X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fileoutput.cpp;h=117f8ab1c3a9a93c5f80f38613c4aefa1c898e32;hb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;hp=2f7639fbbcfec3233f5388e66e2e34637e4d90fe;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed;p=mothur.git

diff --git a/fileoutput.cpp b/fileoutput.cpp
index 2f7639f..117f8ab 100644
--- a/fileoutput.cpp
+++ b/fileoutput.cpp
@@ -16,7 +16,7 @@ ThreeColumnFile::~ThreeColumnFile(){
 	inFile.close();
 	outFile.close();
 	remove(outName.c_str());
-};
+}
 
 /***********************************************************************/
 
@@ -27,7 +27,7 @@ void ThreeColumnFile::initFile(string label){
 			openInputFile(inName, inFile);
 
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 		
 			outFile	<<  inputBuffer << '\t' << label << "\tlci\thci" << endl;
 		}
@@ -40,11 +40,7 @@ void ThreeColumnFile::initFile(string label){
 		outFile.setf(ios::showpoint);
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ThreeColumnFile class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ThreeColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ThreeColumnFile", "initFile");
 		exit(1);
 	}
 }
@@ -55,7 +51,7 @@ void ThreeColumnFile::output(int nSeqs, vector<double> data){
 	try {
 		if(counter != 0){		
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 		
 			outFile	<<  inputBuffer << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
 		}
@@ -64,14 +60,10 @@ void ThreeColumnFile::output(int nSeqs, vector<double> data){
 		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ThreeColumnFile class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ThreeColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ThreeColumnFile", "output");
 		exit(1);
 	}
-};
+}
 
 /***********************************************************************/
 
@@ -85,17 +77,126 @@ void ThreeColumnFile::resetFile(){
 			outFile.close();
 		}
 		counter = 1;
+		
 		remove(inName.c_str());
-		rename(outName.c_str(), inName.c_str());
+		renameOk = rename(outName.c_str(), inName.c_str());
+		
+		//renameFile(outName, inName);
+		
+		//checks to make sure user was able to rename and remove successfully
+		if ((renameOk != 0)) { 
+			m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
+			perror(" : ");
+		}	
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ThreeColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ThreeColumnFile", "resetFile");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ThreeColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+/***********************************************************************/
+/***********************************************************************/
+
+ColumnFile::~ColumnFile(){
+	
+	inFile.close();
+	outFile.close();
+	remove(outName.c_str());
+}
+
+/***********************************************************************/
+
+void ColumnFile::initFile(string label, vector<string> tags){
+	try {
+		if(counter != 0){
+			openOutputFile(outName, outFile);
+			openInputFile(inName, inFile);
+
+			string inputBuffer;
+			inputBuffer = getline(inFile);
+		
+			outFile	<<  inputBuffer << '\t'; 
+			for(int i = 0; i < tags.size(); i++) {
+				outFile << label + tags[i] << '\t';
+			}
+			outFile << endl;
+		}
+		else{
+			openOutputFile(outName, outFile);
+			for(int i = 0; i < tags.size(); i++) {
+				outFile << label + tags[i] << '\t';
+			}
+			outFile << endl;
+		}
+
+		outFile.setf(ios::fixed, ios::floatfield);
+		outFile.setf(ios::showpoint);
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ColumnFile", "initFile");
 		exit(1);
-	}	
+	}
+}
+
+/***********************************************************************/
+
+void ColumnFile::output(vector<double> data){
+	try {
+	
+		if(counter != 0){		
+			string inputBuffer;
+			inputBuffer = getline(inFile);
+
+			outFile << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(iters.length());
+			for (int i = 1; i< data.size(); i++) {
+				outFile << '\t' << data[i]; 
+			}
+			outFile << endl;
+		}
+		else{
+			outFile << setprecision(6) << data[0] << setprecision(iters.length());
+			for (int i = 1; i< data.size(); i++) {
+				outFile << '\t' << data[i]; 
+			}
+			outFile << endl;
+		}
+
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ColumnFile", "output");
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+
+void ColumnFile::resetFile(){
+	try {
+		if(counter != 0){
+			outFile.close();
+			inFile.close();
+		}
+		else{
+			outFile.close();
+		}
+		counter = 1;
+		
+		remove(inName.c_str());
+		renameOk = rename(outName.c_str(), inName.c_str());
+		
+		//renameFile(outName, inName);
+		
+		//checks to make sure user was able to rename and remove successfully
+		if ((renameOk != 0)) { 
+			m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
+			perror(" : ");
+		}	
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ColumnFile", "resetFile");
+		exit(1);
+	}
 }
 
 /***********************************************************************/
@@ -106,7 +207,7 @@ SharedThreeColumnFile::~SharedThreeColumnFile(){
 	inFile.close();
 	outFile.close();
 	remove(outName.c_str());
-};
+}
 
 /***********************************************************************/
 
@@ -117,7 +218,7 @@ void SharedThreeColumnFile::initFile(string label){
 			openInputFile(inName, inFile);
 
