Added "stats" to the project

src/stats/stats.cpp

@@ -0,0 +1,312 @@
+#include <iostream>
+#include <fstream>
+#include <iomanip>
+#include <vector>
+#include <map>
+#include <algorithm>
+#include <math.h>
+
+using namespace std;
+
+// define our program name
+#define PROGRAM_NAME "stats"
+
+// define our parameter checking macro
+#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen)) == 0) && (actualLen == paramLen)
+
+// function declarations
+void ShowHelp(void);
+bool isLineNumeric(string);
+
+int main(int argc, char* argv[]) {
+
+	// our configuration variables
+	bool showHelp = false;
+
+	bool isFile = false;
+	string inFile;
+
+	bool doAll = true;
+	bool doMean = true;
+	bool doGeoMean = false;
+	bool doMode = false;
+	bool doMedian = false;
+	bool doMin = false;
+	bool doMax = false;
+	bool doVariance = false;
+	bool doStdDev = false;
+
+	//###############################################
+	// Parse command line.
+	//###############################################
+
+	for(int i = 1; i < argc; i++) {
+		int parameterLength = (int)strlen(argv[i]);
+		if(PARAMETER_CHECK("-h", 2, parameterLength) || PARAMETER_CHECK("--help", 5, parameterLength)) {
+			showHelp = true;
+		}
+	}
+	if(showHelp) ShowHelp();
+
+	// do some parsing (all of these parameters require 1 string---the are booleans)
+	for(int i = 1; i < argc; i++) {
+
+		int parameterLength = (int)strlen(argv[i]);
+		string parameter = argv[i];
+
+		if(PARAMETER_CHECK("-a", 2, parameterLength)) {
+			doAll = true;
+		} 
+		else if(PARAMETER_CHECK("-mu", 3, parameterLength)) {
+			doMean = true;
+			doAll = false;
+		} 
+		else if(PARAMETER_CHECK("-gm", 3, parameterLength)) {
+			doGeoMean = true;
+			doAll = false;
+		} 
+		else if(PARAMETER_CHECK("-med", 4, parameterLength)) {
+			doMedian = true;
+			doAll = false;			
+		} 
+		else if(PARAMETER_CHECK("-mod", 4, parameterLength)) {
+			doMode = true;
+			doAll = false;			
+		}  
+		else if(PARAMETER_CHECK("-var", 4, parameterLength)) {
+			doVariance = true;
+			doAll = false;			
+		}
+		else if(PARAMETER_CHECK("-std", 4, parameterLength)) {
+			doStdDev = true;
+			doAll = false;			
+		}		
+		else if(PARAMETER_CHECK("-min", 4, parameterLength)) {
+			doMin = true;
+			doAll = false;			
+		}
+		else if(PARAMETER_CHECK("-max", 4, parameterLength)) {
+			doMax = true;
+			doAll = false;			
+		}
+		else if((parameterLength > 0) && (parameter[0] != '-')) {
+			isFile = true;
+			inFile = parameter;
+		}
+		else {
+			cout << "ERROR: Unrecognized parameter: " << argv[i] << endl;
+			showHelp = true;
+			exit(1);
+		}		
+	}
+
+	//###############################################
+	// Main processing.
+	//###############################################
+	string line;
+	double dLine;
+	double sumOfLines = 0.0;
+	double natLogSumOfLines = 0.0;
+	double mean = 0.0;
+	double geoMean = 0.0;
+	double median = 0.0;
+	double mode;
+	double min, max;
+	double variance;
+	double stddev;
+	long totalLines = 0;
+	bool zeroFound = false;
+
+	vector<double> linesVector;
+	map<double,int> linesMap;
+
+	if (isFile) {
+		ifstream inF(inFile.c_str(), ios::in);
+
+		// ensure that the file can be opened
+		if ( !inF ) {
+			cerr << "Error: The requested input file (" << inFile << ") could not be opened.  Exiting!" << endl;
+			exit (1);
+		}
+		while (getline(inF,line)) {
+
+			// increment the count of lines processed
+			totalLines++;	
+
+			if(line.empty()) continue;
+
+			// TO DO: make sure the current line is numeric.  If not, write an error message and quit.
+			dLine = atof(line.c_str());
+
+			// increment the count of lines processed
+			totalLines++;
+
+			// add to the total sum of the lines
+			sumOfLines += dLine; 
+
+			// add to the sum of natural logs.  used for geometric mean
+			natLogSumOfLines += log(dLine);
+
+			// flag if we found a zero.  This prevents a geometric mean from being calculated.
+			if (dLine == 0) zeroFound = true;
+
+			// add the line to the vector and map
+			linesVector.push_back(dLine);
+			linesMap[dLine]++;
+		}
+		cout << "stats from: " << inFile << endl << endl;
+	}
+	else {
+		while (getline(cin,line)) {
+
+			// increment the count of lines processed
+			totalLines++;
+
+			if(line.empty()) continue;
+
+
+			// TO DO: make sure the current line is numeric.  If not, write an error message and quit.
+			dLine = atof(line.c_str());
+
+			// add to the total sum of the lines
+			sumOfLines += dLine; 
+
+			// add to the sum of natural logs.  used for geometric mean
+			natLogSumOfLines += log(dLine);
+
+			// flag if we found a zero.  This prevents a geometric mean from being calculated.
