number (in */
+/* the 1-norm); of a real symmetric packed matrix A using the */
+/* factorization A = U*D*U**T or A = L*D*L**T computed by DSPTRF */
+La_extern void
+F77_NAME(dspcon)(const char* uplo, const int* n,
+		 const double* ap, const int* ipiv,
+		 const double* anorm, double* rcond,
+		 double* work, int* iwork, int* info);
+/* DSPEV - compute all the eigenvalues and, optionally, */
+/* eigenvectors of a real symmetric matrix A in packed storage */
+La_extern void
+F77_NAME(dspev)(const char* jobz, const char* uplo, const int* n,
+		double* ap, double* w, double* z, const int* ldz,
+		double* work, int* info);
+/* DSPEVD - compute all the eigenvalues and, optionally, */
+/* eigenvectors of a real symmetric matrix A in packed storage */
+La_extern void
+F77_NAME(dspevd)(const char* jobz, const char* uplo,
+		 const int* n, double* ap, double* w,
+		 double* z, const int* ldz,
+		 double* work, const int* lwork,
+		 int* iwork, const int* liwork, int* info);
+/* DSPEVX - compute selected eigenvalues and, optionally, */
+/* eigenvectors of a real symmetric matrix A in packed storage */
+La_extern void
+F77_NAME(dspevx)(const char* jobz, const char* range,
+		 const char* uplo, const int* n, double* ap,
+		 const double* vl, const double* vu,
+		 const int* il, const int* iu,
+		 const double* abstol,
+		 int* m, double* w,
+		 double* z, const int* ldz,
+		 double* work, int* iwork,
+		 int* ifail, int* info);
+/* DSPGST - reduce a real symmetric-definite generalized */
+/* eigenproblem to standard form, using packed storage */
+La_extern void
+F77_NAME(dspgst)(const int* itype, const char* uplo,
+		 const int* n, double* ap, double* bp, int* info);
+/* DSPGV - compute all the eigenvalues and, optionally, the */
+/* eigenvectors of a real generalized symmetric-definite */
+/* eigenproblem, of the form A*x=(lambda)*B*x, A*Bx=(lambda)*x, */
+/* or B*A*x=(lambda)*x */
+La_extern void
+F77_NAME(dspgv)(const int* itype, const char* jobz,
+		const char* uplo, const int* n,
+		double* ap, double* bp, double* w,
+		double* z, const int* ldz,
+		double* work, int* info);
+
+/* DSPRFS - improve the computed solution to a system of linear */
+/* equations when the coefficient matrix is symmetric indefinite */
+/* and packed, and provides error bounds and backward error */
+/* estimates for the solution */
+La_extern void
+F77_NAME(dsprfs)(const char* uplo, const int* n,
+		 const int* nrhs, const double* ap,
+		 const double* afp, const int* ipiv,
+		 const double* b, const int* ldb,
+		 double* x, const int* ldx,
+		 double* ferr, double* berr,
+		 double* work, int* iwork, int* info);
+
+/* DSPSV - compute the solution to a real system of linear */
+/* equations  A * X = B, */
+La_extern void
+F77_NAME(dspsv)(const char* uplo, const int* n,
+		const int* nrhs, double* ap, int* ipiv,
+		double* b, const int* ldb, int* info);
+
+/* DSPSVX - use the diagonal pivoting factorization A = U*D*U**T */
+/* or A = L*D*L**T to compute the solution to a real system of */
+/* linear equations A * X = B, where A is an N-by-N symmetric */
+/* matrix stored in packed format and X and B are N-by-NRHS */
+/* matrices */
+La_extern void
+F77_NAME(dspsvx)(const int* fact, const char* uplo,
+		 const int* n, const int* nrhs,
+		 const double* ap, double* afp, int* ipiv,
+		 const double* b, const int* ldb,
+		 double* x, const int* ldx,
+		 double* rcond, double* ferr, double* berr,
+		 double* work, int* iwork, int* info);
+
+/* DSPTRD - reduce a real symmetric matrix A stored in packed */
+/* form to symmetric tridiagonal form T by an orthogonal */
+/* similarity transformation */
+La_extern void
+F77_NAME(dsptrd)(const char* uplo, const int* n,
+		 double* ap, double* d, double* e,
+		 double* tau, int* info);
+
+/* DSPTRF - compute the factorization of a real symmetric matrix */
+/* A stored in packed format using the Bunch-Kaufman diagonal */
+/* pivoting method */
+La_extern void
+F77_NAME(dsptrf)(const char* uplo, const int* n,
+		 double* ap, int* ipiv, int* info);
+
+/* DSPTRI - compute the inverse of a real symmetric indefinite */
+/* matrix A in packed storage using the factorization A = U*D*U**T */
+/* or A = L*D*L**T computed by DSPTRF */
+La_extern void
+F77_NAME(dsptri)(const char* uplo, const int* n,
+		 double* ap, const int* ipiv,
+		 double* work, int* info);
+
+/* DSPTRS - solve a system of linear equations A*X = B with a */
+/* real symmetric matrix A stored in packed format using the */
+/* factorization A = U*D*U**T or A = L*D*L**T computed by DSPTRF */
+La_extern void
+F77_NAME(dsptrs)(const char* uplo, const int* n,
+		 const int* nrhs, const double* ap,
+		 const int* ipiv, double* b, const int* ldb, int* info);
+
+/* Double precision Symmetric Tridiagonal matrices */
+
+/* DSTEBZ - compute the eigenvalues of a symmetric tridiagonal */
+/* matrix T */
+La_extern void
+F77_NAME(dstebz)(const char* range, const char* order, const int* n,
+		 const double* vl, const double* vu,
+		 const int* il, const int* iu,
+		 const double *abstol,
+		 const double* d, const double* e,
+		 int* m, int* nsplit, double* w,
+		 int* iblock, int* isplit,
+		 double* work, int* iwork,
+		 int* info);
+/* DSTEDC - compute all eigenvalues and, optionally, eigenvectors */
+/* of a symmetric tridiagonal matrix using the divide and conquer */
+/* method */
+La_extern void
+F77_NAME(dstedc)(const char* compz, const int* n,
+		 double* d, double* e,
+		 double* z, const int* ldz,
+		 double* work, const int* lwork,
+		 int* iwork, const int* liwork, int* info);
+/* DSTEIN - compute the eigenvectors of a real symmetric */
+/* tridiagonal matrix T corresponding to specified eigenvalues, */
+/* using inverse iteration */
+La_extern void
+F77_NAME(dstein)(const int* n, const double* d, const double* e,
+		 const int* m, const double* w,
+		 const int* iblock, const int* isplit,
+		 double* z, const int* ldz,
+		 double* work, int* iwork,
+		 int* ifail, int* info);
+/* DSTEQR - compute all eigenvalues and, optionally, eigenvectors */
+/* of a symmetric tridiagonal matrix using the implicit QL or QR */
+/* method */
+La_extern void
+F77_NAME(dsteqr)(const char* compz, const int* n, double* d, double* e,
+		 double* z, const int* ldz, double* work, int* info);
+/* DSTERF - compute all eigenvalues of a symmetric tridiagonal */
+/* matrix using the Pal-Walker-Kahan variant of the QL or QR */
+/* algorithm */
+La_extern void
+F77_NAME(dsterf)(const int* n, double* d, double* e, int* info);
+/* DSTEV - compute all eigenvalues and, optionally, eigenvectors */
+/* of a real symmetric tridiagonal matrix A */
+La_extern void
+F77_NAME(dstev)(const char* jobz, const int* n,
+		double* d, double* e,
+		double* z, const int* ldz,
+		double* work, int* info);
+/* DSTEVD - compute all eigenvalues and, optionally, eigenvectors */
+/* of a real symmetric tridiagonal matrix */
+La_extern void
+F77_NAME(dstevd)(const char* jobz, const int* n,
+		 double* d, double* e,
+		 double* z, const int* ldz,
+		 double* work, const int* lwork,
+		 int* iwork, const int* liwork, int* info);
+/* DSTEVX - compute selected eigenvalues and, optionally, */
+/* eigenvectors of a real symmetric tridiagonal matrix A */
+La_extern void
+F77_NAME(dstevx)(const char* jobz, const char* range,
+		 const int* n, double* d, double* e,
+		 const double* vl, const double* vu,
+		 const int* il, const int* iu,
+		 const double* abstol,
+		 int* m, double* w,
+		 double* z, const int* ldz,
+		 double* work, int* iwork,
+		 int* ifail, int* info);
+
+/* Double precision SYmmetric matrices */
+
+/* DSYCON - estimate the reciprocal of the condition number (in */
+/* the 1-norm); of a real symmetric matrix A using the */
+/* factorization A = U*D*U**T or A = L*D*L**T computed by DSYTRF */
+La_extern void
+F77_NAME(dsycon)(const char* uplo, const int* n,
+		 const double* a, const int* lda,
+		 const int* ipiv,
+		 const double* anorm, double* rcond,
+		 double* work, int* iwork, int* info);
+/* DSYEV - compute all eigenvalues and, optionally, eigenvectors */
+/* of a real symmetric matrix A */
+La_extern void
+F77_NAME(dsyev)(const char* jobz, const char* uplo,
+		const int* n, double* a, const int* lda,
+		double* w, double* work, const int* lwork, int* info);
+/* DSYEVD - compute all eigenvalues and, optionally, eigenvectors */
+/* of a real symmetric matrix A */
+La_extern void
+F77_NAME(dsyevd)(const char* jobz, const char* uplo,
+		 const int* n, double* a, const int* lda,
+		 double* w, double* work, const int* lwork,
+		 int* iwork, const int* liwork, int* info);
+/* DSYEVX - compute selected eigenvalues and, optionally, */
+/* eigenvectors of a real symmetric matrix A */
+La_extern void
+F77_NAME(dsyevx)(const char* jobz, const char* range,
+		 const char* uplo, const int* n,
+		 double* a, const int* lda,
+		 const double* vl, const double* vu,
+		 const int* il, const int* iu,
+		 const double* abstol,
+		 int* m, double* w,
+		 double* z, const int* ldz,
+		 double* work, const int* lwork, int* iwork,
+		 int* ifail, int* info);
+/* DSYEVR - compute all eigenvalues and, optionally, eigenvectors   */
+/* of a real symmetric matrix A					   */
+La_extern void
+F77_NAME(dsyevr)(const char *jobz, const char *range, const char *uplo,
+		 const int *n, double *a, const int *lda,
+		 const double *vl, const double *vu,
+		 const int *il, const int *iu,
+		 const double *abstol, int *m, double *w,
+		 double *z, const int *ldz, int *isuppz,
+		 double *work, const int *lwork,
+		 int *iwork, const int *liwork,
+		 int *info);
+/* DSYGS2 - reduce a real symmetric-definite generalized */
+/* eigenproblem to standard form */
+La_extern void
+F77_NAME(dsygs2)(const int* itype, const char* uplo,
+		 const int* n, double* a, const int* lda,
+		 const double* b, const int* ldb, int* info);
+/* DSYGST - reduce a real symmetric-definite generalized */
+/* eigenproblem to standard form */
+La_extern void
+F77_NAME(dsygst)(const int* itype, const char* uplo,
+		 const int* n, double* a, const int* lda,
+		 const double* b, const int* ldb, int* info);
+/* DSYGV - compute all the eigenvalues, and optionally, the */
+/* eigenvectors of a real generalized symmetric-definite */
+/* eigenproblem, of the form A*x=(lambda);*B*x, A*Bx=(lambda);*x, */
+/* or B*A*x=(lambda);*x */
+La_extern void
+F77_NAME(dsygv)(const int* itype, const char* jobz,
+		const char* uplo, const int* n,
+		double* a, const int* lda,
+		double* b, const int* ldb,
+		double* w, double* work, const int* lwork,
+		int* info);
+/* DSYRFS - improve the computed solution to a system of linear */
+/* equations when the coefficient matrix is symmetric indefinite, */
+/* and provides error bounds and backward error estimates for the */
+/* solution */
+La_extern void
+F77_NAME(dsyrfs)(const char* uplo, const int* n,
+		 const int* nrhs,
+		 const double* a, const int* lda,
+		 const double* af, const int* ldaf,
+		 const int* ipiv,
+		 const double* b, const int* ldb,
+		 double* x, const int* ldx,
+		 double* ferr, double* berr,
+		 double* work, int* iwork, int* info);
+
+/* DSYSV - compute the solution to a real system of linear */
+/* equations  A * X = B, */
+La_extern void
+F77_NAME(dsysv)(const char* uplo, const int* n,
+		const int* nrhs,
+		double* a, const int* lda, int* ipiv,
+		double* b, const int* ldb,
+		double* work, const int* lwork, int* info);
+
+/* DSYSVX - use the diagonal pivoting factorization to compute */
+/* the solution to a real system of linear equations A * X = B, */
+La_extern void
+F77_NAME(dsysvx)(const int* fact, const char* uplo,
+		 const int* n, const int* nrhs,
+		 const double* a, const int* lda,
+		 double* af, const int* ldaf, int* ipiv,
+		 const double* b, const int* ldb,
+		 double* x, const int* ldx, double* rcond,
+		 double* ferr, double* berr,
+		 double* work, const int* lwork,
+		 int* iwork, int* info);
+
+/* DSYTD2 - reduce a real symmetric matrix A to symmetric */
+/* tridiagonal form T by an orthogonal similarity transformation */
+La_extern void
+F77_NAME(dsytd2)(const char* uplo, const int* n,
+		 double* a, const int* lda,
+		 double* d, double* e, double* tau,
+		 int* info);
+
+/* DSYTF2 - compute the factorization of a real symmetric matrix */
+/* A using the Bunch-Kaufman diagonal pivoting method */
+La_extern void
+F77_NAME(dsytf2)(const char* uplo, const int* n,
+		 double* a, const int* lda,
+		 int* ipiv, int* info);
+
+/* DSYTRD - reduce a real symmetric matrix A to real symmetric */
+/* tridiagonal form T by an orthogonal similarity transformation */
+La_extern void
+F77_NAME(dsytrd)(const char* uplo, const int* n,
+		 double* a, const int* lda,
+		 double* d, double* e, double* tau,
+		 double* work, const int* lwork, int* info);
+
+/* DSYTRF - compute the factorization of a real symmetric matrix */
+/* A using the Bunch-Kaufman diagonal pivoting method */
+La_extern void
+F77_NAME(dsytrf)(const char* uplo, const int* n,
+		 double* a, const int* lda, int* ipiv,
+		 double* work, const int* lwork, int* info);
+
+/* DSYTRI - compute the inverse of a real symmetric indefinite */
+/* matrix A using the factorization A = U*D*U**T or A = L*D*L**T */
+/* computed by DSYTRF */
+La_extern void
+F77_NAME(dsytri)(const char* uplo, const int* n,
+		 double* a, const int* lda, const int* ipiv,
+		 double* work, int* info);
+
+/* DSYTRS - solve a system of linear equations A*X = B with a */
+/* real symmetric matrix A using the factorization A = U*D*U**T or */
+/* A = L*D*L**T computed by DSYTRF */
+La_extern void
+F77_NAME(dsytrs)(const char* uplo, const int* n,
+		 const int* nrhs,
+		 const double* a, const int* lda,
+		 const int* ipiv,
+		 double* b, const int* ldb, int* info);
+
+/* Double precision Triangular Band matrices */
+
+/* DTBCON - estimate the reciprocal of the condition number of a */
+/* triangular band matrix A, in either the 1-norm or the */
+/* infinity-norm */
+La_extern void
+F77_NAME(dtbcon)(const char* norm, const char* uplo,
+		 const char* diag, const int* n, const int* kd,
+		 const double* ab, const int* ldab,
+		 double* rcond, double* work,
+		 int* iwork, int* info);
+/* DTBRFS - provide error bounds and backward error estimates for */
+/* the solution to a system of linear equations with a triangular */
+/* band coefficient matrix */
+La_extern void
+F77_NAME(dtbrfs)(const char* uplo, const char* trans,
+		 const char* diag, const int* n, const int* kd,
+		 const int* nrhs,
+		 const double* ab, const int* ldab,
+		 const double* b, const int* ldb,
+		 double* x, const int* ldx,
+		 double* ferr, double* berr,
+		 double* work, int* iwork, int* info);
+/* DTBTRS - solve a triangular system of the form   A * X = B or */
+/* A**T * X = B,  */
+La_extern void
+F77_NAME(dtbtrs)(const char* uplo, const char* trans,
+		 const char* diag, const int* n,
+		 const int* kd, const int* nrhs,
+		 const double* ab, const int* ldab,
+		 double* b, const int* ldb, int* info);
+
+/* Double precision Triangular matrices Generalized problems */
+
+/* DTGEVC - compute some or all of the right and/or left */
+/* generalized eigenvectors of a pair of real upper triangular */
+/* matrices (A,B); */
+La_extern void
+F77_NAME(dtgevc)(const char* side, const char* howmny,
+		 const int* select, const int* n,
+		 const double* a, const int* lda,
+		 const double* b, const int* ldb,
+		 double* vl, const int* ldvl,
+		 double* vr, const int* ldvr,
+		 const int* mm, int* m, double* work, int* info);
+
+/* DTGSJA - compute the generalized singular value decomposition */
+/* (GSVD); of two real upper triangular (or trapezoidal); matrices */
+/* A and B */
+La_extern void
+F77_NAME(dtgsja)(const char* jobu, const char* jobv, const char* jobq,
+		 const int* m, const int* p, const int* n,
+		 const int* k, const int* l,
+		 double* a, const int* lda,
+		 double* b, const int* ldb,
+		 const double* tola, const double* tolb,
+		 double* alpha, double* beta,
+		 double* u, const int* ldu,
+		 double* v, const int* ldv,
+		 double* q, const int* ldq,
+		 double* work, int* ncycle, int* info);
+
+/* Double precision Triangular matrices Packed storage */
+
+/* DTPCON - estimate the reciprocal of the condition number of a */
+/* packed triangular matrix A, in either the 1-norm or the */
+/* infinity-norm */
+La_extern void
+F77_NAME(dtpcon)(const char* norm, const char* uplo,
+		 const char* diag, const int* n,
+		 const double* ap, double* rcond,
+		 double* work, int* iwork, int* info);
+
+/* DTPRFS - provide error bounds and backward error estimates for */
+/* the solution to a system of linear equations with a triangular */
+/* packed coefficient matrix */
+La_extern void
+F77_NAME(dtprfs)(const char* uplo, const char* trans,
+		 const char* diag, const int* n,
+		 const int* nrhs, const double* ap,
+		 const double* b, const int* ldb,
+		 double* x, const int* ldx,
+		 double* ferr, double* berr,
+		 double* work, int* iwork, int* info);
+
+/* Double precision TRiangular matrices */
+
+/* DTPTRI - compute the inverse of a real upper or lower */
+/* triangular matrix A stored in packed format */
+La_extern void
+F77_NAME(dtptri)(const char* uplo, const char* diag,
+		 const int* n, double* ap, int* info);
+
+/* DTPTRS - solve a triangular system of the form   A * X = B or */
+/* A**T * X = B, */
+La_extern void
+F77_NAME(dtptrs)(const char* uplo, const char* trans,
+		 const char* diag, const int* n,
+		 const int* nrhs, const double* ap,
+		 double* b, const int* ldb, int* info);
+
+/* DTRCON - estimate the reciprocal of the condition number of a */
+/* triangular matrix A, in either the 1-norm or the infinity-norm */
+La_extern void
+F77_NAME(dtrcon)(const char* norm, const char* uplo,
+		 const char* diag, const int* n,
+		 const double* a, const int* lda,
+		 double* rcond, double* work,
+		 int* iwork, int* info);
+
+/* DTREVC - compute some or all of the right and/or left */
+/* eigenvectors of a real upper quasi-triangular matrix T */
+La_extern void
+F77_NAME(dtrevc)(const char* side, const char* howmny,
+		 const int* select, const int* n,
+		 const double* t, const int* ldt,
+		 double* vl, const int* ldvl,
+		 double* vr, const int* ldvr,
+		 const int* mm, int* m, double* work, int* info);
+
+/* DTREXC - reorder the real Schur factorization of a real matrix */
+/* A = Q*T*Q**T, so that the diagonal block of T with row index */
+/* IFST is moved to row ILST */
+La_extern void
+F77_NAME(dtrexc)(const char* compq, const int* n,
+		 double* t, const int* ldt,
+		 double* q, const int* ldq,
+		 int* ifst, int* ILST,
+		 double* work, int* info);
+
+/* DTRRFS - provide error bounds and backward error estimates for */
+/* the solution to a system of linear equations with a triangular */
+/* coefficient matrix */
+La_extern void
+F77_NAME(dtrrfs)(const char* uplo, const char* trans,
+		 const char* diag, const int* n, const int* nrhs,
+		 const double* a, const int* lda,
+		 const double* b, const int* ldb,
+		 double* x, const int* ldx,
+		 double* ferr, double* berr,
+		 double* work, int* iwork, int* info);
+
+/* DTRSEN - reorder the real Schur factorization of a real matrix */
+/* A = Q*T*Q**T, so that a selected cluster of eigenvalues appears */
+/* in the leading diagonal blocks of the upper quasi-triangular */
+/* matrix T, */
+La_extern void
+F77_NAME(dtrsen)(const char* job, const char* compq,
+		 const int* select, const int* n,
+		 double* t, const int* ldt,
+		 double* q, const int* ldq,
+		 double* wr, double* wi,
+		 int* m, double* s, double* sep,
+		 double* work, const int* lwork,
+		 int* iwork, const int* liwork, int* info);
+
+/* DTRSNA - estimate reciprocal condition numbers for specified */
+/* eigenvalues and/or right eigenvectors of a real upper */
+/* quasi-triangular matrix T (or of any matrix Q*T*Q**T with Q */
+/* orthogonal); */
+La_extern void
+F77_NAME(dtrsna)(const char* job, const char* howmny,
+		 const int* select, const int* n,
+		 const double* t, const int* ldt,
+		 const double* vl, const int* ldvl,
+		 const double* vr, const int* ldvr,
+		 double* s, double* sep, const int* mm,
+		 int* m, double* work, const int* lwork,
+		 int* iwork, int* info);
+
+/* DTRSYL - solve the real Sylvester matrix equation */
+La_extern void
+F77_NAME(dtrsyl)(const char* trana, const char* tranb,
+		 const int* isgn, const int* m, const int* n,
+		 const double* a, const int* lda,
+		 const double* b, const int* ldb,
+		 double* c, const int* ldc,
+		 double* scale, int* info);
+
+/* DTRTI2 - compute the inverse of a real upper or lower */
+/* triangular matrix */
+La_extern void
+F77_NAME(dtrti2)(const char* uplo, const char* diag,
+		 const int* n, double* a, const int* lda,
+		 int* info);
+
+/* DTRTRI - compute the inverse of a real upper or lower */
+/* triangular matrix A */
+La_extern void
+F77_NAME(dtrtri)(const char* uplo, const char* diag,
+		 const int* n, double* a, const int* lda,
+		 int* info);
+
+/* DTRTRS - solve a triangular system of the form   A * X = B or */
+/* A**T * X = B	 */
+La_extern void
+F77_NAME(dtrtrs)(const char* uplo, const char* trans,
+		 const char* diag, const int* n, const int* nrhs,
+		 const double* a, const int* lda,
+		 double* b, const int* ldb, int* info);
+
+/* DTZRQF - reduce the M-by-N ( M<=N ); real upper trapezoidal */
+/* matrix A to upper triangular form by means of orthogonal */
+/* transformations  */
+La_extern void
+F77_NAME(dtzrqf)(const int* m, const int* n,
+		 double* a, const int* lda,
+		 double* tau, int* info);
+
+
+
+/* Double precision utilties in Lapack */
+/* DHGEQZ - implement a single-/double-shift version of the QZ */
+/* method for finding the generalized eigenvalues */
+/* w(j);=(ALPHAR(j); + i*ALPHAI(j););/BETAR(j); of the equation */
+/* det( A - w(i); B ); = 0  In addition, the pair A,B may be */
+/* reduced to generalized Schur form */
+La_extern void
+F77_NAME(dhgeqz)(const char* job, const char* compq, const char* compz,
+		 const int* n, const int *ILO, const int* IHI,
+		 double* a, const int* lda,
+		 double* b, const int* ldb,
+		 double* alphar, double* alphai, const double* beta,
+		 double* q, const int* ldq,
+		 double* z, const int* ldz,
+		 double* work, const int* lwork, int* info);
+/* DHSEIN - use inverse iteration to find specified right and/or */
+/* left eigenvectors of a real upper Hessenberg matrix H */
+La_extern void
+F77_NAME(dhsein)(const char* side, const char* eigsrc,
+		 const char* initv, int* select,
+		 const int* n, double* h, const int* ldh,
+		 double* wr, double* wi,
+		 double* vl, const int* ldvl,
+		 double* vr, const int* ldvr,
+		 const int* mm, int* m, double* work,
+		 int* ifaill, int* ifailr, int* info);
+/* DHSEQR - compute the eigenvalues of a real upper Hessenberg */
+/* matrix H and, optionally, the matrices T and Z from the Schur */
+/* decomposition H = Z T Z**T, where T is an upper */
+/* quasi-triangular matrix (the Schur form);, and Z is the */
+/* orthogonal matrix of Schur vectors */
+La_extern void
+F77_NAME(dhseqr)(const char* job, const char* compz, const int* n,
+		 const int* ilo, const int* ihi,
+		 double* h, const int* ldh,
+		 double* wr, double* wi,
+		 double* z, const int* ldz,
+		 double* work, const int* lwork, int* info);
+/* DLABAD - take as input the values computed by SLAMCH for */
+/* underflow and overflow, and returns the square root of each of */
+/* these values if the log of LARGE is sufficiently large */
+La_extern void
+F77_NAME(dlabad)(double* small, double* large);
+/* DLABRD - reduce the first NB rows and columns of a real */
+/* general m by n matrix A to upper or lower bidiagonal form by an */
+/* orthogonal transformation Q' * A * P, and returns the matrices */
+/* X and Y which are needed to apply the transformation to the */
+/* unreduced part of A */
+La_extern void
+F77_NAME(dlabrd)(const int* m, const int* n, const int* nb,
+		 double* a, const int* lda, double* d, double* e,
+		 double* tauq, double* taup,
+		 double* x, const int* ldx, double* y, const int* ldy);
+/* DLACON - estimate the 1-norm of a square, real matrix A */
+La_extern void
+F77_NAME(dlacon)(const int* n, double* v, double* x,
+		 int* isgn, double* est, int* kase);
+/* DLACPY - copy all or part of a two-dimensional matrix A to */
+/* another matrix B */
+La_extern void
+F77_NAME(dlacpy)(const char* uplo, const int* m, const int* n,
+		 const double* a, const int* lda,
+		 double* b, const int* ldb);
+/* DLADIV - perform complex division in real arithmetic	 */
+La_extern void
+F77_NAME(dladiv)(const double* a, const double* b,
+		 const double* c, const double* d,
+		 double* p, double* q);
+/* DLAE2 - compute the eigenvalues of a 2-by-2 symmetric matrix [ A B ] */
+/*								[ B C ] */
+La_extern void
+F77_NAME(dlae2)(const double* a, const double* b, const double* c,
+		double* rt1, double* rt2);
+/* DLAEBZ - contain the iteration loops which compute and use the */
+/* function N(w);, which is the count of eigenvalues of a */
+/* symmetric tridiagonal matrix T less than or equal to its */
+/* argument w  */
+La_extern void
+F77_NAME(dlaebz)(const int* ijob, const int* nitmax, const int* n,
+		 const int* mmax, const int* minp, const int* nbmin,
+		 const double* abstol, const double* reltol,
+		 const double* pivmin, double* d, double* e,
+		 double* e2, int* nval, double* ab, double* c,
+		 int* mout, int* nab, double* work, int* iwork,
+		 int* info);
+/* DLAED0 - compute all eigenvalues and corresponding */
+/* eigenvectors of a symmetric tridiagonal matrix using the divide */
+/* and conquer method */
+La_extern void
+F77_NAME(dlaed0)(const int* icompq, const int* qsiz, const int* n,
+		 double* d, double* e, double* q, const int* ldq,
+		 double* qstore, const int* ldqs,
+		 double* work, int* iwork, int* info);
+/* DLAED1 - compute the updated eigensystem of a diagonal matrix */
+/* after modification by a rank-one symmetric matrix */
+La_extern void
+F77_NAME(dlaed1)(const int* n, double* d, double* q, const int* ldq,
+		 int* indxq, const double* rho, const int* cutpnt,
+		 double* work, int* iwork, int* info);
+/* DLAED2 - merge the two sets of eigenvalues together into a */
+/* single sorted set */
+La_extern void
+F77_NAME(dlaed2)(const int* k, const int* n, double* d,
+		 double* q, const int* ldq, int* indxq,
+		 double* rho, const int* cutpnt, double* z,
+		 double* dlamda, double* q2, const int *ldq2,
+		 int* indxc, int* w, int* indxp, int* indx,
+		 int* coltyp, int* info);
+/* DLAED3 - find the roots of the secular equation, as defined by */
+/* the values in double* d, W, and RHO, between KSTART and KSTOP */
+La_extern void
+F77_NAME(dlaed3)(const int* k, const int* kstart,
+		 const int *kstop, const int* n,
+		 double* d, double* q, const int* ldq,
+		 const double* rho, const int* cutpnt,
+		 double* dlamda, int* q2, const int* ldq2,
+		 int* indxc, int* ctot, double* w,
+		 double* s, const int* lds, int* info);
+/* DLAED4 - subroutine computes the I-th updated eigenvalue of a */
+/* symmetric rank-one modification to a diagonal matrix whose */
+/* elements are given in the array d, and that	 D(i); < D(j); for */
+/* i < j  and that RHO > 0 */
+La_extern void
+F77_NAME(dlaed4)(const int* n, const int* i, const double* d,
+		 const double* z, const double* delta,
+		 const double* rho, double* dlam, int* info);
+/* DLAED5 - subroutine computes the I-th eigenvalue of a */
+/* symmetric rank-one modification of a 2-by-2 diagonal matrix */
+/* diag( D ); + RHO  The diagonal elements in the array D are */
+/* assumed to satisfy	D(i); < D(j); for i < j	 */
+La_extern void
+F77_NAME(dlaed5)(const int* i, const double* d, const double* z,
+		 double* delta, const double* rho, double* dlam);
+/* DLAED6 - compute the positive or negative root (closest to the */
+/* origin); of	z(1); z(2); z(3); f(x); = rho + --------- + */
+/* ---------- + ---------  d(1);-x d(2);-x d(3);-x  It is assumed */
