X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothur.h;h=102b44d57030561244c8ba6205f7c02c831b9b36;hp=07bb971347d974066ab5449614172c5e68d4c2a6;hb=d1faab5efe1c28700890bdec5b4d8e817fa1dab2;hpb=a8f5a612bba54ceb74e17efc027d3a7f5aa93c9a

diff --git a/mothur.h b/mothur.h
index 07bb971..102b44d 100644
--- a/mothur.h
+++ b/mothur.h
@@ -1,7 +1,6 @@
 #ifndef MOTHUR_H
 #define MOTHUR_H
 
-using namespace std;
 
 
 /*
@@ -22,6 +21,8 @@ using namespace std;
 #include <iomanip>
 #include <fstream>
 #include <sstream>
+#include <signal.h>
+
 
 //exception
 #include <stdexcept>
@@ -35,13 +36,59 @@ using namespace std;
 #include <map>
 #include <string>
 #include <list>
+#include <string.h>
 
 //math
 #include <cmath>
 #include <math.h>
 #include <algorithm>
+#include <numeric>
+
+//misc
+#include <cerrno>
+#include <ctime>
+#include <limits>
+
+#ifdef USE_MPI
+	#include "mpi.h"
+#endif
+/***********************************************************************/
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+	#include <sys/wait.h>
+	#include <sys/time.h>
+	#include <sys/resource.h>
+	#include <sys/types.h>
+	#include <sys/stat.h>
+	#include <unistd.h>
+	
+	#ifdef USE_READLINE
+		#include <readline/readline.h>
+		#include <readline/history.h>
+	#endif
+
+#else
+	#include <conio.h> //allows unbuffered screen capture from stdin
+	#include <direct.h> //get cwd
+	#include <windows.h>
+	#include <psapi.h>
+	#include <direct.h>
+	#include <tchar.h>
+
+#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 long ull;
+typedef unsigned long ull;
+typedef unsigned short intDist;
 
 struct IntNode {
 	int lvalue;
@@ -50,515 +97,296 @@ struct IntNode {
 	int rcoef;
 	IntNode* left;
 	IntNode* right;
-};
 	
-/***********************************************************************/
-
-// 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){ }
+	IntNode(int lv, int rv, IntNode* l, IntNode* r) : lvalue(lv), rvalue(rv), left(l), right(r) {};
+	IntNode() {};
 };
 
-//**********************************************************************************************************************
-
-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 << "'" << s << "' is unable to be converted into an integer.\n";
-		return false;
-	} 
-	return true;
-}
-
-//**********************************************************************************************************************
-
-template<typename T>
-string toString(const T&x){
-    stringstream output;
-    output << x;
-    return output.str();
-}
-
-//**********************************************************************************************************************
+struct ThreadNode {
+	int* pid;
+	IntNode* left;
+	IntNode* right;
+};
 
-template<typename T>
-string toHex(const T&x){
-	stringstream output;
+struct diffPair {
+	float	prob;
+	float	reverseProb;
 	
-	output << hex << x;
-
-    return output.str();
-}
-//**********************************************************************************************************************
+	diffPair() {
+		prob = 0; reverseProb = 0;
+	}
+	diffPair(float p, float rp) {
+		prob = p;
+		reverseProb = rp;
+	}
+};
 
-template<typename T>
-string toString(const T&x, int i){
-	stringstream output;
+/**********************************************************/
+struct CommonHeader {
+	unsigned int magicNumber;
+	string version;
+	unsigned long long indexOffset;
+	unsigned int indexLength;
+	unsigned int numReads;
+	unsigned short headerLength;
+	unsigned short keyLength;
+	unsigned short numFlowsPerRead;
+	int flogramFormatCode;
+	string flowChars; //length depends on number flow reads
+	string keySequence; //length depends on key length
 	
-	output.precision(i);
-    output << fixed << x;
-	
-    return output.str();
-}
-
-
-/***********************************************************************/
-
-inline void gobble(istream& f){
+	CommonHeader(){ magicNumber=0; indexOffset=0; indexLength=0; numReads=0; headerLength=0; keyLength=0; numFlowsPerRead=0; flogramFormatCode='s'; }
+	~CommonHeader() { }
+};
+/**********************************************************/
+struct Header {
+	unsigned short headerLength;
+	unsigned short nameLength;
+	unsigned int numBases;
+	unsigned short clipQualLeft;
+	unsigned short clipQualRight;
+	unsigned short clipAdapterLeft;
+	unsigned short clipAdapterRight;
+	string name; //length depends on nameLength
+	string timestamp;
+	string region;
+	string xy;
 	
