X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=f839328cd2c304330fb18f31fb97eea531ef625a;hb=a5afca18544555fba2d9c3670ad1f8574916b0a0;hp=e5c389005df83b47e45504433269ac7735f6a8c4;hpb=bfbc55964f1977da72c2cea984288a427d370a59;p=mothur.git

diff --git a/mothur.h b/mothur.h
index e5c3890..f839328 100644
--- a/mothur.h
+++ b/mothur.h
@@ -1,7 +1,6 @@
 #ifndef MOTHUR_H
 #define MOTHUR_H
 
-using namespace std;
 
 
 /*
@@ -13,14 +12,16 @@ using namespace std;
  *
  */
 
-/* This file contains all the standard incudes we use in the project. */
+/* This file contains all the standard incudes we use in the project as well as some common utilities. */
 
+//#include <cstddef>
 
 //io libraries
 #include <iostream>
 #include <iomanip>
 #include <fstream>
 #include <sstream>
+#include <signal.h>
 
 //exception
 #include <stdexcept>
@@ -40,5 +41,740 @@ using namespace std;
 #include <math.h>
 #include <algorithm>
 
+//misc
+#include <cerrno>
+#include <ctime>
+#include <limits>
+
+/***********************************************************************/
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+	#include <sys/wait.h>
+	#include <unistd.h>
+	
+	#ifdef USE_READLINE
+		#include <readline/readline.h>
+		#include <readline/history.h>
+	#endif
+
+	//#include <readline/readline.h>
+	//#include <readline/history.h>
+#else
+	#include <conio.h> //allows unbuffered screen capture from stdin
+#endif
+
+using namespace std;
+
+#define exp(x) (exp((double) x))
+#define sqrt(x) (sqrt((double) x))
+#define log10(x) (log10((double) x))
+#define log2(x) (log10(x)/log10(2))
+#define isnan(x) ((x) != (x))
+#define isinf(x) (fabs(x) == std::numeric_limits<double>::infinity())
+
+
+typedef unsigned long ull;
+
+struct IntNode {
+	int lvalue;
+	int rvalue;
+	int lcoef;
+	int rcoef;
+	IntNode* left;
+	IntNode* right;
+	
+	IntNode(int lv, int rv, IntNode* l, IntNode* r) : lvalue(lv), rvalue(rv), left(l), right(r) {};
+	IntNode() {};
+};
+
+struct ThreadNode {
+	int* pid;
+	IntNode* left;
+	IntNode* right;
+};
+
+/************************************************************/
+struct clusterNode {
+	int numSeq;
+	int parent;
+	int smallChild; //used to make linkTable work with list and rabund. represents bin number of this cluster node
+	clusterNode(int num, int par, int kid) : numSeq(num), parent(par), smallChild(kid) {};
+};
+
+/***********************************************************************/
+
+// snagged from http://www.parashift.com/c++-faq-lite/misc-technical-issues.html#faq-39.2
+// works for now, but there should be a way to do it without killing the whole program
+
+class BadConversion : public runtime_error {
+public:
+	BadConversion(const string& s) : runtime_error(s){ }
+};
+
+//**********************************************************************************************************************
+
+template<typename T>
+inline void convert(const string& s, T& x, bool failIfLeftoverChars = true){
+	istringstream i(s);
+	char c;
+	if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
+		throw BadConversion(s);
+}
+
+//**********************************************************************************************************************
+
+template<typename T>
+inline bool convertTestFloat(const string& s, T& x, bool failIfLeftoverChars = true){
+	istringstream i(s);
+	char c;
+	if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
+	{
+		return false;
+	} 
+	return true;
+}
+
+//**********************************************************************************************************************
+
+template<typename T>
+inline bool convertTest(const string& s, T& x, bool failIfLeftoverChars = true){
+	istringstream i(s);
+	char c;
+	if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
+	{
+		cout << "unable to be converted into an integer.\n" << endl;
+		return false;
+	} 
+	return true;
+}
+
+//**********************************************************************************************************************