+/* that	  if ORGATI = .true  */
+La_extern void
+F77_NAME(dlaed6)(const int* kniter, const int* orgati,
+		 const double* rho, const double* d,
+		 const double* z, const double* finit,
+		 double* tau, int* info);
+/* DLAED7 - compute the updated eigensystem of a diagonal matrix */
+/* after modification by a rank-one symmetric matrix */
+La_extern void
+F77_NAME(dlaed7)(const int* icompq, const int* n,
+		 const int* qsiz, const int* tlvls,
+		 const int* curlvl, const int* curpbm,
+		 double* d, double* q, const int* ldq,
+		 int* indxq, const double* rho, const int* cutpnt,
+		 double* qstore, double* qptr, const int* prmptr,
+		 const int* perm, const int* givptr,
+		 const int* givcol, const double* givnum,
+		 double* work, int* iwork, int* info);
+/* DLAED8 - merge the two sets of eigenvalues together into a */
+/* single sorted set */
+La_extern void
+F77_NAME(dlaed8)(const int* icompq, const int* k,
+		 const int* n, const int* qsiz,
+		 double* d, double* q, const int* ldq,
+		 const int* indxq, double* rho,
+		 const int* cutpnt, const double* z,
+		 double* dlamda, double* q2, const int* ldq2,
+		 double* w, int* perm, int* givptr,
+		 int* givcol, double* givnum, int* indxp,
+		 int* indx, int* info);
+/* DLAED9 - find the roots of the secular equation, as defined by */
+/* the values in double* d, Z, and RHO, between KSTART and KSTOP */
+La_extern void
+F77_NAME(dlaed9)(const int* k, const int* kstart, const int* kstop,
+		 const int* n, double* d, double* q, const int* ldq,
+		 const double* rho, const double* dlamda,
+		 const double* w, double* s, const int* lds, int* info);
+/* DLAEDA - compute the Z vector corresponding to the merge step */
+/* in the CURLVLth step of the merge process with TLVLS steps for */
+/* the CURPBMth problem */
+La_extern void
+F77_NAME(dlaeda)(const int* n, const int* tlvls, const int* curlvl,
+		 const int* curpbm, const int* prmptr, const int* perm,
+		 const int* givptr, const int* givcol,
+		 const double* givnum, const double* q,
+		 const int* qptr, double* z, double* ztemp, int* info);
+/* DLAEIN - use inverse iteration to find a right or left */
+/* eigenvector corresponding to the eigenvalue (WR,WI); of a real */
+/* upper Hessenberg matrix H */
+La_extern void
+F77_NAME(dlaein)(const int* rightv, const int* noinit, const int* n,
+		 const double* h, const int* ldh,
+		 const double* wr, const double* wi,
+		 double* vr, double* vi,
+		 double* b, const int* ldb, double* work,
+		 const double* eps3, const double* smlnum,
+		 const double* bignum, int* info);
+/* DLAEV2 - compute the eigendecomposition of a 2-by-2 symmetric */
+/* matrix  [ A B ]  [ B C ] */
+La_extern void
+F77_NAME(dlaev2)(const double* a, const double* b, const double* c,
+		 double* rt1, double* rt2, double* cs1, double *sn1);
+/* DLAEXC - swap adjacent diagonal blocks T11 and T22 of order 1 */
+/* or 2 in an upper quasi-triangular matrix T by an orthogonal */
+/* similarity transformation */
+La_extern void
+F77_NAME(dlaexc)(const int* wantq, const int* n, double* t, const int* ldt,
+		  double* q, const int* ldq, const int* j1,
+		 const int* n1, const int* n2, double* work, int* info);
+/* DLAG2 - compute the eigenvalues of a 2 x 2 generalized */
+/* eigenvalue problem A - w B, with scaling as necessary to aextern void */
+/* over-/underflow */
+La_extern void
+F77_NAME(dlag2)(const double* a, const int* lda, const double* b,
+		const int* ldb, const double* safmin,
+		double* scale1, double* scale2,
+		double* wr1, double* wr2, double* wi);
+/* DLAGS2 - compute 2-by-2 orthogonal matrices U, V and Q, such */
+/* that if ( UPPER ); then   U'*A*Q = U'*( A1 A2 );*Q = ( x 0 ); */
+/* ( 0 A3 ); ( x x ); and  V'*B*Q = V'*( B1 B2 );*Q = ( x 0 );	( */
+/* 0 B3 ); ( x x );  or if ( .NOT.UPPER ); then	  U'*A*Q = U'*( A1 */
+/* 0 );*Q = ( x x );  ( A2 A3 ); ( 0 x ); and  V'*B*Q = V'*( B1 0 */
+/* );*Q = ( x x );  ( B2 B3 ); ( 0 x );	 The rows of the */
+/* transformed A and B are parallel, where   U = ( CSU SNU );, V = */
+/* ( CSV SNV );, Q = ( CSQ SNQ );  ( -SNU CSU ); ( -SNV CSV ); ( */
+/* -SNQ CSQ );	Z' denotes the transpose of Z */
+La_extern void
+F77_NAME(dlags2)(const int* upper,
+		 const double* a1, const double* a2, const double* a3,
+		 const double* b1, const double* b2, const double* b3,
+		 double* csu, double* snu,
+		 double* csv, double* snv, double *csq, double *snq);
+/* DLAGTF - factorize the matrix (T - lambda*I);, where T is an n */
+/* by n tridiagonal matrix and lambda is a scalar, as	T - */
+/* lambda*I = PLU, */
+La_extern void
+F77_NAME(dlagtf)(const int* n, double* a, const double* lambda,
+		 double* b, double* c, const double *tol,
+		 double* d, int* in, int* info);
+/* DLAGTM - perform a matrix-vector product of the form	  B := */
+/* alpha * A * X + beta * B  where A is a tridiagonal matrix of */
+/* order N, B and X are N by NRHS matrices, and alpha and beta are */
+/* real scalars, each of which may be 0., 1., or -1 */
+La_extern void
+F77_NAME(dlagtm)(const char* trans, const int* n, const int* nrhs,
+		 const double* alpha, const double* dl,
+		 const double* d, const double* du,
+		 const double* x, const int* ldx, const double* beta,
+		 double* b, const int* ldb);
+/* DLAGTS - may be used to solve one of the systems of equations */
+/* (T - lambda*I);*x = y or (T - lambda*I);'*x = y, */
+La_extern void
+F77_NAME(dlagts)(const int* job, const int* n,
+		 const double* a, const double* b,
+		 const double* c, const double* d,
+		 const int* in, double* y, double* tol, int* info);
+/* DLAHQR - an auxiliary routine called by DHSEQR to update the */
+/* eigenvalues and Schur decomposition already computed by DHSEQR, */
+/* by dealing with the Hessenberg submatrix in rows and columns */
+/* ILO to IHI */
+La_extern void
+F77_NAME(dlahqr)(const int* wantt, const int* wantz, const int* n,
+		 const int* ilo, const int* ihi,
+		 double* H, const int* ldh, double* wr, double* wi,
+		 const int* iloz, const int* ihiz,
+		 double* z, const int* ldz, int* info);
+/* DLAHRD - reduce the first NB columns of a real general */
+/* n-by-(n-k+1); matrix A so that elements below the k-th */
+/* subdiagonal are zero */
+La_extern void
+F77_NAME(dlahrd)(const int* n, const int* k, const int* nb,
+		 double* a, const int* lda,
+		 double* tau, double* t, const int* ldt,
+		 double* y, const int* ldy);
+/* DLAIC1 - apply one step of incremental condition estimation in */
+/* its simplest version */
+La_extern void
+F77_NAME(dlaic1)(const int* job, const int* j, const double* x,
+		 const double* sest, const double* w,
+		 const double* gamma, double* sestpr,
+		 double* s, double* c);
+/* DLALN2 - solve a system of the form (ca A - w D ); X = s B or */
+/* (ca A' - w D); X = s B with possible scaling ("s"); and */
+/* perturbation of A */
+La_extern void
+F77_NAME(dlaln2)(const int* ltrans, const int* na, const int* nw,
+		 const double* smin, const double* ca,
+		 const double* a, const int* lda,
+		 const double* d1, const double* d2,
+		 const double* b, const int* ldb,
+		 const double* wr, const double* wi,
+		 double* x, const int* ldx, double* scale,
+		 double* xnorm, int* info);
+/* DLAMCH - determine double precision machine parameters */
+La_extern double
+F77_NAME(dlamch)(const char* cmach);
+/* DLAMRG - will create a permutation list which will merge the */
+/* elements of A (which is composed of two independently sorted */
+/* sets); into a single set which is sorted in ascending order */
+La_extern void
+F77_NAME(dlamrg)(const int* n1, const int* n2, const double* a,
+		 const int* dtrd1, const int* dtrd2, int* index);
+/* DLANGB - return the value of the one norm, or the Frobenius */
+/* norm, or the infinity norm, or the element of largest absolute */
+/* value of an n by n band matrix A, with kl sub-diagonals and ku */
+/* super-diagonals */
+La_extern double
+F77_NAME(dlangb)(const char* norm, const int* n,
+		 const int* kl, const int* ku, const double* ab,
+		 const int* ldab, double* work);
+/* DLANGE - return the value of the one norm, or the Frobenius */
+/* norm, or the infinity norm, or the element of largest absolute */
+/* value of a real matrix A */
+La_extern double
+F77_NAME(dlange)(const char* norm, const int* m, const int* n,
+		 const double* a, const int* lda, double* work);
+/* DLANGT - return the value of the one norm, or the Frobenius */
+/* norm, or the infinity norm, or the element of largest absolute */
+/* value of a real tridiagonal matrix A */
+La_extern double
+F77_NAME(dlangt)(const char* norm, const int* n,
+		 const double* dl, const double* d,
+		 const double* du);
+/* DLANHS - return the value of the one norm, or the Frobenius */
+/* norm, or the infinity norm, or the element of largest absolute */
+/* value of a Hessenberg matrix A */
+La_extern double
+F77_NAME(dlanhs)(const char* norm, const int* n,
+		 const double* a, const int* lda, double* work);
+/* DLANSB - return the value of the one norm, or the Frobenius */
+/* norm, or the infinity norm, or the element of largest absolute */
+/* value of an n by n symmetric band matrix A, with k */
+/* super-diagonals */
+La_extern double
+F77_NAME(dlansb)(const char* norm, const char* uplo,
+		 const int* n, const int* k,
+		 const double* ab, const int* ldab, double* work);
+/* DLANSP - return the value of the one norm, or the Frobenius */
+/* norm, or the infinity norm, or the element of largest absolute */
+/* value of a real symmetric matrix A, supplied in packed form */
+La_extern double
+F77_NAME(dlansp)(const char* norm, const char* uplo,
+		 const int* n, const double* ap, double* work);
+/* DLANST - return the value of the one norm, or the Frobenius */
+/* norm, or the infinity norm, or the element of largest absolute */
+/* value of a real symmetric tridiagonal matrix A */
+La_extern double
+F77_NAME(dlanst)(const char* norm, const int* n,
+		 const double* d, const double* e);
+/* DLANSY - return the value of the one norm, or the Frobenius */
+/* norm, or the infinity norm, or the element of largest absolute */
+/* value of a real symmetric matrix A */
+La_extern double
+F77_NAME(dlansy)(const char* norm, const char* uplo, const int* n,
+		 const double* a, const int* lda, double* work);
+/* DLANTB - return the value of the one norm, or the Frobenius */
+/* norm, or the infinity norm, or the element of largest absolute */
+/* value of an n by n triangular band matrix A, with ( k + 1 ) diagonals */
+La_extern double
+F77_NAME(dlantb)(const char* norm, const char* uplo,
+		 const char* diag, const int* n, const int* k,
+		 const double* ab, const int* ldab, double* work);
+/* DLANTP - return the value of the one norm, or the Frobenius */
+/* norm, or the infinity norm, or the element of largest absolute */
+/* value of a triangular matrix A, supplied in packed form */
+La_extern double
+F77_NAME(dlantp)(const char* norm, const char* uplo, const char* diag,
+		 const int* n, const double* ap, double* work);
+/* DLANTR - return the value of the one norm, or the Frobenius */
+/* norm, or the infinity norm, or the element of largest absolute */
+/* value of a trapezoidal or triangular matrix A */
+La_extern double
+F77_NAME(dlantr)(const char* norm, const char* uplo,
+		 const char* diag, const int* m, const int* n,
+		 const double* a, const int* lda, double* work);
+/* DLANV2 - compute the Schur factorization of a real 2-by-2 */
+/* nonsymmetric matrix in standard form */
+La_extern void
+F77_NAME(dlanv2)(double* a, double* b, double* c, double* d,
+		 double* rt1r, double* rt1i, double* rt2r, double* rt2i,
+		 double* cs, double *sn);
+/* DLAPLL - two column vectors X and Y, let A = ( X Y ); */
+La_extern void
+F77_NAME(dlapll)(const int* n, double* x, const int* incx,
+		 double* y, const int* incy, double* ssmin);
+/* DLAPMT - rearrange the columns of the M by N matrix X as */
+/* specified by the permutation K(1);,K(2);,...,K(N); of the */
+/* integers 1,...,N */
+La_extern void
+F77_NAME(dlapmt)(const int* forwrd, const int* m, const int* n,
+		 double* x, const int* ldx, const int* k);
+/* DLAPY2 - return sqrt(x**2+y**2);, taking care not to cause */
+/* unnecessary overflow */
+La_extern double
+F77_NAME(dlapy2)(const double* x, const double* y);
+/* DLAPY3 - return sqrt(x**2+y**2+z**2);, taking care not to */
+/* cause unnecessary overflow */
+La_extern double
+F77_NAME(dlapy3)(const double* x, const double* y, const double* z);
+/* DLAQGB - equilibrate a general M by N band matrix A with KL */
+/* subdiagonals and KU superdiagonals using the row and scaling */
+/* factors in the vectors R and C */
+La_extern void
+F77_NAME(dlaqgb)(const int* m, const int* n,
+		 const int* kl, const int* ku,
+		 double* ab, const int* ldab,
+		 double* r, double* c,
+		 double* rowcnd, double* colcnd,
+		 const double* amax, char* equed);
+/* DLAQGE - equilibrate a general M by N matrix A using the row */
+/* and scaling factors in the vectors R and C */
+La_extern void
+F77_NAME(dlaqge)(const int* m, const int* n,
+		 double* a, const int* lda,
+		 double* r, double* c,
+		 double* rowcnd, double* colcnd,
+		 const double* amax, char* equed);
+/* DLAQSB - equilibrate a symmetric band matrix A using the */
+/* scaling factors in the vector S */
+La_extern void
+F77_NAME(dlaqsb)(const char* uplo, const int* n, const int* kd,
+		 double* ab, const int* ldab, const double* s,
+		 const double* scond, const double* amax, char* equed);
+/* DLAQSP - equilibrate a symmetric matrix A using the scaling */
+/* factors in the vector S */
+La_extern void
+F77_NAME(dlaqsp)(const char* uplo, const int* n,
+		 double* ap, const double* s, const double* scond,
+		 const double* amax, int* equed);
+/* DLAQSY - equilibrate a symmetric matrix A using the scaling */
+/* factors in the vector S */
+La_extern void
+F77_NAME(dlaqsy)(const char* uplo, const int* n,
+		 double* a, const int* lda,
+		 const double* s, const double* scond,
+		 const double* amax, int* equed);
+/* DLAQTR - solve the real quasi-triangular system   */
+/* op(T) * p = scale*c */
+La_extern void
+F77_NAME(dlaqtr)(const int* ltran, const int* lreal, const int* n,
+		 const double* t, const int* ldt,
+		 const double* b, const double* w,
+		 double* scale, double* x, double* work, int* info);
+/* DLAR2V - apply a vector of real plane rotations from both */
+/* sides to a sequence of 2-by-2 real symmetric matrices, defined */
+/* by the elements of the vectors x, y and z  */
+La_extern void
+F77_NAME(dlar2v)(const int* n, double* x, double* y,
+		 double* z, const int* incx,
+		 const double* c, const double* s,
+		 const int* incc);
+/* DLARF - apply a real elementary reflector H to a real m by n */
+/* matrix C, from either the left or the right */
+La_extern void
+F77_NAME(dlarf)(const char* side, const int* m, const int* n,
+		const double* v, const int* incv, const double* tau,
+		double* c, const int* ldc, double* work);
+/* DLARFB - apply a real block reflector H or its transpose H' */
+/* to a real m by n matrix C, from either the left or the right */
+La_extern void
+F77_NAME(dlarfb)(const char* side, const char* trans,
+		 const char* direct, const char* storev,
+		 const int* m, const int* n, const int* k,
+		 const double* v, const int* ldv,
+		 const double* t, const int* ldt,
+		 double* c, const int* ldc,
+		 double* work, const int* lwork);
+/* DLARFG - generate a real elementary reflector H of order n, */
+/* such that   H * ( alpha ) = ( beta ), H' * H = I */
+La_extern void
+F77_NAME(dlarfg)(const int* n, const double* alpha,
+		 double* x, const int* incx, double* tau);
+/* DLARFT - form the triangular factor T of a real block */
+/* reflector H of order n, which is defined as a product of k */
+/* elementary reflectors */
+La_extern void
+F77_NAME(dlarft)(const char* direct, const char* storev,
+		 const int* n, const int* k, double* v, const int* ldv,
+		 const double* tau, double* t, const int* ldt);
+/* DLARFX - apply a real elementary reflector H to a real m by n */
+/* matrix C, from either the left or the right */
+La_extern void
+F77_NAME(dlarfx)(const char* side, const int* m, const int* n,
+		 const double* v, const double* tau,
+		 double* c, const int* ldc, double* work);
+/* DLARGV - generate a vector of real plane rotations, determined */
+/* by elements of the real vectors x and y */
+La_extern void
+F77_NAME(dlargv)(const int* n, double* x, const int* incx,
+		 double* y, const int* incy, double* c, const int* incc);
+/* DLARNV - return a vector of n random real numbers from a */
+/* uniform or normal distribution */
+La_extern void
+F77_NAME(dlarnv)(const int* idist, int* iseed, const int* n, double* x);
+/* DLARTG - generate a plane rotation so that	[ CS SN ]  */
+La_extern void
+F77_NAME(dlartg)(const double* f, const double* g, double* cs,
+		 double* sn, double *r);
+/* DLARTV - apply a vector of real plane rotations to elements of */
+/* the real vectors x and y */
+La_extern void
+F77_NAME(dlartv)(const int* n, double* x, const int* incx,
+		 double* y, const int* incy,
+		 const double* c, const double* s,
+		 const int* incc);
+/* DLARUV - return a vector of n random real numbers from a */
+/* uniform (0,1); */
+La_extern void
+F77_NAME(dlaruv)(int* iseed, const int* n, double* x);
+
+/* DLAS2 - compute the singular values of the 2-by-2 matrix */
+/* [ F G ]  [ 0 H ] */
+La_extern void
+F77_NAME(dlas2)(const double* f, const double* g, const double* h,
+		 double* ssmin, double* ssmax);
+
+/* DLASCL - multiply the M by N real matrix A by the real scalar */
+/* CTO/CFROM */
+La_extern void
+F77_NAME(dlascl)(const char* type,
+		 const int* kl,const int* ku,
+		 double* cfrom, double* cto,
+		 const int* m, const int* n,
+		 double* a, const int* lda, int* info);
+
+/* DLASET - initialize an m-by-n matrix A to BETA on the diagonal */
+/* and ALPHA on the offdiagonals */
+La_extern void
+F77_NAME(dlaset)(const char* uplo, const int* m, const int* n,
+		 const double* alpha, const double* beta,
+		 double* a, const int* lda);
+/* DLASQ1 - DLASQ1 computes the singular values of a real N-by-N */
+/* bidiagonal  matrix with diagonal D and off-diagonal E */
+La_extern void
+F77_NAME(dlasq1)(const int* n, double* d, double* e,
+		 double* work, int* info);
+/* DLASQ2 - DLASQ2 computes the singular values of a real N-by-N */
+/* unreduced  bidiagonal matrix with squared diagonal elements in */
+/* Q and  squared off-diagonal elements in E */
+La_extern void
+F77_NAME(dlasq2)(const int* m, double* q, double* e,
+		 double* qq, double* ee, const double* eps,
+		 const double* tol2, const double* small2,
+		 double* sup, int* kend, int* info);
+/* DLASQ3 - DLASQ3 is the workhorse of the whole bidiagonal SVD */
+/* algorithm */
+La_extern void
+F77_NAME(dlasq3)(int* n, double* q, double* e, double* qq,
+		 double* ee, double* sup, double *sigma,
+		 int* kend, int* off, int* iphase,
+		 const int* iconv, const double* eps,
+		 const double* tol2, const double* small2);
+/* DLASQ4 - DLASQ4 estimates TAU, the smallest eigenvalue of a */
+/* matrix */
+La_extern void
+F77_NAME(dlasq4)(const int* n, const double* q, const double* e,
+		 double* tau, double* sup);
+/* DLASR - perform the transformation	A := P*A, when SIDE = 'L' */
+/* or 'l' ( Left-hand side );	A := A*P', when SIDE = 'R' or 'r' */
+/* ( Right-hand side );	 where A is an m by n real matrix and P is */
+/* an orthogonal matrix, */
+La_extern void
+F77_NAME(dlasr)(const char* side, const char* pivot,
+		const char* direct, const int* m, const int* n,
+		const double* c, const double* s,
+		double* a, const int* lda);
+/* DLASRT - the numbers in D in increasing order (if ID = 'I'); */
+/* or in decreasing order (if ID = 'D' ); */
+La_extern void
+F77_NAME(dlasrt)(const char* id, const int* n, double* d, int* info);
+/* DLASSQ - return the values scl and smsq such that   ( scl**2 */
+/* );*smsq = x( 1 );**2 +...+ x( n );**2 + ( scale**2 );*sumsq, */
+La_extern void
+F77_NAME(dlassq)(const int* n, const double* x, const int* incx,
+		 double* scale, double* sumsq);
+/* DLASV2 - compute the singular value decomposition of a 2-by-2 */
+/* triangular matrix  [ F G ]  [ 0 H ] */
+La_extern void
+F77_NAME(dlasv2)(const double* f, const double* g, const double* h,
+		 double* ssmin, double* ssmax, double* snr, double* csr,
+		 double* snl, double* csl);
+/* DLASWP - perform a series of row interchanges on the matrix A */
+La_extern void
+F77_NAME(dlaswp)(const int* n, double* a, const int* lda,
+		 const int* k1, const int* k2,
+		 const int* ipiv, const int* incx);
+/* DLASY2 - solve for the N1 by N2 matrix double* x, 1 <= N1,N2 <= 2, in */
+/* op(TL);*X + ISGN*X*op(TR); = SCALE*B, */
+La_extern void
+F77_NAME(dlasy2)(const int* ltranl, const int* ltranr,
+		 const int* isgn, const int* n1, const int* n2,
+		 const double* tl, const int* ldtl,
+		 const double* tr, const int* ldtr,
+		 const double* b, const int* ldb,
+		 double* scale, double* x, const int* ldx,
+		 double* xnorm, int* info);
+/* DLASYF - compute a partial factorization of a real symmetric */
+/* matrix A using the Bunch-Kaufman diagonal pivoting method */
+La_extern void
+F77_NAME(dlasyf)(const char* uplo, const int* n,
+		 const int* nb, const int* kb,
+		 double* a, const int* lda, int* ipiv,
+		 double* w, const int* ldw, int* info);
+/* DLATBS - solve one of the triangular systems	  A *x = s*b or */
+/* A'*x = s*b  with scaling to prevent overflow, where A is an */
+/* upper or lower triangular band matrix */
+La_extern void
+F77_NAME(dlatbs)(const char* uplo, const char* trans,
+		 const char* diag, const char* normin,
+		 const int* n, const int* kd,
+		 const double* ab, const int* ldab,
+		 double* x, double* scale, double* cnorm, int* info);
+/* DLATPS - solve one of the triangular systems	  A *x = s*b or */
+/* A'*x = s*b  with scaling to prevent overflow, where A is an */
+/* upper or lower triangular matrix stored in packed form */
+La_extern void
+F77_NAME(dlatps)(const char* uplo, const char* trans,
+		 const char* diag, const char* normin,
+		 const int* n, const double* ap,
+		 double* x, double* scale, double* cnorm, int* info);
+/* DLATRD - reduce NB rows and columns of a real symmetric matrix */
+/* A to symmetric tridiagonal form by an orthogonal similarity */
+/* transformation Q' * A * Q, and returns the matrices V and W */
+/* which are needed to apply the transformation to the unreduced */
+/* part of A */
+La_extern void
+F77_NAME(dlatrd)(const char* uplo, const int* n, const int* nb,
+		 double* a, const int* lda, double* e, double* tau,
+		 double* w, const int* ldw);
+/* DLATRS - solve one of the triangular systems	  A *x = s*b or */
+/* A'*x = s*b  with scaling to prevent overflow */
+La_extern void
+F77_NAME(dlatrs)(const char* uplo, const char* trans,
+		 const char* diag, const char* normin,
+		 const int* n, const double* a, const int* lda,
+		 double* x, double* scale, double* cnorm, int* info);
+/* DLATZM - apply a Householder matrix generated by DTZRQF to a */
+/* matrix */
+La_extern void
+F77_NAME(dlatzm)(const char* side, const int* m, const int* n,
+		 const double* v, const int* incv,
+		 const double* tau, double* c1, double* c2,
+		 const int* ldc, double* work);
+/* DLAUU2 - compute the product U * U' or L' * const int* l, where the */
+/* triangular factor U or L is stored in the upper or lower */
+/* triangular part of the array A */
+La_extern void
+F77_NAME(dlauu2)(const char* uplo, const int* n,
+		 double* a, const int* lda, int* info);
+/* DLAUUM - compute the product U * U' or L' * L, where the */
+/* triangular factor U or L is stored in the upper or lower */
+/* triangular part of the array A */
+La_extern void
+F77_NAME(dlauum)(const char* uplo, const int* n,
+		 double* a, const int* lda, int* info);
+
+
+/* ======================================================================== */
+
+/* Selected Double Complex Lapack Routines
+   ========
+ */
+
+/* IZMAX1 finds the index of the element whose real part has maximum
+ * absolute value. */
+La_extern int
+F77_NAME(izmax1)(const int *n, Rcomplex *cx, const int *incx);
+
+
+/*  ZGECON estimates the reciprocal of the condition number of a general
+ *  complex matrix A, in either the 1-norm or the infinity-norm, using
+ *  the LU factorization computed by ZGETRF.
+ */
+La_extern void
+F77_NAME(zgecon)(const char *norm, const int *n,
+		 const Rcomplex *a, const int *lda,
+		 const double *anorm, double *rcond,
+		 Rcomplex *work, double *rwork, int *info);
+
+/* ZGESV computes the solution to a complex system of linear equations */
+La_extern void
+F77_NAME(zgesv)(const int *n, const int *nrhs, Rcomplex *a,
+		const int *lda, int *ipiv, Rcomplex *b,
+		const int *ldb, int *info);
+
+/*  ZGEQP3 computes a QR factorization with column pivoting */
+La_extern void
+F77_NAME(zgeqp3)(const int *m, const int *n,
+		 Rcomplex *a, const int *lda,
+		 int *jpvt, Rcomplex *tau,
+		 Rcomplex *work, const int *lwork,
+		 double *rwork, int *info);
+
+/* ZUNMQR applies Q or Q**H from the Left or Right */
+La_extern void
+F77_NAME(zunmqr)(const char *side, const char *trans,
+		 const int *m, const int *n, const int *k,
+		 Rcomplex *a, const int *lda,
+		 Rcomplex *tau,
+		 Rcomplex *c, const int *ldc,
+		 Rcomplex *work, const int *lwork, int *info);
+
+/*  ZTRTRS solves triangular systems */
+La_extern void
+F77_NAME(ztrtrs)(const char *uplo, const char *trans, const char *diag,
+		 const int *n, const int *nrhs,
+		 Rcomplex *a, const int *lda,
+		 Rcomplex *b, const int *ldb, int *info);
+/* ZGESVD - compute the singular value decomposition (SVD); of a   */
+/* real M-by-N matrix A, optionally computing the left and/or	   */
+/* right singular vectors					   */
+La_extern void
+F77_NAME(zgesvd)(const char *jobu, const char *jobvt,
+		 const int *m, const int *n,
+		 Rcomplex *a, const int *lda, double *s,
+		 Rcomplex *u, const int *ldu,
+		 Rcomplex *vt, const int *ldvt,
+		 Rcomplex *work, const int *lwork, double *rwork,
+		 int *info);
+
+/* ZGHEEV - compute all eigenvalues and, optionally, eigenvectors */
+/* of a Hermitian matrix A */
+La_extern void
+F77_NAME(zheev)(const char *jobz, const char *uplo,
+		const int *n, Rcomplex *a, const int *lda,
+		double *w, Rcomplex *work, const int *lwork,
+		double *rwork, int *info);
+
+/* ZGGEEV - compute all eigenvalues and, optionally, eigenvectors */
+/* of a complex non-symmetric matrix A */
+La_extern void
+F77_NAME(zgeev)(const char *jobvl, const char *jobvr,
+		const int *n, Rcomplex *a, const int *lda,
+		Rcomplex *wr, Rcomplex *vl, const int *ldvl,
+		Rcomplex *vr, const int *ldvr,
+		Rcomplex *work, const int *lwork,
+		double *rwork, int *info);
+
+
+/* NOTE: The following entry points were traditionally in this file,
+   but are not provided by R's libRlapack */
+
+/* DZSUM1 - take the sum of the absolute values of a complex */
+/* vector and returns a double precision result	 */
+La_extern double
+F77_NAME(dzsum1)(const int *n, Rcomplex *CX, const int *incx);
+
+/*  ZLACN2 estimates the 1-norm of a square, complex matrix A.
+ *  Reverse communication is used for evaluating matrix-vector products.
+*/
+La_extern void
+F77_NAME(zlacn2)(const int *n, Rcomplex *v, Rcomplex *x,
+                 double *est, int *kase, int *isave);
+
+/* ZLANTR  -  return the value of the one norm, or the Frobenius norm, */
+/* or the infinity norm, or the element of largest absolute value of */
+/* a trapezoidal or triangular matrix A */
+La_extern double
+F77_NAME(zlantr)(const char *norm, const char *uplo, const char *diag,
+		 const int *m, const int *n, Rcomplex *a,
+		 const int *lda, double *work);
+
+/* ======================================================================== */
+
+/* Other double precision and double complex Lapack routines
+   provided by libRlapack.
+
+   These are extracted from the CLAPACK headers.
