added bootstrap.shared command and fixed some bugs with heatmap

[mothur.git] / parsimonycommand.cpp

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 4fa4ec5ed0943614bf4da9d5a1f03b5d8f706a42..b5c59e87104cb7d413ca4984fee751fbe8707ba4 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -21,15 +21,13 @@ ParsimonyCommand::ParsimonyCommand() {
                if (randomtree == "") { 
                        T = globaldata->gTree;
                        tmap = globaldata->gTreemap;
-                       parsFile = globaldata->getTreeFile() + ".parsimony";
-                       parsFileout = globaldata->getTreeFile() + "temp" + ".parsimony";
+                       output = new ColumnFile(globaldata->getTreeFile()  +  ".parsimony");
                        sumFile = globaldata->getTreeFile() + ".psummary";
                        openOutputFile(sumFile, outSum);
                }else { //user wants random distribution
                        savetmap = globaldata->gTreemap;
                        getUserInput();
-                       parsFile = randomtree;
-                       parsFileout = globaldata->getTreeFile() + "temp";
+                       output = new ColumnFile(randomtree);
                }
                
                //set users groups to analyze
@@ -223,12 +221,16 @@ int ParsimonyCommand::execute() {
 void ParsimonyCommand::printParsimonyFile() {
        try {
                vector<double> data;
+               vector<string> tags;
                
-               //format output
-               out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+               if (randomtree == "") {
+                       tags.push_back("Score"); tags.push_back("UserFreq"); tags.push_back("UserCumul"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
+               }else {
+                       tags.push_back("Score"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
+               }
 
                for(int a = 0; a < numComp; a++) {
-                       initFile(groupComb[a]);
+                       output->initFile(groupComb[a], tags);
                        //print each line
                        for (it = validScores.begin(); it != validScores.end(); it++) { 
                                if (randomtree == "") {
@@ -236,15 +238,11 @@ void ParsimonyCommand::printParsimonyFile() {
                                }else{
                                        data.push_back(it->first);  data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]); 
                                }
-                               output(data);
+                               output->output(data);
                                data.clear();
                        } 
-                       resetFile();
+                       output->resetFile();
                }
-               
-               out.close();
-               inFile.close();
-               remove(parsFileout.c_str());
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function printParsimonyFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -340,102 +338,7 @@ void ParsimonyCommand::getUserInput() {
                exit(1);
        }
 }
-/*****************************************************************/
-
-void ParsimonyCommand::initFile(string label){
-       try {
-               if(counter != 0){
-                       openOutputFile(parsFileout, out);
-                       openInputFile(parsFile, inFile);
-
-                       string inputBuffer;
-                       getline(inFile, inputBuffer);
-                       
-                       if (randomtree == "") {
-                               out <<  inputBuffer << '\t' << label + "Score" << '\t' << label + "UserFreq" << '\t' << label + "UserCumul" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
-                       }else {
-                               out <<  inputBuffer << '\t' << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
-                       }
-               }else{
-                       openOutputFile(parsFileout, out);
-                       //column headers
-                       if (randomtree == "") {
-                               out << label + "Score" << '\t' << label + "UserFreq" << '\t' << label + "UserCumul" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
-                       }else {
-                               out << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
-                       }
-               }
-
-               out.setf(ios::fixed, ios::floatfield);
-               out.setf(ios::showpoint);
-       }
-       catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the ParsimonyCommand class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-}
-
-/***********************************************************************/
 
-void ParsimonyCommand::output(vector<double> data){
-       try {
-               if(counter != 0){               
-                       string inputBuffer;
-                       getline(inFile, inputBuffer);
-               
-                       if (randomtree == "") {
-                               out << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length())  << '\t' << data[1] << '\t' << data[2] << '\t' << data[3] << '\t' << data[4] << endl;
-                       }else{
-                               out << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length())  << '\t' << data[1] << '\t' << data[2] << endl;
-                       }
-               }
-               else{
-                       if (randomtree == "") {
-                               out << setprecision(6) << data[0] << setprecision(globaldata->getIters().length())  << '\t' << data[1] << '\t' << data[2] << '\t' << data[3] << '\t' << data[4] << 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 ParsimonyCommand class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the ParsimonyCommand class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-void ParsimonyCommand::resetFile(){
-       try {
-               if(counter != 0){
-                       out.close();
-                       inFile.close();
-               }
-               else{
-                       out.close();
-               }
-               counter = 1;
-               
-               remove(parsFile.c_str());
-               rename(parsFileout.c_str(), parsFile.c_str());
-       }
-       catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the ParsimonyCommand class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
-}
+/***********************************************************/