X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=ec56c506c8c0c7654c4e436afa16222f14b1224f;hb=e7fe6dd9db877b98c362f9524c3130bbbd037200;hp=36d7b28ebf45dd3f4bf1d0555c74f4e99c841fe9;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d;p=mothur.git

diff --git a/mothur.h b/mothur.h
index 36d7b28..ec56c50 100644
--- a/mothur.h
+++ b/mothur.h
@@ -15,6 +15,7 @@ using namespace std;
 
 /* This file contains all the standard incudes we use in the project as well as some common utilities. */
 
+//#include <cstddef>
 
 //io libraries
 #include <iostream>
@@ -39,9 +40,32 @@ using namespace std;
 #include <cmath>
 #include <math.h>
 #include <algorithm>
+#include <ctime>
+
+#ifdef _WIN32
+	#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))
+#endif
+
 
 typedef unsigned long long ull;
 
+struct IntNode {
+	int lvalue;
+	int rvalue;
+	int lcoef;
+	int rcoef;
+	IntNode* left;
+	IntNode* right;
+};
+
+struct ThreadNode {
+	int* pid;
+	IntNode* left;
+	IntNode* right;
+};
 
 /***********************************************************************/
 
@@ -64,6 +88,19 @@ inline void convert(const string& s, T& x, bool failIfLeftoverChars = true){
 }
 //**********************************************************************************************************************
 
+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);
@@ -95,7 +132,6 @@ string toHex(const T&x){
 
     return output.str();
 }
-
 //**********************************************************************************************************************
 
 template<typename T>
@@ -118,6 +154,13 @@ inline void gobble(istream& f){
 	f.putback(d);
 	
 }
+/***********************************************************************/
+
+inline bool isTrue(string f){
+	
+	if ((f == "TRUE") || (f == "T")	|| (f == "true") || (f == "t")) {	return true;	}
+	else {	return false;  }
+}
 
 /***********************************************************************/
 
@@ -206,11 +249,30 @@ inline string getSimpleName(string longName){
 
 /***********************************************************************/
 
+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){
+	if(longName.find_last_of('/') != longName.npos){
 		int pos = longName.find_last_of('/')+1;
 		rootPathName = longName.substr(0, pos);
 	}
@@ -220,6 +282,20 @@ inline string getPathName(string longName){
 
 /***********************************************************************/
 
+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 int openInputFile(string fileName, ifstream& fileHandle){
 
 	fileHandle.open(fileName.c_str());
@@ -246,6 +322,31 @@ inline int openOutputFile(string fileName, ofstream& fileHandle){
 		return 0;
 	}
 
+}
+/***********************************************************************/
+
+inline int openOutputFileAppend(string fileName, ofstream& fileHandle){
+	
+	fileHandle.open(fileName.c_str(), ios::app);
+	if(!fileHandle) {
+		cerr << "Error: Could not open " << fileName << endl;
+		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;
+
 }
 
 /***********************************************************************/
@@ -424,8 +525,87 @@ inline bool inUsersGroups(string groupname, vector<string> Groups) {
 	}
 }
 
-/**************************************************************************************************/
+/***********************************************************************/
+//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