+*/
+
+La_extern void
+F77_NAME(dbdsdc)(char *uplo, char *compq, int *n, double *
+	d, double *e, double *u, int *ldu, double *vt,
+	int *ldvt, double *q, int *iq, double *work, int * iwork, int *info);
+
+La_extern void
+F77_NAME(dgegs)(char *jobvsl, char *jobvsr, int *n,
+	double *a, int *lda, double *b, int *ldb, double *
+	alphar, double *alphai, double *beta, double *vsl,
+	int *ldvsl, double *vsr, int *ldvsr, double *work,
+	int *lwork, int *info);
+
+La_extern void
+F77_NAME(dgelsd)(int *m, int *n, int *nrhs,
+	double *a, int *lda, double *b, int *ldb, double *
+	s, double *rcond, int *rank, double *work, int *lwork,
+	 int *iwork, int *info);
+
+La_extern void
+F77_NAME(dgelsx)(int *m, int *n, int *nrhs,
+	double *a, int *lda, double *b, int *ldb, int *
+	jpvt, double *rcond, int *rank, double *work, int *
+	info);
+
+La_extern void
+F77_NAME(dgesc2)(int *n, double *a, int *lda,
+	double *rhs, int *ipiv, int *jpiv, double *scale);
+
+/* DGESDD - compute the singular value decomposition (SVD); of a   */
+/* real M-by-N matrix A, optionally computing the left and/or	   */
+/* right singular vectors.  If singular vectors are desired, it uses a */
+/* divide-and-conquer algorithm.				   */
+La_extern void
+F77_NAME(dgesdd)(const char *jobz,
+		 const int *m, const int *n,
+		 double *a, const int *lda, double *s,
+		 double *u, const int *ldu,
+		 double *vt, const int *ldvt,
+		 double *work, const int *lwork, int *iwork, int *info);
+
+La_extern void
+F77_NAME(dgetc2)(int *n, double *a, int *lda, int
+	*ipiv, int *jpiv, int *info);
+
+typedef int (*L_fp)();
+La_extern void
+F77_NAME(dggesx)(char *jobvsl, char *jobvsr, char *sort, L_fp
+	delctg, char *sense, int *n, double *a, int *lda,
+	double *b, int *ldb, int *sdim, double *alphar,
+	double *alphai, double *beta, double *vsl, int *ldvsl,
+	 double *vsr, int *ldvsr, double *rconde, double *
+	rcondv, double *work, int *lwork, int *iwork, int *
+	liwork, int *bwork, int *info);
+
+La_extern void
+F77_NAME(dggev)(char *jobvl, char *jobvr, int *n, double *
+	a, int *lda, double *b, int *ldb, double *alphar,
+	double *alphai, double *beta, double *vl, int *ldvl,
+	double *vr, int *ldvr, double *work, int *lwork,
+	int *info);
+
+La_extern void
+F77_NAME(dggevx)(char *balanc, char *jobvl, char *jobvr, char *
+	sense, int *n, double *a, int *lda, double *b,
+	int *ldb, double *alphar, double *alphai, double *
+	beta, double *vl, int *ldvl, double *vr, int *ldvr,
+	int *ilo, int *ihi, double *lscale, double *rscale,
+	double *abnrm, double *bbnrm, double *rconde, double *
+	rcondv, double *work, int *lwork, int *iwork, int *
+	bwork, int *info);
+
+La_extern void
+F77_NAME(dggsvp)(char *jobu, char *jobv, char *jobq, int *m,
+	int *p, int *n, double *a, int *lda, double *b,
+	int *ldb, double *tola, double *tolb, int *k, int
+	*l, double *u, int *ldu, double *v, int *ldv,
+	double *q, int *ldq, int *iwork, double *tau,
+	double *work, int *info);
+
+La_extern void
+F77_NAME(dgtts2)(int *itrans, int *n, int *nrhs,
+	double *dl, double *d, double *du, double *du2,
+	int *ipiv, double *b, int *ldb);
+La_extern void
+F77_NAME(dlagv2)(double *a, int *lda, double *b, int *ldb, double *alphar,
+		 double *alphai, double * beta, double *csl, double *snl,
+		 double *csr, double * snr);
+
+La_extern void
+F77_NAME(dlals0)(int *icompq, int *nl, int *nr,
+	int *sqre, int *nrhs, double *b, int *ldb, double
+	*bx, int *ldbx, int *perm, int *givptr, int *givcol,
+	int *ldgcol, double *givnum, int *ldgnum, double *
+	poles, double *difl, double *difr, double *z, int *
+	k, double *c, double *s, double *work, int *info);
+
+La_extern void
+F77_NAME(dlalsa)(int *icompq, int *smlsiz, int *n,
+	int *nrhs, double *b, int *ldb, double *bx, int *
+	ldbx, double *u, int *ldu, double *vt, int *k,
+	double *difl, double *difr, double *z, double *
+	poles, int *givptr, int *givcol, int *ldgcol, int *
+	perm, double *givnum, double *c, double *s, double *
+	work, int *iwork, int *info);
+
+La_extern void
+F77_NAME(dlalsd)(char *uplo, int *smlsiz, int *n, int
+	*nrhs, double *d, double *e, double *b, int *ldb,
+	double *rcond, int *rank, double *work, int *iwork,
+	int *info);
+
+La_extern void
+F77_NAME(dlamc1)(int *beta, int *t, int *rnd, int
+	*ieee1);
+
+La_extern void
+F77_NAME(dlamc2)(int *beta, int *t, int *rnd,
+	double *eps, int *emin, double *rmin, int *emax,
+	double *rmax);
+
+La_extern double
+F77_NAME(dlamc3)(double *a, double *b);
+
+La_extern void
+F77_NAME(dlamc4)(int *emin, double *start, int *base);
+
+La_extern void
+F77_NAME(dlamc5)(int *beta, int *p, int *emin,
+	int *ieee, int *emax, double *rmax);
+
+La_extern void
+F77_NAME(dlaqp2)(int *m, int *n, int *offset,
+	double *a, int *lda, int *jpvt, double *tau,
+	double *vn1, double *vn2, double *work);
+
+La_extern void
+F77_NAME(dlaqps)(int *m, int *n, int *offset, int
+	*nb, int *kb, double *a, int *lda, int *jpvt,
+	double *tau, double *vn1, double *vn2, double *auxv,
+	double *f, int *ldf);
+
+La_extern void
+F77_NAME(dlar1v)(int *n, int *b1, int *bn, double
+	*sigma, double *d, double *l, double *ld, double *
+	lld, double *gersch, double *z, double *ztz, double
+	*mingma, int *r, int *isuppz, double *work);
+
+La_extern void
+F77_NAME(dlarrb)(int *n, double *d, double *l,
+	double *ld, double *lld, int *ifirst, int *ilast,
+	double *sigma, double *reltol, double *w, double *
+	wgap, double *werr, double *work, int *iwork, int *
+	info);
+
+La_extern void
+F77_NAME(dlarre)(int *n, double *d, double *e,
+	double *tol, int *nsplit, int *isplit, int *m,
+	double *w, double *woff, double *gersch, double *work,
+	 int *info);
+
+La_extern void
+F77_NAME(dlarrf)(int *n, double *d, double *l,
+	double *ld, double *lld, int *ifirst, int *ilast,
+	double *w, double *dplus, double *lplus, double *work,
+	 int *iwork, int *info);
+
+La_extern void
+F77_NAME(dlarrv)(int *n, double *d, double *l,
+	int *isplit, int *m, double *w, int *iblock,
+	double *gersch, double *tol, double *z, int *ldz,
+	int *isuppz, double *work, int *iwork, int *info);
+
+La_extern void
+F77_NAME(dlarz)(char *side, int *m, int *n, int *l,
+	double *v, int *incv, double *tau, double *c,
+	int *ldc, double *work);
+
+La_extern void
+F77_NAME(dlarzb)(char *side, char *trans, char *direct, char *
+	storev, int *m, int *n, int *k, int *l, double *v,
+	 int *ldv, double *t, int *ldt, double *c, int *
+	ldc, double *work, int *ldwork);
+
+La_extern void
+F77_NAME(dlarzt)(char *direct, char *storev, int *n, int *
+	k, double *v, int *ldv, double *tau, double *t,
+	int *ldt);
+
+La_extern void
+F77_NAME(dlasd0)(int *n, int *sqre, double *d,
+	double *e, double *u, int *ldu, double *vt, int *
+	ldvt, int *smlsiz, int *iwork, double *work, int *
+	info);
+
+La_extern void
+F77_NAME(dlasd1)(int *nl, int *nr, int *sqre,
+	double *d, double *alpha, double *beta, double *u,
+	int *ldu, double *vt, int *ldvt, int *idxq, int *
+	iwork, double *work, int *info);
+
+La_extern void
+F77_NAME(dlasd2)(int *nl, int *nr, int *sqre, int
+	*k, double *d, double *z, double *alpha, double *
+	beta, double *u, int *ldu, double *vt, int *ldvt,
+	double *dsigma, double *u2, int *ldu2, double *vt2,
+	int *ldvt2, int *idxp, int *idx, int *idxc, int *
+	idxq, int *coltyp, int *info);
+
+La_extern void
+F77_NAME(dlasd3)(int *nl, int *nr, int *sqre, int
+	*k, double *d, double *q, int *ldq, double *dsigma,
+	double *u, int *ldu, double *u2, int *ldu2,
+	double *vt, int *ldvt, double *vt2, int *ldvt2,
+	int *idxc, int *ctot, double *z, int *info);
+
+La_extern void
+F77_NAME(dlasd4)(int *n, int *i, double *d,
+	double *z, double *delta, double *rho, double *
+	sigma, double *work, int *info);
+
+La_extern void
+F77_NAME(dlasd5)(int *i, double *d, double *z,
+	double *delta, double *rho, double *dsigma, double *
+	work);
+
+La_extern void
+F77_NAME(dlasd6)(int *icompq, int *nl, int *nr,
+	int *sqre, double *d, double *vf, double *vl,
+	double *alpha, double *beta, int *idxq, int *perm,
+	int *givptr, int *givcol, int *ldgcol, double *givnum,
+	 int *ldgnum, double *poles, double *difl, double *
+	difr, double *z, int *k, double *c, double *s,
+	double *work, int *iwork, int *info);
+
+La_extern void
+F77_NAME(dlasd7)(int *icompq, int *nl, int *nr,
+	int *sqre, int *k, double *d, double *z,
+	double *zw, double *vf, double *vfw, double *vl,
+	double *vlw, double *alpha, double *beta, double *
+	dsigma, int *idx, int *idxp, int *idxq, int *perm,
+	int *givptr, int *givcol, int *ldgcol, double *givnum,
+	 int *ldgnum, double *c, double *s, int *info);
+
+La_extern void
+F77_NAME(dlasd8)(int *icompq, int *k, double *d,
+	double *z, double *vf, double *vl, double *difl,
+	double *difr, int *lddifr, double *dsigma, double *
+	work, int *info);
+
+La_extern void
+F77_NAME(dlasd9)(int *icompq, int *ldu, int *k,
+	double *d, double *z, double *vf, double *vl,
+	double *difl, double *difr, double *dsigma, double *
+	work, int *info);
+
+La_extern void
+F77_NAME(dlasda)(int *icompq, int *smlsiz, int *n,
+	int *sqre, double *d, double *e, double *u, int
+	*ldu, double *vt, int *k, double *difl, double *difr,
+	double *z, double *poles, int *givptr, int *givcol,
+	int *ldgcol, int *perm, double *givnum, double *c,
+	double *s, double *work, int *iwork, int *info);
+
+La_extern void
+F77_NAME(dlasdq)(char *uplo, int *sqre, int *n, int *
+	ncvt, int *nru, int *ncc, double *d, double *e,
+	double *vt, int *ldvt, double *u, int *ldu,
+	double *c, int *ldc, double *work, int *info);
+
+La_extern void
+F77_NAME(dlasdt)(int *n, int *lvl, int *nd, int *
+	inode, int *ndiml, int *ndimr, int *msub);
+
+La_extern void
+F77_NAME(dlasq5)(int *i0, int *n0, double *z,
+	int *pp, double *tau, double *dmin, double *dmin1,
+	double *dmin2, double *dn, double *dnm1, double *dnm2,
+	 int *ieee);
+
+La_extern void
+F77_NAME(dlasq6)(int *i0, int *n0, double *z,
+	int *pp, double *dmin, double *dmin1, double *dmin2,
+	 double *dn, double *dnm1, double *dnm2);
+
+La_extern void
+F77_NAME(dlatdf)(int *ijob, int *n, double *z,
+	int *ldz, double *rhs, double *rdsum, double *rdscal,
+	int *ipiv, int *jpiv);
+
+La_extern void
+F77_NAME(dlatrz)(int *m, int *n, int *l, double *
+	a, int *lda, double *tau, double *work);
+
+La_extern void
+F77_NAME(dormr3)(char *side, char *trans, int *m, int *n,
+	int *k, int *l, double *a, int *lda, double *tau,
+	double *c, int *ldc, double *work, int *info);
+
+La_extern void
+F77_NAME(dormrz)(char *side, char *trans, int *m, int *n,
+	int *k, int *l, double *a, int *lda, double *tau,
+	double *c, int *ldc, double *work, int *lwork,
+	int *info);
+
+La_extern void
+F77_NAME(dptts2)(int *n, int *nrhs, double *d,
+	double *e, double *b, int *ldb);
+
+La_extern void
+F77_NAME(dsbgvd)(char *jobz, char *uplo, int *n, int *ka,
+	int *kb, double *ab, int *ldab, double *bb, int *
+	ldbb, double *w, double *z, int *ldz, double *work,
+	int *lwork, int *iwork, int *liwork, int *info);
+
+La_extern void
+F77_NAME(dsbgvx)(char *jobz, char *range, char *uplo, int *n,
+	int *ka, int *kb, double *ab, int *ldab, double *
+	bb, int *ldbb, double *q, int *ldq, double *vl,
+	double *vu, int *il, int *iu, double *abstol, int
+	*m, double *w, double *z, int *ldz, double *work,
+	int *iwork, int *ifail, int *info);
+
+La_extern void
+F77_NAME(dspgvd)(int *itype, char *jobz, char *uplo, int *
+	n, double *ap, double *bp, double *w, double *z,
+	int *ldz, double *work, int *lwork, int *iwork,
+	int *liwork, int *info);
+
+La_extern void
+F77_NAME(dspgvx)(int *itype, char *jobz, char *range, char *
+	uplo, int *n, double *ap, double *bp, double *vl,
+	double *vu, int *il, int *iu, double *abstol, int
+	*m, double *w, double *z, int *ldz, double *work,
+	int *iwork, int *ifail, int *info);
+
+La_extern void
+F77_NAME(dstegr)(char *jobz, char *range, int *n, double *
+	d, double *e, double *vl, double *vu, int *il,
+	int *iu, double *abstol, int *m, double *w,
+	double *z, int *ldz, int *isuppz, double *work,
+	int *lwork, int *iwork, int *liwork, int *info);
+
+La_extern void
+F77_NAME(dstevr)(char *jobz, char *range, int *n, double *
+	d, double *e, double *vl, double *vu, int *il,
+	int *iu, double *abstol, int *m, double *w,
+	double *z, int *ldz, int *isuppz, double *work,
+	int *lwork, int *iwork, int *liwork, int *info);
+
+La_extern void
+F77_NAME(dsygvd)(int *itype, char *jobz, char *uplo, int *
+	n, double *a, int *lda, double *b, int *ldb,
+	double *w, double *work, int *lwork, int *iwork,
+	int *liwork, int *info);
+
+La_extern void
+F77_NAME(dsygvx)(int *itype, char *jobz, char *range, char *
+	uplo, int *n, double *a, int *lda, double *b, int
+	*ldb, double *vl, double *vu, int *il, int *iu,
+	double *abstol, int *m, double *w, double *z,
+	int *ldz, double *work, int *lwork, int *iwork,
+	int *ifail, int *info);
+
+La_extern void
+F77_NAME(dtgex2)(int *wantq, int *wantz, int *n,
+	double *a, int *lda, double *b, int *ldb, double *
+	q, int *ldq, double *z, int *ldz, int *j1, int *
+	n1, int *n2, double *work, int *lwork, int *info);
+
+La_extern void
+F77_NAME(dtgexc)(int *wantq, int *wantz, int *n,
+	double *a, int *lda, double *b, int *ldb, double *
+	q, int *ldq, double *z, int *ldz, int *ifst,
+	int *ilst, double *work, int *lwork, int *info);
+
+La_extern void
+F77_NAME(dtgsen)(int *ijob, int *wantq, int *wantz,
+	int *select, int *n, double *a, int *lda, double *
+	b, int *ldb, double *alphar, double *alphai, double *
+	beta, double *q, int *ldq, double *z, int *ldz,
+	int *m, double *pl, double *pr, double *dif,
+	double *work, int *lwork, int *iwork, int *liwork,
+	int *info);
+
+La_extern void
+F77_NAME(dtgsna)(char *job, char *howmny, int *select,
+	int *n, double *a, int *lda, double *b, int *ldb,
+	double *vl, int *ldvl, double *vr, int *ldvr,
+	double *s, double *dif, int *mm, int *m, double *
+	work, int *lwork, int *iwork, int *info);
+
+La_extern void
+F77_NAME(dtgsy2)(char *trans, int *ijob, int *m, int *
+	n, double *a, int *lda, double *b, int *ldb,
+	double *c, int *ldc, double *d, int *ldd,
+	double *e, int *lde, double *f, int *ldf, double *
+	scale, double *rdsum, double *rdscal, int *iwork, int
+	*pq, int *info);
+
+La_extern void
+F77_NAME(dtgsyl)(char *trans, int *ijob, int *m, int *
+	n, double *a, int *lda, double *b, int *ldb,
+	double *c, int *ldc, double *d, int *ldd,
+	double *e, int *lde, double *f, int *ldf, double *
+	scale, double *dif, double *work, int *lwork, int *
+	iwork, int *info);
+
+La_extern void
+F77_NAME(dtzrzf)(int *m, int *n, double *a, int *
+	lda, double *tau, double *work, int *lwork, int *info);
+
+La_extern void
+F77_NAME(dpstrf)(const char* uplo, const int* n,
+		 double* a, const int* lda, int* piv, int* rank,
+		 double* tol, double *work, int* info);
+
+
+La_extern int
+F77_NAME(lsame)(char *ca, char *cb);
+
+La_extern void
+F77_NAME(zbdsqr)(char *uplo, int *n, int *ncvt, int *
+	nru, int *ncc, double *d, double *e, Rcomplex *vt,
+	int *ldvt, Rcomplex *u, int *ldu, Rcomplex *c,
+	int *ldc, double *rwork, int *info);
+
+La_extern void
+F77_NAME(zdrot)(int *n, Rcomplex *cx, int *incx,
+	Rcomplex *cy, int *incy, double *c, double *s);
+
+La_extern void
+F77_NAME(zgebak)(char *job, char *side, int *n, int *ilo,
+	int *ihi, double *scale, int *m, Rcomplex *v,
+	int *ldv, int *info);
+
+La_extern void
+F77_NAME(zgebal)(char *job, int *n, Rcomplex *a, int
+	*lda, int *ilo, int *ihi, double *scale, int *info);
+
+La_extern void
+F77_NAME(zgebd2)(int *m, int *n, Rcomplex *a,
+	int *lda, double *d, double *e, Rcomplex *tauq,
+	Rcomplex *taup, Rcomplex *work, int *info);
+
+La_extern void
+F77_NAME(zgebrd)(int *m, int *n, Rcomplex *a,
+	int *lda, double *d, double *e, Rcomplex *tauq,
+	Rcomplex *taup, Rcomplex *work, int *lwork, int *
+	info);
+La_extern void
+F77_NAME(zgehd2)(int *n, int *ilo, int *ihi,
+	Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *
+	work, int *info);
+
+La_extern void
+F77_NAME(zgehrd)(int *n, int *ilo, int *ihi,
+	Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *
+	work, int *lwork, int *info);
+
+La_extern void
+F77_NAME(zgelq2)(int *m, int *n, Rcomplex *a,
+	int *lda, Rcomplex *tau, Rcomplex *work, int *info);
+
+La_extern void
+F77_NAME(zgelqf)(int *m, int *n, Rcomplex *a,
+	int *lda, Rcomplex *tau, Rcomplex *work, int *lwork,
+	 int *info);
+
+La_extern void
+F77_NAME(zgeqr2)(int *m, int *n, Rcomplex *a,
+	int *lda, Rcomplex *tau, Rcomplex *work, int *info);
+
+La_extern void
+F77_NAME(zgeqrf)(int *m, int *n, Rcomplex *a,
+		 int *lda, Rcomplex *tau, Rcomplex *work, int *lwork,
+		 int *info);
+
+La_extern void
+F77_NAME(zgetf2)(int *m, int *n, Rcomplex *a,
+	int *lda, int *ipiv, int *info);
+
+La_extern void
+F77_NAME(zgetrf)(int *m, int *n, Rcomplex *a,
+	int *lda, int *ipiv, int *info);
+
+La_extern void
+F77_NAME(zgetrs)(char *trans, int *n, int *nrhs,
+	Rcomplex *a, int *lda, int *ipiv, Rcomplex *b,
+	int *ldb, int *info);
+
+
+La_extern void
+F77_NAME(zhetd2)(char *uplo, int *n, Rcomplex *a, int *lda, double *d,
+		 double *e, Rcomplex *tau, int *info);
+
+La_extern void
+F77_NAME(zhetrd)(char *uplo, int *n, Rcomplex *a,
+	int *lda, double *d, double *e, Rcomplex *tau,
+	Rcomplex *work, int *lwork, int *info);
+
+La_extern void
+F77_NAME(zhseqr)(char *job, char *compz, int *n, int *ilo,
+	 int *ihi, Rcomplex *h, int *ldh, Rcomplex *w,
+	Rcomplex *z, int *ldz, Rcomplex *work, int *lwork,
+	 int *info);
+
+La_extern void
+F77_NAME(zlabrd)(int *m, int *n, int *nb,
+	Rcomplex *a, int *lda, double *d, double *e,
+	Rcomplex *tauq, Rcomplex *taup, Rcomplex *x, int *
+	ldx, Rcomplex *y, int *ldy);
+
+La_extern void
+F77_NAME(zlacgv)(int *n, Rcomplex *x, int *incx);
+
+La_extern void
+F77_NAME(zlacpy)(char *uplo, int *m, int *n,
+	Rcomplex *a, int *lda, Rcomplex *b, int *ldb);
+
+La_extern void
+F77_NAME(zlahqr)(int *wantt, int *wantz, int *n,
+	int *ilo, int *ihi, Rcomplex *h, int *ldh,
+	Rcomplex *w, int *iloz, int *ihiz, Rcomplex *z,
+	int *ldz, int *info);
+
+La_extern void
+F77_NAME(zlahrd)(int *n, int *k, int *nb,
+	Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *t,
+	int *ldt, Rcomplex *y, int *ldy);
+
+La_extern double
+F77_NAME(zlange)(char *norm, int *m, int *n, Rcomplex *a, int *lda,
+		 double *work);
+
+La_extern double
+F77_NAME(zlanhe)(char *norm,  char *uplo, int *n, Rcomplex *a,
+		 int *lda, double *work);
+
+La_extern double
+F77_NAME(zlanhs)(char *norm, int *n, Rcomplex *a, int *lda, double *work);
+
+
+La_extern void
+F77_NAME(zlaqp2)(int *m, int *n, int *offset,
+	Rcomplex *a, int *lda, int *jpvt, Rcomplex *tau,
+	double *vn1, double *vn2, Rcomplex *work);
+
+La_extern void
+F77_NAME(zlaqps)(int *m, int *n, int *offset, int
+	*nb, int *kb, Rcomplex *a, int *lda, int *jpvt,
+	Rcomplex *tau, double *vn1, double *vn2, Rcomplex *
+	auxv, Rcomplex *f, int *ldf);
+
+La_extern void
+F77_NAME(zlarf)(char *side, int *m, int *n, Rcomplex
+	*v, int *incv, Rcomplex *tau, Rcomplex *c, int *
+	ldc, Rcomplex *work);
+
+La_extern void
+F77_NAME(zlarfb)(char *side, char *trans, char *direct, char *
+	storev, int *m, int *n, int *k, Rcomplex *v, int
+	*ldv, Rcomplex *t, int *ldt, Rcomplex *c, int *
+	ldc, Rcomplex *work, int *ldwork);
+
+La_extern void
+F77_NAME(zlarfg)(int *n, Rcomplex *alpha, Rcomplex *
+	x, int *incx, Rcomplex *tau);
+
+La_extern void
+F77_NAME(zlarft)(char *direct, char *storev, int *n, int *
+	k, Rcomplex *v, int *ldv, Rcomplex *tau, Rcomplex *
+	t, int *ldt);
+
+La_extern void
+F77_NAME(zlarfx)(char *side, int *m, int *n,
+	Rcomplex *v, Rcomplex *tau, Rcomplex *c, int *
+	ldc, Rcomplex *work);
+
+La_extern void
+F77_NAME(zlascl)(char *type, int *kl, int *ku,
+	double *cfrom, double *cto, int *m, int *n,
+	Rcomplex *a, int *lda, int *info);
+
+La_extern void
+F77_NAME(zlaset)(char *uplo, int *m, int *n,
+	Rcomplex *alpha, Rcomplex *beta, Rcomplex *a, int *
+	lda);
+
+La_extern void
+F77_NAME(zlasr)(char *side, char *pivot, char *direct, int *m,
+	 int *n, double *c, double *s, Rcomplex *a,
+	int *lda);
+
+La_extern void
+F77_NAME(zlassq)(int *n, Rcomplex *x, int *incx,
+	double *scale, double *sumsq);
+
+La_extern void
+F77_NAME(zlaswp)(int *n, Rcomplex *a, int *lda,
+	int *k1, int *k2, int *ipiv, int *incx);
+
+La_extern void
+F77_NAME(zlatrd)(char *uplo, int *n, int *nb,
+	Rcomplex *a, int *lda, double *e, Rcomplex *tau,
+	Rcomplex *w, int *ldw);
+
+La_extern void
+F77_NAME(zlatrs)(char *uplo, char *trans, char *diag, char *
+	normin, int *n, Rcomplex *a, int *lda, Rcomplex *x,
+	double *scale, double *cnorm, int *info);
+
+La_extern void
+F77_NAME(zsteqr)(char *compz, int *n, double *d,
+	double *e, Rcomplex *z, int *ldz, double *work,
+	int *info);
+
+/* ZTRCON estimates the reciprocal of the condition number of a
+ * triangular matrix A, in either the 1-norm or the infinity-norm.
+ */
+La_extern void
+F77_NAME(ztrcon)(const char *norm, const char *uplo, const char *diag,
+                 const int *n, const Rcomplex *a, const int *lda,
+		 double *rcond, Rcomplex *work, double *rwork, int *info);
+
+La_extern void
+F77_NAME(ztrevc)(char *side, char *howmny, int *select,
+	int *n, Rcomplex *t, int *ldt, Rcomplex *vl,
+	int *ldvl, Rcomplex *vr, int *ldvr, int *mm, int
+	*m, Rcomplex *work, double *rwork, int *info);
+
+La_extern void
+F77_NAME(zung2l)(int *m, int *n, int *k,
+	Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *
+	work, int *info);
+
+La_extern void
+F77_NAME(zung2r)(int *m, int *n, int *k,
+	Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *
+	work, int *info);
+
+La_extern void
+F77_NAME(zungbr)(char *vect, int *m, int *n, int *k,
+	Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *
+	work, int *lwork, int *info);
+
+La_extern void
+F77_NAME(zunghr)(int *n, int *ilo, int *ihi,
+	Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *
+	work, int *lwork, int *info);
+
+La_extern void
+F77_NAME(zungl2)(int *m, int *n, int *k,
+	Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *
+	work, int *info);
+
+La_extern void
+F77_NAME(zunglq)(int *m, int *n, int *k,
+	Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *
+	work, int *lwork, int *info);
+
+La_extern void
+F77_NAME(zungql)(int *m, int *n, int *k,
+	Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *
+	work, int *lwork, int *info);
+
+La_extern void
+F77_NAME(zungqr)(int *m, int *n, int *k,
+	Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *
+	work, int *lwork, int *info);
+
+La_extern void
+F77_NAME(zungr2)(int *m, int *n, int *k,
+	Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *
+	work, int *info);
+
+La_extern void
+F77_NAME(zungrq)(int *m, int *n, int *k,
+	Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *
+	work, int *lwork, int *info);
+
+La_extern void
+F77_NAME(zungtr)(char *uplo, int *n, Rcomplex *a,
+	int *lda, Rcomplex *tau, Rcomplex *work, int *lwork,
+	 int *info);
+
+La_extern void
+F77_NAME(zunm2r)(char *side, char *trans, int *m, int *n,
+	int *k, Rcomplex *a, int *lda, Rcomplex *tau,
+	Rcomplex *c, int *ldc, Rcomplex *work, int *info);
+
+La_extern void
+F77_NAME(zunmbr)(char *vect, char *side, char *trans, int *m,
+	int *n, int *k, Rcomplex *a, int *lda, Rcomplex
+	*tau, Rcomplex *c, int *ldc, Rcomplex *work, int *
+	lwork, int *info);
+
+La_extern void
+F77_NAME(zunml2)(char *side, char *trans, int *m, int *n,
+	int *k, Rcomplex *a, int *lda, Rcomplex *tau,
+	Rcomplex *c, int *ldc, Rcomplex *work, int *info);
+
+La_extern void
+F77_NAME(zunmlq)(char *side, char *trans, int *m, int *n,
+	int *k, Rcomplex *a, int *lda, Rcomplex *tau,
+	Rcomplex *c, int *ldc, Rcomplex *work, int *lwork,
+	 int *info);
+
+#ifdef	__cplusplus
+}
+#endif
+
+#endif /* R_LAPACK_H */
diff --git a/var_lib_genenet_bnw/localscore/Linpack.h b/var_lib_genenet_bnw/localscore/Linpack.h
new file mode 100644
index 00000000..95cb753e
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/Linpack.h
@@ -0,0 +1,89 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 1997        Robert Gentleman and Ross Ihaka
+ *  Copyright (C) 1999-2002   The R Core Team.
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/* 
+   C declarations of double-precision LINPACK Fortran subroutines
+   included in R, and some others.