+
+template<typename T>
+string toString(const T&x){
+    stringstream output;
+    output << x;
+    return output.str();
+}
+
+//**********************************************************************************************************************
+
+template<typename T>
+string toHex(const T&x){
+	stringstream output;
+	
+	output << hex << x;
+
+    return output.str();
+}
+//**********************************************************************************************************************
+
+template<typename T>
+string toString(const T&x, int i){
+	stringstream output;
+	
+	output.precision(i);
+    output << fixed << x;
+	
+    return output.str();
+}
+/***********************************************************************/
+
+inline int openOutputFileAppend(string fileName, ofstream& fileHandle){
+	
+	fileHandle.open(fileName.c_str(), ios::app);
+	if(!fileHandle) {
+		cout << "Error: Could not open " <<  fileName << endl; 
+		return 1;
+	}
+	else {
+		return 0;
+	}
+
+}
+/***********************************************************************/
+
+inline void gobble(istream& f){
+	
+	char d;
+    while(isspace(d=f.get()))		{;}
+	f.putback(d);
+	
+}
+/***********************************************************************/
+
+inline string getline(ifstream& fileHandle) {
+	try {
+	
+		string line = "";
+		
+		while (!fileHandle.eof())	{
+			//get next character
+			char c = fileHandle.get(); 
+			
+			//are you at the end of the line
+			if ((c == '\n') || (c == '\r') || (c == '\f')){  break;	}	
+			else {		line += c;		}
+		}
+		
+		return line;
+		
+	}
+	catch(exception& e) {
+		cout << "Error in mothur function getline" << endl;
+		exit(1);
+	}
+}
+
+/**************************************************************************************************/
+
+inline void mothurOut(string message) {
+	try{
+		ofstream out;
+		string logFileName = "mothur.logFile";
+		openOutputFileAppend(logFileName, out);
+		
+		cout << message;
+		out << message;
+		
+		out.close();
+	}
+	catch(exception& e) {
+		cout << "Error in mothur class mothurOut" << endl;
+		exit(1);
+	}
+}
+/**************************************************************************************************/
+
+inline void mothurOut(string message, string precision) {
+	try{
+		ofstream out;
+		string logFileName = "mothur.logFile";
+		openOutputFileAppend(logFileName, out);
+		
+		cout << precision << message;
+		out << precision << message;
+		
+		out.close();
+	}
+	catch(exception& e) {
+		cout << "Error in mothur class mothurOut" << endl;
+		exit(1);
+	}
+}
+
+/**************************************************************************************************/
+
+inline void mothurOutEndLine() {
+	try {
+		ofstream out;
+		string logFileName = "mothur.logFile";
+		openOutputFileAppend(logFileName, out);
+		
+		cout << endl;  
+		out << endl;
+		
+		out.close();
+	}
+	catch(exception& e) {
+		cout << "error in mothur mothurOutEndLine" << endl;
+		exit(1);
+	}
+}
+
+
+/**************************************************************************************************/
+
+inline void errorOut(exception& e, string object, string function) {
+	
+		mothurOut("Error: ");
+		mothurOut(toString(e.what()));
+		mothurOut(" has occurred in the " + object + " class function " + function + ". Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.");
+		mothurOutEndLine();
+	
+}
+
+/***********************************************************************/
+
+inline bool isTrue(string f){
+	
+	if ((f == "TRUE") || (f == "T")	|| (f == "true") || (f == "t")) {	return true;	}
+	else {	return false;  }
+}
+
+/***********************************************************************/
+
+inline float roundDist(float dist, int precision){
+	
+	return int(dist * precision + 0.5)/float(precision);
+	
+}
+
+/***********************************************************************/
+