-	char d;
-    while(isspace(d=f.get()))		{;}
-	f.putback(d);
+	Header() { headerLength=0; nameLength=0; numBases=0; clipQualLeft=0; clipQualRight=0; clipAdapterLeft=0; clipAdapterRight=0; }
+	~Header() { }
+};
+/**********************************************************/
+struct seqRead {
+	vector<unsigned short> flowgram;
+	vector<unsigned int> flowIndex;
+	string bases;
+	vector<unsigned int> qualScores;
 	
-}
+	seqRead() { }
+	~seqRead() { }
+};
 
 /***********************************************************************/
-
-inline float roundDist(float dist, int precision){
-	
-	return int(dist * precision + 0.5)/float(precision);
-	
-}
-
+struct PDistCell{
+	ull index;
+	float dist;
+	PDistCell() :  index(0), dist(0) {};
+	PDistCell(ull c, float d) :  index(c), dist(d) {}
+};
 /***********************************************************************/
-
-inline int getNumNames(string names){
-	
-	int count = 0;
-	
-	if(names != ""){
-		count = 1;
-		for(int i=0;i<names.size();i++){
-			if(names[i] == ','){
-				count++;
-			}
-		}
-	}
+struct consTax{
+	string name;
+    string taxonomy;
+    int abundance;
+	consTax() :  name(""), taxonomy("unknown"), abundance(0) {};
+	consTax(string n, string t, int a) :  name(n), taxonomy(t), abundance(a) {}
+};
+/***********************************************************************/
+struct consTax2{
+    string taxonomy;
+    int abundance;
+	consTax2() :  taxonomy("unknown"), abundance(0) {};
+	consTax2(string t, int a) :  taxonomy(t), abundance(a) {}
+};
+/************************************************************/
+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) {};
+};
+/************************************************************/
+struct seqDist {
+	int seq1;
+	int seq2;
+	double dist;
+	seqDist() {}
+	seqDist(int s1, int s2, double d) : seq1(s1), seq2(s2), dist(d) {}
+	~seqDist() {}
+};
+/************************************************************/
+struct distlinePair {
+	int start;
+	int end;
 	
-	return count;
+};
+/************************************************************/
+struct seqPriorityNode {
+	int numIdentical;
+	string seq;
+	string name;
+	seqPriorityNode() {}
+	seqPriorityNode(int n, string s, string nm) : numIdentical(n), seq(s), name(nm) {}
+	~seqPriorityNode() {}
+};
+/************************************************************/
+struct compGroup {
+	string group1;
+	string group2;
+	compGroup() {}
+	compGroup(string s, string nm) : group1(s), group2(nm) {}
+    string getCombo() { return group1+"-"+group2; }
+	~compGroup() {}
+};
+/***************************************************************/
+struct spearmanRank {
+	string name;
+	float score;
 	
+	spearmanRank(string n, float s) : name(n), score(s) {}
+};
+//***********************************************************************
+inline bool compareIndexes(PDistCell left, PDistCell right){
+	return (left.index > right.index);	
 }
-
-/**************************************************************************************************/
-
-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 bool compareSpearman(spearmanRank left, spearmanRank right){
+	return (left.score < right.score);	
 }
-
-/***********************************************************************/
-
-inline string getRootName(string longName){
+//********************************************************************************************************************
+inline double max(double left, double right){
+    if (left > right) { return left; }
+    else { return right; }
+}
+//********************************************************************************************************************
+inline double max(int left, double right){
+    double value = left;
+    if (left > right) { return value; }
+    else { return right; }
+}
+//********************************************************************************************************************
+inline double max(double left, int right){
+    double value = right;
+    if (left > value) { return left; }
+    else { return value; }
+}
+//********************************************************************************************************************
+//sorts highest to lowest
+inline bool compareSeqPriorityNodes(seqPriorityNode left, seqPriorityNode right){
+	if (left.numIdentical > right.numIdentical) {
+        return true;
+    }else if (left.numIdentical == right.numIdentical) {
+        if (left.seq > right.seq) { return true; }
+        else { return false; }
+    }
+    return false;	
+} 
  
-	string rootName = longName;
-	
-	if(longName.find_last_of(".") != longName.npos){
-		int pos = longName.find_last_of('.')+1;
-		rootName = longName.substr(0, pos);
-	}
-
-	return rootName;
+/************************************************************/
+//sorts lowest to highest
+inline bool compareDistLinePairs(distlinePair left, distlinePair right){
+	return (left.end < right.end);	
+} 
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareSequenceDistance(seqDist left, seqDist right){
+	return (left.dist < right.dist);	
+}
+//********************************************************************************************************************
+//returns sign of double
+inline double sign(double temp){
+	//find sign
+    if (temp > 0)       { return 1.0;   }
+    else if (temp < 0)  { return -1.0;  }
+    return 0;
 }
 /***********************************************************************/
 
-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());
-	}
+// 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
 
