X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=25e534e43880497955512ce7dc2240adf99157e9;hb=d6c0a11d1cecfac18b323285e7ffadb7f58e848f;hp=90d6f37434d7cb4df231817be6d1759df80b45bb;hpb=4c5e7a20a03ddc6feb49ff9d21fcb4c79bc5508d;p=mothur.git

diff --git a/mothurout.cpp b/mothurout.cpp
index 90d6f37..25e534e 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -212,8 +212,8 @@ void MothurOut::mothurOut(string output) {
 			if (pid == 0) { //only one process should output to screen
 		#endif
 		
-		cout << output;
 		out << output;
+        logger() << output;
 		
 		#ifdef USE_MPI
 			}
@@ -234,8 +234,8 @@ void MothurOut::mothurOutEndLine() {
 			if (pid == 0) { //only one process should output to screen
 		#endif
 		
-		cout << endl;
 		out << endl;
+        logger() << endl;
 		
 		#ifdef USE_MPI
 			}
@@ -257,13 +257,15 @@ void MothurOut::mothurOut(string output, ofstream& outputFile) {
 		if (pid == 0) { //only one process should output to screen
 #endif
 			
-			cout << output;
+			
 			out << output;
 			outputFile << output;
+            logger() << output;
 			
 #ifdef USE_MPI
 		}
 #endif
+        
 	}
 	catch(exception& e) {
 		errorOut(e, "MothurOut", "MothurOut");
@@ -280,9 +282,9 @@ void MothurOut::mothurOutEndLine(ofstream& outputFile) {
 		if (pid == 0) { //only one process should output to screen
 #endif
 			
-			cout << endl;
 			out << endl;
 			outputFile << endl;
+            logger() << endl;
 			
 #ifdef USE_MPI
 		}
@@ -726,7 +728,7 @@ string MothurOut::getFullPathName(string fileName){
 					}else if (path[(pos-1)] == '/') { //you want the current working dir ./
 						path = path.substr(0, pos);
 					}else if (pos == 1) { break;  //you are at the end
-					}else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
+					}else { mothurOut("cannot resolve path for " +  fileName + "\n"); return fileName; }
 				}
 			
 				for (int i = index; i >= 0; i--) {
@@ -772,7 +774,7 @@ string MothurOut::getFullPathName(string fileName){
 					}else if (path[(pos-1)] == '\\') { //you want the current working dir ./
 						path = path.substr(0, pos);
 					}else if (pos == 1) { break;  //you are at the end
-					}else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
+					}else { mothurOut("cannot resolve path for " +  fileName + "\n"); return fileName; }
 				}
 			
 				for (int i = index; i >= 0; i--) {
@@ -1151,7 +1153,7 @@ vector<unsigned long long> MothurOut::setFilePosEachLine(string filename, int& n
 					while(isspace(d) && (d != in.eof()))		{ d=in.get(); count++;}
 				}
 				positions.push_back(count-1);
-				cout << count-1 << endl;
+				//cout << count-1 << endl;
 			}
 			in.close();
 		
@@ -1182,7 +1184,6 @@ 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 +1191,7 @@ 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 +1200,9 @@ 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 +1222,10 @@ 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
@@ -1233,14 +1239,18 @@ vector<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
 		
 		//save end pos
 		filePos.push_back(size);
-
+		
 		//sanity check filePos
 		for (int i = 0; i < (filePos.size()-1); i++) {
 			if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
 		}
 
 		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) {
@@ -1469,16 +1479,121 @@ int MothurOut::getNumNames(string names){
 }
 /***********************************************************************/
 
-void MothurOut::mothurRemove(string filename){
+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);
-		remove(filename.c_str());
+		int error = remove(filename.c_str());
+		//if (error != 0) { 
+		//	if (errno != ENOENT) { //ENOENT == file does not exist
+		//		string message = "Error deleting file " + filename;
+		//		perror(message.c_str()); 
+		//	}
+		//}
+		return error;
 	}
 	catch(exception& e) {
 		errorOut(e, "MothurOut", "mothurRemove");
 		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){
@@ -2020,6 +2135,46 @@ bool MothurOut::isContainingOnlyDigits(string input) {
 	}
 }
 /**************************************************************************************************/
+int MothurOut::removeConfidences(string& tax) {
+	try {
+		
+		string taxon;
+		string newTax = "";
+		
+		while (tax.find_first_of(';') != -1) {
+			
+			if (control_pressed) { return 0; }
+			
+			//get taxon
+			taxon = tax.substr(0,tax.find_first_of(';'));
+	
+			int pos = taxon.find_last_of('(');
+			if (pos != -1) {
+				//is it a number?
+				int pos2 = taxon.find_last_of(')');
+				if (pos2 != -1) {
+					string confidenceScore = taxon.substr(pos+1, (pos2-(pos+1)));
+					if (isNumeric1(confidenceScore)) {
+						taxon = taxon.substr(0, pos); //rip off confidence 
+					}
+				}
+			}
+			taxon += ";";
+			
+			tax = tax.substr(tax.find_first_of(';')+1, tax.length());
+			newTax += taxon;
+		}
+		
+		tax = newTax;
+		
+		return 0;
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "removeConfidences");
+		exit(1);
+	}
+}
+/**************************************************************************************************/