+inline int getNumNames(string names){
+	
+	int count = 0;
+	
+	if(names != ""){
+		count = 1;
+		for(int i=0;i<names.size();i++){
+			if(names[i] == ','){
+				count++;
+			}
+		}
+	}
+	
+	return count;
+	
+}
+
+/**************************************************************************************************/
+
+inline vector<vector<double> > binomial(int maxOrder){
+	
+	vector<vector<double> > binomial(maxOrder+1);
+	
+    for(int i=0;i<=maxOrder;i++){
+		binomial[i].resize(maxOrder+1);
+		binomial[i][0]=1;
+		binomial[0][i]=0;
+    }
+    binomial[0][0]=1;
+	
+    binomial[1][0]=1;
+    binomial[1][1]=1;
+	
+    for(int i=2;i<=maxOrder;i++){
+		binomial[1][i]=0;
+    }
+	
+    for(int i=2;i<=maxOrder;i++){
+		for(int j=1;j<=maxOrder;j++){
+			if(i==j){	binomial[i][j]=1;									}
+			if(j>i)	{	binomial[i][j]=0;									}
+			else	{	binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j];	}
+		}
+    }
+	
+	return binomial;
+}
+
+/***********************************************************************/
+
+inline string getRootName(string longName){
+ 
+	string rootName = longName;
+	
+	if(longName.find_last_of(".") != longName.npos){
+		int pos = longName.find_last_of('.')+1;
+		rootName = longName.substr(0, pos);
+	}
+
+	return rootName;
+}
+/***********************************************************************/
+
+inline string getSimpleName(string longName){
+ 
+	string simpleName = longName;
+	
+	if(longName.find_last_of("/") != longName.npos){
+		int pos = longName.find_last_of('/')+1;
+		simpleName = longName.substr(pos, longName.length());
+	}
+
+	return simpleName;
+}
+
+/***********************************************************************/
+
+inline int factorial(int num){
+	int total = 1;
+	
+	for (int i = 1; i <= num; i++) {
+		total *= i;
+	}
+	
+	return total;
+}
+/**************************************************************************************************
+
+double min(double x, double y)
+{
+    if(x<y){	return x;    }
+    else   {	return y;    }
+}
+
+/***********************************************************************/
+
+inline string getPathName(string longName){
+ 
+	string rootPathName = longName;
+	
+	if(longName.find_last_of('/') != longName.npos){
+		int pos = longName.find_last_of('/')+1;
+		rootPathName = longName.substr(0, pos);
+	}
+
+	return rootPathName;
+}
+
+/***********************************************************************/
+
+inline string getExtension(string longName){
+	
+	string extension = longName;
+	
+	if(longName.find_last_of('.') != longName.npos){
+		int pos = longName.find_last_of('.');
+		extension = longName.substr(pos, longName.length());
+	}
+	
+	return extension;
+}
+/***********************************************************************/
+inline bool isBlank(string fileName){
+	
+	ifstream fileHandle;
+	fileHandle.open(fileName.c_str());
+	if(!fileHandle) {
+		mothurOut("Error: Could not open " + fileName);  mothurOutEndLine();
+		return false;
+	}else {
+		//check for blank file
+		gobble(fileHandle);
+		if (fileHandle.eof()) { fileHandle.close(); return true;  }
+	}
+	return false;
+}
+/***********************************************************************/
+
+inline int openInputFile(string fileName, ifstream& fileHandle){
+
+	fileHandle.open(fileName.c_str());
+	if(!fileHandle) {
+		mothurOut("Error: Could not open " + fileName);  mothurOutEndLine();
+		return 1;
+	}
+	else {
+		//check for blank file
+		gobble(fileHandle);
+		if (fileHandle.eof()) { mothurOut(fileName + " is blank. Please correct."); mothurOutEndLine();  return 1;  }
+		
+		return 0;
+	}
+	
+}
+
+/***********************************************************************/
+
+inline int openOutputFile(string fileName, ofstream& fileHandle){
+	
+	fileHandle.open(fileName.c_str(), ios::trunc);
+	if(!fileHandle) {
+		mothurOut("Error: Could not open " + fileName);  mothurOutEndLine();
+		return 1;
+	}
+	else {
+		return 0;
+	}
+
+}
+