-	return simpleName;
-}
-/***********************************************************************/
+class BadConversion : public runtime_error {
+public:
+	BadConversion(const string& s) : runtime_error(s){ }
+};
 
-inline int factorial(int num){
-	int total = 1;
+//**********************************************************************************************************************
+template<typename T>
+void convert(const string& s, T& x, bool failIfLeftoverChars = true){
 	
-	for (int i = 1; i <= num; i++) {
-		total *= i;
-	}
+		istringstream i(s);
+		char c;
+		if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
+			throw BadConversion(s);
 	
-	return total;
 }
-/**************************************************************************************************
-
-double min(double x, double y)
-{
-    if(x<y){	return x;    }
-    else   {	return y;    }
-}
-
-/***********************************************************************/
+//**********************************************************************************************************************
+template <typename T> int sgn(T val){ return (val > T(0)) - (val < T(0)); }
+//**********************************************************************************************************************
 
-inline string getPathName(string longName){
- 
-	string rootPathName = longName;
+template<typename T>
+bool convertTestFloat(const string& s, T& x, bool failIfLeftoverChars = true){
 	
-	if(longName.find_last_of("/") != longName.npos){
-		int pos = longName.find_last_of('/')+1;
-		rootPathName = longName.substr(0, pos);
-	}
-
-	return rootPathName;
-}
-
-/***********************************************************************/
-
-inline int openInputFile(string fileName, ifstream& fileHandle){
-
-	fileHandle.open(fileName.c_str());
-	if(!fileHandle) {
-		cerr << "Error: Could not open " << fileName << endl;
-		return 1;
-	}
-	else {
-		return 0;
-	}
+		istringstream i(s);
+		char c;
+		if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
+		{
+			return false;
+		} 
+		return true;
 	
 }
 
-/***********************************************************************/
+//**********************************************************************************************************************
 
-inline int openOutputFile(string fileName, ofstream& fileHandle){
+template<typename T>
+bool convertTest(const string& s, T& x, bool failIfLeftoverChars = true){
+	
+		istringstream i(s);
+		char c;
+		if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
+		{
+			return false;
+		} 
+		return true;
 	
-	fileHandle.open(fileName.c_str(), ios::trunc);
-	if(!fileHandle) {
-		cerr << "Error: Could not open " << fileName << endl;
-		return 1;
-	}
-	else {
-		return 0;
-	}
-
 }
-/***********************************************************************/
-
-inline int openOutputFileAppend(string fileName, ofstream& fileHandle){
+//**********************************************************************************************************************
+template<typename T>
+string toString(const T&x){
+	
+		stringstream output;
+		output << x;
+		return output.str();
 	
-	fileHandle.open(fileName.c_str(), ios::app);
-	if(!fileHandle) {
-		cerr << "Error: Could not open " << fileName << endl;
-		return 1;
-	}
-	else {
-		return 0;
-	}
-
 }
 
+//**********************************************************************************************************************
 
-/***********************************************************************/
-
-//This function parses the estimator options and puts them in a vector
-inline void splitAtDash(string& estim, vector<string>& container) {
-	try {
-		string individual;
+template<typename T>
+string toHex(const T&x){
+	
+		stringstream output;
 		
-		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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the mothur class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
+		output << hex << x;
 
+		return output.str();
+	
 }
+//**********************************************************************************************************************
 
-/***********************************************************************/
-//This function parses the label options and puts them in a set
-inline void splitAtDash(string& estim, set<string>& container) {
-	try {
-		string individual;
+template<typename T>
+string toString(const T&x, int i){
+	
+		stringstream output;
 		
-		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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the mothur class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		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;
+		output.precision(i);
+		output << fixed << x;
 		
-		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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the mothur class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the mothur class function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the mothur class function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-
+		return output.str();
+	
 }
-/***********************************************************************/
-
-//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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the mothur class function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the mothur class function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
+template<class T>
+T fromString(const string& s){
+	istringstream stream (s);
+	T t;
+	stream >> t;
+	return t;
 }
 
-/***********************************************************************/
-//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 == "") {  cout << *it << " is not a valid label." << endl;  }
-				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 == "") { cout << "Your file does not include the label unique." <<  endl; }
-					userLabels.erase("unique");
-				}
-				else {  
-					if (errorOff == "") { cout << "Your file does not include the label "; }
-					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 == "") { cout << s << ". I will use the next smallest distance. "  <<  endl; }
-				}
-			//since they are sorted once you find a bigger one stop looking
-			}else { break; }
-		}
-		
-		return smaller;
-						
-	}
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function anyLabelsToProcess. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the mothur class function anyLabelsToProcess. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-
-}
+//**********************************************************************************************************************
 
-/**************************************************************************************************/
 #endif