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Very first version. Updating for efficiency and handling increased complexity to be done.

Calculator.cpp

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+// GAGS  
+// Developed by Andrew R Wood
+// [email protected]
+
+#include "Calculator.h"
+#include <math.h>
+#include <vector>
+#include <cmath>
+
+using namespace std;
+
+
+double CalcVariance(vector<double>& v) {
+    double s;
+    double m;
+    int    i;
+    s=0;
+    for (i=0;i<v.size();++i) {
+        s+=v[i];
+    }
+    m=s/(double) v.size();
+    s=0;
+    for (i=0;i<v.size();++i) {
+        s+=(v[i]-m)*(v[i]-m);
+    }
+    return (s/(v.size()-1)) ;
+}
+
+
+double CalcMean(vector<double>& v) {
+    double s;
+    s=0;
+    for (int i=0;i<v.size();++i) {
+        s+=v[i];
+    }
+    return s/v.size();
+}
+
+
+double CalcSum(vector<double>& v) {
+    double s;
+    s=0;
+    for (int i=0;i<v.size();++i) {
+        s+=v[i];
+    }
+    return s;
+}
+
+
+bool doubleEqual(double l, double r, double e) {
+    return (fabs(l-r)<e);
+}
+
+
+bool doubleLess(double l, double r, double e, bool orequal) {
+    if (fabs(l-r)<e) {
+        // within epsilon so considered equal
+        return orequal;
+    }
+    return (l<r);
+}
+
+
+bool doubleGreater(double l, double r, double e, bool orequal) {
+    if (fabs(l-r)<e) {
+       	// within epsilon so considered equal
+       	return orequal;
+    }
+    return (l>r);
+}

Calculator.h

@@ -0,0 +1,13 @@
+#ifndef __CALCULATOR__
+#define __CALCULATOR__
+
+#include <vector>
+#include <string>
+
+double CalcVariance(std::vector<double>&);
+double CalcMean(std::vector<double>&);
+bool   doubleEqual(double, double, double);
+bool   doubleLess(double, double, double, bool);
+bool   doubleGreater(double, double, double, bool);
+
+#endif

ExclusionListProcessor.cpp

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+// GAGS
+// Developed by Andrew R Wood
+// [email protected]
+
+#include "ExclusionListProcessor.h"
+#include <iostream>
+#include <fstream>
+#include <stdlib.h>
+
+using namespace std;
+
+void ReadExclusionsFile(string f, map<string, int>& m) {
+    string line, id;
+    ifstream inFile(f.c_str());
+    if (inFile.is_open()) {
+        while (inFile.good()) {
+            getline (inFile, line);
+            if (!line.empty()) {
+                m[line] = 0;
+            }
+        }
+        inFile.close();
+    }
+    else {
+        cout << "Unable to open " << f << " for reading" << endl;
+        exit(EXIT_FAILURE);
+    }
+}

ExclusionListProcessor.h

@@ -0,0 +1,9 @@
+#ifndef __ExclusionListProcessor__
+#define __ExclusionListProcessor__
+
+#include <string>
+#include <map>
+
+void ReadExclusionsFile(std::string, std::map<std::string, int>&);
+
+#endif 

FileWriter.cpp

@@ -0,0 +1,73 @@
+// GAGS
+// Developed by Andrew R Wood
+// [email protected]
+
+#include "FileWriter.h"
+#include <iostream>
+#include <fstream>
+#include <stdlib.h>
+
+using namespace std;
+
+void OutputSolution(vector<string>& s, map<string,double>& m, vector<int>& n, string& o, int& g) {
+    ofstream outFile;
+    outFile.open(o.c_str(), ios_base::out);
+    if (outFile.is_open()) {
+        int index  = 0;
+        //int group  = 0;
+        int offset = 0;
+        outFile << "Group\tID\tPhenotype\n";   
+        for (int i = 0; i < n.size(); ++i) {
+            //group++;
+            while (index < n[i] + offset) {
+                outFile << g << "\t" << s[index] << "\t" << m[s[index]] << endl;
+                index++;
+            }
+            offset = offset + index;
+            g++;
+        }
+        outFile.close();
+    }
+    else {
+        cout << "Can not open " << o << " for writing" << endl;
+        exit(EXIT_FAILURE);
+    }
+}
+
+void OutputIndependentSolution(vector<string>& s, map<string,double>& m, vector<int>& n, string& o, int& g) {
+
+    ofstream outFile;
+
+    if (g == 1) {
+        outFile.open(o.c_str(), ios_base::out);
+        if (outFile.is_open()) {
+            outFile << "Group\tID\tPhenotype\n";   
+            for (int i = 0; i < n.size(); ++i) {
+                for (int j = 0; j < n[i]; ++j) {
+                    outFile << g << "\t" << s[j] << "\t" << m[s[j]] << endl;
+                }
+            }
+            outFile.close();
+        }
+        else {
+            cout << "Can not open " << o << " for writing" << endl;
+            exit(EXIT_FAILURE);
+        }
+    }
+    else {
+        outFile.open(o.c_str(), ios_base::app);
+        if (outFile.is_open()) {
+            for (int i = 0; i < n.size(); ++i) {
+                for (int j = 0; j < n[i]; ++j) {
+                    outFile << g << "\t" << s[j] << "\t" << m[s[j]] << endl;
+                }
+            }
+            outFile.close();
+        }
+        else {
+            cout << "Can not open " << o << " for appending" << endl;
+            exit(EXIT_FAILURE);
+        }
+    }
+}
+

FileWriter.h

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+#ifndef __FILEWRITER__
+#define __FILEWRITER__
+
+#include <string>
+#include <vector>
+#include <map>
+
+void OutputSolution(std::vector<std::string>&, std::map<std::string, double>&, std::vector<int>&, std::string&, int&);
+void OutputIndependentSolution(std::vector<std::string>&, std::map<std::string, double>&, std::vector<int>&, std::string&, int&);
+
+#endif