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 		
 			outFile	<<  inputBuffer << '\t' << label << "\tlci\thci" << endl;
 		}
@@ -130,11 +231,7 @@ void SharedThreeColumnFile::initFile(string label){
 		outFile.setf(ios::showpoint);
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedThreeColumnFile class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedThreeColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedThreeColumnFile", "initFile");
 		exit(1);
 	}
 }
@@ -145,7 +242,7 @@ void SharedThreeColumnFile::output(int nSeqs, vector<double> data){
 	try {
 		if(counter != 0){		
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 		
 			outFile	<<  inputBuffer << setprecision(4) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
 		}
@@ -155,14 +252,10 @@ void SharedThreeColumnFile::output(int nSeqs, vector<double> data){
 		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedThreeColumnFile class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedThreeColumnFile", "output");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedThreeColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-};
+}
 
 /***********************************************************************/
 
@@ -176,17 +269,22 @@ void SharedThreeColumnFile::resetFile(){
 			outFile.close();
 		}
 		counter = 1;
+		
 		remove(inName.c_str());
-		rename(outName.c_str(), inName.c_str());
+		renameOk = rename(outName.c_str(), inName.c_str());
+		
+		//renameFile(outName, inName);
+		
+		//checks to make sure user was able to rename and remove successfully
+		if ((renameOk != 0)) { 
+			m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
+			perror(" : ");
+		}	
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedThreeColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedThreeColumnFile", "resetFile");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedThreeColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/
@@ -198,7 +296,7 @@ OneColumnFile::~OneColumnFile(){
 	inFile.close();
 	outFile.close();
 	remove(outName.c_str());	
-};
+}
 
 /***********************************************************************/
 
@@ -209,26 +307,22 @@ void OneColumnFile::initFile(string label){
 			openInputFile(inName, inFile);
 		
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 		
 			outFile	<<  inputBuffer << '\t' << label << endl;
 		}
 		else{
 			openOutputFile(outName, outFile);
-			outFile << "numsequences\t" << label << endl;
+			outFile << "numsampled\t" << label << endl;
 		}
 	
 		outFile.setf(ios::fixed, ios::floatfield);
 		outFile.setf(ios::showpoint);
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "OneColumnFile", "initFile");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the OneColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/
@@ -237,7 +331,7 @@ void OneColumnFile::output(int nSeqs, vector<double> data){
 	try {	
 		if(counter != 0){		
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 		
 			outFile	<<  inputBuffer << setprecision(4) << '\t'  << data[0] << endl;
 		}
@@ -246,14 +340,10 @@ void OneColumnFile::output(int nSeqs, vector<double> data){
 		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "OneColumnFile", "output");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the OneColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
-};
+}
 
 /***********************************************************************/
 
@@ -262,22 +352,27 @@ void OneColumnFile::resetFile(){
 		if(counter != 0){
 			outFile.close();
 			inFile.close();
-		}
-		else{
+		}else{
 			outFile.close();
 		}	
 		counter = 1;
+		
 		remove(inName.c_str());
-		rename(outName.c_str(), inName.c_str());
+		renameOk = rename(outName.c_str(), inName.c_str());
+		
+		//renameFile(outName, inName);
+		
+		//checks to make sure user was able to rename and remove successfully
+		if ((renameOk != 0)) { 
+			m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
+			perror(" : ");
+		}	
+
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "OneColumnFile", "resetFile");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the OneColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/
@@ -288,7 +383,7 @@ SharedOneColumnFile::~SharedOneColumnFile(){
 	inFile.close();
 	outFile.close();
 	remove(outName.c_str());	
-};
+}
 
 /***********************************************************************/
 
@@ -299,7 +394,7 @@ void SharedOneColumnFile::initFile(string label){
 			openInputFile(inName, inFile);
 		
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 		
 			outFile	<<  inputBuffer << '\t' << label  << endl;
 
@@ -314,13 +409,9 @@ void SharedOneColumnFile::initFile(string label){
 		outFile.setf(ios::showpoint);
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedOneColumnFile", "initFile");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the OneColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/
@@ -336,7 +427,7 @@ void SharedOneColumnFile::output(int nSeqs, vector<double> data){
 			}
 			if(counter != 0){		
 				string inputBuffer;
-				getline(inFile, inputBuffer);
+				inputBuffer = getline(inFile);
 
 				outFile	<<  inputBuffer << setprecision(2) << '\t' << dataOutput << endl;
 			}
@@ -345,14 +436,10 @@ void SharedOneColumnFile::output(int nSeqs, vector<double> data){
 			}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedOneColumnFile", "output");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the OneColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
-};
+}
 
 /***********************************************************************/
 
@@ -366,17 +453,22 @@ void SharedOneColumnFile::resetFile(){
 			outFile.close();
 		}	
 		counter = 1;
+
 		remove(inName.c_str());
-		rename(outName.c_str(), inName.c_str());
+		renameOk = rename(outName.c_str(), inName.c_str());
+		
+		//renameFile(outName, inName);
+		
+		//checks to make sure user was able to rename and remove successfully
+		if ((renameOk != 0)) { 
+			m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
+			perror(" : ");
+		}	
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the OneColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedOneColumnFile", "resetFile");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the OneColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/