+   
+   Those which are listed as part of R are in the API
+ */
+
+#ifndef R_LINPACK_H_
+#define R_LINPACK_H_
+
+#include <R_ext/RS.h>		/* for F77_... */
+#include <R_ext/BLAS.h>
+
+#ifdef  __cplusplus
+extern "C" {
+#endif
+
+	/* Double Precision Linpack */
+
+extern void F77_NAME(dchdc)(double*, int*, int*, double*, int*, int*, int*);
+extern void F77_NAME(dpbfa)(double*, int*, int*, int*, int*);
+extern void F77_NAME(dpbsl)(double*, int*, int*, int*, double*);
+extern void F77_NAME(dpoco)(double*, int*, int*, double*, double*, int*);
+extern void F77_NAME(dpodi)(double*, int*, int*, double*, int*);
+extern void F77_NAME(dpofa)(double*, int*, int*, int*);
+extern void F77_NAME(dposl)(double*, int*, int*, double*);
+extern void F77_NAME(dqrdc)(double*, int*, int*, int*, double*, int*, double*, int*);
+extern void F77_NAME(dqrsl)(double*, int*, int*, int*, double*, double*, double*, double*, double*, double*, double*, int*, int*);
+extern void F77_NAME(dsvdc)(double*, int*, int*, int*, double*, double*, double*, int*, double*, int*, double*, int*, int*);
+extern void F77_NAME(dtrco)(double*, int*, int*, double*, double*, int*);
+extern void F77_NAME(dtrsl)(double*, int*, int*, double*, int*, int*);
+
+
+/* The following routines are listed as they have always been declared
+   here, but they are not currently included in R */
+extern void F77_NAME(dchdc)(double*, int*, int*, double*, int*, int*, int*);
+extern void F77_NAME(dchdd)(double*, int*, int*, double*, double*, int*, int*, double*, double*, double*, double*, int*);
+extern void F77_NAME(dchex)(double*, int*, int*, int*, int*, double*, int*, int*, double*, double*, int*);
+extern void F77_NAME(dchud)(double*, int*, int*, double*, double*, int*, int*, double*, double*, double*, double*);
+extern void F77_NAME(dgbco)(double*, int*, int*, int*, int*, int*, double*, double*);
+extern void F77_NAME(dgbdi)(double*, int*, int*, int*, int*, int*, double*);
+extern void F77_NAME(dgbfa)(double*, int*, int*, int*, int*, int*, int*);
+extern void F77_NAME(dgbsl)(double*, int*, int*, int*, int*, int*, double*, int*);
+extern void F77_NAME(dgeco)(double*, int*, int*, int*, double*, double*);
+extern void F77_NAME(dgedi)(double*, int*, int*, int*, double*, double*, int*);
+extern void F77_NAME(dgefa)(double*, int*, int*, int*, int*);
+extern void F77_NAME(dgesl)(double*, int*, int*, int*, double*, int*);
+extern void F77_NAME(dgtsl)(int*, double*, double*, double*, double*, int*);
+extern void F77_NAME(dpbco)(double*, int*, int*, int*, double*, double*, int*);
+extern void F77_NAME(dpbdi)(double*, int*, int*, int*, double*);
+extern void F77_NAME(dppco)(double*, int*, double*, double*, int*);
+extern void F77_NAME(dppdi)(double*, int*, double*, int*);
+extern void F77_NAME(dppfa)(double*, int*, int*);
+extern void F77_NAME(dppsl)(double*, int*, double*);
+extern void F77_NAME(dptsl)(int*, double*, double*, double*);
+extern void F77_NAME(dsico)(double*, int*, int*, int*, double*, double*);
+extern void F77_NAME(dsidi)(double*, int*, int*, int*, double*, int*, double*, int*);
+extern void F77_NAME(dsifa)(double*, int*, int*, int*, int*);
+extern void F77_NAME(dsisl)(double*, int*, int*, int*, double*);
+extern void F77_NAME(dspco)(double*, int*, int*, double*, double*);
+extern void F77_NAME(dspdi)(double*, int*, int*, double*, int*, double*, int*);
+extern void F77_NAME(dspfa)(double*, int*, int*, int*);
+extern void F77_NAME(dspsl)(double*, int*, int*, double*);
+
+#ifdef  __cplusplus
+}
+#endif
+
+#endif /* R_LINPACK_H_ */
diff --git a/var_lib_genenet_bnw/localscore/MathThreads.h b/var_lib_genenet_bnw/localscore/MathThreads.h
new file mode 100644
index 00000000..41234442
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/MathThreads.h
@@ -0,0 +1,39 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2000, 2001 The R Core Team.
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/*
+  Experimental: included by src/library/stats/src/distance.c
+*/
+
+#ifndef R_EXT_MATHTHREADS_H_
+#define R_EXT_MATHTHREADS_H_
+
+#ifdef  __cplusplus
+extern "C" {
+#endif
+
+#include <R_ext/libextern.h>
+LibExtern int R_num_math_threads;
+LibExtern int R_max_num_math_threads;
+
+#ifdef  __cplusplus
+}
+#endif
+
+#endif /* R_EXT_MATHTHREADS_H_ */
diff --git a/var_lib_genenet_bnw/localscore/Memory.h b/var_lib_genenet_bnw/localscore/Memory.h
new file mode 100644
index 00000000..306c9835
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/Memory.h
@@ -0,0 +1,49 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 1998-2007  The R Core Team
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ *
+ *
+ * Memory Allocation (garbage collected) --- INCLUDING S compatibility ---
+ */
+
+/* Included by R.h: API */
+
+#ifndef R_EXT_MEMORY_H_
+#define R_EXT_MEMORY_H_
+
+#ifndef NO_C_HEADERS
+# include <stddef.h> /* for size_t */
+#endif
+
+#ifdef  __cplusplus
+extern "C" {
+#endif
+
+void*	vmaxget(void);
+void	vmaxset(const void *);
+
+void	R_gc(void);
+
+char*	R_alloc(size_t, int);
+char*	S_alloc(long, int);
+char*	S_realloc(char *, long, long, int);
+
+#ifdef  __cplusplus
+}
+#endif
+
+#endif /* R_EXT_MEMORY_H_ */
diff --git a/var_lib_genenet_bnw/localscore/Parse.h b/var_lib_genenet_bnw/localscore/Parse.h
new file mode 100644
index 00000000..a1d8cc87
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/Parse.h
@@ -0,0 +1,47 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 1998-2006 R Core Team
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation; either version 2 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/* NOTE:
+   This file exports a part of the current internal parse interface.
+   It is subject to change at any minor (x.y.0) version of R.
+ */
+
+#ifndef R_EXT_PARSE_H_
+#define R_EXT_PARSE_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* PARSE_NULL will not be returned by R_ParseVector */
+typedef enum {
+    PARSE_NULL,
+    PARSE_OK,
+    PARSE_INCOMPLETE,
+    PARSE_ERROR,
+    PARSE_EOF
+} ParseStatus;
+
+SEXP R_ParseVector(SEXP, int, ParseStatus *, SEXP);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/var_lib_genenet_bnw/localscore/Print.h b/var_lib_genenet_bnw/localscore/Print.h
new file mode 100644
index 00000000..7beeaf17
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/Print.h
@@ -0,0 +1,50 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 1998-2010    The R Core Team
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/* Included by R.h: API */
+
+#ifndef R_EXT_PRINT_H_
+#define R_EXT_PRINT_H_
+
+#ifdef  __cplusplus
+/* If the vprintf interface is defined at all in C++ it may only be
+   defined in namespace std. */
+# ifdef R_USE_C99_IN_CXX
+#  include <cstdarg>
+#  ifdef __SUNPRO_CC
+using _STLP_VENDOR_CSTD::va_list;
+#  endif
+# endif
+extern "C" {
+#else
+# include <stdarg.h>
+#endif
+
+void Rprintf(const char *, ...);
+void REprintf(const char *, ...);
+#if !defined(__cplusplus) || defined R_USE_C99_IN_CXX
+void Rvprintf(const char *, va_list);
+void REvprintf(const char *, va_list);
+#endif
+
+#ifdef  __cplusplus
+}
+#endif
+
+#endif /* R_EXT_PRINT_H_ */
diff --git a/var_lib_genenet_bnw/localscore/PrtUtil.h b/var_lib_genenet_bnw/localscore/PrtUtil.h
new file mode 100644
index 00000000..1ef06d9a
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/PrtUtil.h
@@ -0,0 +1,71 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 1998-2012    The R Core Team
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/*
+ *  These functions are not part of the API.
+ */
+#ifndef PRTUTIL_H_
+#define PRTUTIL_H_
+
+#include <R_ext/Complex.h>
+#include <R_ext/Print.h>
+
+#define formatLogical      Rf_formatLogical
+#define formatInteger      Rf_formatInteger
+#define formatReal         Rf_formatReal
+#define formatComplex      Rf_formatComplex
+#define EncodeLogical      Rf_EncodeLogical
+#define EncodeInteger      Rf_EncodeInteger
+#define EncodeReal         Rf_EncodeReal
+#define EncodeComplex      Rf_EncodeComplex
+#define VectorIndex        Rf_VectorIndex
+#define printIntegerVector Rf_printIntegerVector
+#define printRealVector    Rf_printRealVector
+#define printComplexVector Rf_printComplexVector
+
+#ifdef  __cplusplus
+extern "C" {
+#endif
+
+/* Computation of printing formats */
+void formatLogical(int *, int, int *);
+void formatInteger(int *, int, int *);
+void formatReal(double *, int, int *, int *, int *, int);
+void formatComplex(Rcomplex *, int, int *, int *, int *, int *, int *, int *, int);
+
+/* Formating of values */
+const char *EncodeLogical(int, int);
+const char *EncodeInteger(int, int);
+const char *EncodeReal(double, int, int, int, char);
+const char *EncodeComplex(Rcomplex, int, int, int, int, int, int, char);
+
+/* Printing */
+void VectorIndex(int, int);
+
+void printLogicalVector(int *, int, int);
+void printIntegerVector(int *, int, int);
+void printRealVector   (double *, int, int);
+void printComplexVector(Rcomplex *,int, int);
+
+/* char *Rsprintf(char*, ...); */
+#ifdef  __cplusplus
+}
+#endif
+
+#endif /* PRTUTIL_H_ */
diff --git a/var_lib_genenet_bnw/localscore/QuartzDevice.h b/var_lib_genenet_bnw/localscore/QuartzDevice.h
new file mode 100644
index 00000000..ceb513e2
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/QuartzDevice.h
@@ -0,0 +1,235 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2007  The R Core Team
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation; either version 2 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ *
+ *---------------------------------------------------------------------
+ *  This header file constitutes the (unofficial) API to the Quartz
+ *  device. Being unofficial, the API may change at any point without
+ *  warning.
+ *
+ *  Quartz is a general device-independent way of drawing in Mac OS X,
+ *  therefore the Quartz device modularizes the actual drawing target
+ *  implementation into separate modules (e.g. Carbon and Cocoa for
+ *  on-screen display and PDF, Bitmap for off-screen drawing). The API
+ *  below is used by the modules to talk to the Quartz device without
+ *  having to know anything about R graphics device API.
+ *
+ *  Key functions are listed here:
+ *  QuartzDevice_Create - creates a Quartz device
+ *  QuartzDevice_ResetContext - should be called after the target
+ *    context has been created to initialize it.
+ *  QuartzDevice_Kill - closes the Quartz device (e.g. on window close)
+ *  QuartzDevice_SetScaledSize - resize device (does not include
+ *    re-painting, it should be followed by a call to
+ *    QuartzDevice_ReplayDisplayList)
+ *  QuartzDevice_ReplayDisplayList - replays all plot commands
+ *
+ *  Key concepts
+ *  - all Quartz modules are expected to provide a device context
+ *    (CGContextRef) for drawing. A device can temporarily return NULL
+ *    (e.g. if the context is not available immediately) and replay
+ *    the display list later to catch up.
+ *
+ *  - interactive devices can use QuartzDevice_SetScaledSize to resize
+ *    the device (no context is necessary), then prepare the context
+ *    (call QuartzDevice_ResetContext if a new context was created)
+ *    and finally re-draw using QuartzDevice_ReplayDisplayList.
+ *
+ *  - snapshots can be created either off the current display list
+ *    (last=0) or off the last known one (last=1). NewPage callback
+ *    can only use last=1 as there is no display list during that
+ *    call. Restored snapshots become the current display list and
+ *    thus can be extended by further painting (yet the original saved
+ *    copy is not influenced). Also note that all snapshots are SEXPs
+ *    (the declaration doesn't use SEXP as to not depend on
+ *    Rinternals.h) therefore must be protected or preserved immediately
+ *    (i.e. the Quartz device does NOT protect them - except in the
+ *    call to RestoreSnapshot).
+ *
+ *  - dirty flag: the dirty flag is not used internally by the Quartz
+ *    device, but can be useful for the modules to determine whether
+ *    the current graphics is a restored copy or in-progress
+ *    drawing. The Quartz device manages the flag as follows: a)
+ *    display list replay does NOT change the flag, b) snapshot
+ *    restoration resets the flag, c) all other paint operations
+ *    (i.e. outside of restore/replay) set the flag. Most common use
+ *    is to determine whether restored snapshots have been
+ *    subsequently modified.
+ *
+ *  - history: currently the history management is not used by any
+ *    modules and as such is untested and strictly experimental. It
+ *    may be removed in the future as it is not clear whether it makes
+ *    sense to be part of the device. See Cocoa module for a
+ *    module-internal implementation of the display history.
+ *
+ *  Quartz device creation path:
+ *    quartz() function -> SEXP Quartz(args) ->
+ *    setup QuartzParameters_t, call backend constructor
+ *    [e.g. QuartzCocoa_DeviceCreate(dd, fn, QuartzParameters_t *pars)] ->
+ *    create backend definition (QuartzBackend_t backend) -> 
+ *    fn->Create(dd, &backend), return the result
+ */
+
+#ifndef R_EXT_QUARTZDEVICE_H_
+#define R_EXT_QUARTZDEVICE_H_
+
+/* FIXME: this is installed, but can it really work without config.h */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#ifdef __cplusplus
+extern "C" {
+#endif   
+ 
+#if HAVE_AQUA
+#include <ApplicationServices/ApplicationServices.h>
+#else
+    typedef void* CGContextRef;
+#endif
+
+/* flags passed to the newPage callback */
+#define QNPF_REDRAW 0x0001 /* is set when NewPage really means re-draw of an existing page */
+
+/* flags passed to QuartzDevice_Create (as fs parameter) */
+#define QDFLAG_DISPLAY_LIST 0x0001
+#define QDFLAG_INTERACTIVE  0x0002 
+#define QDFLAG_RASTERIZED   0x0004 /* rasterized media - may imply disabling AA paritally for rects etc. */
+
+/* parameter flags (they should not conflict with QDFLAGS to allow chaining) */
+#define QPFLAG_ANTIALIAS 0x0100
+
+typedef void* QuartzDesc_t;
+
+typedef struct QuartzBackend_s {
+    int    size;                          /* structure size */
+    double width, height;
+    double scalex, scaley, pointsize;
+    int    bg, canvas;
+    int    flags;
+    void*  userInfo;
+    CGContextRef (*getCGContext)(QuartzDesc_t dev, void*userInfo); /* Get the context for this device */
+    int          (*locatePoint)(QuartzDesc_t dev, void*userInfo, double*x, double*y);
+    void         (*close)(QuartzDesc_t dev, void*userInfo);
+    void         (*newPage)(QuartzDesc_t dev, void*userInfo, int flags);
+    void         (*state)(QuartzDesc_t dev, void*userInfo, int state);
+    void*        (*par)(QuartzDesc_t dev, void*userInfo, int set, const char *key, void *value);
+    void         (*sync)(QuartzDesc_t dev, void*userInfo);
+    void*        (*cap)(QuartzDesc_t dev, void*userInfo);
+} QuartzBackend_t;
+
+/* parameters that are passed to functions that create backends */
+typedef struct QuartzParameters_s {
+    int        size;                   /* structure size */
+    const char *type, *file, *title;
+    double     x, y, width, height, pointsize;
+    const char *family;
+    int        flags;
+    int        connection;
+    int        bg, canvas;
+    double     *dpi;
+    /* the following parameters can be used to pass custom parameters when desired */
+    double     pard1, pard2;
+    int        pari1, pari2;
+    const char *pars1, *pars2;
+    void       *parv;
+} QuartzParameters_t;
+    
+/* all device implementations have to call this general Quartz device constructor at some point */
+QuartzDesc_t QuartzDevice_Create(void *dd, QuartzBackend_t* def);
+    
+typedef struct QuartzFunctons_s {
+    void*  (*Create)(void *, QuartzBackend_t *);  /* create a new device */
+    int    (*DevNumber)(QuartzDesc_t desc);       /* returns device number */
+    void   (*Kill)(QuartzDesc_t desc);            /* call to close the device */
+    void   (*ResetContext)(QuartzDesc_t desc);    /* notifies Q back-end that the implementation has created a new context */
+    double (*GetWidth)(QuartzDesc_t desc);        /* get device width (in inches) */
+    double (*GetHeight)(QuartzDesc_t desc);       /* get device height (in inches) */
+    void   (*SetSize)(QuartzDesc_t desc, double width, double height); /* set device size (in inches) */
+    
+    double (*GetScaledWidth)(QuartzDesc_t desc);  /* get device width (in pixels) */
+    double (*GetScaledHeight)(QuartzDesc_t desc); /* get device height (in pixels) */
+    void   (*SetScaledSize)(QuartzDesc_t desc, double width, double height); /* set device size (in pixels) */
+
+    double (*GetXScale)(QuartzDesc_t desc);     /* get x scale factor (px/pt ratio) */
+    double (*GetYScale)(QuartzDesc_t desc);     /* get y scale factor (px/pt ratio) */
+    void   (*SetScale)(QuartzDesc_t desc,double scalex, double scaley); /* sets both scale factors (px/pt ratio) */
+
+    void   (*SetTextScale)(QuartzDesc_t desc,double scale); /* sets text scale factor */
+    double (*GetTextScale)(QuartzDesc_t desc);  /* sets text scale factor */
+
+    void   (*SetPointSize)(QuartzDesc_t desc,double ps); /* sets point size */
+    double (*GetPointSize)(QuartzDesc_t desc);  /* gets point size */
+
+    int    (*GetDirty)(QuartzDesc_t desc);        /* sets dirty flag */
+    void   (*SetDirty)(QuartzDesc_t desc,int dirty); /* gets dirty flag */
+
+    void   (*ReplayDisplayList)(QuartzDesc_t desc); /* replay display list
+     Note: it inhibits sync calls during repaint,
+     the caller is responsible for calling sync if needed.
+     Dirty flag is kept unmodified */
+    void*  (*GetSnapshot)(QuartzDesc_t desc, int last);    
+    /* create a (replayable) snapshot of the device contents. 
+       when 'last' is set then the last stored display list is used, 
+       otherwise a new snapshot is created */
+    void   (*RestoreSnapshot)(QuartzDesc_t desc,void* snapshot);
+    /* restore a snapshot. also clears the dirty flag */
+
+    int    (*GetAntialias)(QuartzDesc_t desc);    /* get anti-alias flag */
+    void   (*SetAntialias)(QuartzDesc_t desc, int aa); /* set anti-alias flag */
+
+    int    (*GetBackground)(QuartzDesc_t desc);   /* get background color */
+    void   (*Activate)(QuartzDesc_t desc);        /* activate/select the device */
+    /* get/set Quartz-specific parameters. desc can be NULL for global parameters */
+    void*  (*SetParameter)(QuartzDesc_t desc, const char *key, void *value);
+    void*  (*GetParameter)(QuartzDesc_t desc, const char *key);
+} QuartzFunctions_t;
+
+#define QuartzParam_EmbeddingFlags "embeddeding flags" /* value: int[1] */
+#define QP_Flags_CFLoop 0x0001  /* drives application event loop */
+#define QP_Flags_Cocoa  0x0002  /* Cocoa is fully initialized */
+#define QP_Flags_Front  0x0004  /* is front application */
+
+/* from unix/aqua.c - loads grDevices if necessary and returns NULL on failure */
+QuartzFunctions_t *getQuartzFunctions();
+
+/* type of a Quartz contructor */
+typedef QuartzDesc_t (*quartz_create_fn_t)(void *dd, QuartzFunctions_t *fn, QuartzParameters_t *par);
+
+/* grDevices currently supply following constructors:
+   QuartzCocoa_DeviceCreate, QuartzCarbon_DeviceCreate,
+   QuartzBitmap_DeviceCreate, QuartzPDF_DeviceCreate */
+
+/* embedded Quartz support hook (defined in unix/aqua.c):
+     dd = should be passed-through to QuartzDevice_Create
+     fn = Quartz API functions
+     par = parameters (see above) */
+#ifndef IN_AQUA_C
+    extern
+#endif
+    QuartzDesc_t (*ptr_QuartzBackend)(void *dd, QuartzFunctions_t *fn, QuartzParameters_t *par);
+
+/* C version of the Quartz call (experimental)
+   returns 0 on success, error code on failure */
+QuartzDesc_t Quartz_C(QuartzParameters_t *par, quartz_create_fn_t q_create, int *errorCode);
+
+#ifdef __cplusplus
+}
+#endif   
+
+#endif
diff --git a/var_lib_genenet_bnw/localscore/R-ftp-http.h b/var_lib_genenet_bnw/localscore/R-ftp-http.h
new file mode 100644
index 00000000..665bfb87
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/R-ftp-http.h
@@ -0,0 +1,65 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2001-6 The R Core Team.
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/* Advertized entry points, for that part of libxml included in
+ * the internet module.
+ */
+
+#ifndef R_FTP_HTTP_H_
+#define R_FTP_HTTP_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+void *R_HTTPOpen(const char *url);
+int   R_HTTPRead(void *ctx, char *dest, int len);
+void  R_HTTPClose(void *ctx);
+
+void *R_FTPOpen(const char *url);
+int   R_FTPRead(void *ctx, char *dest, int len);
+void  R_FTPClose(void *ctx);
+
+void *	RxmlNanoHTTPOpen(const char *URL, char **contentType, const char *headers, int cacheOK);
+int	RxmlNanoHTTPRead(void *ctx, void *dest, int len);
+void	RxmlNanoHTTPClose(void *ctx);
+int 	RxmlNanoHTTPReturnCode(void *ctx);
+char * 	RxmlNanoHTTPStatusMsg(void *ctx);
+int 	RxmlNanoHTTPContentLength(void *ctx);
+char *	RxmlNanoHTTPContentType(void *ctx);
+void	RxmlNanoHTTPTimeout(int delay);
+
+void *	RxmlNanoFTPOpen(const char *URL);
+int	RxmlNanoFTPRead(void *ctx, void *dest, int len);
+int	RxmlNanoFTPClose(void *ctx);
+void	RxmlNanoFTPTimeout(int delay);
+int 	RxmlNanoFTPContentLength(void *ctx);
+
+void    RxmlMessage(int level, const char *format, ...);
+
+/* not currently used */
+
+void RxmlNanoFTPCleanup(void);
+void RxmlNanoHTTPCleanup(void);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* R_FTP_HTTP_H_ */
diff --git a/var_lib_genenet_bnw/localscore/R.h b/var_lib_genenet_bnw/localscore/R.h
new file mode 100644
index 00000000..5c5696b3
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/R.h
@@ -0,0 +1,65 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2000-2010 The R Core Team.
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+#ifndef R_R_H
+#define R_R_H
+
+#ifndef USING_R
+# define USING_R
+#endif
+
+#ifndef NO_C_HEADERS
+#include <stdlib.h>
+#include <stdio.h>  /* Used by several packages, remove in due course */
+#include <limits.h> /* for INT_MAX */
+#include <math.h>
+#endif
+
+#include "Rconfig.h"
+#include "Arith.h"      /* R_FINITE, ISNAN, ... */
+#include "Boolean.h"    /* Rboolean type */
+#include "Complex.h"    /* Rcomplex type */
+#include "Constants.h"  /* PI, DOUBLE_EPS, etc */
+#include "Error.h"      /* error and warning */
+#include "Memory.h"     /* R_alloc and S_alloc */
+#include "Print.h"      /* Rprintf etc */
+#include "Random.h"     /* RNG interface */
+#include "Utils.h"      /* sort routines et al */
+#include "RS.h"
+/* for PROBLEM ... Calloc, Realloc, Free, Memcpy, F77_xxxx */
+
+
+typedef double Sfloat;
+typedef int Sint;
+#define SINT_MAX INT_MAX
+#define SINT_MIN INT_MIN
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+void R_FlushConsole(void);
+/* always declared, but only usable under Win32 and Aqua */
+void R_ProcessEvents(void);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* !R_R_H */
diff --git a/var_lib_genenet_bnw/localscore/RConverters.h b/var_lib_genenet_bnw/localscore/RConverters.h
new file mode 100644
index 00000000..9ac0da33
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/RConverters.h
@@ -0,0 +1,131 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 1998-2006   The R Core Team
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ *
+ *
+ */
+
+/*
+  Not part of the API, concerns .C() converters which are deprecated.
+ */
+
+#ifndef R_CCONVERTERS_H
+#define R_CCONVERTERS_H
+
+#include <Rinternals.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#define freeCConverter RC_freeCConverter
+#define R_addToCConverter RC_addToCConverter
+#define R_converterMatchClass RC_converterMatchClass
+#define R_converterMatchClass RC_converterMatchClass
+#define R_getToCConverterByDescription RC_getToCConverterByDescription
+#define R_getToCConverterByIndex RC_getToCConverterByIndex
+#define R_getToCConverterByIndex RC_getToCConverterByIndex
+#define R_removeToCConverter RC_removeToCConverter
+
+  /* Context information controlling how the conversion is performed, passed 
+     to RObjToCPtr in dotcode.c and the different user level converters. */
+  typedef struct {
+    int  naok;
+    int  narg;
+    int  dup;
+    int  Fort;
+ 
+    char const * name ;
+
+    SEXP classes;
+  } R_CConvertInfo;
+
+
+  /* Typedefs for structs defined below with future/cross-referencing. */
+  typedef struct RtoCConverter R_toCConverter;
+  typedef struct RFromCConvertInfo R_FromCConvertInfo;
+
+
+  /* The matching routine which determines whether the converter can process the given SEXP. */
+  typedef Rboolean (*R_ToCPredicate)(SEXP obj, R_CConvertInfo *info, R_toCConverter *el);
+
+  /* The converter routine that returns the value to be passed to the C routine.
+     (We may have to make the return type a union to handle the different types.) */
+  typedef void*    (*R_ToCConverter)(SEXP obj, R_CConvertInfo *info, R_toCConverter *el);
+
+  /* The reverse converter from the C argument to the R object that is returned via the .C() call. */ 
+  typedef SEXP     (*R_FromCConverter)(void *value, SEXP arg, R_FromCConvertInfo *info, 
+				       R_toCConverter *el);
+
+
+  /* The definition of the converter element which are stored as a linked list. */
+  struct RtoCConverter {
+    R_ToCPredicate    matcher; /* check if converter applies to R object */
+    R_ToCConverter    converter; /* convert the R object to C value */
+    R_FromCConverter  reverse;   /* convert the C value back to an R object. */
+    char             *description; /* user-readable string describing the converter. */
+    void             *userData;    /* additional information used in (any of) the matcher,
+                                      converter, and reverse routines to parameterize them. */
+    Rboolean          active;  /* allows the converter to be in the list but ignored temporarily. */
+
+    R_toCConverter   *next;    /* next element in the linked list. */
+  };
+
+
+  /*   Information used to convert C values to R objects at the end of do_dotCode() */
+  struct RFromCConvertInfo {
+    const char *functionName; /* the name of the routine being called (S's name for it). */
+   
+    int         argIndex; /* the pariticular argument being processed. */
+
+    /* We provide all of the arguments and the corresponding C values. 
+       This gives the full context of the call to the reverse converter */
+    SEXP        allArgs;
+    void      **cargs;
+    int         nargs;
+  };
+
+
+
+  /* Internal mechanism for employing the converter mechanism, used in do_dotCode() in dotcode.c */
+  void *Rf_convertToC(SEXP s, R_CConvertInfo *info, int *success, R_toCConverter **converter);
+
+  /* Converter management facilities. */
+  R_toCConverter *R_addToCConverter(R_ToCPredicate match, R_ToCConverter converter,
+				    R_FromCConverter reverse, 
+				    void *userData, char *desc);
+  R_toCConverter *R_getToCConverterByIndex(int which);
+  R_toCConverter *R_getToCConverterByDescription(const char *desc);
+  void R_removeToCConverter(R_toCConverter *el);
+
+  Rboolean R_converterMatchClass(SEXP obj, R_CConvertInfo *inf, R_toCConverter *el);
+  void freeCConverter(R_toCConverter *el);
+
+  /* The routines corresponding to the .Internal() providing access to the
+     management facilities of the converter list.
+  */
+  SEXP do_getNumRtoCConverters(SEXP call, SEXP op, SEXP args, SEXP env);
+  SEXP do_getRtoCConverterDescriptions(SEXP call, SEXP op, SEXP args, SEXP env);
+  SEXP do_getRtoCConverterStatus(SEXP call, SEXP op, SEXP args, SEXP env);
+  SEXP do_setToCConverterActiveStatus(SEXP call, SEXP op, SEXP args, SEXP env);
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* R_CCONVERTERS_H */
diff --git a/var_lib_genenet_bnw/localscore/RS.h b/var_lib_genenet_bnw/localscore/RS.h
new file mode 100644
index 00000000..e8ce2ef2
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/RS.h
@@ -0,0 +1,96 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 1999-2007 The R Core Team.