+			if (dLine == 0) zeroFound = true;
+
+			// add the line to the vector and map
+			linesVector.push_back(dLine);
+			linesMap[dLine]++;
+		}
+		cout << "stats from: stdin" << endl << endl;
+	}
+
+	//###############################################
+	// Report the results.
+	//###############################################
+	cout << "Total lines:\t\t" << setprecision (15) << totalLines << endl;
+	cout << "Sum of lines:\t\t" << setprecision (15) << sumOfLines << endl; 
+
+	if (doMean || doAll) {
+		// compute the mean
+		mean = sumOfLines / totalLines;
+		cout << "Ari. Mean:\t\t" << setprecision (15) << mean << endl; 
+	}	
+	if (doGeoMean || doAll) {
+		// compute the mean
+		if (!zeroFound) {
+			geoMean = exp(natLogSumOfLines / totalLines);
+			cout << "Geo. Mean:\t\t" << setprecision (15) << geoMean << endl; 
+		}
+		else {
+			cout << "Geo. Mean:\t\t" << "undef (zero found in data)"<< endl; 
+		}
+	}		
+	if (doMedian || doAll) {
+		//sort the vector of values in ascending order.  We will then pick the "middle element"
+		sort(linesVector.begin(), linesVector.end());
+
+		if ((totalLines % 2) > 0) {
+			long mid;
+			mid = totalLines / 2;
+			median = linesVector[mid];
+		}
+		else {
+			long midLow;
+			long midHigh;
+
+			midLow = (totalLines / 2) - 1;
+			midHigh = (totalLines / 2);
+
+			median = (linesVector[midLow] + linesVector[midHigh]) / 2.0;
+		}
+		cout << "Median:\t\t\t" << setprecision (15) << median << endl;
+	}
+	if (doMode || doAll) {
+		// get the mode
+		int count = 0;
+		int minCount = INT_MAX;
+		double antiMode;
+		for(map<double,int>::const_iterator iter = linesMap.begin(); iter != linesMap.end(); ++iter) {
+			if (iter->second > count) {
+				mode = iter->first;
+				count = iter->second;
+			}
+			if (iter->second < minCount) {
+				antiMode = iter->first;
+				minCount = iter->second;
+			}
+		}
+		float freq = count / totalLines;
+		cout << "Mode:\t\t\t" << setprecision (15) << mode << " (N=" << count << ")" << endl;
+		cout << "Anti-Mode:\t\t" << setprecision (15) << antiMode << " (N=" << minCount << ")" << endl;
+	}
+	if (doMin || doAll) {
+		// get the min value
+		min = *min_element(linesVector.begin(), linesVector.end());
+		cout << "Minimum:\t\t" << setprecision (15) << min << endl;
+	}
+	if (doMax || doAll) {
+		// get the min value
+		max = *max_element(linesVector.begin(), linesVector.end());
+		cout << "Maximum:\t\t" << setprecision (15) << max << endl;
+	}
+	if (doVariance || doStdDev || doAll) {
+		double totalVariance = 0.0;
+		for(vector<double>::const_iterator iter = linesVector.begin(); iter != linesVector.end(); ++iter) {
+			totalVariance += pow((*iter - mean),2);
+		}
+		variance = totalVariance / totalLines;
+		cout << "Variance:\t\t" << setprecision (15) << variance << endl;
+	}
+	if (doStdDev || doAll) {
+		stddev = sqrt(variance);
+		cout << "StdDev:\t\t\t" << setprecision (15) << stddev << endl;
+	}
+
+	return 0;
+}
+
+
+// function to show a help menu
+void ShowHelp(void) {
+
+	cout << "===============================================================================" << endl;
+	cout << PROGRAM_NAME << ": compute descriptive statistics on data in a file or stdin." << endl << endl;
+	cout << "Aaron Quinlan, Ph.D." << endl;
+	cout << "Marth Laboratory" << endl;
+	cout << "Dept. of Biology, Boston College" << endl; 
+	cout << "===============================================================================" << endl << endl;
+
+	cout << "Usage: " << PROGRAM_NAME << " <file (opt.)> [-a, -mu, -med, -mod, -min, -max, -var, -std]" << endl << endl;
+	cout << "Default: " << "By default, " << PROGRAM_NAME << " will report all of the metrics below." << endl << endl;
+
+	cout << "Options:" << endl;
+	cout << "  -a                       Return all metrics below (default)." << endl;
+	cout << "  -mu  <arithmetic mean>   Return the arithmetic mean (opt.)" << endl;
+	cout << "  -med <median>            Return the median (opt.)" << endl;
+	cout << "  -mod <mode>              Return the mode (opt.)" << endl;
+	cout << "  -min <min>               Return the minimum value (opt.)" << endl;
+	cout << "  -max <min>               Return the maximum value (opt.)" << endl;	
+	cout << "  -var <variance>          Return the variance (opt.)" << endl;	
+	cout << "  -std <std. dev.>         Return the standard deviation (opt.)" << endl;		
+	cout << "\nHelp:" << endl;
+	cout << "  -h                       Shows this help text" << endl;
+
+	// end the program here
+	exit(1);
+}
+
+// test to see if a string is numeric
+inline bool isLineNumeric(string l) {
+	// check to make sure there are no alphanumeric characters in the data
+	for(int i = 0; i < strlen(l.c_str()); i++) {
+		if (isalpha(l[i])) {
+			return false;
+		}
+	}
+	return true;
+}