added bootstrap.shared command and fixed some bugs with heatmap

[mothur.git] / unifracweightedcommand.cpp

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index 5f7b4ad5363a2660aa2df7ac9ecb8f3fa998a13d..6dfbd710765478d3e7b5c8dc21ab844fa4a6b231 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -56,9 +56,8 @@ int UnifracWeightedCommand::execute() {
                        counter = 0;
                        rScores.resize(numComp);  //data[0] = weightedscore AB, data[1] = weightedscore AC...
                        uScores.resize(numComp);  //data[0] = weightedscore AB, data[1] = weightedscore AC...
-                       //weightedFile = globaldata->getTreeFile()  + toString(i+1) + ".weighted";
-                       //weightedFileout = globaldata->getTreeFile() + "temp." + toString(i+1) + ".weighted";
-                       output = new ThreeColumnFile2(globaldata->getTreeFile()  + toString(i+1) + ".weighted");
+                       
+                       output = new ColumnFile(globaldata->getTreeFile()  + toString(i+1) + ".weighted");
 
                        userData = weighted->getValues(T[i]);  //userData[0] = weightedscore
                        
@@ -163,11 +162,6 @@ void UnifracWeightedCommand::printWeightedFile() {
                        } 
                        output->resetFile();
                }
-               
-               //out.close();
-               //inFile.close();
-               //remove(weightedFileout.c_str());
-               
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -284,92 +278,8 @@ void UnifracWeightedCommand::calculateFreqsCumuls() {
 
 }
 
-/*****************************************************************
-
-void UnifracWeightedCommand::initFile(string label){
-       try {
-               if(counter != 0){
-                       openOutputFile(weightedFileout, out);
-                       openInputFile(weightedFile, inFile);
-
-                       string inputBuffer;
-                       getline(inFile, inputBuffer);
-               
-                       out     <<  inputBuffer << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;           
-               }else{
-                       openOutputFile(weightedFileout, out);
-                       out     << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
-               }
-
-               out.setf(ios::fixed, ios::floatfield);
-               out.setf(ios::showpoint);
-       }
-       catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the UnifracWeightedCommand class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-}
-
-/***********************************************************************
-
-void UnifracWeightedCommand::output(vector<double> data){
-       try {
-               if(counter != 0){               
-                       string inputBuffer;
-                       getline(inFile, inputBuffer);
-
-                       out << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length())  << '\t' << data[1] << '\t' << data[2] << endl;
-               }
-               else{
-                       out << setprecision(6) << data[0] << setprecision(globaldata->getIters().length())  << '\t' << data[1] << '\t' << data[2] << endl;
-
-               }
-               
-       }
-       catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the UnifracWeightedCommand class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-};
-
-/***********************************************************************
-
-void UnifracWeightedCommand::resetFile(){
-       try {
-               if(counter != 0){
-                       out.close();
-                       inFile.close();
-               }
-               else{
-                       out.close();
-               }
-               counter = 1;
-               
-               remove(weightedFile.c_str());
-               rename(weightedFileout.c_str(), weightedFile.c_str());
-       }
-       catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the UnifracWeightedCommand class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       
-       
-                       
-}
+/***********************************************************/
 
-*/