X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fileoutput.cpp;h=597a05a6ad9a892caff5f0b6f69269ae6af4013d;hb=5a9f3cce3e2e053c249e3e97507ce180f0854d76;hp=c8df770c8054b42d1bdcf7c654700a284ee2aa8f;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/fileoutput.cpp b/fileoutput.cpp
index c8df770..597a05a 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";
+		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";
+		errorOut(e, "ThreeColumnFile", "output");
 		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";
-		exit(1);
-	}
-};
+}
 
 /***********************************************************************/
 
@@ -85,17 +77,118 @@ 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());
+		
+		//checks to make sure user was able to rename and remove successfully
+		if ((renameOk != 0)) {	mothurOut("Unable to rename necessary files."); mothurOutEndLine(); }
+
+	}
+	catch(exception& e) {
+		errorOut(e, "ThreeColumnFile", "resetFile");
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+/***********************************************************************/
+
+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) {
+		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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ThreeColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "ColumnFile", "output");
 		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";
+}
+
+/***********************************************************************/
+
+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());
+		
+		//checks to make sure user was able to rename and remove successfully
+		if ((renameOk != 0)) { mothurOut("Unable to rename necessary files."); mothurOutEndLine(); }
+
+	}
+	catch(exception& e) {
+		errorOut(e, "ColumnFile", "resetFile");
 		exit(1);
-	}	
+	}
 }
 
 /***********************************************************************/
@@ -106,7 +199,7 @@ SharedThreeColumnFile::~SharedThreeColumnFile(){
 	inFile.close();
 	outFile.close();
 	remove(outName.c_str());
-};
+}
 
 /***********************************************************************/
 
@@ -117,7 +210,7 @@ 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 +223,7 @@ 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";
+		errorOut(e, "SharedThreeColumnFile", "initFile");
 		exit(1);
 	}
 }
@@ -145,7 +234,7 @@ 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 +244,10 @@ 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";
+		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);
-	}
-};
+}
 
 /***********************************************************************/
 
@@ -177,16 +262,16 @@ void SharedThreeColumnFile::resetFile(){
 		}
 		counter = 1;
 		remove(inName.c_str());
-		rename(outName.c_str(), inName.c_str());
+		renameOk = rename(outName.c_str(), inName.c_str());
+		
+		//checks to make sure user was able to rename and remove successfully
+		if ((renameOk != 0)) { mothurOut("Unable to rename necessary files."); mothurOutEndLine(); }
+
 	}
 	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";
+		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 +283,7 @@ OneColumnFile::~OneColumnFile(){
 	inFile.close();
 	outFile.close();
 	remove(outName.c_str());	
-};
+}
 
 /***********************************************************************/
 
@@ -209,7 +294,7 @@ void OneColumnFile::initFile(string label){
 			openInputFile(inName, inFile);
 		
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 		
 			outFile	<<  inputBuffer << '\t' << label << endl;
 		}
@@ -222,13 +307,9 @@ void OneColumnFile::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";
+		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 +318,7 @@ 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 +327,10 @@ 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";
+		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);
-	}	
-};
+}
 
 /***********************************************************************/
 
@@ -268,27 +345,27 @@ void OneColumnFile::resetFile(){
 		}	
 		counter = 1;
 		remove(inName.c_str());
-		rename(outName.c_str(), inName.c_str());
+		renameOk = rename(outName.c_str(), inName.c_str());
+		
+		//checks to make sure user was able to rename and remove successfully
+		if ((renameOk != 0)) { mothurOut("Unable to rename necessary files."); mothurOutEndLine(); }
+
 	}
 	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";
+		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);
-	}	
 }
 
 /***********************************************************************/
 /***********************************************************************/
 
-SharedOneColumnFile::~OneColumnFile(){
+SharedOneColumnFile::~SharedOneColumnFile(){
 	
 	inFile.close();
 	outFile.close();
 	remove(outName.c_str());	
-};
+}
 
 /***********************************************************************/
 
@@ -299,7 +376,7 @@ void SharedOneColumnFile::initFile(string label){
 			openInputFile(inName, inFile);
 		
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 		
 			outFile	<<  inputBuffer << '\t' << label  << endl;
 
@@ -314,13 +391,9 @@ 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";
+		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 +409,7 @@ 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 +418,10 @@ 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";
+		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 +435,19 @@ 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());
+		
+		//checks to make sure user was able to rename and remove successfully
+		if ((renameOk != 0)) { mothurOut("Unable to rename necessary files."); mothurOutEndLine(); }
+
+		
 	}
 	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";
+		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);
-	}	
 }
 
 /***********************************************************************/