+/***********************************************************************/
+
+inline int getNumSeqs(ifstream& file){
+	
+	int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
+	file.seekg(0);
+	return numSeqs;
+
+}
+/***********************************************************************/
+
+inline bool inVector(string member, vector<string> group){
+	
+	for (int i = 0; i < group.size(); i++) {
+		if (group[i] == member) {  return true; 	}
+	}
+	
+	return false;
+}
+/***********************************************************************/
+
+//This function parses the estimator options and puts them in a vector
+inline void splitAtDash(string& estim, vector<string>& container) {
+	try {
+		string individual;
+		
+		while (estim.find_first_of('-') != -1) {
+			individual = estim.substr(0,estim.find_first_of('-'));
+			if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
+				estim = estim.substr(estim.find_first_of('-')+1, estim.length());
+				container.push_back(individual);
+			}
+		}
+		//get last one
+		container.push_back(estim);
+	}
+	catch(exception& e) {
+		errorOut(e, "mothur", "splitAtDash");
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+//This function parses the label options and puts them in a set
+inline void splitAtDash(string& estim, set<string>& container) {
+	try {
+		string individual;
+		
+		while (estim.find_first_of('-') != -1) {
+			individual = estim.substr(0,estim.find_first_of('-'));
+			if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
+				estim = estim.substr(estim.find_first_of('-')+1, estim.length());
+				container.insert(individual);
+			}
+		}
+		//get last one
+		container.insert(estim);
+	}
+	catch(exception& e) {
+		errorOut(e, "mothur", "splitAtDash");
+		exit(1);
+	}
+}
+/***********************************************************************/
+//This function parses the line options and puts them in a set
+inline void splitAtDash(string& estim, set<int>& container) {
+	try {
+		string individual;
+		int lineNum;
+		
+		while (estim.find_first_of('-') != -1) {
+			individual = estim.substr(0,estim.find_first_of('-'));
+			if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
+				estim = estim.substr(estim.find_first_of('-')+1, estim.length());
+				convert(individual, lineNum); //convert the string to int
+				container.insert(lineNum);
+			}
+		}
+		//get last one
+		convert(estim, lineNum); //convert the string to int
+		container.insert(lineNum);
+	}
+	catch(exception& e) {
+		errorOut(e, "mothur", "splitAtDash");
+		exit(1);
+	}
+}
+/***********************************************************************/
+//This function parses the a string and puts peices in a vector
+inline void splitAtComma(string& estim, vector<string>& container) {
+	try {
+		string individual;
+		
+		while (estim.find_first_of(',') != -1) {
+			individual = estim.substr(0,estim.find_first_of(','));
+			if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
+				estim = estim.substr(estim.find_first_of(',')+1, estim.length());
+				container.push_back(individual);
+			}
+		}
+		//get last one
+		container.push_back(estim);
+	}
+	catch(exception& e) {
+		errorOut(e, "mothur", "splitAtComma");
+		exit(1);
+	}
+}
+/***********************************************************************/
+
+//This function splits up the various option parameters
+inline void splitAtComma(string& prefix, string& suffix){
+	try {
+		prefix = suffix.substr(0,suffix.find_first_of(','));
+		if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
+			suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
+			string space = " ";
+			while(suffix.at(0) == ' ')
+				suffix = suffix.substr(1, suffix.length());
+		}
+
+	}
+	catch(exception& e) {
+		errorOut(e, "mothur", "splitAtComma");
+		exit(1);
+	}
+}
+/***********************************************************************/
+
+//This function separates the key value from the option value i.e. dist=96_...
