added bootstrap.shared command and fixed some bugs with heatmap

[mothur.git] / fileoutput.cpp

diff --git a/fileoutput.cpp b/fileoutput.cpp
index e6f069dd894e7fe5702b63e5fe6e4c3ce85bc25e..9c1f9c0f0c61fe3b27d84f699482d8708ad1e660 100644 (file)
--- a/fileoutput.cpp
+++ b/fileoutput.cpp
@@ -90,7 +90,7 @@ 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; }
+               if ((renameOk != 0)) {  cout << "Unable to rename necessary files." << endl;  cout << outName << "  g   " << inName << endl;}
 
        }
        catch(exception& e) {
@@ -106,7 +106,7 @@ void ThreeColumnFile::resetFile(){
 /***********************************************************************/
 /***********************************************************************/
 
-ThreeColumnFile2::~ThreeColumnFile2(){
+ColumnFile::~ColumnFile(){
        
        inFile.close();
        outFile.close();
@@ -115,7 +115,7 @@ ThreeColumnFile2::~ThreeColumnFile2(){
 
 /***********************************************************************/
 
-void ThreeColumnFile2::initFile(string label, vector<string> tags){
+void ColumnFile::initFile(string label, vector<string> tags){
        try {
                if(counter != 0){
                        openOutputFile(outName, outFile);
@@ -125,7 +125,7 @@ void ThreeColumnFile2::initFile(string label, vector<string> tags){
                        getline(inFile, inputBuffer);
                
                        outFile <<  inputBuffer << '\t'; 
-                       for(int i = 1; i < tags.size(); i++) {
+                       for(int i = 0; i < tags.size(); i++) {
                                outFile << label + tags[i] << '\t';
                        }
                        outFile << endl;
@@ -136,52 +136,58 @@ void ThreeColumnFile2::initFile(string label, vector<string> tags){
                                outFile << label + tags[i] << '\t';
                        }
                        outFile << endl;
-
                }
 
                outFile.setf(ios::fixed, ios::floatfield);
                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";
+               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 ThreeColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               cout << "An unknown error has occurred in the ColumnFile class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
                exit(1);
        }
 }
 
 /***********************************************************************/
 
-void ThreeColumnFile2::output(vector<double> data){
+void ColumnFile::output(vector<double> data){
        try {
        
                if(counter != 0){               
                        string inputBuffer;
                        getline(inFile, inputBuffer);
 
-                       outFile << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length())  << '\t' << data[1] << '\t' << data[2] << endl;
+                       outFile << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().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())  << '\t' << data[1] << '\t' << data[2] << endl;
-
+                       outFile << setprecision(6) << data[0] << setprecision(globaldata->getIters().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 ThreeColumnFile2 class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               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 ThreeColumnFile2 class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               cout << "An unknown error has occurred in the ColumnFile class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
                exit(1);
        }
 };
 
 /***********************************************************************/
 
-void ThreeColumnFile2::resetFile(){
+void ColumnFile::resetFile(){
        try {
                if(counter != 0){
                        outFile.close();
@@ -200,11 +206,11 @@ void ThreeColumnFile2::resetFile(){
 
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ThreeColumnFile2 class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               cout << "Standard Error: " << e.what() << " has occurred in the ColumnFile class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
                exit(1);
        }
        catch(...) {
-               cout << "An unknown error has occurred in the ThreeColumnFile2 class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               cout << "An unknown error has occurred in the ColumnFile class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
                exit(1);
        }       
 }