X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=9dcdc80e761f1483059297dbcd996a0a06b43e5b;hb=0ca63a8165baa0afa459e644ebe140ba496d5ba0;hp=bc5e24efffc6d79291112870d74ac4686c39d42b;hpb=88fbc534a92cb91900e98a3288dfa1f68828b69b;p=mothur.git

diff --git a/mothurout.cpp b/mothurout.cpp
index bc5e24e..9dcdc80 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -1182,7 +1182,6 @@ vector<unsigned long long> MothurOut::setFilePosEachLine(string filename, int& n
 
 vector<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
 	try{
-	
 		vector<unsigned long long> filePos;
 		filePos.push_back(0);
 		
@@ -1190,7 +1189,7 @@ vector<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
 		unsigned long long size;
 		
 		filename = getFullPathName(filename);
-		
+	
 		//get num bytes in file
 		pFile = fopen (filename.c_str(),"rb");
 		if (pFile==NULL) perror ("Error opening file");
@@ -1199,7 +1198,9 @@ vector<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
 			size=ftell (pFile);
 			fclose (pFile);
 		}
-	
+		
+	#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				
 		//estimate file breaks
 		unsigned long long chunkSize = 0;
 		chunkSize = size / proc;
@@ -1219,7 +1220,10 @@ vector<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
 			unsigned long long newSpot = spot;
 			while (!in.eof()) {
 			   char c = in.get();
+				
 			   if (c == '>') {   in.putback(c); newSpot = in.tellg(); break;  }
+			   else if (int(c) == -1) { break; }
+				
 			}
 		
 			//there was not another sequence before the end of the file
@@ -1240,7 +1244,11 @@ vector<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
 		}
 
 		proc = (filePos.size() - 1);
-		
+#else
+		mothurOut("[ERROR]: Windows version should not be calling the divideFile function."); mothurOutEndLine();
+		proc=1;
+		filePos.push_back(size);
+#endif
 		return filePos;
 	}
 	catch(exception& e) {
@@ -1469,6 +1477,26 @@ int MothurOut::getNumNames(string names){
 }
 /***********************************************************************/
 
+int MothurOut::getNumChar(string line, char c){
+	try {
+		int count = 0;
+		
+		if(line != ""){
+			for(int i=0;i<line.size();i++){
+				if(line[i] == c){
+					count++;
+				}
+			}
+		}
+		
+		return count;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "getNumChar");
+		exit(1);
+	}
+}
+/***********************************************************************/
 int MothurOut::mothurRemove(string filename){
 	try {
 		filename = getFullPathName(filename);
@@ -1486,6 +1514,84 @@ int MothurOut::mothurRemove(string filename){
 		exit(1);
 	}
 }
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, int& num){
+	try {
+		bool error = false;
+		
+		if (isNumeric1(item)) {
+			convert(item, num);
+		}else {
+			num = 0;
+			error = true;
+			mothurOut("[ERROR]: cannot convert " + item + " to an integer."); mothurOutEndLine();
+			commandInputsConvertError = true;
+		}
+		
+		return error;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "mothurConvert");
+		exit(1);
+	}
+}
+/***********************************************************************/
+bool MothurOut::isNumeric1(string stringToCheck){
+	try {
+		bool numeric = false;
+		
+		if(stringToCheck.find_first_not_of("0123456789.-") == string::npos) { numeric = true; }
+			
+		return numeric;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "isNumeric1");
+		exit(1);
+	}
+	
+}
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, float& num){
+	try {
+		bool error = false;
+		
+		if (isNumeric1(item)) {
+			convert(item, num);
+		}else {
+			num = 0;
+			error = true;
+			mothurOut("[ERROR]: cannot convert " + item + " to a float."); mothurOutEndLine();
+			commandInputsConvertError = true;
+		}
+		
+		return error;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "mothurConvert");
+		exit(1);
+	}
+}
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, double& num){
+	try {
+		bool error = false;
+		
+		if (isNumeric1(item)) {
+			convert(item, num);
+		}else {
+			num = 0;
+			error = true;
+			mothurOut("[ERROR]: cannot convert " + item + " to a double."); mothurOutEndLine();
+			commandInputsConvertError = true;
+		}
+		
+		return error;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "mothurConvert");
+		exit(1);
+	}
+}
 /**************************************************************************************************/
 
 vector<vector<double> > MothurOut::binomial(int maxOrder){