+inline void splitAtEquals(string& key, string& value){		
+	try {
+		if(value.find_first_of('=') != -1){
+			key = value.substr(0,value.find_first_of('='));
+			if ((value.find_first_of('=')+1) <= value.length()) {
+				value = value.substr(value.find_first_of('=')+1, value.length());
+			}
+		}else{
+			key = value;
+			value = 1;
+		}
+	}
+	catch(exception& e) {
+		errorOut(e, "mothur", "splitAtEquals");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
+
+inline bool inUsersGroups(string groupname, vector<string> Groups) {
+	try {
+		for (int i = 0; i < Groups.size(); i++) {
+			if (groupname == Groups[i]) { return true; }
+		}
+		return false;
+	}
+	catch(exception& e) {
+		errorOut(e, "mothur", "inUsersGroups");
+		exit(1);
+	}
+}
+
+/**************************************************************************************************/
+
+inline void mothurOutJustToLog(string message) {
+	try {
+		ofstream out;
+		string logFileName = "mothur.logFile";
+		openOutputFileAppend(logFileName, out);
+		
+		out << message;
+		
+		out.close();
+	}
+	catch(exception& e) {
+		errorOut(e, "mothur", "mothurOutJustToLog");
+		exit(1);
+	}
+}
+
+
+/**************************************************************************************************/
+
+inline void mothurOut(float num) {
+	try {
+		ofstream out;
+		string logFileName = "mothur.logFile";
+		openOutputFileAppend(logFileName, out);
+		
+		cout << num;  
+		out << num;
+		
+		out.close();
+	}
+	catch(exception& e) {
+		cout << "Error in mothur class mothurOut float" << endl;
+		exit(1);
+	}
+}
+/***********************************************************************/
+inline void mothurOut(double value) {
+	try {
+		ofstream out;
+		string logFileName = "mothur.logFile";
+		openOutputFileAppend(logFileName, out);
+		
+		cout << value;  
+		out << value;
+		
+		out.close();
+	}
+	catch(exception& e) {
+		cout << "Error in mothur class mothurOut double" << endl;
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+//this function determines if the user has given us labels that are smaller than the given label.
+//if so then it returns true so that the calling function can run the previous valid distance.
+//it's a "smart" distance function.  It also checks for invalid labels.
+inline bool anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
+	try {
+		set<string>::iterator it;
+		vector<float> orderFloat;
+		map<string, float> userMap;  //the conversion process removes trailing 0's which we need to put back
+		map<string, float>::iterator it2;
+		float labelFloat;
+		bool smaller = false;
+		
+		//unique is the smallest line
+		if (label == "unique") {  return false;  }
+		else { convert(label, labelFloat); }
+		
+		//go through users set and make them floats
+		for(it = userLabels.begin(); it != userLabels.end(); ++it) {
+			
+			float temp;
+			if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
+				convert(*it, temp);
+				orderFloat.push_back(temp);
+				userMap[*it] = temp;
+			}else if (*it == "unique") { 
+				orderFloat.push_back(-1.0);
+				userMap["unique"] = -1.0;
+			}else {
+				if (errorOff == "") {  mothurOut(*it + " is not a valid label."); mothurOutEndLine();  }
+				userLabels.erase(*it); 
+				it--;
+			}
+		}
+		
+		//sort order
+		sort(orderFloat.begin(), orderFloat.end());
+		
+		/*************************************************/
+		//is this label bigger than any of the users labels
+		/*************************************************/
+				
+		//loop through order until you find a label greater than label
+		for (int i = 0; i < orderFloat.size(); i++) {
+			if (orderFloat[i] < labelFloat) {
+				smaller = true;
+				if (orderFloat[i] == -1) { 
+					if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); }
+					userLabels.erase("unique");
+				}
+				else {  
+					if (errorOff == "") { mothurOut("Your file does not include the label "); mothurOutEndLine(); }
+					string s = "";
+					for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {  
+						if (it2->second == orderFloat[i]) {  
+							s = it2->first;  
+							//remove small labels
+							userLabels.erase(s);
+							break;
+						}
+					}
+					if (errorOff == "") { mothurOut(s + ". I will use the next smallest distance. "); mothurOutEndLine(); }
+				}
+			//since they are sorted once you find a bigger one stop looking
+			}else { break; }
+		}
+		
+		return smaller;
+						
+	}
+	catch(exception& e) {
+		errorOut(e, "mothur", "anyLabelsToProcess");
+		exit(1);
+	}
+}
+
+/**************************************************************************************************/
 #endif