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/* Included by R.h: API */
+
+#ifndef R_RS_H
+#define R_RS_H
+
+#ifndef NO_C_HEADERS
+# include <string.h>		/* for memcpy */
+#endif
+
+#include "Rconfig.h"		/* for F77_APPEND_UNDERSCORE */
+
+#ifdef  __cplusplus
+extern "C" {
+#endif
+
+/* S Like Error Handling */
+
+#include "Error.h"	/* for error and warning */
+
+#ifndef STRICT_R_HEADERS
+
+#define R_PROBLEM_BUFSIZE	4096
+/* Parentheses added for FC4 with gcc4 and -D_FORTIFY_SOURCE=2 */
+#define PROBLEM			{char R_problem_buf[R_PROBLEM_BUFSIZE];(sprintf)(R_problem_buf,
+#define MESSAGE                 {char R_problem_buf[R_PROBLEM_BUFSIZE];(sprintf)(R_problem_buf,
+#define ERROR			),error(R_problem_buf);}
+#define RECOVER(x)		),error(R_problem_buf);}
+#define WARNING(x)		),warning(R_problem_buf);}
+#define LOCAL_EVALUATOR		/**/
+#define NULL_ENTRY		/**/
+#define WARN			WARNING(NULL)
+
+#endif
+
+/* S Like Memory Management */
+
+extern void *R_chk_calloc(size_t, size_t);
+extern void *R_chk_realloc(void *, size_t);
+extern void R_chk_free(void *);
+
+#ifndef STRICT_R_HEADERS
+/* S-PLUS 3.x but not 5.x NULLs the pointer in the following */
+#define Calloc(n, t)   (t *) R_chk_calloc( (size_t) (n), sizeof(t) )
+#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
+#define Free(p)        (R_chk_free( (void *)(p) ), (p) = NULL)
+#endif
+#define R_Calloc(n, t)   (t *) R_chk_calloc( (size_t) (n), sizeof(t) )
+#define R_Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
+#define R_Free(p)      (R_chk_free( (void *)(p) ), (p) = NULL)
+
+#define Memcpy(p,q,n)  memcpy( p, q, (size_t)( (n) * sizeof(*p) ) )
+
+#define CallocCharBuf(n) (char *) R_chk_calloc((size_t) ((n)+1), sizeof(char))
+
+/* S Like Fortran Interface */
+/* These may not be adequate everywhere. Convex had _ prepending common
+   blocks, and some compilers may need to specify Fortran linkage */
+
+#ifdef HAVE_F77_UNDERSCORE
+# define F77_CALL(x)	x ## _
+#else
+# define F77_CALL(x)	x
+#endif
+#define F77_NAME(x)    F77_CALL(x)
+#define F77_SUB(x)     F77_CALL(x)
+#define F77_COM(x)     F77_CALL(x)
+#define F77_COMDECL(x) F77_CALL(x)
+
+#ifndef NO_CALL_R
+void	call_R(char*, long, void**, char**, long*, char**, long, char**);
+#endif
+
+#ifdef  __cplusplus
+}
+#endif
+
+#endif /* R_RS_H */
diff --git a/var_lib_genenet_bnw/localscore/RStartup.h b/var_lib_genenet_bnw/localscore/RStartup.h
new file mode 100644
index 00000000..5b89e7fe
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/RStartup.h
@@ -0,0 +1,107 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 1999-2010  The R Core Team
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation; either version 2 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/*
+  C functions to be called from alternative front-ends.
+
+  Part of the API for such front-ends but not for packages.
+*/
+
+#ifndef R_EXT_RSTARTUP_H_
+#define R_EXT_RSTARTUP_H_
+
+#include <R_ext/Boolean.h>	/* TRUE/FALSE */
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#ifdef Win32
+typedef int (*blah1) (const char *, char *, int, int);
+typedef void (*blah2) (const char *, int);
+typedef void (*blah3) (void);
+typedef void (*blah4) (const char *);
+/* Return value here is expected to be 1 for Yes, -1 for No and 0 for Cancel:
+   symbolic constants in graphapp.h */
+typedef int (*blah5) (const char *);
+typedef void (*blah6) (int);
+typedef void (*blah7) (const char *, int, int);
+typedef enum {RGui, RTerm, LinkDLL} UImode;
+#endif
+
+/* Startup Actions */
+typedef enum {
+    SA_NORESTORE,/* = 0 */
+    SA_RESTORE,
+    SA_DEFAULT,/* was === SA_RESTORE */
+    SA_NOSAVE,
+    SA_SAVE,
+    SA_SAVEASK,
+    SA_SUICIDE
+} SA_TYPE;
+
+typedef struct
+{
+    Rboolean R_Quiet;
+    Rboolean R_Slave;
+    Rboolean R_Interactive;
+    Rboolean R_Verbose;
+    Rboolean LoadSiteFile;
+    Rboolean LoadInitFile;
+    Rboolean DebugInitFile;
+    SA_TYPE RestoreAction;
+    SA_TYPE SaveAction;
+    size_t vsize;
+    size_t nsize;
+    size_t max_vsize;
+    size_t max_nsize;
+    size_t ppsize;
+    int NoRenviron;
+
+#ifdef Win32
+    char *rhome;               /* R_HOME */
+    char *home;                /* HOME  */
+    blah1 ReadConsole;
+    blah2 WriteConsole;
+    blah3 CallBack;
+    blah4 ShowMessage;
+    blah5 YesNoCancel;
+    blah6 Busy;
+    UImode CharacterMode;
+    blah7 WriteConsoleEx; /* used only if WriteConsole is NULL */
+#endif
+} structRstart;
+
+typedef structRstart *Rstart;
+
+void R_DefParams(Rstart);
+void R_SetParams(Rstart);
+void R_SetWin32(Rstart);
+void R_SizeFromEnv(Rstart);
+void R_common_command_line(int *, char **, Rstart);
+
+void R_set_command_line_arguments(int argc, char **argv);
+
+void setup_Rmainloop(void); // also in Rembedded.h
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/var_lib_genenet_bnw/localscore/Random.h b/var_lib_genenet_bnw/localscore/Random.h
new file mode 100644
index 00000000..1615778d
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/Random.h
@@ -0,0 +1,75 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 1998-2011    The R Core Team
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/* Included by R.h: API */
+
+#ifndef R_RANDOM_H
+#define R_RANDOM_H
+
+#ifdef  __cplusplus
+extern "C" {
+#endif
+
+#include "Boolean.h"
+
+typedef enum {
+    WICHMANN_HILL,
+    MARSAGLIA_MULTICARRY,
+    SUPER_DUPER,
+    MERSENNE_TWISTER,
+    KNUTH_TAOCP,
+    USER_UNIF,
+    KNUTH_TAOCP2,
+    LECUYER_CMRG
+} RNGtype;
+
+/* Different kinds of "N(0,1)" generators :*/
+typedef enum {
+    BUGGY_KINDERMAN_RAMAGE,
+    AHRENS_DIETER,
+    BOX_MULLER,
+    USER_NORM,
+    INVERSION,
+    KINDERMAN_RAMAGE
+} N01type;
+
+
+void GetRNGstate(void);
+void PutRNGstate(void);
+
+double unif_rand(void);
+/* These are also defined in Rmath.h */
+double norm_rand(void);
+double exp_rand(void);
+
+typedef unsigned int Int32;
+double * user_unif_rand(void);
+void user_unif_init(Int32);
+int * user_unif_nseed(void);
+int * user_unif_seedloc(void);
+
+double * user_norm_rand(void);
+
+void FixupProb(double *, int, int, Rboolean);
+
+#ifdef  __cplusplus
+}
+#endif
+
+#endif /* R_RANDOM_H */
diff --git a/var_lib_genenet_bnw/localscore/Rconfig.h b/var_lib_genenet_bnw/localscore/Rconfig.h
new file mode 100644
index 00000000..2541c8a9
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/Rconfig.h
@@ -0,0 +1,20 @@
+/* Rconfig.h.  Generated automatically */
+#ifndef R_RCONFIG_H
+#define R_RCONFIG_H
+
+#ifndef R_CONFIG_H
+
+#define HAVE_F77_UNDERSCORE 1
+#define IEEE_754 1
+/* #undef WORDS_BIGENDIAN */
+#define R_INLINE inline
+#define HAVE_VISIBILITY_ATTRIBUTE 1
+#define SUPPORT_UTF8 1
+#define SUPPORT_MBCS 1
+#define ENABLE_NLS 1
+/* #undef HAVE_AQUA */
+#define SUPPORT_OPENMP 1
+
+#endif /* not R_CONFIG_H */
+
+#endif /* not R_RCONFIG_H */
diff --git a/var_lib_genenet_bnw/localscore/Rdynload.h b/var_lib_genenet_bnw/localscore/Rdynload.h
new file mode 100644
index 00000000..982b571a
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/Rdynload.h
@@ -0,0 +1,129 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2001-12  The R Core Team.
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/*
+  C functions used to register compiled code in packages.
+
+  Those needed for that purpose are part of the API.
+ */
+
+#ifndef  R_EXT_DYNLOAD_H_
+#define  R_EXT_DYNLOAD_H_
+
+#include <R_ext/Boolean.h>
+
+/* called with a variable argument set */
+typedef void * (*DL_FUNC)();
+
+typedef unsigned int R_NativePrimitiveArgType;
+
+#define SINGLESXP 302 /* Don't have a single type for this. */
+
+/* In the future, we will want to allow people register their own types
+   and then refer to these in other contexts. Something like the Gtk type 
+   system may be appropriate.
+*/
+typedef unsigned int R_NativeObjectArgType;
+
+
+/* In the near future, we may support registering 
+   information about the arguments of native routines 
+   and whether they are used to return information.
+   The hope is that we can minimize copying objects even 
+   further. Not currently in use.
+*/
+typedef enum {R_ARG_IN, R_ARG_OUT, R_ARG_IN_OUT, R_IRRELEVANT} R_NativeArgStyle;
+
+
+
+/* 
+ These are very similar to those in  unix/dynload.c
+ but we maintain them separately to give us more freedom to do
+ some computations on the internal versions that are derived from
+ these definitions.
+*/
+typedef struct {
+    const char *name;
+    DL_FUNC     fun;
+    int         numArgs;
+  
+    R_NativePrimitiveArgType *types;
+    R_NativeArgStyle         *styles; 
+    
+} R_CMethodDef;
+
+typedef R_CMethodDef R_FortranMethodDef;
+
+
+
+typedef struct {
+    const char *name;
+    DL_FUNC     fun;
+    int         numArgs;
+/* In the future, we will put types in here for the different arguments.
+   We need a richer type system to do this effectively so that one
+   can specify types for new classes.
+*/
+} R_CallMethodDef;
+typedef R_CallMethodDef R_ExternalMethodDef;
+
+
+typedef struct _DllInfo DllInfo;
+
+/* 
+  Currently ignore the graphics routines, accessible via .External.graphics()
+  and .Call.graphics().
+ */
+#ifdef __cplusplus 
+extern "C" {
+#endif
+int R_registerRoutines(DllInfo *info, const R_CMethodDef * const croutines,
+		       const R_CallMethodDef * const callRoutines, 
+		       const R_FortranMethodDef * const fortranRoutines,
+                       const R_ExternalMethodDef * const externalRoutines);
+
+Rboolean R_useDynamicSymbols(DllInfo *info, Rboolean value);
+
+DllInfo *R_getDllInfo(const char *name);
+
+/* to be used by applications embedding R to register their symbols
+   that are not related to any dynamic module */
+DllInfo *R_getEmbeddingDllInfo(void);
+
+typedef struct Rf_RegisteredNativeSymbol R_RegisteredNativeSymbol;
+typedef enum {R_ANY_SYM=0, R_C_SYM, R_CALL_SYM, R_FORTRAN_SYM, R_EXTERNAL_SYM} NativeSymbolType;
+
+
+DL_FUNC R_FindSymbol(char const *, char const *, 
+                       R_RegisteredNativeSymbol *symbol);
+
+
+/* Experimental interface for exporting and importing functions from
+   one package for use from C code in a package.  The registration
+   part probably ought to be integrated with the other registrations.
+   The naming of these routines may be less than ideal. */
+
+void R_RegisterCCallable(const char *package, const char *name, DL_FUNC fptr);
+DL_FUNC R_GetCCallable(const char *package, const char *name);
+
+#ifdef __cplusplus 
+}
+#endif
+
+#endif /* R_EXT_DYNLOAD_H_ */
diff --git a/var_lib_genenet_bnw/localscore/Riconv.h b/var_lib_genenet_bnw/localscore/Riconv.h
new file mode 100644
index 00000000..13864ee6
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/Riconv.h
@@ -0,0 +1,46 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2005     the R Core Team
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/*
+  Interface to R's platform-independent implementation of iconv.
+
+  Part of the API.
+*/
+
+#ifndef R_ICONV_H
+#define R_ICONV_H
+
+#ifdef  __cplusplus
+extern "C" {
+#endif
+
+/* from sysutils.c */
+#undef Riconv_open
+#undef Riconv
+#undef Riconv_close
+void * Riconv_open (const char* tocode, const char* fromcode);
+size_t Riconv (void * cd, const char **inbuf, size_t *inbytesleft,
+	       char  **outbuf, size_t *outbytesleft);
+int Riconv_close (void * cd);
+
+#ifdef  __cplusplus
+}
+#endif
+
+#endif /* R_ICONV_H */
diff --git a/var_lib_genenet_bnw/localscore/Rmath.h b/var_lib_genenet_bnw/localscore/Rmath.h
new file mode 100644
index 00000000..1acd1dbb
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/Rmath.h
@@ -0,0 +1,657 @@
+/* -*- C -*-
+ *  Mathlib : A C Library of Special Functions
+ *  Copyright (C) 1998-2011  The R Core Team
+ *  Copyright (C) 2004       The R Foundation
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ *
+
+ * Rmath.h  should contain ALL headers from R's C code in `src/nmath'
+   -------  such that ``the Math library'' can be used by simply
+
+   ``#include <Rmath.h> ''
+
+   and nothing else.
+
+   It is part of the API and supports 'standalone Rmath'.
+
+*/
+#ifndef RMATH_H
+#define RMATH_H
+
+/* Note that on some systems we need to include math.h before the
+   defines below, to avoid redefining ftrunc */
+#ifndef NO_C_HEADERS
+# include <math.h>
+#endif
+
+/*-- Mathlib as part of R --  define this for standalone : */
+/* #undef MATHLIB_STANDALONE */
+
+#define R_VERSION_STRING "2.15.2"
+
+#ifndef HAVE_EXPM1
+# define HAVE_EXPM1 1
+#endif
+
+#ifndef HAVE_HYPOT
+# define HAVE_HYPOT 1
+#endif
+
+#ifndef HAVE_LOG1P
+# define HAVE_LOG1P 1
+#endif
+
+#ifndef HAVE_WORKING_LOG1P
+# define HAVE_WORKING_LOG1P 1
+#endif
+
+#if defined(HAVE_LOG1P) && !defined(HAVE_WORKING_LOG1P)
+/* remap to avoid problems with getting the right entry point */
+double  Rlog1p(double);
+#define log1p Rlog1p
+#endif
+
+
+	/* Undo SGI Madness */
+
+#ifdef ftrunc
+# undef ftrunc
+#endif
+#ifdef qexp
+# undef qexp
+#endif
+#ifdef qgamma
+# undef qgamma
+#endif
+
+
+/* ----- The following constants and entry points are part of the R API ---- */
+
+/* 30 Decimal-place constants */
+/* Computed with bc -l (scale=32; proper round) */
+
+/* SVID & X/Open Constants */
+/* Names from Solaris math.h */
+
+#ifndef M_E
+#define M_E		2.718281828459045235360287471353	/* e */
+#endif
+
+#ifndef M_LOG2E
+#define M_LOG2E		1.442695040888963407359924681002	/* log2(e) */
+#endif
+
+#ifndef M_LOG10E
+#define M_LOG10E	0.434294481903251827651128918917	/* log10(e) */
+#endif
+
+#ifndef M_LN2
+#define M_LN2		0.693147180559945309417232121458	/* ln(2) */
+#endif
+
+#ifndef M_LN10
+#define M_LN10		2.302585092994045684017991454684	/* ln(10) */
+#endif
+
+#ifndef M_PI
+#define M_PI		3.141592653589793238462643383280	/* pi */
+#endif
+
+#ifndef M_2PI
+#define M_2PI		6.283185307179586476925286766559	/* 2*pi */
+#endif
+
+#ifndef M_PI_2
+#define M_PI_2		1.570796326794896619231321691640	/* pi/2 */
+#endif
+
+#ifndef M_PI_4
+#define M_PI_4		0.785398163397448309615660845820	/* pi/4 */
+#endif
+
+#ifndef M_1_PI
+#define M_1_PI		0.318309886183790671537767526745	/* 1/pi */
+#endif
+
+#ifndef M_2_PI
+#define M_2_PI		0.636619772367581343075535053490	/* 2/pi */
+#endif
+
+#ifndef M_2_SQRTPI
+#define M_2_SQRTPI	1.128379167095512573896158903122	/* 2/sqrt(pi) */
+#endif
+
+#ifndef M_SQRT2
+#define M_SQRT2		1.414213562373095048801688724210	/* sqrt(2) */
+#endif
+
+#ifndef M_SQRT1_2
+#define M_SQRT1_2	0.707106781186547524400844362105	/* 1/sqrt(2) */
+#endif
+
+/* R-Specific Constants */
+
+#ifndef M_SQRT_3
+#define M_SQRT_3	1.732050807568877293527446341506	/* sqrt(3) */
+#endif
+
+#ifndef M_SQRT_32
+#define M_SQRT_32	5.656854249492380195206754896838	/* sqrt(32) */
+#endif
+
+#ifndef M_LOG10_2
+#define M_LOG10_2	0.301029995663981195213738894724	/* log10(2) */
+#endif
+
+#ifndef M_SQRT_PI
+#define M_SQRT_PI	1.772453850905516027298167483341	/* sqrt(pi) */
+#endif
+
+#ifndef M_1_SQRT_2PI
+#define M_1_SQRT_2PI	0.398942280401432677939946059934	/* 1/sqrt(2pi) */
+#endif
+
+#ifndef M_SQRT_2dPI
+#define M_SQRT_2dPI	0.797884560802865355879892119869	/* sqrt(2/pi) */
+#endif
+
+
+#ifndef M_LN_SQRT_PI
+#define M_LN_SQRT_PI	0.572364942924700087071713675677	/* log(sqrt(pi))
+								   == log(pi)/2 */
+#endif
+
+#ifndef M_LN_SQRT_2PI
+#define M_LN_SQRT_2PI	0.918938533204672741780329736406	/* log(sqrt(2*pi))
+								 == log(2*pi)/2 */
+#endif
+
+#ifndef M_LN_SQRT_PId2
+#define M_LN_SQRT_PId2	0.225791352644727432363097614947	/* log(sqrt(pi/2)) */
+#endif
+
+
+#ifdef MATHLIB_STANDALONE
+# ifndef R_EXT_BOOLEAN_H_
+/* "copy-paste" R_ext/Boolean.h if not already included: */
+ #define R_EXT_BOOLEAN_H_
+ #undef FALSE
+ #undef TRUE
+ typedef enum { FALSE = 0, TRUE } Rboolean;
+# endif
+#else
+# include "Boolean.h"
+#endif
+
+
+#ifndef MATHLIB_STANDALONE
+#define bessel_i	Rf_bessel_i
+#define bessel_j	Rf_bessel_j
+#define bessel_k	Rf_bessel_k
+#define bessel_y	Rf_bessel_y
+#define bessel_i_ex	Rf_bessel_i_ex
+#define bessel_j_ex	Rf_bessel_j_ex
+#define bessel_k_ex	Rf_bessel_k_ex
+#define bessel_y_ex	Rf_bessel_y_ex
+#define beta		Rf_beta
+#define choose		Rf_choose
+#define dbeta		Rf_dbeta
+#define dbinom		Rf_dbinom
+#define dcauchy		Rf_dcauchy
+#define dchisq		Rf_dchisq
+#define dexp		Rf_dexp
+#define df		Rf_df
+#define dgamma		Rf_dgamma
+#define dgeom		Rf_dgeom
+#define dhyper		Rf_dhyper
+#define digamma		Rf_digamma
+#define dlnorm		Rf_dlnorm
+#define dlogis		Rf_dlogis
+#define dnbeta		Rf_dnbeta
+#define dnbinom		Rf_dnbinom
+#define dnchisq		Rf_dnchisq
+#define dnf		Rf_dnf
+#define dnorm4		Rf_dnorm4
+#define dnt		Rf_dnt
+#define dpois		Rf_dpois
+#define dpsifn		Rf_dpsifn
+#define dsignrank	Rf_dsignrank
+#define dt		Rf_dt
+#define dtukey		Rf_dtukey
+#define dunif		Rf_dunif
+#define dweibull	Rf_dweibull
+#define dwilcox		Rf_dwilcox
+#define fmax2		Rf_fmax2
+#define fmin2		Rf_fmin2
+#define fprec		Rf_fprec
+#define fround		Rf_fround
+#define ftrunc		Rf_ftrunc
+#define fsign		Rf_fsign
+#define gammafn		Rf_gammafn
+#define imax2		Rf_imax2
+#define imin2		Rf_imin2
+#define lbeta		Rf_lbeta
+#define lchoose		Rf_lchoose
+#define lgammafn	Rf_lgammafn
+#define lgammafn_sign	Rf_lgammafn_sign
+#define lgamma1p	Rf_lgamma1p
+#define log1pmx		Rf_log1pmx
+#define logspace_add	Rf_logspace_add
+#define logspace_sub	Rf_logspace_sub
+#define pbeta		Rf_pbeta
+#define pbeta_raw	Rf_pbeta_raw
+#define pbinom		Rf_pbinom
+#define pcauchy		Rf_pcauchy
+#define pchisq		Rf_pchisq
+#define pentagamma	Rf_pentagamma
+#define pexp		Rf_pexp
+#define pf		Rf_pf
+#define pgamma		Rf_pgamma
+#define pgeom		Rf_pgeom
+#define phyper		Rf_phyper
+#define plnorm		Rf_plnorm
+#define plogis		Rf_plogis
+#define pnbeta		Rf_pnbeta
+#define pnbinom		Rf_pnbinom
+#define pnchisq		Rf_pnchisq
+#define pnf		Rf_pnf
+#define pnorm5		Rf_pnorm5
+#define pnorm_both	Rf_pnorm_both
+#define pnt		Rf_pnt
+#define ppois		Rf_ppois
+#define psignrank	Rf_psignrank
+#define psigamma	Rf_psigamma
+#define pt		Rf_pt
+#define ptukey		Rf_ptukey
+#define punif		Rf_punif
+#define pythag		Rf_pythag
+#define pweibull	Rf_pweibull
+#define pwilcox		Rf_pwilcox
+#define qbeta		Rf_qbeta
+#define qbinom		Rf_qbinom
+#define qcauchy		Rf_qcauchy
+#define qchisq		Rf_qchisq
+#define qchisq_appr	Rf_qchisq_appr
+#define qexp		Rf_qexp
+#define qf		Rf_qf
+#define qgamma		Rf_qgamma
+#define qgeom		Rf_qgeom
+#define qhyper		Rf_qhyper
+#define qlnorm		Rf_qlnorm
+#define qlogis		Rf_qlogis
+#define qnbeta		Rf_qnbeta
+#define qnbinom		Rf_qnbinom
+#define qnchisq		Rf_qnchisq
+#define qnf		Rf_qnf
+#define qnorm5		Rf_qnorm5
+#define qnt		Rf_qnt
+#define qpois		Rf_qpois
+#define qsignrank	Rf_qsignrank
+#define qt		Rf_qt
+#define qtukey		Rf_qtukey
+#define qunif		Rf_qunif
+#define qweibull	Rf_qweibull
+#define qwilcox		Rf_qwilcox
+#define rbeta		Rf_rbeta
+#define rbinom		Rf_rbinom
+#define rcauchy		Rf_rcauchy
+#define rchisq		Rf_rchisq
+#define rexp		Rf_rexp
+#define rf		Rf_rf
+#define rgamma		Rf_rgamma
+#define rgeom		Rf_rgeom
+#define rhyper		Rf_rhyper
+#define rlnorm		Rf_rlnorm
+#define rlogis		Rf_rlogis
+#define rnbeta		Rf_rnbeta
+#define rnbinom		Rf_rnbinom
+#define rnchisq		Rf_rnchisq
+#define rnf		Rf_rnf
+#define rnorm		Rf_rnorm
+#define rnt		Rf_rnt
+#define rpois		Rf_rpois
+#define rsignrank	Rf_rsignrank
+#define rt		Rf_rt
+#define rtukey		Rf_rtukey
+#define runif		Rf_runif
+#define rweibull	Rf_rweibull
+#define rwilcox		Rf_rwilcox
+#define sign		Rf_sign
+#define tetragamma	Rf_tetragamma
+#define trigamma	Rf_trigamma
+#endif
+
+#define	rround	fround
+#define	prec	fprec
+#undef trunc
+#define	trunc	ftrunc
+
+#ifdef  __cplusplus
+extern "C" {
+#endif
+	/* R's versions with !R_FINITE checks */
+
+double R_pow(double x, double y);
+double R_pow_di(double, int);
+
+	/* Random Number Generators */
+
+double	norm_rand(void);
+double	unif_rand(void);
+double	exp_rand(void);
+#ifdef MATHLIB_STANDALONE
+void	set_seed(unsigned int, unsigned int);
+void	get_seed(unsigned int *, unsigned int *);
+#endif
+
+	/* Normal Distribution */
+
+#define pnorm pnorm5
+#define qnorm qnorm5
+#define dnorm dnorm4
+
+double	dnorm(double, double, double, int);
+double	pnorm(double, double, double, int, int);
+double	qnorm(double, double, double, int, int);
+double	rnorm(double, double);
+void	pnorm_both(double, double *, double *, int, int);/* both tails */
+
+	/* Uniform Distribution */
+
+double	dunif(double, double, double, int);
+double	punif(double, double, double, int, int);
+double	qunif(double, double, double, int, int);
+double	runif(double, double);
+
+	/* Gamma Distribution */
+
+double	dgamma(double, double, double, int);
+double	pgamma(double, double, double, int, int);
+double	qgamma(double, double, double, int, int);
+double	rgamma(double, double);
+
+double  log1pmx(double);
+double  log1pexp(double); // <-- ../nmath/plogis.c
+double  lgamma1p(double);
+double  logspace_add(double, double);
+double  logspace_sub(double, double);
+
+	/* Beta Distribution */
+
+double	dbeta(double, double, double, int);
+double	pbeta(double, double, double, int, int);
+double	qbeta(double, double, double, int, int);
+double	rbeta(double, double);
+
+	/* Lognormal Distribution */
+
+double	dlnorm(double, double, double, int);
+double	plnorm(double, double, double, int, int);
+double	qlnorm(double, double, double, int, int);
+double	rlnorm(double, double);
+
+	/* Chi-squared Distribution */
+
+double	dchisq(double, double, int);
+double	pchisq(double, double, int, int);
+double	qchisq(double, double, int, int);
+double	rchisq(double);
+
+	/* Non-central Chi-squared Distribution */
+
+double	dnchisq(double, double, double, int);
+double	pnchisq(double, double, double, int, int);
+double	qnchisq(double, double, double, int, int);
+double	rnchisq(double, double);
+
+	/* F Distibution */
+
+double	df(double, double, double, int);
+double	pf(double, double, double, int, int);
+double	qf(double, double, double, int, int);
+double	rf(double, double);
+
+	/* Student t Distibution */
+
+double	dt(double, double, int);
+double	pt(double, double, int, int);
+double	qt(double, double, int, int);
+double	rt(double);
+
+	/* Binomial Distribution */
+
+double	dbinom(double, double, double, int);
+double	pbinom(double, double, double, int, int);
+double	qbinom(double, double, double, int, int);
+double	rbinom(double, double);
+
+	/* Multnomial Distribution */
+
+void	rmultinom(int, double*, int, int*);
+
+	/* Cauchy Distribution */
+
+double	dcauchy(double, double, double, int);
+double	pcauchy(double, double, double, int, int);
+double	qcauchy(double, double, double, int, int);
+double	rcauchy(double, double);
+
+	/* Exponential Distribution */
+
+double	dexp(double, double, int);
+double	pexp(double, double, int, int);
+double	qexp(double, double, int, int);
+double	rexp(double);
+
+	/* Geometric Distribution */
+
+double	dgeom(double, double, int);
+double	pgeom(double, double, int, int);
+double	qgeom(double, double, int, int);
+double	rgeom(double);
+
+	/* Hypergeometric Distibution */
+
+double	dhyper(double, double, double, double, int);
+double	phyper(double, double, double, double, int, int);
+double	qhyper(double, double, double, double, int, int);
+double	rhyper(double, double, double);
+
+	/* Negative Binomial Distribution */
+
+double	dnbinom(double, double, double, int);
+double	pnbinom(double, double, double, int, int);
+double	qnbinom(double, double, double, int, int);
+double	rnbinom(double, double);
+
+double	dnbinom_mu(double, double, double, int);
+double	pnbinom_mu(double, double, double, int, int);
+double	qnbinom_mu(double, double, double, int, int);
+double	rnbinom_mu(double, double);
+
+	/* Poisson Distribution */
+
+double	dpois(double, double, int);
+double	ppois(double, double, int, int);
+double	qpois(double, double, int, int);
+double	rpois(double);
+
+	/* Weibull Distribution */
+
+double	dweibull(double, double, double, int);
+double	pweibull(double, double, double, int, int);
+double	qweibull(double, double, double, int, int);
+double	rweibull(double, double);
+
+	/* Logistic Distribution */
+
+double	dlogis(double, double, double, int);
+double	plogis(double, double, double, int, int);
+double	qlogis(double, double, double, int, int);
+double	rlogis(double, double);
+
+	/* Non-central Beta Distribution */
+
+double	dnbeta(double, double, double, double, int);
+double	pnbeta(double, double, double, double, int, int);
+double	qnbeta(double, double, double, double, int, int);
+double	rnbeta(double, double, double);
+
+	/* Non-central F Distribution */
+
+double  dnf(double, double, double, double, int);
+double	pnf(double, double, double, double, int, int);
+double	qnf(double, double, double, double, int, int);
+
+	/* Non-central Student t Distribution */
+
+double	dnt(double, double, double, int);
+double	pnt(double, double, double, int, int);
+double	qnt(double, double, double, int, int);
+
+	/* Studentized Range Distribution */
+
+double	ptukey(double, double, double, double, int, int);
+double	qtukey(double, double, double, double, int, int);
+
+	/* Wilcoxon Rank Sum Distribution */
+
+double dwilcox(double, double, double, int);
+double pwilcox(double, double, double, int, int);
+double qwilcox(double, double, double, int, int);
+double rwilcox(double, double);
+
+	/* Wilcoxon Signed Rank Distribution */
+
+double dsignrank(double, double, int);
+double psignrank(double, double, int, int);
+double qsignrank(double, double, int, int);
+double rsignrank(double);
+
+	/* Gamma and Related Functions */
+double	gammafn(double);
+double	lgammafn(double);
+double	lgammafn_sign(double, int*);
+void    dpsifn(double, int, int, int, double*, int*, int*);
+double	psigamma(double, double);
+double	digamma(double);
+double	trigamma(double);
+double	tetragamma(double);
+double	pentagamma(double);
+
+double	beta(double, double);
+double	lbeta(double, double);
+
+double	choose(double, double);
+double	lchoose(double, double);
+
+	/* Bessel Functions */
+
+double	bessel_i(double, double, double);
+double	bessel_j(double, double);
+double	bessel_k(double, double, double);
+double	bessel_y(double, double);
+double	bessel_i_ex(double, double, double, double *);
+double	bessel_j_ex(double, double, double *);
+double	bessel_k_ex(double, double, double, double *);
+double	bessel_y_ex(double, double, double *);
+
+
+	/* General Support Functions */
+
+#ifndef HAVE_HYPOT
+double 	hypot(double, double);
+#endif
+double 	pythag(double, double);
+#ifndef HAVE_EXPM1
+double  expm1(double); /* = exp(x)-1 {care for small x} */
+#endif
+#ifndef HAVE_LOG1P
+double  log1p(double); /* = log(1+x) {care for small x} */
+#endif
+int	imax2(int, int);
+int	imin2(int, int);
+double	fmax2(double, double);
+double	fmin2(double, double);
+double	sign(double);
+double	fprec(double, double);
+double	fround(double, double);
+double	fsign(double, double);
+double	ftrunc(double);
+
+double  log1pmx(double); /* Accurate log(1+x) - x, {care for small x} */
+double  lgamma1p(double);/* accurate log(gamma(x+1)), small x (0 < x < 0.5) */
+
+/* Compute the log of a sum or difference from logs of terms, i.e.,
+ *
+ *     log (exp (logx) + exp (logy))
+ * or  log (exp (logx) - exp (logy))
+ *
+ * without causing overflows or throwing away too much accuracy:
+ */
+double  logspace_add(double logx, double logy);
+double  logspace_sub(double logx, double logy);
+
+
+
+
+/* ----------------- Private part of the header file ------------------- */
+
+	/* old-R Compatibility */
+
+#ifdef OLD_RMATH_COMPAT
+# define snorm	norm_rand
+# define sunif	unif_rand
+# define sexp	exp_rand
+#endif
+
+#if defined(MATHLIB_STANDALONE) && !defined(MATHLIB_PRIVATE_H)
+/* second is defined by nmath.h */
+
+/* If isnan is a macro, as C99 specifies, the C++
+   math header will undefine it. This happens on OS X */
+# ifdef __cplusplus
+  int R_isnancpp(double); /* in mlutils.c */
+#  define ISNAN(x)     R_isnancpp(x)
+# else
+#  define ISNAN(x)     (isnan(x)!=0)
+# endif
+
+# define R_FINITE(x)    R_finite(x)
+int R_finite(double);
+
+# ifdef WIN32  /* not Win32 as no config information */
+#  ifdef RMATH_DLL
+#   define R_EXTERN extern __declspec(dllimport)
+#  else
+#   define R_EXTERN extern
+#  endif
+R_EXTERN double NA_REAL;
+R_EXTERN double R_PosInf;
+R_EXTERN double R_NegInf;
+R_EXTERN int N01_kind;
+#  undef R_EXTERN
+#else
+extern int N01_kind;
+# endif
+
+#endif /* MATHLIB_STANDALONE */
+
+#ifdef  __cplusplus
+}
+#endif
+
+#endif /* RMATH_H */
diff --git a/var_lib_genenet_bnw/localscore/Utils.h b/var_lib_genenet_bnw/localscore/Utils.h
new file mode 100644
index 00000000..61efaaaa
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/Utils.h
@@ -0,0 +1,115 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 1998-2005    The R Core Team
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ *
+ *
+ * Generally useful  UTILITIES  *NOT* relying on R internals (from Defn.h)
+ */
+
+/* Included by R.h: API */
+
+#ifndef R_EXT_UTILS_H_
+#define R_EXT_UTILS_H_
+
+#include "Boolean.h"
+#include "Complex.h"
+
+#define revsort       Rf_revsort
+#define iPsort        Rf_iPsort
+#define rPsort        Rf_rPsort
+#define cPsort        Rf_cPsort
+#define IndexWidth    Rf_IndexWidth
+#define setIVector    Rf_setIVector
+#define setRVector    Rf_setRVector
+#define StringFalse   Rf_StringFalse
+#define StringTrue    Rf_StringTrue
+#define isBlankString Rf_isBlankString
+#define hsv2rgb       Rf_hsv2rgb
+#define rgb2hsv       Rf_rgb2hsv
+
+#ifdef  __cplusplus
+extern "C" {
+#endif
+
+/* ../../main/sort.c : */
+void	R_isort(int*, int);
+void	R_rsort(double*, int);
+void	R_csort(Rcomplex*, int);
+void    rsort_with_index(double *, int *, int);
+void	revsort(double*, int*, int);/* reverse; sort i[] alongside */
+void	iPsort(int*,    int, int);
+void	rPsort(double*, int, int);
+void	cPsort(Rcomplex*, int, int);
+
+/* ../../main/qsort.c : */
+void R_qsort    (double *v,         int i, int j);
+void R_qsort_I  (double *v, int *I, int i, int j);
+void R_qsort_int  (int *iv,         int i, int j);
+void R_qsort_int_I(int *iv, int *I, int i, int j);
+#ifdef R_RS_H
+void F77_NAME(qsort4)(double *v, int *indx, int *ii, int *jj);
+void F77_NAME(qsort3)(double *v,            int *ii, int *jj);
+#endif
+
+/* ../../main/printutils.c : */
+int	IndexWidth(int);
+/* ../../main/util.c  and others : */
+const char *R_ExpandFileName(const char *);
+void	setIVector(int*, int, int);
+void	setRVector(double*, int, double);
+Rboolean StringFalse(const char *);
+Rboolean StringTrue(const char *);
+Rboolean isBlankString(const char *);
+
+/* These two are guaranteed to use '.' as the decimal point,
+   and to accept "NA".
