bugs for 1.5

[mothur.git] / fileoutput.cpp

diff --git a/fileoutput.cpp b/fileoutput.cpp
index 63130a83ba6c850bc8db4ea720ba51a15d80ff81..597a05a6ad9a892caff5f0b6f69269ae6af4013d 100644 (file)
--- 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;
                }
@@ -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;
                }
@@ -110,7 +110,7 @@ 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++) {
@@ -142,7 +142,7 @@ 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++) {
@@ -210,7 +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;
                }
@@ -234,7 +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;
                }
@@ -294,7 +294,7 @@ void OneColumnFile::initFile(string label){
                        openInputFile(inName, inFile);
                
                        string inputBuffer;
-                       getline(inFile, inputBuffer);
+                       inputBuffer = getline(inFile);
                
                        outFile <<  inputBuffer << '\t' << label << endl;
                }
@@ -318,7 +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;
                }
@@ -376,7 +376,7 @@ void SharedOneColumnFile::initFile(string label){
                        openInputFile(inName, inFile);
                
                        string inputBuffer;
-                       getline(inFile, inputBuffer);
+                       inputBuffer = getline(inFile);
                
                        outFile <<  inputBuffer << '\t' << label  << endl;
 
@@ -409,7 +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;
                        }