bugs fixes while testing for 1.5 release

[mothur.git] / fileoutput.cpp

diff --git a/fileoutput.cpp b/fileoutput.cpp
index 9c1f9c0f0c61fe3b27d84f699482d8708ad1e660..df1bfecfc0de7e3183ace1e826ef9d536f9dc5c3 100644 (file)
--- a/fileoutput.cpp
+++ b/fileoutput.cpp
@@ -16,7 +16,7 @@ ThreeColumnFile::~ThreeColumnFile(){
        inFile.close();
        outFile.close();
        remove(outName.c_str());
-};
+}
 
 /***********************************************************************/
 
@@ -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);
        }
 }
@@ -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";
+               errorOut(e, "ThreeColumnFile", "output");
                exit(1);
        }
-};
+}
 
 /***********************************************************************/
 
@@ -90,17 +82,13 @@ void ThreeColumnFile::resetFile(){
                renameOk = rename(outName.c_str(), inName.c_str());
                
                //checks to make sure user was able to rename and remove successfully
-               if ((renameOk != 0)) {  cout << "Unable to rename necessary files." << endl;  cout << outName << "  g   " << inName << endl;}
+               if ((renameOk != 0)) {  mothurOut("Unable to rename necessary files."); mothurOutEndLine(); }
 
        }
        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, "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";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/
@@ -111,7 +99,7 @@ ColumnFile::~ColumnFile(){
        inFile.close();
        outFile.close();
        remove(outName.c_str());
-};
+}
 
 /***********************************************************************/
 
@@ -142,11 +130,7 @@ void ColumnFile::initFile(string label, vector<string> tags){
                outFile.setf(ios::showpoint);
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ColumnFile class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the ColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ColumnFile", "initFile");
                exit(1);
        }
 }
@@ -160,14 +144,14 @@ void ColumnFile::output(vector<double> data){
                        string inputBuffer;
                        getline(inFile, inputBuffer);
 
-                       outFile << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length());
+                       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(globaldata->getIters().length());
+                       outFile << setprecision(6) << data[0] << setprecision(iters.length());
                        for (int i = 1; i< data.size(); i++) {
                                outFile << '\t' << data[i]; 
                        }
@@ -176,14 +160,10 @@ void ColumnFile::output(vector<double> data){
 
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ColumnFile class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the ColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ColumnFile", "output");
                exit(1);
        }
-};
+}
 
 /***********************************************************************/
 
@@ -202,17 +182,13 @@ void ColumnFile::resetFile(){
                renameOk = rename(outName.c_str(), inName.c_str());
                
                //checks to make sure user was able to rename and remove successfully
-               if ((renameOk != 0)) { cout << "Unable to rename necessary files." << endl; }
+               if ((renameOk != 0)) { mothurOut("Unable to rename necessary files."); mothurOutEndLine(); }
 
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ColumnFile", "resetFile");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/
@@ -223,7 +199,7 @@ SharedThreeColumnFile::~SharedThreeColumnFile(){
        inFile.close();
        outFile.close();
        remove(outName.c_str());
-};
+}
 
 /***********************************************************************/
 
@@ -247,11 +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);
        }
 }
@@ -272,14 +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";
-               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";
+               errorOut(e, "SharedThreeColumnFile", "output");
                exit(1);
        }
-};
+}
 
 /***********************************************************************/
 
@@ -297,17 +265,13 @@ void SharedThreeColumnFile::resetFile(){
                renameOk = rename(outName.c_str(), inName.c_str());
                
                //checks to make sure user was able to rename and remove successfully
-               if ((renameOk != 0)) { cout << "Unable to rename necessary files." << endl; }
+               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);
-       }       
 }
 
 /***********************************************************************/
@@ -319,7 +283,7 @@ OneColumnFile::~OneColumnFile(){
        inFile.close();
        outFile.close();
        remove(outName.c_str());        
-};
+}
 
 /***********************************************************************/
 
@@ -343,13 +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);
-       }       
 }
 
 /***********************************************************************/
@@ -367,14 +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);
-       }       
-};
+}
 
 /***********************************************************************/
 
@@ -392,17 +348,13 @@ void OneColumnFile::resetFile(){
                renameOk = rename(outName.c_str(), inName.c_str());
                
                //checks to make sure user was able to rename and remove successfully
-               if ((renameOk != 0)) { cout << "Unable to rename necessary files." << endl; }
+               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);
-       }       
 }
 
 /***********************************************************************/
@@ -413,7 +365,7 @@ SharedOneColumnFile::~SharedOneColumnFile(){
        inFile.close();
        outFile.close();
        remove(outName.c_str());        
-};
+}
 
 /***********************************************************************/
 
@@ -439,13 +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);
-       }       
 }
 
 /***********************************************************************/
@@ -461,7 +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;
                        }
@@ -470,14 +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);
-       }       
-};
+}
 
 /***********************************************************************/
 
@@ -496,18 +440,14 @@ void SharedOneColumnFile::resetFile(){
                renameOk = rename(outName.c_str(), inName.c_str());
                
                //checks to make sure user was able to rename and remove successfully
-               if ((renameOk != 0)) { cout << "Unable to rename necessary files." << endl; }
+               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);
-       }       
 }
 
 /***********************************************************************/