+ */
+double R_atof(const char *str);
+double R_strtod(const char *c, char **end);
+
+char *R_tmpnam(const char *prefix, const char *tempdir);
+char *R_tmpnam2(const char *prefix, const char *tempdir, const char *fileext);
+
+void	hsv2rgb(double h, double s, double v,
+		double *r, double *g, double *b);
+void	rgb2hsv(double r, double g, double b,
+		double *h, double *s, double *v);
+
+void R_CheckUserInterrupt(void);
+void R_CheckStack(void);
+    
+
+/* ../../appl/interv.c: also in Applic.h */
+int findInterval(double *xt, int n, double x,
+		 Rboolean rightmost_closed,  Rboolean all_inside, int ilo,
+		 int *mflag);
+#ifdef R_RS_H
+int F77_SUB(interv)(double *xt, int *n, double *x,
+		    Rboolean *rightmost_closed, Rboolean *all_inside,
+		    int *ilo, int *mflag);
+#endif
+void find_interv_vec(double *xt, int *n,	double *x,   int *nx,
+		     int *rightmost_closed, int *all_inside, int *indx);
+
+/* ../../appl/maxcol.c: also in Applic.h */
+void R_max_col(double *matrix, int *nr, int *nc, int *maxes, int *ties_meth);
+
+#ifdef  __cplusplus
+}
+#endif
+
+#endif /* R_EXT_UTILS_H_ */
diff --git a/var_lib_genenet_bnw/localscore/Visibility.h b/var_lib_genenet_bnw/localscore/Visibility.h
new file mode 100644
index 00000000..aa35e342
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/Visibility.h
@@ -0,0 +1,39 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2008    the R Core Team
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/*
+  Definitions controlling visibility on some platforms.
+
+  Part of the API.
+*/
+
+#ifndef R_EXT_VISIBILITY_H_
+#define R_EXT_VISIBILITY_H_
+
+#include <Rconfig.h>
+
+#ifdef HAVE_VISIBILITY_ATTRIBUTE
+# define attribute_visible __attribute__ ((visibility ("default")))
+# define attribute_hidden __attribute__ ((visibility ("hidden")))
+#else
+# define attribute_visible
+# define attribute_hidden
+#endif
+
+#endif /* R_EXT_VISIBILITY_H_ */
diff --git a/var_lib_genenet_bnw/localscore/eventloop.h b/var_lib_genenet_bnw/localscore/eventloop.h
new file mode 100644
index 00000000..842cf9bb
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/eventloop.h
@@ -0,0 +1,97 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2000-2007 The R Core Team.
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/* 
+   For use by alternative front-ends and packages which need to share
+   the R event loop (on all platforms).
+
+   Not part of the API and subject to change without notice.
+ */
+
+#ifndef R_EXT_EVENTLOOP_H
+#define R_EXT_EVENTLOOP_H
+
+#ifndef NO_C_HEADERS
+#ifdef HAVE_SYS_SELECT_H
+# include <sys/select.h>	/* for fd_set according to recent POSIX */
+#endif
+/* NOTE: Needed at least on FreeBSD so that fd_set is defined. */
+# include <sys/types.h>
+#endif
+
+#ifdef  __cplusplus
+extern "C" {
+#endif
+
+#define XActivity 1
+#define StdinActivity 2
+
+typedef void (*InputHandlerProc)(void *userData); 
+
+typedef struct _InputHandler {
+
+  int activity;
+  int fileDescriptor;
+  InputHandlerProc handler;
+
+  struct _InputHandler *next;
+
+    /* Whether we should be listening to this file descriptor or not. */
+  int active;
+
+    /* Data that can be passed to the routine as its only argument.
+       This might be a user-level function or closure when we implement
+       a callback to R mechanism. 
+     */
+  void *userData;
+
+} InputHandler;
+
+
+extern InputHandler *initStdinHandler(void);
+extern void consoleInputHandler(unsigned char *buf, int len);
+
+extern InputHandler *addInputHandler(InputHandler *handlers, int fd, InputHandlerProc handler, int activity);
+extern InputHandler *getInputHandler(InputHandler *handlers, int fd);
+extern int           removeInputHandler(InputHandler **handlers, InputHandler *it);
+extern InputHandler *getSelectedHandler(InputHandler *handlers, fd_set *mask);
+extern fd_set *R_checkActivity(int usec, int ignore_stdin);
+extern fd_set *R_checkActivityEx(int usec, int ignore_stdin, void (*intr)(void));
+extern void R_runHandlers(InputHandler *handlers, fd_set *mask);
+
+extern int R_SelectEx(int  n,  fd_set  *readfds,  fd_set  *writefds,
+		      fd_set *exceptfds, struct timeval *timeout,
+		      void (*intr)(void));
+
+#ifdef __SYSTEM__
+#ifndef __cplusplus   /* Would get duplicate conflicting symbols*/
+InputHandler *R_InputHandlers;
+#endif
+#else
+extern InputHandler *R_InputHandlers;
+#endif
+
+extern void (* R_PolledEvents)(void);
+extern int R_wait_usec;
+
+#ifdef  __cplusplus
+}
+#endif
+
+#endif /* R_EXT_EVENTLOOP_H */
diff --git a/var_lib_genenet_bnw/localscore/libRmath.so b/var_lib_genenet_bnw/localscore/libRmath.so
new file mode 100644
index 00000000..8c56eb4f
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/libRmath.so
Binary files differdiff --git a/var_lib_genenet_bnw/localscore/libextern.h b/var_lib_genenet_bnw/localscore/libextern.h
new file mode 100644
index 00000000..3f61fb1e
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/libextern.h
@@ -0,0 +1,48 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2001, 2004  The R Core Team.
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+/* Included by R.h: API on Windows */
+
+/* don't disallow including this one more than once */
+
+/* This is intended to be called from other header files, so not callable
+   from C++ */
+
+#undef LibExtern
+#undef LibImport
+#undef LibExport
+
+/* Don't try to include CYGWIN here: decorating some symbols breaks
+   the auto-export that it relies on, even if R_DLL_BUILD were set. */
+#ifdef WIN32 /* WIN32 as does not depend on config.h */
+#define LibImport __declspec(dllimport)
+#define LibExport __declspec(dllexport)
+#else
+#define LibImport
+#define LibExport
+#endif
+
+#ifdef __MAIN__
+#define LibExtern LibExport
+#define extern
+#elif defined(R_DLL_BUILD)
+#define LibExtern extern
+#else
+#define LibExtern extern LibImport
+#endif
diff --git a/var_lib_genenet_bnw/localscore/matrix.h b/var_lib_genenet_bnw/localscore/matrix.h
new file mode 100644
index 00000000..b37772b4
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/matrix.h
@@ -0,0 +1,42 @@
+/*                               -*- Mode: C -*- 
+ * matrix.h --- 
+ * Author          : Claus Dethlefsen
+ * Created On      : Thu Mar 14 06:47:52 2002
+ * Last Modified By: Claus Dethlefsen
+ * Last Modified On: Tue May 07 09:39:46 2002
+ * Update Count    : 22
+ * Status          : Unknown, Use with caution!
+ */
+
+/*
+  ##
+##    Copyright (C) 2002  Susanne Gammelgaard Bøttcher, Claus Dethlefsen
+##
+##    This program is free software; you can redistribute it and/or modify
+##    it under the terms of the GNU General Public License as published by
+##    the Free Software Foundation; either version 2 of the License, or
+##    (at your option) any later version.
+##
+##    This program is distributed in the hope that it will be useful,
+##    but WITHOUT ANY WARRANTY; without even the implied warranty of
+##    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+##    GNU General Public License for more details.
+##
+##    You should have received a copy of the GNU General Public License
+##    along with this program; if not, write to the Free Software
+##    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+######################################################################
+*/
+
+extern double **   dmatrix( int, int, int, int );
+extern int *       ivector( int, int );
+extern void        free_ivector( int    *, int, int );
+
+extern int         invers(double **a, int n, double **b, int m);
+extern void        printmat( double **, int, int);
+extern void        asmatrix( double *, double **, int, int);
+extern double**    matcopy(double **, int, int);
+extern double**    matmult(double **,double **, int, int, int);
+extern double**    matsum(double **a, double **b, int nr, int nc);
+extern double**    matminus(double **a, double **b, int nr, int nc);
+extern double**    transp (double **a, int n, int m); 
diff --git a/var_lib_genenet_bnw/localscore/modified_matrix.c b/var_lib_genenet_bnw/localscore/modified_matrix.c
new file mode 100644
index 00000000..8737b51b
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/modified_matrix.c
@@ -0,0 +1,252 @@
+/*                               -*- Mode: C -*- 
+ * matrix.c --- Simple matrix functions for use with postc.c
+ * Author          : Claus Dethlefsen
+ * Created On      : Thu Mar 14 06:48:02 2002
+ * Last Modified By: Claus Dethlefsen
+ * Last Modified On: Wed Jun 04 11:56:23 2003
+ * Update Count    : 36
+ * Status          : Ready
+ */
+
+/*
+  ##
+##    Copyright (C) 2002  Susanne Gammelgaard Bøttcher, Claus Dethlefsen
+##
+##    This program is free software; you can redistribute it and/or modify
+##    it under the terms of the GNU General Public License as published by
+##    the Free Software Foundation; either version 2 of the License, or
+##    (at your option) any later version.
+##
+##    This program is distributed in the hope that it will be useful,
+##    but WITHOUT ANY WARRANTY; without even the implied warranty of
+##    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+##    GNU General Public License for more details.
+##
+##    You should have received a copy of the GNU General Public License
+##    along with this program; if not, write to the Free Software
+##    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+######################################################################
+*/
+
+
+#include "matrix.h"
+#include "R.h"
+#include "Rmath.h"
+
+
+int *ivector(int nl, int nh)
+{
+   int *v;
+
+   v=(int *) calloc((unsigned) (nh-nl+1)*sizeof(int),sizeof(int));
+   if ( v == NULL ){
+      //error("memory allocation failure in ivector()"); return(NULL);
+   }
+   return v-nl;
+}
+
+void free_ivector(int *v, int nl, int nh) { free((char*) (v+nl)); }
+
+double **dmatrix(int nrl, int nrh, int ncl, int nch)
+{
+   int i;
+   double **m;
+
+   m=(double **) calloc((unsigned) (nrh-nrl+1)*sizeof(double*),sizeof(double*));
+  
+   m -= nrl;
+
+   for(i=nrl;i<=nrh;i++) {
+	   m[i]=(double *) calloc((unsigned) (nch-ncl+1)*sizeof(double),sizeof(double));
+      
+      m[i] -= ncl;
+   }
+   return m;
+}
+
+void free_dmatrix(double **m, int nrl, int nrh, int ncl, int nch)
+{
+	int i;
+
+	for(i=nrh;i>=nrl;i--) free((char*) (m[i]+ncl));
+	free((char*) (m+nrl));
+}
+
+void printmat(double **mat, int nr, int nc) {
+	int i,j;
+
+}
+
+void asmatrix(double *vek, double **mat, int nr, int nc) {
+	int i,j;
+	for (i=1; i<=nr; i++) {
+		for (j=1; j<=nc; j++) {
+			mat[i][j] = vek[j-1+(i-1)*nc];
+		}
+	}
+
+}
+
+double** matcopy(double **mat, int nr, int nc) {
+	/* copy mat[i][j] into nat[i][j] */
+	int i,j;
+	double **nat;
+	nat = dmatrix(1,nr,1,nc);
+/*	Rprintf("(nr=%d,nc=%d)\n",nr,nc);
+	Rprintf("(mat=%d)\n",mat);
+	Rprintf("(mat[1][1]=%f)\n",mat[1][1]);
+*/
+
+	for (i=1; i<=nr; i++) {
+		for (j=1; j<=nc; j++) {
+			 nat[i][j] = mat[i][j];
+		}
+	}
+	return(nat);
+}
+
+double** matmult(double **a, double **b, int nra, int nca, int ncb) {
+	double **c;
+	int i,j,k;
+	c = dmatrix(1,nra,1,ncb);
+	for (i=1; i<=nra; i++)
+		for (j=1; j<=ncb; j++)
+			c[i][j] = 0.0;
+
+	for (i=1; i<=nra; i++) 
+		for (k=1; k<=ncb; k++)
+			for (j=1; j<=nca; j++)
+				c[i][k] += a[i][j]*b[j][k];
+	return(c);
+}
+
+
+double** modified_matmult(double **a, double **b, int nra, int nca, int ncb) {
+	double **c;
+	int i,j,k;
+	c = dmatrix(1,nra,1,ncb);
+	for (i=1; i<=nra; i++)
+		for (j=1; j<=ncb; j++)
+			c[i][j] = 0.0;
+
+	for (i=1; i<=nra; i++) 
+		for (k=1; k<=ncb; k++)
+			for (j=1; j<=nca; j++)
+				c[i][k] += a[i][j]*b[j][k];
+
+	for (i=1; i<=nra; i++)
+		{
+                 for (j=1; j<=ncb; j++)
+			printf("%lf\t",c[i][j]);
+                 printf("\n");
+              } 
+
+
+	return(c);
+}
+
+
+double** matsum(double **a, double **b, int nr, int nc) {
+	double **c;
+	int i,j;
+	c = dmatrix(1,nr,1,nc);
+
+	for (i=1; i<=nr; i++)
+		for (j=1; j<=nc; j++)
+			c[i][j] = a[i][j] + b[i][j];
+	return(c);
+}
+
+double** matminus(double **a, double **b, int nr, int nc) {
+	double **c;
+	int i,j;
+	c = dmatrix(1,nr,1,nc);
+
+	for (i=1; i<=nr; i++)
+		for (j=1; j<=nc; j++)
+			c[i][j] = a[i][j] - b[i][j];
+	return(c);
+}
+
+double** transp (double **a, int n, int m) {
+	double **b;
+	int i,j;
+	b = dmatrix(1,m,1,n);
+	for (i=1; i<=n; i++)
+		for (j=1; j<=m; j++)
+			b[j][i] = a[i][j];
+	return(b);
+}
+
+int invers(double **a, int n, double **b, int m)
+{
+   int *indxc,*indxr,*ipiv;
+   int i,icol=1,irow=1,j,k,l,ll;
+   double big,dum,pivinv;
+
+//   if( (indxc = ivector(1,n)) == NULL){ return(-1); }
+ //  if( (indxr = ivector(1,n)) == NULL){ return(-1); }
+ //  if( (ipiv  = ivector(1,n)) == NULL){ return(-1); }
+  if( (indxc=(int *)calloc((unsigned)(n+1)*sizeof(int),sizeof(int))) == NULL){ return(-1); }
+  if( (indxr=(int *)calloc((unsigned)(n+1)*sizeof(int),sizeof(int))) == NULL){ return(-1); }
+  if( (ipiv=(int *)calloc((unsigned)(n+1)*sizeof(int),sizeof(int))) == NULL){ return(-1); }
+
+  
+   for (j=1;j<=n;j++) ipiv[j]=0;
+   for (i=1;i<=n;i++) {
+      big=0.0;
+      for (j=1;j<=n;j++)
+         if (ipiv[j] != 1)
+            for (k=1;k<=n;k++) {
+               if (ipiv[k] == 0) {
+                  if (fabs(a[j][k]) >= big) {
+                     big=fabs(a[j][k]);
+                     irow=j;
+                     icol=k;
+                  }
+               } else if (ipiv[k] > 1){
+                 
+                  return(-1);
+               }
+            }
+      ++(ipiv[icol]);
+      if (irow != icol) {
+         for (l=1;l<=n;l++){
+            double temp=a[irow][l]; a[irow][l]=a[icol][l]; a[icol][l]=temp;
+         }
+         for (l=1;l<=m;l++){
+            double temp=b[irow][l]; b[irow][l]=b[icol][l]; b[icol][l]=temp;
+         }
+      }
+      indxr[i]=irow;
+      indxc[i]=icol;
+      if (a[icol][icol] == 0.0){
+         //error("Invers: Singular Matrix-2");
+         return(-1);
+      }
+      pivinv=1.0/a[icol][icol];
+      a[icol][icol]=1.0;
+      for (l=1;l<=n;l++) a[icol][l] *= pivinv;
+      for (l=1;l<=m;l++) b[icol][l] *= pivinv;
+      for (ll=1;ll<=n;ll++)
+         if (ll != icol) {
+            dum=a[ll][icol];
+            a[ll][icol]=0.0;
+            for (l=1;l<=n;l++) a[ll][l] -= a[icol][l]*dum;
+            for (l=1;l<=m;l++) b[ll][l] -= b[icol][l]*dum;
+         }
+   }
+   for (l=n;l>=1;l--) {
+      if (indxr[l] != indxc[l]){
+         for (k=1;k<=n;k++){
+            double temp     = a[k][indxr[l]];
+            a[k][indxr[l]] = a[k][indxc[l]];
+            a[k][indxc[l]] = temp;
+         }
+      }
+   }
+   free(indxc); free(indxr); free(ipiv);
+   return(0);
+}
+
+
diff --git a/var_lib_genenet_bnw/localscore/modified_postc.c b/var_lib_genenet_bnw/localscore/modified_postc.c
new file mode 100644
index 00000000..f223fdb8
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/modified_postc.c
@@ -0,0 +1,171 @@
+/*                               -*- Mode: C -*- 
+ * postc.c --- Posterior for continuous node with continuous parents
+ * Author          : Claus Dethlefsen
+ * Created On      : Tue Mar 12 06:44:35 2002
+ * Last Modified By: Claus Dethlefsen
+ * Last Modified On: Wed Jun 04 11:56:51 2003
+ * Update Count    : 227
+ * Status          : Unknown, Use with caution!
+ */
+
+/*
+  ##
+##    Copyright (C) 2002  Susanne Gammelgaard Bøttcher, Claus Dethlefsen
+##
+##    This program is free software; you can redistribute it and/or modify
+##    it under the terms of the GNU General Public License as published by
+##    the Free Software Foundation; either version 2 of the License, or
+##    (at your option) any later version.
+##
+##    This program is distributed in the hope that it will be useful,
+##    but WITHOUT ANY WARRANTY; without even the implied warranty of
+##    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+##    GNU General Public License for more details.
