X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fileoutput.cpp;h=117f8ab1c3a9a93c5f80f38613c4aefa1c898e32;hb=2df35fdeea85f574630d75b11fb5b08c39aec31a;hp=63130a83ba6c850bc8db4ea720ba51a15d80ff81;hpb=03193ff423c9526ff6525040cab60ff715d8cc48;p=mothur.git

diff --git a/fileoutput.cpp b/fileoutput.cpp
index 63130a8..117f8ab 100644
--- a/fileoutput.cpp
+++ b/fileoutput.cpp
@@ -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;
 		}
@@ -40,7 +40,7 @@ void ThreeColumnFile::initFile(string label){
 		outFile.setf(ios::showpoint);
 	}
 	catch(exception& e) {
-		errorOut(e, "ThreeColumnFile", "initFile");
+		m->errorOut(e, "ThreeColumnFile", "initFile");
 		exit(1);
 	}
 }
@@ -51,7 +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;
 		}
@@ -60,7 +60,7 @@ void ThreeColumnFile::output(int nSeqs, vector<double> data){
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "ThreeColumnFile", "output");
+		m->errorOut(e, "ThreeColumnFile", "output");
 		exit(1);
 	}
 }
@@ -81,12 +81,16 @@ void ThreeColumnFile::resetFile(){
 		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)) {	mothurOut("Unable to rename necessary files."); mothurOutEndLine(); }
-
+		if ((renameOk != 0)) { 
+			m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
+			perror(" : ");
+		}	
 	}
 	catch(exception& e) {
-		errorOut(e, "ThreeColumnFile", "resetFile");
+		m->errorOut(e, "ThreeColumnFile", "resetFile");
 		exit(1);
 	}
 }
@@ -110,7 +114,7 @@ void ColumnFile::initFile(string label, vector<string> tags){
 			openInputFile(inName, inFile);
 
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 		
 			outFile	<<  inputBuffer << '\t'; 
 			for(int i = 0; i < tags.size(); i++) {
@@ -130,7 +134,7 @@ void ColumnFile::initFile(string label, vector<string> tags){
 		outFile.setf(ios::showpoint);
 	}
 	catch(exception& e) {
-		errorOut(e, "ColumnFile", "initFile");
+		m->errorOut(e, "ColumnFile", "initFile");
 		exit(1);
 	}
 }
@@ -142,7 +146,7 @@ void ColumnFile::output(vector<double> data){
 	
 		if(counter != 0){		
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 
 			outFile << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(iters.length());
 			for (int i = 1; i< data.size(); i++) {
@@ -160,7 +164,7 @@ void ColumnFile::output(vector<double> data){
 
 	}
 	catch(exception& e) {
-		errorOut(e, "ColumnFile", "output");
+		m->errorOut(e, "ColumnFile", "output");
 		exit(1);
 	}
 }
@@ -181,12 +185,16 @@ void ColumnFile::resetFile(){
 		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)) { mothurOut("Unable to rename necessary files."); mothurOutEndLine(); }
-
+		if ((renameOk != 0)) { 
+			m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
+			perror(" : ");
+		}	
 	}
 	catch(exception& e) {
-		errorOut(e, "ColumnFile", "resetFile");
+		m->errorOut(e, "ColumnFile", "resetFile");
 		exit(1);
 	}
 }
@@ -210,7 +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;
 		}
@@ -223,7 +231,7 @@ void SharedThreeColumnFile::initFile(string label){
 		outFile.setf(ios::showpoint);
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedThreeColumnFile", "initFile");
+		m->errorOut(e, "SharedThreeColumnFile", "initFile");
 		exit(1);
 	}
 }
@@ -234,7 +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;
 		}
@@ -244,7 +252,7 @@ void SharedThreeColumnFile::output(int nSeqs, vector<double> data){
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedThreeColumnFile", "output");
+		m->errorOut(e, "SharedThreeColumnFile", "output");
 		exit(1);
 	}
 }
@@ -261,15 +269,20 @@ void SharedThreeColumnFile::resetFile(){
 			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)) { mothurOut("Unable to rename necessary files."); mothurOutEndLine(); }
-
+		if ((renameOk != 0)) { 
+			m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
+			perror(" : ");
+		}	
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedThreeColumnFile", "resetFile");
+		m->errorOut(e, "SharedThreeColumnFile", "resetFile");
 		exit(1);
 	}
 }
@@ -294,20 +307,20 @@ 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) {
-		errorOut(e, "OneColumnFile", "initFile");
+		m->errorOut(e, "OneColumnFile", "initFile");
 		exit(1);
 	}
 }
@@ -318,7 +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;
 		}
@@ -327,7 +340,7 @@ void OneColumnFile::output(int nSeqs, vector<double> data){
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "OneColumnFile", "output");
+		m->errorOut(e, "OneColumnFile", "output");
 		exit(1);
 	}
 }
@@ -339,20 +352,25 @@ void OneColumnFile::resetFile(){
 		if(counter != 0){
 			outFile.close();
 			inFile.close();
-		}
-		else{
+		}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)) { mothurOut("Unable to rename necessary files."); mothurOutEndLine(); }
+		if ((renameOk != 0)) { 
+			m->mothurOut("Unable to rename " + outName); m->mothurOutEndLine();
+			perror(" : ");
+		}	
 
 	}
 	catch(exception& e) {
-		errorOut(e, "OneColumnFile", "resetFile");
+		m->errorOut(e, "OneColumnFile", "resetFile");
 		exit(1);
 	}
 }
@@ -376,7 +394,7 @@ void SharedOneColumnFile::initFile(string label){
 			openInputFile(inName, inFile);
 		
 			string inputBuffer;
-			getline(inFile, inputBuffer);
+			inputBuffer = getline(inFile);
 		
 			outFile	<<  inputBuffer << '\t' << label  << endl;
 
@@ -391,7 +409,7 @@ void SharedOneColumnFile::initFile(string label){
 		outFile.setf(ios::showpoint);
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedOneColumnFile", "initFile");
+		m->errorOut(e, "SharedOneColumnFile", "initFile");
 		exit(1);
 	}
 }
@@ -409,7 +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;
 			}
@@ -418,7 +436,7 @@ void SharedOneColumnFile::output(int nSeqs, vector<double> data){
 			}
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedOneColumnFile", "output");
+		m->errorOut(e, "SharedOneColumnFile", "output");
 		exit(1);
 	}
 }
@@ -435,17 +453,20 @@ void SharedOneColumnFile::resetFile(){
 			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(); }
-
+		//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) {
-		errorOut(e, "SharedOneColumnFile", "resetFile");
+		m->errorOut(e, "SharedOneColumnFile", "resetFile");
 		exit(1);
 	}
 }