+##
+##    You should have received a copy of the GNU General Public License
+##    along with this program; if not, write to the Free Software
+##    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+######################################################################
+*/
+
+#include "R.h"
+#include "Rmath.h"
+#include "matrix.h"
+#include "modified_matrix.c"
+
+void postc(double *mu, double *tau, double *rho, double *phi, double
+	    *loglik, double *y, double *z, int *n, int *d)
+{
+	int i,j,ii,jj;
+	double logscale,logk,mscore;
+	double **mtau, **mmu, **tauinv=0;
+	double **zero, **zi, **ziy;
+       double **oldtau, **oldmu;
+       //temp pointers
+       double **tm1,**tm2,**tm3,**tm4,**mm1,**sm1,**sm2,**tt1,**tt2;  
+
+	/* allocate space for matrices */
+	mtau   = dmatrix(1,*d,1,*d);
+     	oldtau   = dmatrix(1,*d,1,*d);
+
+	zi     = dmatrix(1,*d,1,1);
+	ziy    = dmatrix(1,*d,1,1);
+	mmu    = dmatrix(1,*d,1,1);
+	oldmu    = dmatrix(1,*d,1,1);
+	zero   = dmatrix(1,*d,1,1);
+     	tauinv   = dmatrix(1,*d,1,*d);
+
+     
+
+	/* copy arguments into the matrices */
+	asmatrix(mu,mmu,*d,1);
+	asmatrix(tau,mtau,*d,*d);
+	
+	/* show input */
+
+	for(i = 1; i <= *n; i++) {
+			for (ii=1; ii<=*d; ii++) {
+					for (jj=1; jj<=*d; jj++) {
+						 tauinv[ii][jj] = mtau[ii][jj];
+					}
+			}
+
+		invers(tauinv, *d, zero, 1);
+
+		for (j=1; j<=*d; j++) {
+			zi[j][1] = z[j-1+(i-1)*(*d)];
+		}
+              //define once		
+              tt1=transp(zi,*d,1);
+  
+              tm1=matmult(tauinv,zi,*d,*d,1);
+              tm2=matmult(tt1,tm1,1,*d,1);
+
+		logscale = log(*phi) + log1p(tm2[1][1]);
+                 		
+             free_dmatrix(tm1,1,*d,1,*d);
+	      free_dmatrix(tm2,1,1,1,*d);
+
+
+		logk = lgammafn( 0.5*(1.0+*rho) ) - lgammafn(*rho*0.5);
+		logk -= 0.5*(logscale + log(M_PI));
+		
+              tm1=matmult(tt1,mmu,1,*d,1);
+                           
+
+		mscore =  logk - 0.5*(*rho+1)*log1p((y[i-1] - tm1[1][1])*(y[i-1] - tm1[1][1])/exp(logscale));
+		*loglik += mscore;
+          
+             free_dmatrix(tm1,1,1,1,1);
+
+		for (ii=1; ii<=*d; ii++) {
+				for (jj=1; jj<=*d; jj++) {
+					 oldtau[ii][jj] = mtau[ii][jj];
+				}
+		}
+
+
+		for (jj=1; jj<=*d; jj++) {
+			 oldmu[jj][1] = mmu[jj][1];
+		}
+           
+              tm1=matmult(zi,tt1,*d,1,*d);
+              sm1=matsum(mtau,tm1,*d,*d);               
+              free_dmatrix(mtau,1,*d,1,*d);
+		mtau = sm1;
+              free_dmatrix(tm1,1,*d,1,*d);
+
+		for (ii=1; ii<=*d; ii++) {
+					for (jj=1; jj<=*d; jj++) {
+						 tauinv[ii][jj] = mtau[ii][jj];
+					}
+		}
+
+
+		invers(tauinv, *d, zero, 1);
+
+		for (j=1;j<=*d;j++)
+			ziy[j][1] = zi[j][1]*y[i-1];
+
+              
+              tm1=matmult(oldtau,mmu,*d,*d,1);
+              sm2=matsum(tm1,ziy,*d,1);
+              free_dmatrix(mmu,1,*d,1,1);
+              mmu=matmult(tauinv,sm2,*d,*d,1);
+              free_dmatrix(tm1,1,*d,1,*d);
+              free_dmatrix(sm2,1,*d,1,1);
+
+
+		(*rho)++;
+
+               tm1=matmult(tt1,mmu,1,*d,1);
+               mm1=matminus(oldmu,mmu,*d,1);             
+               tt2=transp(mm1,*d,1);
+               tm3=matmult(oldtau,oldmu,*d,*d,1);
+               tm4=matmult(tt2,tm3,1,*d,1);
+
+		 (*phi) += (y[i-1]-tm1[1][1])*y[i-1] + tm4[1][1];
+
+                  
+              free_dmatrix(tm1,1,1,1,*d);
+              free_dmatrix(mm1,1,*d,1,1);
+		free_dmatrix(tt2,1,1,1,*d);
+              free_dmatrix(tm3,1,*d,1,*d);
+              free_dmatrix(tm4,1,1,1,*d);
+
+              free_dmatrix(tt1,1,1,1,*d);
+
+
+	} 
+
+       free_dmatrix(mtau,1,*d,1,*d);
+	free_dmatrix(zi,1,*d,1,1);
+	free_dmatrix(ziy,1,*d,1,1);
+	free_dmatrix(mmu,1,*d,1,1);
+	free_dmatrix(zero,1,*d,1,1);
+	free_dmatrix(tauinv,1,*d,1,*d);
+	free_dmatrix(oldtau,1,*d,1,*d);
+	free_dmatrix(oldmu,1,*d,1,1);
+    
+} 
+
diff --git a/var_lib_genenet_bnw/localscore/network_score.c b/var_lib_genenet_bnw/localscore/network_score.c
new file mode 100644
index 00000000..69e84aab
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/network_score.c
@@ -0,0 +1,1434 @@
+#include<stdio.h>
+#include <stdlib.h>
+#include<string.h>
+#define MATHLIB_STANDALONE 1
+#include "matrix.h"
+#include "postc0.c"
+#include "modified_postc.c" // only line that has been changed in this code
+//#define OUT_DIR "./Result/"  //WHERE BENE READ DATA FOR STRUCTURE LEARNING //change it to #define OUT_DIR "/var/www/html/compbio/BNW/bene-0.9-4/example/resdir/" for server. Also change   from sprintf(line+9,"%d",i);  to sprintf(line+52,"%d",i);
+
+struct white{
+int n;
+int *list;
+};
+
+struct ban{
+int n;
+int *list;
+};
+
+struct ndata{
+int idx,type,score_i;
+char **ddata;
+char **label;              //for descrete node
+int lindex;
+double *prob,*cdata,*post_alpha;	
+double score_zeroparent;
+double *score;
+struct white wlist;
+struct ban blist;
+};
+
+
+struct nd{
+int num,nd,*discrete,nc,*continuous,row;
+double score;
+struct ndata *node;
+};
+
+void get_next_seq(int *,int *,int);
+void  learn_node(struct nd *);
+double learn_parent(struct nd  *,int,int);
+
+double run_strtof (const char * input)  //Convert string to double
+{
+    double output;
+    char * end;
+    output = strtod (input, & end);
+    if (end == input) {
+     return 0.0;    
+    }
+    else {
+        return output;
+    }
+}
+
+ 
+char* itoa(int val, int base){  //convert number to string
+	
+	static char buf[32] = {0};
+	
+	int i = 30;
+	
+	for(; val && i ; --i, val /= base)
+	
+		buf[i] = "0123456789abcdef"[val % base];
+	
+	return &buf[i+1];
+	
+}
+
+double standarizedata(double val,double mean,double std)
+{
+  return (val-mean)/std;
+
+}
+
+double mean(double *a,int l)
+{
+int i;
+double m;
+m=0;
+for(i=0;i<l;i++)
+{
+	m+=a[i];
+}
+m=m/l;
+return m;
+}
+
+
+double stdev(double *a,int l,double m)
+{
+int i;
+double sqsum=0.0;
+
+for(i=0;i<l;i++)
+{
+   sqsum+=(a[i]-m)*(a[i]-m);
+ 
+}
+
+return sqrt(sqsum/(l-1));
+}
+
+
+main(int argc, char *argv[])
+{
+ FILE * pFile,*banf,*whitef;
+ int i,s_i,j,k,l,m,id,ic,c,row,imatch,flag,bit,bit_count,ccount,maxccount;
+ int n = 0,ban_flag,white_flag,white_flag_all;
+ char line[2500],nf[250],nt[250],*file_name;
+ char **name;  //name of variables
+ double tc,tcm,score_val;
+ struct nd network;
+ int MAX_PARENT;
+ FILE **inputFiles;
+ 
+
+ double min_score; 
+ 
+
+ if(argc<=5)
+ {
+   printf("Use 5 arguments: 1. input data file name. 2. ban list file name. 3. white list file name. 4. integer value of the maximum number of parents are allowed and 5. output file directory\n");
+   return; 
+ } 
+
+ 
+ 
+ pFile=fopen (argv[1],"r");
+
+  
+ if (pFile==NULL) perror ("Error opening file");
+ else
+ {//reading data from input file
+    
+
+    	row=0;
+    	do{   row++;
+    	} while (fgets (line,2500,pFile)!=NULL);  
+  
+    	row-=3;  
+    	network.row=row;
+    	fclose(pFile);
+   	pFile=fopen (argv[1],"r");
+       ccount=0;  
+       maxccount=0;
+   	do {
+      		c = fgetc (pFile);
+      		if (c == '\t') 
+              {     
+                   n++;
+                   if(maxccount<ccount)
+                      maxccount=ccount;
+                   ccount=0;
+              }
+              else
+                  ccount++;
+               
+
+    	} while (c != '\n');
+    
+
+    	network.num=n+1;
+    	network.discrete=(int *)malloc(sizeof(int)*network.num);
+    	network.continuous=(int *)malloc(sizeof(int)*network.num); 
+    	network.node=(struct ndata *)malloc(sizeof(struct ndata)*network.num);
+
+       MAX_PARENT=atoi(argv[4]);  //maximum number of parents for each node
+       if(MAX_PARENT==0)  //no restriction on parents
+           MAX_PARENT=network.num+1;
+
+       name=(char **)malloc(sizeof(char *)*network.num);
+
+    	for(i=0;i<network.num;i++)
+           name[i]=(char *)malloc(sizeof(char)*(maxccount+1));
+
+
+    
+ 	id=0;
+       ic=0; 
+    	for(i=0;i<=n;i++)
+     	{
+	  	fscanf(pFile,"%d",&c);
+	  	network.node[i].idx=i;
+	  	network.node[i].type=c;
+	  	if(c==1)
+	  	{
+	    		network.continuous[ic]=i;
+	    		ic++;	
+	    		network.node[i].prob=(double *)malloc(sizeof(double)*2); //probability array of size 2 for continuous node
+	    		network.node[i].prob[0]=0.0;  //initialization
+	    		network.node[i].prob[1]=0.0; 
+	    	       network.node[i].cdata=(double *)malloc(sizeof(double)*row); //data matrix for continuous node
+	  	}
+	  	else
+	  	{
+	  		network.discrete[id]=i; 
+              	network.node[i].post_alpha=(double *)calloc(network.node[i].type,sizeof(double));  //prepare total count of each discrete data lebel initialize with zero by calloc which is used in learnnode
+			id++;
+	    		network.node[i].prob=(double *)malloc(sizeof(double)*c); //probability array of size equals to number of levels for discrete node 
+	    		network.node[i].ddata=(char **)malloc(sizeof(char *)*row); //data matrix for continuous node
+	    		network.node[i].label=(char **)malloc(sizeof(char *)*c);  //label array
+	    		for(j=0;j<c;j++)
+			   network.node[i].prob[j]=1.0/c;
+	  	}
+    	 }
+	 network.nd=id;  network.nc=ic; 
+        j=0;
+   	 
+        do{  //calculate average and prob for each node
+     	 	for(i=0;i<=n;i++) //n is nimber of column in the data matrix
+     		{
+     			if(network.node[i].type==1)   //if continuous
+     			{
+     	         		fscanf(pFile,"%s",line);
+     	         		tc=run_strtof(line);
+		  		//network.node[i].prob[1]+=tc;   //summation for average
+		  		network.node[i].cdata[j]=tc;  // data values in data column vector
+     			}
+     			else   //discrete
+     	 	       {
+				fscanf(pFile,"%s",line);
+				network.node[i].ddata[j]=(char *)malloc(sizeof(char)*strlen(line));
+				if(j==0)    //first iteration of do while
+				{ 
+	    	         		network.node[i].lindex=0;
+		   	  		network.node[i].label[0]=(char *)malloc(sizeof(char)*strlen(line));
+		   	  		strcpy(network.node[i].label[0],line);  //new label assigned to label list
+		   	  		network.node[i].post_alpha[0]=1;
+		   	
+				}
+				else  //store different label for discrete node also count number of ocarance of each label for calculation of post alpha score
+				{
+		   	 		imatch=0;
+		   	 		for(k=0;k<=network.node[i].lindex;k++)
+		   	 		{
+		   	   	 		if(strcmp(network.node[i].label[k],line)==0)
+		   	   	 		{
+		   	   	    			imatch=1; 
+							network.node[i].post_alpha[k]+=1;	
+		   	   	    			break; 	
+		   	   	 		}
+		   	   		}
+		   	 		if(imatch==0)
+		   	 		{
+		   	       		network.node[i].lindex++;
+		   	       		k=network.node[i].lindex;
+		   	       		network.node[i].label[k]=(char *)malloc(sizeof(char)*strlen(line));
+		   	       		strcpy(network.node[i].label[k],line);  //new label assigned to label list
+						network.node[i].post_alpha[k]+=1;
+		   	 		}
+				}
+				strcpy(network.node[i].ddata[j],line);
+     	 		}
+     	
+     		}
+      		j++;  
+    	} while (fgets (line,250,pFile)!=NULL);  //end of do while to read the input file  
+     
+       //////////////normalize continuous data/////////////
+       for(i=0;i<=n;i++)
+   	{
+     		if(network.node[i].type==1)  
+     		{    	  		
+
+                     tcm=mean(network.node[i].cdata,row);
+                     tc=stdev(network.node[i].cdata,row,tcm);
+          	  	for(j=0;j<row;j++)
+		  	{
+			    network.node[i].cdata[j]=standarizedata(network.node[i].cdata[j],tcm,tc); //dataval.data mean, standard deviation
+			}
+     		}
+	 } 
+     
+       //////////////////adjust average and prob for normalized data
+     	for(i=0;i<=n;i++)
+   	{
+     		if(network.node[i].type==1)  //claculate average and prob for continuous nodes
+     		{
+     	  		network.node[i].prob[1]=mean(network.node[i].cdata,row);
+	
+          	  	for(j=0;j<row;j++)
+		  	{
+			    network.node[i].prob[0]+=(network.node[i].cdata[j]-network.node[i].prob[1])*(network.node[i].cdata[j]-network.node[i].prob[1]);
+			}
+       	  	network.node[i].prob[0]*=1.0/(double)(row-1);	
+		  	network.node[i].prob[0]*=(double)(row-1.0)/(double)row;                    
+
+     		}
+	 } 
+
+  fclose (pFile);
+  }//end of else part for open input file
+
+  pFile=fopen (argv[1],"r");
+
+  for(i=0;i<network.num;i++)
+      fscanf(pFile,"%s",name[i]);
+
+  fclose(pFile);
+
+  learn_node(&network);    //call function to learn network and get local score whell 0 parent for all nodes
+
+
+
+  //printf("%.2lf\n",learn_parent(&network,6,176));
+  // printf("%.2lf\n",learn_parent(&network,6,47));
+  // printf("%.2lf\n",learn_parent(&network,6,18));
+  //printf("%.2lf\n",learn_parent(&network,7,80));
+  ////////printing trylist to a file////////////////////////////////
+
+  //fprintf(outfile,"Number of nodes\n%d\n",network.num);
+  //fprintf(outfile,"Possible sets of parents per node\n");
+  j=(int)pow(2.0,network.nd-1);  //possible number of parents for discrete node
+  k=(int)pow(2.0,network.num-1); //possible number of parents for continuous nodes
+
+
+  for(i=0;i<network.num;i++)
+  {
+     network.node[i].score=(double *)malloc(sizeof(double)*(k+1));
+     network.node[i].score_i=0;
+
+ 
+     network.node[i].wlist.n=0;
+     network.node[i].blist.n=0;
+     network.node[i].blist.list=(int *)malloc(sizeof(int)*network.num);
+     network.node[i].wlist.list=(int *)malloc(sizeof(int)*network.num);
+    // if(network.node[i].type>1)  //discrete
+      //     fprintf(outfile,"%d\t",j);
+     //else   //continuous
+       //    fprintf(outfile,"%d\t",k);
+  }
+
+  banf=fopen (argv[2],"r");  //ban list file name
+  whitef=fopen (argv[3],"r");  //white list file name
+
+  //read banlist
+strcpy(nf,"");
+strcpy(nt,"");
+
+while (fgets (line,2500,banf)!=NULL){  
+  
+   fscanf(banf,"%s",nf);  //node from
+   fscanf(banf,"%s",nt);  //node to
+   
+   for(i=0;i<network.num;i++)
+   {
+       if(strcmp(name[i],nt)==0)
+       {
+              j=network.node[i].blist.n;
+              for(l=0;l<network.num;l++)
+   		{
+                    if(strcmp(name[l],nf)==0)
+                    {
+                        ban_flag=0;
+                        for(k=0;k<network.node[i].blist.n;k++)
+                             {    
+                                 if(network.node[i].blist.list[k]==l)
+                                  {           		   
+                       		         ban_flag=1;
+                          		         break;
+                                  }
+                             }
+                        if(ban_flag==0) 
+                        {
+                             network.node[i].blist.list[j]=l;
+                             j++;
+                             network.node[i].blist.n=j;
+                        }
+
+                        
+                    } 
+              }
+       }   
+  }
+
+}   
+
+
+
+//read whitelist
+strcpy(nf,"");
+strcpy(nt,"");
+
+while (fgets (line,2500,whitef)!=NULL){  
+
+fscanf(whitef,"%s",nf);  //node from
+fscanf(whitef,"%s",nt);  //node to
+
+for(i=0;i<network.num;i++)
+  {
+       if(strcmp(name[i],nt)==0)
+       {
+              j=network.node[i].wlist.n;
+              for(l=0;l<network.num;l++)
+   		{
+                    if(strcmp(name[l],nf)==0)
+                    {
+                         white_flag=0;
+                        for(k=0;k<network.node[i].wlist.n;k++)
+                             {    
+                                 if(network.node[i].wlist.list[k]==l)
+                                  {           		   
+                       		         white_flag=1;
+                          		         break;
+                                  }
+                             }
+                             if(white_flag==0) 
+                             {
+
+                                 network.node[i].wlist.list[j]=l;
+                                 j++;
+                                 network.node[i].wlist.n=j;
+                             }
+
+ 
+                    } 
+              }
+       }   
+  }
+
+}   
+
+  //fprintf(outfile,"\nChild	Parents	Score\n");
+
+  m=(int)pow(2.0,network.num)-1; //number of combinations of parents
+  min_score=1.0;
+  for(i=0;i<network.num;i++)
+  {
+ 
+    if(network.node[i].wlist.n==0)
+    {
+            network.node[i].score[0]=network.node[i].score_zeroparent;
+            if(min_score>network.node[i].score_zeroparent)
+                min_score=network.node[i].score_zeroparent;
+
+            //fprintf(outfile,"%d\t0\t%lf\n",i+1,network.node[i].score_zeroparent);  //printing score for zero parent 
+    }
+    else
+    {
+          network.node[i].score[0]=1.0;
+          //fprintf(outfile,"%d\t0\t0.0\n",i+1);
+          
+     }
+    network.node[i].score_i=1;
+
+
+     for(j=0;j<m;j++)
+     {   
+
+     
+
+         bit= (j+1 >> i) & 1;
+
+         if(bit!=1)  //check if the child itself is present in parent list
+         { 
+
+          		bit_count=0;
+               	//fprintf(outfile,"%d\t",i+1);
+      			for(l=0;l<network.num;l++)
+                     {
+                       		bit= (j+1 >> l) & 1;
+                           		if(bit==1)
+                           		{
+                                         	//fprintf(outfile,"%d",l+1);
+                   				bit_count++;
+ 	            				
+                                   }  
+
+                     }
+
+
+    	            if(network.node[i].type>1)  //if discrete node checck if any continuous node is included in the parent list
+              	    {     
+                  		flag=0;
+                              ban_flag=0;
+
+                  		for(l=0;l<network.num;l++)
+                  		{
+                        		bit= (j+1 >> l) & 1;
+                        
+	  	          		if(bit==1 && network.node[l].type==1) //check if continuous is parent of discrete
+ 	   	           		{   
+                             		 flag=1;
+                             		 break;
+                         		}
+	  	          		if(bit==1)
+                                   { 
+                                           for(k=0;k<network.node[i].blist.n;k++)
+                                           {    
+                                               if(network.node[i].blist.list[k]==l)
+                                                {           		   
+                             		         ban_flag=1;
+                             		         break;
+                                                }
+                                           }
+
+
+                                           if(ban_flag==1)
+                                              break;
+                         		}
+
+
+
+                   		}
+                   		if(flag==0)  //if no continuous parent for discrete node then learn the network with the list of parents  
+                   		{
+
+					if(bit_count>MAX_PARENT)
+                                   {
+                                              //fprintf(outfile,"\t0.0\n");   
+
+                                              s_i=network.node[i].score_i;
+                                              network.node[i].score[s_i]=1.0;
+                                              network.node[i].score_i=s_i+1;
+
+
+
+                                   }
+                                   else if(ban_flag==1)
+                                    {        
+                                              //fprintf(outfile,"\t0.0\n");   
+                                              s_i=network.node[i].score_i;
+                                              network.node[i].score[s_i]=1.0;
+                                              network.node[i].score_i=s_i+1;
+                                    }
+                                   else  // calculate score if white list check get satisfied
+                         		{
+                                          if(network.node[i].wlist.n==0)
+                                           {  
+                                              score_val=learn_parent(&network,i,j);
+
+            					    if(min_score>score_val)
+					                min_score=score_val;
+
+
+
+                                              //fprintf(outfile,"\t%lf\n",score_val);   
+                                              s_i=network.node[i].score_i;
+                                              network.node[i].score[s_i]=score_val;
+                                              network.node[i].score_i=s_i+1;
+                                           }                                                 
+                                          else if(bit_count<network.node[i].wlist.n)  //white list is greater than list of parents
+                                          {
+						    //fprintf(outfile,"\tfor white\t0.0\n"); 
+                                              s_i=network.node[i].score_i;
+                                              network.node[i].score[s_i]=1.0;
+                                              network.node[i].score_i=s_i+1;
+                                          }
+                                          else
+                                          {
+                                                white_flag=0;  
+                                                white_flag_all=0;  
+
+     			                          for(l=0;l<network.num;l++)
+                        		            {
+                            	          	  bit= (j+1 >> l) & 1;
+
+                            		         if(bit==1)
+                                		         {
+                                                        for(k=0;k<network.node[i].wlist.n;k++)
+                                                        {     
+                                                               if(network.node[i].wlist.list[k]==l)
+                                                               {           		   
+                             		                        white_flag=1;
+                             		                        break;
+                                                               }
+                                                        }
+                                                        if(white_flag!=1)
+                                                        {    
+                                                              white_flag_all=1;
+                                                              break; 
+
+                                          	        }  
+                        
+                                    	           }
+                                                }
+                                                if(white_flag_all==0)
+                                       	      {
+                                                      score_val=learn_parent(&network,i,j);
+	             					     if(min_score>score_val)
+					                        min_score=score_val;
+
+                                                      //fprintf(outfile,"\t%lf\n",score_val);   
+                                                      s_i=network.node[i].score_i;
+                                                      network.node[i].score[s_i]=score_val;
+                                                      network.node[i].score_i=s_i+1;
+                                                }
+                                                else
+                                                { 
+                                                     //fprintf(outfile,"\t0.0\n");  
+	                                              s_i=network.node[i].score_i;
+	                                              network.node[i].score[s_i]=1.0;
+	                                              network.node[i].score_i=s_i+1;
+							}
+
+                                           } 
+                                   }
+
+                   		}
+                            else  //fill up data when continuous is parent of discrete
+                            {
+					//fprintf(outfile,"\t0.0\n"); 
+                                   s_i=network.node[i].score_i;
+                                   network.node[i].score[s_i]=1.0;
+                                   network.node[i].score_i=s_i+1;
+
+                             }  
+               	}
+               	else  //if continuous node then learn the network with the parent set
+               	{
+
+                            ban_flag=0;
+
+       
+                   		for(l=0;l<network.num;l++)
+                   		{
+                       		bit= (j+1 >> l) & 1;
+                       		if(bit==1)
+                            	{
+
+                                           for(k=0;k<network.node[i].blist.n;k++)
+                                           {    
+                                               if(network.node[i].blist.list[k]==l)
+                                                {           		   
+                             		         ban_flag=1;
+                             		         break;
+                                                }
+                                           }
+                                           if(ban_flag==1)
+                                              break;
+                         		}
+
+
+                   		}
+				if(bit_count>MAX_PARENT)
+                            {
+                                   //fprintf(outfile,"\t0.0\n"); 
+                                   s_i=network.node[i].score_i;
+                                   network.node[i].score[s_i]=1.0;
+                                   network.node[i].score_i=s_i+1;
+                            } 
+                            else if(ban_flag==1)
+                            {
+					//fprintf(outfile,"\t0.0\n"); 
+                                   s_i=network.node[i].score_i;
+                                   network.node[i].score[s_i]=1.0;
+                                   network.node[i].score_i=s_i+1;
+				}				
+                            else
+                            {
+                                          if(network.node[i].wlist.n==0)
+                                      	 {
+                                                      score_val=learn_parent(&network,i,j);
+       	      					     if(min_score>score_val)
+						                min_score=score_val;
+
+                                                      //fprintf(outfile,"\t%lf\n",score_val);   
+                                                      s_i=network.node[i].score_i;
+                                                      network.node[i].score[s_i]=score_val;
+                                                      network.node[i].score_i=s_i+1;
+                                            }
+                                          else if(bit_count<network.node[i].wlist.n)  //white list is greater than list of parents
+                                          {
+                                                     //fprintf(outfile,"\t0.0\n"); 
+                                                     s_i=network.node[i].score_i;
+                                                     network.node[i].score[s_i]=1.0;
+                                                     network.node[i].score_i=s_i+1;
+                                           } 
+                                          else
+                                          {
+                                                white_flag=0;  
+                                                white_flag_all=0;  
+
+     			                          for(l=0;l<network.num;l++)
+                        		            {
+                            	          	  bit= (j+1 >> l) & 1;
+
+                            		         if(bit==1)
+                                		         {
+                                                        for(k=0;k<network.node[i].wlist.n;k++)
+                                                        {     
+                                                               if(network.node[i].wlist.list[k]==l)
+                                                               {           		   
+                             		                        white_flag=1;
+                             		                        break;
+                                                               }
+                                                        }
+                                                        if(white_flag!=1)
+                                                        {    
+                                                              white_flag_all=1;
+                                                              break; 
+
+                                          	        }  
+                        
+                                    	           }
+                                                }
+                                                if(white_flag_all==0)
+                                      	      {
+                                                      score_val=learn_parent(&network,i,j);
+            					            if(min_score>score_val)
+					                       min_score=score_val;
+
+                                                      //fprintf(outfile,"\t%lf\n",score_val);   
+                                                      s_i=network.node[i].score_i;
+                                                      network.node[i].score[s_i]=score_val;
+                                                      network.node[i].score_i=s_i+1;
+                                                }
+                                                else
+                                                {
+       						    // fprintf(outfile,"\t0.0\n");  
+                                              	     s_i=network.node[i].score_i;
+	                                               network.node[i].score[s_i]=1.0;
+	                                               network.node[i].score_i=s_i+1;
+							}
+
+                                           } 
+                              }
+
+
+                	}
+
+
+           }  
+       }
+  }  
+
+
+//print scores to separate files
+
+min_score*=10;
+inputFiles= (FILE **) malloc(network.num * sizeof(FILE*));
+
+
+for(i=0;i<network.num;i++)
+{
+  strcpy(line,argv[5]);
+  k=strlen(line);
+  sprintf(line+k,"/%d",i); 
+
+  inputFiles[i] = fopen(line, "wb");
+
+  //print content  
+  for(j=0;j<network.node[i].score_i;j++)
+  {      
+          if(network.node[i].score[j]<1.0)
+            fwrite(&network.node[i].score[j],sizeof(double),1,inputFiles[i]); // fprintf(inputFiles[i],"%lf\n",network.node[i].score[j]);
+          else 
+            fwrite(&min_score,sizeof(double),1,inputFiles[i]); //fprintf(inputFiles[i],"%lf\n",min_score);
+  }  
+
+  fclose(inputFiles[i]);
+}
+
+
+
+
+
+
+fclose(banf);
+fclose(whitef);
+
+
+// printf("Time elapsed: %f\n", ((double)clock() - start) / CLOCKS_PER_SEC);
+
+}
+
+
+/* learn the network for zero parent */
+
+void  learn_node(struct nd  *net)
+{
+  int i,j,k,nk,l,m,i1,j1;
+  long num,temp;
+  double n,N,s2;
+  struct nd network=*net; //create a local copy
+  double *alpha,nu,rho,mu,phi,tau;
+  double post_nu,post_rho,post_mu,post_phi,post_tau;
+  double loglik,post_loglik;
+ 
+  num=network.num;
+
+  nk=1;
+  
+  for(i=0;i<num;i++)
+  {
+     if(network.node[i].type>1)
+        nk*=network.node[i].type;
+  }
+  
+  	   
+
+
+  for(i=0;i<num;i++)
+  {	   
+     if(network.node[i].type>1)
+     {
+	      	
+	  alpha=(double *)malloc(sizeof(double)*network.node[i].type);
+	  k=1;
+			  
+	   for(j=0;j<num;j++)
+          {
+          	  if(i!=j && network.node[j].type>1)
+                 k*=network.node[j].type;
+		          	
+          }
+          N=0.0; n=0.0;
+	   for(j=0;j<network.node[i].type;j++)
+          {
+              alpha[j]=2.0*k;
+              network.node[i].post_alpha[j]+=alpha[j];
+          ////////update loglik from udisclik
+              n+=alpha[j]; 
+              N+=network.node[i].post_alpha[j];
+          }
+     
+	  
+         loglik=0.0;
+         post_loglik=0.0;
+  
+     	  for(j=0;j<network.node[i].type;j++)
+             post_loglik+=lgammafn(network.node[i].post_alpha[j])-lgammafn(alpha[j]);
+
+          post_loglik+=lgammafn(n);
+          post_loglik-=lgammafn(N);
+ 
+     
+	}
+	else
+	{
+	    	nu=nk*2.0;
+	    	tau=nu;
+	    	rho=nk*2.0;	
+		mu=network.node[i].prob[1];
+		phi=network.node[i].prob[0]*nk;
+		loglik=0.0;
+              post_mu=mu;
+              post_tau=tau;
+              post_rho=rho;
+              post_phi=phi;
+	       post_loglik=loglik; 
+
+              postc0(&post_mu,&post_tau,&post_rho,&post_phi,&post_loglik,network.node[i].cdata,&network.row);
+
+     		    	
+	}
+      network.node[i].score_zeroparent=post_loglik; // store the zero parent score 
+		  
+   }
+    	
+   if(nk!=1)
+     free(alpha);
+
+   *net=network;  //coppied back to original	
+}
+
+
+/*
+learn node for a list of parents
+*/
+
+double learn_parent(struct nd  *net,int child,int p)
+{
+  int i,j,jj,k,nk,l,m,i1,j1,k1,k2,cn_send;
+  long num,temp;
+  double n,N,s2;
+  struct nd network=*net; //create a local copy
+  int cn,ds,bit,*discrete,*continuous;
+  double alpha,*postalpha,alpha_parent,*postalpha_parent,nu,rho,mu,phi,tau;
+  double post_nu,post_rho,*post_mu,post_phi,post_tau;
+  double loglik,post_loglik=0,post_loglik_parent=0;
+  double *mu_mat,**tau_mat,tau11,tau12,tau22,div,phiinv;
+  char **label; 
+  int *a,*l_list,flag,y_count,z_count;
+  double *y,mu_p,phi_p,*tau_send,*z_send,loglik_sum;
+
+
+
+  num=network.num;
+
+  continuous=(int *)malloc(sizeof(int)*network.nc);
+  discrete=(int *)malloc(sizeof(int)*network.nd); 
+
+  nk=1;
+  for(i=0;i<num;i++)
+  {
+	if(network.node[i].type>1)
+	    nk*=network.node[i].type;
+  }
+	   
+//list of discrete snd continuous parents
+  cn=0;
+  ds=0;
+  alpha_parent=0;
+  alpha=2;
+ 
+  k1=network.node[child].type;
+  k2=1;
+ 
+ //printf("%d\n",child);
+  for(j=0;j<network.num;j++)   //list the continuous parents and discrete parents
+	 {
+	  	bit= (p+1 >> j) & 1;
+              
+              
+	  	if(bit==1 && j!=child)
+	  	{   
+                 
+	  	   if(network.node[j].type>1)
+	  	    {
+			   discrete[ds]=j;
+                        //printf("discrete parent=%d\n",j);
+                        k1*=network.node[j].type;
+                        k2*=network.node[j].type;
+     			   ds++;
+	  	    }
+	   	    else
+	  	    {
+			   continuous[cn]=j; 
+                        //printf("continuous parent=%d\n",j);
+			   cn++;
+	  	    }	
+	  	}
+              else if(j!=child)
+              {
+                 alpha*=network.node[j].type;
+              }  
+	 }
+    
+       if(network.nd<=2)
+          alpha=2; 
+
+       i=child;   //i is the node with changes in its parrent nodes 
+         
+       if(network.node[i].type>1 && cn==0)  // no continuous node  //prepare alpha and post alpha and then calculate local score
+	{   
+         
+	   k=k1;
+      	   postalpha=(double *)calloc(network.node[i].type,sizeof(double));
+  
+          label=(char **)malloc(sizeof(char *)*(ds+1)); //label array
+  	   a=(int *)calloc((ds+1),sizeof(int));
+          l_list=(int *)malloc(sizeof(int)*(ds+1));
+
+          for(j=0;j<=ds;j++)
+              label[j]=(char *)malloc(sizeof(char)*100);
+       	   
+          for(j=0;j<ds;j++)
+          {
+               l=discrete[j];
+               l_list[j]=network.node[l].type; 
+              
+          }
+          l_list[ds]=network.node[i].type;
+                   
+          for(j=0;j<k;j++)                
+          {
+ 	     
+	             get_next_seq(a,l_list,ds+1);   // prepare a new combination of labels for parent
+       	      for(i1=0;i1<ds;i1++)
+             		{
+                 		j1=a[i1];
+                 		l=discrete[i1];
+                 		strcpy(label[i1],network.node[l].label[j1]); 
+                     }  
+                     
+             		j1=a[i1];
+                     strcpy(label[i1],network.node[child].label[j1]); 
+                     for(i1=0;i1<network.node[i].type;i1++)
+               		postalpha[i1]=0;
+             		for(i1=0;i1<network.row;i1++)  // search through parents data and count how many number of matches for current label list. prepare post alpha from count+alpha
+             		{
+                     	flag=0;
+                     	for(m=0;m<ds;m++)
+                     	{
+                        		j1=a[m];
+                       		 l=discrete[m];
+                        		if(strcmp(label[m],network.node[l].ddata[i1])!=0)
+                        		{
+                          			flag=1;
+                        		}      
+                     	}  
+                    		j1=a[m];
+                    		if(strcmp(label[m],network.node[child].ddata[i1])!=0)
+                        	{
+                          		flag=1;
+                        	}     
+                   		if(flag==0)
+                   		{
+                        		j1=a[ds];
+                        		postalpha[j1]+=1;
+
+                   		}
+             		}
+             		for(m=0;m<network.node[i].type;m++)
+                     {   
+                             if(postalpha[m]!=0)
+                             {
+  	                        	postalpha[m]+=alpha;
+                                   post_loglik+=lgammafn(postalpha[m])-lgammafn(alpha);
+                             }
+                     } 
+          }
+
+	
+          k=k2;   // repeat the last step of preparing alpha and post alpha for only parent set. this time exclude the child node label from computation. prepare alpha_parent and post_alphaparent
+	   l=discrete[ds-1];       
+	   postalpha_parent=(double *)calloc(network.node[l].type,sizeof(double));
+
+	   for(j=0;j<ds;j++)
+	   {
+	  	    l=discrete[j];
+	      	    l_list[j]=network.node[l].type;
+	           a[j]=0; 
+
+	    }
+           for(j=0;j<k1/k2;j++)
+                 alpha_parent+=alpha; 
+	    for(j=0;j<k;j++)
+	    {
+		    	get_next_seq(a,l_list,ds);
+
+	      		for(i1=0;i1<ds;i1++)
+			{
+		  		j1=a[i1];
+		  		l=discrete[i1];
+		  		strcpy(label[i1],network.node[l].label[j1]);
+                            
+			}
+
+	      		l=discrete[ds-1]; 
+	      		for(i1=0;i1<network.node[l].type;i1++)
+				postalpha_parent[i1]=0;
+             
+			for(i1=0;i1<network.row;i1++)
+			{
+		  		flag=0;
+		  		for(m=0;m<ds;m++)
+		    		{
+		      			j1=a[m];
+		      			l=discrete[m];
+		      			if(strcmp(label[m],network.node[l].ddata[i1])!=0)
+                        		{
+                          			flag=1;
+                        		}
+		    		}
+                    
+		  		if(flag==0)
+		    		{
+		      			j1=a[ds-1];
+		       		postalpha_parent[j1]+=1;
+
+		    		}
+			}
+	      		l=discrete[ds-1];
+	      		for(m=0;m<network.node[l].type;m++)
+			{ 
+                             if(postalpha_parent[m]!=0)
+                              {  
+                                    postalpha_parent[m]+=alpha_parent;
+       	                      post_loglik_parent+=lgammafn(postalpha_parent[m])-lgammafn(alpha_parent);
+                              }
+			}
+	    }
+
+      
+         loglik=post_loglik-post_loglik_parent;
+	  free(postalpha);
+         free(postalpha_parent);
+         for(j=0;j<=ds;j++)
+             free(label[j]);
+	  free(label);
+ 	  free(a);
+ 	  free(l_list);
+
+	}
+       else if(network.node[i].type==1 && ds==0)  // no discrete node  //prepare continuous parameter set
+	{
+           z_count=0;
+           tau_mat=(double **)malloc(sizeof(double *)*(cn+1));
+
+           z_send=(double *)malloc(sizeof(double)*(cn+1)*network.row);
+           tau_send=(double *)malloc(sizeof(double)*(cn+1)*(cn+1));
+  
+	    mu_mat=(double *)malloc(sizeof(double)*(cn+1));
+           nu=nk*2.0;  rho=nk*2.0+cn; 
+           mu_mat[0]=network.node[i].prob[1];
+           for(j=0;j<cn;j++)
+           {
+              mu_mat[j+1]=0;
+              tau_mat[j]=(double *)malloc(sizeof(double)*(cn+1));
+ 
+           } 
+         
+           tau_mat[j]=(double *)malloc(sizeof(double)*(cn+1));
+
+           for(j=0;j<network.row;j++)
+           {
+               z_send[z_count]=1;
+               z_count++;
+               for(j1=0;j1<cn;j1++)
+               {
+                  l=continuous[j1];
+                  z_send[z_count]=network.node[l].cdata[j];   
+                  z_count++;                                            
+               }
+                  
+           }
+           
+             phi=network.node[i].prob[0]*nk;	
+               
+             //preparing tau
+      
+             //**tau_mat
+               for(j=0;j<=cn;j++)
+                     for(m=0;m<=cn;m++)
+                     {
+                      tau_mat[j][m]=1.0;
+                     }
+              
+              for(j=0;j<cn;j++)
+              {
+                 l=continuous[j];
+                 mu_p=network.node[l].prob[1];
+                 phi_p=network.node[l].prob[0]*nk;
+                 phiinv=1/phi_p; 
+                 tau11 = 1/nu + mu_p*phiinv*mu_p;
+                 tau22 = phiinv;
+                 tau12 = -mu_p*phiinv;
+                 div=tau11*tau22-tau12*tau12;
+                 if(j==0) 
+                    tau_mat[0][0]=tau22/div;
+                 tau_mat[0][j+1]=-tau12/div;
+                 tau_mat[j+1][0]=tau_mat[0][j+1];
+                 tau_mat[j+1][j+1]=tau11/div;
+              }
+
+               for(j=0;j<=cn;j++)
+                     for(m=0;m<=cn;m++)
+                     {
+                       if(tau_mat[j][m]==1.0)
+                          { 
+                                tau_mat[j][m]=tau_mat[0][j]*(tau_mat[0][m]/tau_mat[0][0]);
+                               
+                          }
+                       j1=j*(cn+1)+m;
+                       tau_send[j1]=tau_mat[j][m];
+                      
+                     }
+                      
+              loglik=0.0;
+              
+              cn_send=cn+1; 
+              
+              postc(mu_mat,tau_send,&rho,&phi,&loglik,network.node[i].cdata,z_send,&network.row,&cn_send);
+             
+ 	
+ 		free(z_send);
+ 		free(tau_send);
+              for(j=0;j<=cn;j++)
+                 free(tau_mat[j]);
+  		free(tau_mat);
+ 		free(mu_mat);
+ 		    	
+	}
+       else  //hybrid cases
+       {
+              if(cn==0)   //if parents are all discrete and child is continuous
+              { 
+   
+                     ///////////////////prepare y array and run c code////////////////////////////////
+              	loglik_sum=0;
+              	k=k2;
+      	       	y=(double *)calloc(network.row,sizeof(double));
+              	label=(char **)malloc(sizeof(char *)*(ds));  //label array
+  	       	a=(int *)calloc((ds+1),sizeof(int));
+              	l_list=(int *)malloc(sizeof(int)*(ds));
+
+          		for(j=0;j<ds;j++)
+              		label[j]=(char *)malloc(sizeof(char)*100);
+       	   
+          		for(j=0;j<ds;j++)
+          		{
+              		l=discrete[j];
+               		l_list[j]=network.node[l].type; 
+              
+          		}
+
+                   
+          		for(j=0;j<k;j++)                
+              	{
+
+                     	nu=(nk*2.0)/k2;
+	    			tau=nu;
+	    			rho=nu;	
+				mu=network.node[i].prob[1];
+				phi=network.node[i].prob[0]*nu/2;
+				loglik=0.0;
+
+ 	               	get_next_seq(a,l_list,ds);   // prepare a new combination of labels for parent
+       	      		for(i1=0;i1<ds;i1++)
+             			{
+                 			j1=a[i1];
+                 			l=discrete[i1];
+                 			strcpy(label[i1],network.node[l].label[j1]); 
+                     	}  
+             	       	y_count=0; 	
+             			for(i1=0;i1<network.row;i1++)  // search through parents data and count how many number of matches for current label list. prepare post alpha from count+alpha
+             			{
+                     		flag=0;
+                     		for(m=0;m<ds;m++)
+                     		{
+                        		
+                       			l=discrete[m];
+                        			if(strcmp(label[m],network.node[l].ddata[i1])!=0)
+                        			{
+                          				flag=1;
+                        			}      
+                     		}  
+                    		     
+                   			if(flag==0)
+                   			{
+                        			y[y_count]=network.node[i].cdata[i1];
+                        			y_count++;
+             
+                   			}
+             			}
+          
+             			postc0(&mu,&tau,&rho,&phi,&loglik,y,&y_count);
+                     	loglik_sum+=loglik;
+          
+
+              	}
+
+              	loglik=loglik_sum;
+                      
+                     free(y);
+                     for(j=0;j<ds;j++)
+                         free(label[j]);
+			free(label);
+			free(a);
+			free(l_list);
+          
+ 
+              }//end of continuous node discrete parent check
+              else //all the other hybrid cases when parents are both continuous and discrete 
+              {
+                     
+                   
+          	      tau_mat=(double **)malloc(sizeof(double *)*(cn+1));
+		      z_send=(double *)malloc(sizeof(double)*(cn+1)*network.row);
+         	      tau_send=(double *)malloc(sizeof(double)*(cn+1)*(cn+1));
+	    	      mu_mat=(double *)malloc(sizeof(double)*(cn+1));
+           	      
+           	       for(j=0;j<cn;j++)
+           		{
+              	   tau_mat[j]=(double *)malloc(sizeof(double)*(cn+1));
+ 	              } 
+         
+      		       
+           		tau_mat[j]=(double *)malloc(sizeof(double)*(cn+1));          
+
+                     ///////////////////prepare parameters  and run c code////////////////////////////////
+              	loglik_sum=0.0;
+              	k=k2;
+      	       	y=(double *)calloc(network.row,sizeof(double));
+              	label=(char **)malloc(sizeof(char *)*(ds));  //label array
+  	       	a=(int *)calloc((ds+1),sizeof(int));
+              	l_list=(int *)malloc(sizeof(int)*(ds));
+
+          		for(j=0;j<ds;j++)
+              		label[j]=(char *)malloc(sizeof(char)*100);
+       	   
+          		for(j=0;j<ds;j++)
+          		{
+              		l=discrete[j];
+               		l_list[j]=network.node[l].type; 
+              
+          		}
+
+                   
+          		for(jj=0;jj<k;jj++)                
+              	{
+
+                     	nu=(nk*2.0)/k2;
+	      			rho=nu+cn;	
+				mu_mat[0]=network.node[i].prob[1];
+
+                            for(j1=0;j1<cn;j1++)
+           		            mu_mat[j1+1]=0;
+
+				phi=network.node[i].prob[0]*nu/2;
+	                    //preparing tau
+                   		//**tau_mat
+             			for(j=0;j<=cn;j++)
+                               for(m=0;m<=cn;m++)
+                               {
+                   			   tau_mat[j][m]=1.0;
+                     	    }
+             
+              		for(j=0;j<cn;j++)
+              		{
+                 			l=continuous[j];
+                 			mu_p=network.node[l].prob[1];
+                 			phi_p=network.node[l].prob[0]*(nk/k2);
+                
+                 			phiinv=1/phi_p; 
+                 			tau11 = 1/nu + mu_p*phiinv*mu_p;
+                 			tau22 = phiinv;
+                 			tau12 = -mu_p*phiinv;
+                 			div=tau11*tau22-tau12*tau12;
+                 			if(j==0) 
+                  			    tau_mat[0][0]=tau22/div;
+                 
+			              tau_mat[0][j+1]=-tau12/div;
+                 			tau_mat[j+1][0]=tau_mat[0][j+1];
+                 			tau_mat[j+1][j+1]=tau11/div;
+       
+                
+              		}
+               		for(j=0;j<=cn;j++)
+                    			 for(m=0;m<=cn;m++)
+                    			 {
+			                       if(tau_mat[j][m]==1.0)
+                       		         { 
+			                            tau_mat[j][m]=tau_mat[0][j]*(tau_mat[0][m]/tau_mat[0][0]);
+                              		  }
+
+                       			j1=j*(cn+1)+m;
+                       			tau_send[j1]=tau_mat[j][m];
+                                           
+                     		   //printf("%.2lf\t",tau_mat[j][m]);
+                                    }
+                                    //printf("\n");
+              	       loglik=0.0;
+              
+  	      
+             		       cn_send=cn+1; 
+
+ 	               	
+                            get_next_seq(a,l_list,ds);   // prepare a new combination of labels for parent
+       	      		for(i1=0;i1<ds;i1++)
+             			{
+                 			j1=a[i1];
+                 			l=discrete[i1];
+                 			strcpy(label[i1],network.node[l].label[j1]); 
+                     	}  
+             	       	y_count=0;
+                            z_count=0; 	
+             			for(i1=0;i1<network.row;i1++)  // search through parents data and count how many number of matches for current label list. prepare post alpha from count+alpha
+             			{
+                     		flag=0;
+                     		for(m=0;m<ds;m++)
+                     		{
+                        		
+                       			l=discrete[m];
+                        			if(strcmp(label[m],network.node[l].ddata[i1])!=0)
+                        			{
+                          				flag=1;
+                        			}      
+                     		}  
+                    		     
+                   			if(flag==0)
+                   			{
+                        			y[y_count]=network.node[i].cdata[i1];
+
+                                          //prepare z send matrix
+                                          z_send[z_count]=1;
+                                          z_count++;
+                                          for(j1=0;j1<cn;j1++)
+                                          {
+                 			          l=continuous[j1];
+                 			          z_send[z_count]=network.node[l].cdata[i1];   
+                                             z_count++;                                            
+                                          }
+                        			y_count++;
+                   			}
+             			}
+          
+                            postc(mu_mat,tau_send,&rho,&phi,&loglik,y,z_send,&y_count,&cn_send);
+ 
+                     	loglik_sum+=loglik;
+          
+
+              	}
+
+              	loglik=loglik_sum;
+                        
+                     free(y);
+ 			//free(z);
+ 			free(z_send);
+ 			free(tau_send);
+                     for(j=0;j<=cn;j++)
+                        free(tau_mat[j]);
+          	       free(tau_mat);
+ 			free(mu_mat);
+                     for(j=0;j<ds;j++)
+                         free(label[j]);  
+ 			free(label);
+ 			free(a);
+ 			free(l_list);       
+
+              }//end of else part for hybrid when parents are mixed       
+
+       }//end of else part for hybrid
+       
+ free(continuous);
+ free(discrete); 
+ return loglik;
+
+	
+}
+
+void get_next_seq(int *a,int *l,int size)
+{
+  int j,idx;
+  idx=size-1;
+  a[idx]+=1;
+  if(a[idx]==l[idx])
+  {
+      a[idx]=0;
+      for(j=idx-1;j>=0;j--){
+        a[j]+=1;
+        if(a[j]==l[j])
+           a[j]=0;
+        else
+            break;
+      }
+  }
+}
+
+
diff --git a/var_lib_genenet_bnw/localscore/postc0.c b/var_lib_genenet_bnw/localscore/postc0.c
new file mode 100644
index 00000000..16e9ccec
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/postc0.c
@@ -0,0 +1,81 @@
+/*                               -*- Mode: C -*- 
+ * postc0.c --- Posterior for continuous node with 0 parents
+ * Author          : Claus Dethlefsen
+ * Created On      : Tue Mar 12 06:44:35 2002
+ * Last Modified By: Claus Dethlefsen
+ * Last Modified On: Wed Jun 04 11:57:10 2003
+ * Update Count    : 55
+ * Status          : Unknown, Use with caution!
+ */
+
+/*
+  ##
+##    Copyright (C) 2002  Susanne Gammelgaard Bøttcher, Claus Dethlefsen
+##
+##    This program is free software; you can redistribute it and/or modify
+##    it under the terms of the GNU General Public License as published by
+##    the Free Software Foundation; either version 2 of the License, or
+##    (at your option) any later version.
+##
+##    This program is distributed in the hope that it will be useful,
+##    but WITHOUT ANY WARRANTY; without even the implied warranty of
+##    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+##    GNU General Public License for more details.
+##
+##    You should have received a copy of the GNU General Public License
+##    along with this program; if not, write to the Free Software
+##    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+######################################################################
+*/
+
+#include "R.h"
+#include "Rmath.h"
+
+
+void postc0(double *mu, double *tau, double *rho, double *phi, double
+	    *loglik, double *y, int *n)
+{
+	int i;
+	double logscale,logk,mscore;
+	double oldtau,oldmu;
+
+/*	Rprintf("her er mu=%f\n",*mu);
+	Rprintf("her er tau=%f\n",*tau);
+	Rprintf("her er rho=%f\n",*rho);
+	Rprintf("her er phi=%f\n",*phi);
+	Rprintf("her er loglik=%f\n",*loglik);
+*/
+
+	for(i = 0; i < *n; i++) {
+		
+		logscale = log(*phi)+log1p(1.0/(*tau));
+		logk = lgammafn( 0.5*(1.0+*rho) ) - lgammafn(*rho*0.5);
+		logk -= 0.5*(logscale + log(M_PI));
+		mscore = logk - 0.5*(*rho+1.0)*log1p( (y[i]-*mu)*(y[i]-*mu)/exp(logscale));
+		*loglik += mscore;
+
+		oldtau = *tau;
+		oldmu  = *mu;
+
+		(*tau)++;
+		(*rho)++;
+/*	Rprintf("her er oldmu=%f\n",oldmu);
+	Rprintf("her er oldtau=%f\n",oldtau);
+	Rprintf("her er mu=%f\n",*mu);
+	Rprintf("her er tau=%f\n",*tau);
+*/
+		*mu = (oldtau*(*mu)+y[i])/(*tau);
+		*phi+= (y[i]-(*mu))*y[i] + (oldmu-(*mu))*oldtau*oldmu;
+/*		Rprintf("logscale=%f\n",logscale);
+		Rprintf("logk=%f\n",logk);
+		Rprintf("mscore=%f\n",mscore);
+		Rprintf("loglik=%f\n",*loglik);
+		
+	Rprintf("her er mu=%f\n",*mu);
+	Rprintf("her er tau=%f\n",*tau);
+	Rprintf("her er rho=%f\n",*rho);
+	Rprintf("her er phi=%f\n",*phi);
+	Rprintf("her er loglik=%f\n",*loglik);
+*/
+	}
+}
diff --git a/var_lib_genenet_bnw/localscore/rlocale.h b/var_lib_genenet_bnw/localscore/rlocale.h
new file mode 100644
index 00000000..ac08f341
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/rlocale.h
@@ -0,0 +1,118 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2005-12   The R Core Team
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation; either version 2 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+
+/*  This file was contributed by Ei-ji Nakama.
+ *  See also the comments in src/main/rlocale.c.
+
+ * For use in R only. 
+ */
+
+#ifndef R_LOCALE_H
+#define R_LOCALE_H
+
+#ifndef NO_C_HEADERS
+#include <wchar.h>
+#include <ctype.h>
+#include <wctype.h>
+#endif
+
+#ifdef  __cplusplus
+extern "C" {
+#endif
+
+extern const char *locale2charset(const char *);
+
+/*
+ * Windows CJK
+ * In Unicode, there is not a rule about character width. 
+ * A letter of breadth is used in a CJK (China, Japan, Korea,
+ * Taiwan, Hong Kong, and Singapore) area, and there are a
+ * letter and a standard (character width is not still prescribed)
+ * of a cord in a country.
+ * Letter width is a problem of a font, but it is a rule route
+ * besides a alphanumeric character that use a breadth letter.
+ * It is generally defined as a breadth letter for a font such
+ * as Japanese.
+ * - Win32
+
+ *  Attempted explanation by BDR
+ *  The display widths of characters are not prescribed in Unicode.
+ *  Double-width characters are used in the CJK area: their width can
+ *  be font-specific, with different fonts in use in different parts
+ *  of the CJK area.  The tables supplied in many OSes and by Marcus
+ *  Kuhn are not do not take the exact locale into account.  The
+ *  tables supplied in rlocale_data.h allow different widths for
+ *  different parts of the CJK area, and also where needed different
+ *  widths on Windows.  (The Windows differences are in zh_CN, and
+ *  apply to European characters.)
+ *
+ */
+extern int Ri18n_wcwidth(wchar_t);
+extern int Ri18n_wcswidth (const wchar_t *, size_t);
+
+/* Mac OSX CJK and WindowXP(Japanese)
+ * iswctypes of MacOSX calls isctypes. no i18n.
+ * For example, iswprint of Windows does not accept a macron of
+ * Japanese "a-ru" of R as a letter. 
+ * Therefore Japanese "Buraian.Ripuri-" of "Brian Ripley" is
+ * shown of hex-string.:-)
+ * We define alternatives to be used if
+ * defined(Win32) || defined(__APPLE_CC__) || defined(_AIX)
+ */
+extern wctype_t Ri18n_wctype(const char *);
+extern int      Ri18n_iswctype(wint_t, wctype_t);
+
+#ifndef IN_RLOCALE_C
+/* We want to avoid these redefinitions in rlocale.c itself */
+#undef iswupper
+#undef iswlower
+#undef iswalpha
+#undef iswdigit
+#undef iswxdigit
+#undef iswspace
+#undef iswprint
+#undef iswgraph
+#undef iswblank
+#undef iswcntrl
+#undef iswpunct
+#undef iswalnum
+#undef wctype
+#undef iswctype
+
+#define iswupper(__x)     Ri18n_iswctype(__x, Ri18n_wctype("upper"))
+#define iswlower(__x)     Ri18n_iswctype(__x, Ri18n_wctype("lower"))
+#define iswalpha(__x)     Ri18n_iswctype(__x, Ri18n_wctype("alpha"))
+#define iswdigit(__x)     Ri18n_iswctype(__x, Ri18n_wctype("digit"))
+#define iswxdigit(__x)    Ri18n_iswctype(__x, Ri18n_wctype("xdigit"))
+#define iswspace(__x)     Ri18n_iswctype(__x, Ri18n_wctype("space"))
+#define iswprint(__x)     Ri18n_iswctype(__x, Ri18n_wctype("print"))
+#define iswgraph(__x)     Ri18n_iswctype(__x, Ri18n_wctype("graph"))
+#define iswblank(__x)     Ri18n_iswctype(__x, Ri18n_wctype("blank"))
+#define iswcntrl(__x)     Ri18n_iswctype(__x, Ri18n_wctype("cntrl"))
+#define iswpunct(__x)     Ri18n_iswctype(__x, Ri18n_wctype("punct"))
+#define iswalnum(__x)     Ri18n_iswctype(__x, Ri18n_wctype("alnum"))
+#define wctype(__x)       Ri18n_wctype(__x)
+#define iswctype(__x,__y) Ri18n_iswctype(__x,__y)
+#endif
+
+#ifdef  __cplusplus
+}
+#endif
+#endif /* R_LOCALE_H */
diff --git a/var_lib_genenet_bnw/localscore/stats_package.h b/var_lib_genenet_bnw/localscore/stats_package.h
new file mode 100644
index 00000000..3717c482
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/stats_package.h
@@ -0,0 +1,71 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2007  The R Core Team.
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+#ifndef R_STATS_PACKAGE_H
+#define R_STATS_PACKAGE_H
+#include <Rconfig.h>
+
+#ifdef HAVE_VISIBILITY_ATTRIBUTE
+# define attribute_hidden __attribute__ ((visibility ("hidden")))
+#else
+# define attribute_hidden
+#endif
+
+enum AlgType {NREG = 1, OPT = 2};
+				/* 0-based indices into v */
+enum  VPos {F = 9, F0 = 12, FDIF = 10, G = 27, HC = 70};
+				/* 0-based indices into iv */
+enum IVPos {AI = 90, AM = 94, ALGSAV = 50, COVMAT = 25,
+	    COVPRT = 13, COVREQ = 14, DRADPR = 100,
+	    DTYPE = 15, IERR = 74, INITH = 24, INITS = 24,
+	    IPIVOT = 75, IVNEED =  2, LASTIV = 42, LASTV = 44,
+	    LMAT =  41, MXFCAL = 16, MXITER = 17, NEXTV  = 46,
+	    NFCALL =  5, NFCOV = 51, NFGCAL = 6, NGCOV = 52,
+	    NITER = 30, NVDFLT = 49, NVSAVE = 8, OUTLEV = 18,
+	    PARPRT = 19, PARSAV = 48, PERM = 57, PRUNIT = 20,
+	    QRTYP = 79, RDREQ = 56, RMAT = 77, SOLPRT = 21,
+	    STATPR = 22, TOOBIG = 1, VNEED = 3, VSAVE = 59,
+	    X0PRT = 23};
+
+void attribute_hidden
+S_Rf_divset(int alg, int iv[], int liv, int lv, double v[]);
+
+void attribute_hidden
+S_nlsb_iterate(double b[], double d[], double dr[], int iv[],
+	       int liv, int lv, int n, int nd, int p,
+	       double r[], double rd[], double v[], double x[]);
+
+void attribute_hidden
+S_nlminb_iterate(double b[], double d[], double fx, double g[],
+		 double h[], int iv[], int liv, int lv, int n,
+		 double v[], double x[]);
+
+static R_INLINE int S_v_length(int alg, int n)
+{
+    return (alg - 1) ? (105 + (n * (2 * n + 20))) :
+	(130 + (n * (n + 27))/2);
+}
+
+static R_INLINE int S_iv_length(int alg, int n)
+{
+    return (alg - 1) ? (82 + 4 * n) : (78 + 3 * n);
+}
+
+#endif /* R_STATS_PACKAGE_H */
+
diff --git a/var_lib_genenet_bnw/localscore/stats_stubs.h b/var_lib_genenet_bnw/localscore/stats_stubs.h
new file mode 100644
index 00000000..bc46821e
--- /dev/null
+++ b/var_lib_genenet_bnw/localscore/stats_stubs.h
@@ -0,0 +1,68 @@
+/*
+ *  R : A Computer Language for Statistical Data Analysis
+ *  Copyright (C) 2007  The R Core Team.
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as published by
+ *  the Free Software Foundation; either version 2.1 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License
+ *  along with this program; if not, a copy is available at
+ *  http://www.r-project.org/Licenses/
+ */
+
+#include <Rconfig.h>
+#include <Rinternals.h>
+#include <R_ext/Rdynload.h>
+
+#ifdef HAVE_VISIBILITY_ATTRIBUTE
+# define attribute_hidden __attribute__ ((visibility ("hidden")))
+#else
+# define attribute_hidden
+#endif
+
+void attribute_hidden
+S_Rf_divset(int alg, int iv[], int liv, int lv, double v[])
+{
+    static void(*fun)(int,int[],int,int,double[]) = NULL;
+    if (fun == NULL)
+	fun = (void(*)(int,int[],int,int,double[]))
+	    R_GetCCallable("stats", "Rf_divset");
+    fun(alg, iv, liv, lv, v);
+}
+
+void attribute_hidden
+S_nlminb_iterate(double b[], double d[], double fx, double g[], double h[],
+		 int iv[], int liv, int lv, int n, double v[], double x[])
+{
+    static void(*fun)(double[],double[],double,double[],double[],
+		      int[],int,int,int,double[],double[]) = NULL;
+    if (fun == NULL)
+	fun = (void(*)(double[],double[],double,double[],double[],
+			  int[],int,int,int,double[],double[]))
+	    R_GetCCallable("stats", "nlminb_iterate");
+    fun(b, d, fx, g, h, iv, liv, lv, n, v, x);
+}
+
+void attribute_hidden
+S_nlsb_iterate(double b[], double d[], double dr[], int iv[], int liv,
+	       int lv, int n, int nd, int p, double r[], double rd[],
+	       double v[], double x[])
+{
+    static void(*fun)(double[],double[],double[],int[],int,int,
+		      int,int,int,double[],double[],double[],
+		      double[]) = NULL;
+    if (fun == NULL)
+	fun = (void(*)(double[],double[],double[],int[],int,
+		       int, int,int,int,double[],
+		       double[],double[],double[]))
+	    R_GetCCallable("stats", "nlsb_iterate");
+    fun(b, d, dr, iv, liv, lv, n, nd, p, r, rd, v, x);
+}
+
diff --git a/var_lib_genenet_bnw/network_score b/var_lib_genenet_bnw/network_score
new file mode 100644
index 00000000..bd062e72
--- /dev/null
+++ b/var_lib_genenet_bnw/network_score
Binary files differdiff --git a/var_lib_genenet_bnw/print_structure/structure.c b/var_lib_genenet_bnw/print_structure/structure.c
new file mode 100644
index 00000000..0b490324
--- /dev/null
+++ b/var_lib_genenet_bnw/print_structure/structure.c
@@ -0,0 +1,86 @@
+#include<stdio.h>
+#include<stdlib.h>
+#include<string.h>
+#include<math.h>
+
+struct st{
+char *name;	
+double *data;	
+}*st_tab;
+
+main(int argc,char *argv[])
+{
+FILE *fp1,*fp2,*fp3;
+char line[2500];
+int i,j,rd;
+double d,row;
+double thr=atof(argv[5]);
+
+fp1=fopen(argv[2],"r");
+fp2=fopen(argv[3],"w");
+
+fp3=fopen(argv[4],"w");
+
+
+row=0.0;
+while(fgets(line,2500,fp1)!=NULL)
+   row++;
+
+rd=(int)sqrt(row);
+
+printf("%d\n",rd);
+
+fclose(fp1);
+fp1=fopen(argv[1],"r");
+
+st_tab=(struct st *)malloc(sizeof(struct st)*rd);
+
+for(i=0;i<rd;i++)
+{
+   fscanf(fp1,"%s",line);	
+   st_tab[i].name=(char *)malloc(sizeof(char)*(sizeof(line)+1));
+   strcpy(st_tab[i].name,line);
+   st_tab[i].data=(double *)calloc(rd,sizeof(double));
+}
+
+fclose(fp1);
+fp1=fopen(argv[2],"r");
+
+for(i=0;i<rd;i++)
+{
+    for(j=0;j<rd;j++)
+    {
+          fscanf(fp1,"%s",line);
+	   fscanf(fp1,"%s",line);
+	   fscanf(fp1,"%s",line);		
+   	   fscanf(fp1,"%lf",&d);
+          st_tab[i].data[j]=d;
+    
+    }
+}
+
+
+
+for(i=0;i<rd;i++)
+{ 
+    fprintf(fp2,"%s\t",st_tab[i].name);
+    fprintf(fp3,"%s\t",st_tab[i].name);
+}
+fprintf(fp2,"\n");
+fprintf(fp3,"\n");
+
+for(i=0;i<rd;i++)
+{ 
+    for(j=0;j<rd;j++)
+    {
+   	   fprintf(fp2,"%lf\t",st_tab[j].data[i]);
+          if(st_tab[j].data[i]>thr)	
+   	     fprintf(fp3,"1\t");
+          else 	
+   	     fprintf(fp3,"0\t");
+    }
+    fprintf(fp2,"\n");
+    fprintf(fp3,"\n");
+}
+
+}
diff --git a/var_lib_genenet_bnw/run.sh b/var_lib_genenet_bnw/run.sh
new file mode 100644
index 00000000..d7389dad
--- /dev/null
+++ b/var_lib_genenet_bnw/run.sh
@@ -0,0 +1,58 @@
+#!/bin/bash
+d=`dirname $0`
+#Name of the data directory
+data=$1
+
+DIR="$d/$data/tmp"
+DIR_1="$d/$data/tmp/"
+
+mkdir -p $DIR
+#Arguments. User can modify these arguments.
+
+#Input data file name.
+input="$d/$data/input.txt"
+
+#Input banlist file
+ban="$d/$data/banlist.txt"
+
+#Input whitelist file
+white="$d/$data/whitelist.txt"
+
+#Max parents. We set the number of maximum parents to 4 
+maxparent=4
+
+#k is the numbeer of structure considered in each step of k-best structure learning algorithm. We set the value of k=100
+k=100
+
+#Model averaging threshold. We set the model averaging threshold to 0.5
+THR=0.5
+
+
+echo "Dataset with number of variables:"
+head -1 $input|wc -w
+echo "Dataset with number of samples:"
+wc -l $input|cut -d' ' -f1
+echo "Parameters are: max parent = $maxparent, k= $k and model averaging threshold = $THR"
+
+start_time1=`date +%s`
+#execute local score
+./network_score $input $ban $white $maxparent $DIR
+end_time=`date +%s`
+echo "Local score execution time was `expr $end_time - $start_time1` s."
+
+start_time=`date +%s`
+#execute k-best structure learning
+sh $d/k-best/src/data2netk_poster.sh $input $DIR $k $maxparent
+
+end_time=`date +%s`
+echo "k-best parent total execution time was `expr $end_time - $start_time` s."
+
+start_time=`date +%s`
+#execute print structure
+./structure $input $DIR/postProbEachEdge.txt $d/$data/model_averaging_probabilities.txt $d/$data/model_structure.txt $THR
+
+end_time1=`date +%s`
+echo "Preparing structure output file from model averaging matrix. Execution time was `expr $end_time1 - $start_time` s."
+echo "Total execution time was `expr $end_time1 - $start_time1` s."
+rm -r $DIR_1*
+rmdir $DIR
diff --git a/var_lib_genenet_bnw/structure b/var_lib_genenet_bnw/structure
new file mode 100644
index 00000000..b8680416
--- /dev/null
+++ b/var_lib_genenet_bnw/structure
Binary files differ