fixed memory leak in parsimony calculator and added progress bars to parsimony and...

[mothur.git] / unifracunweightedcommand.cpp

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 6fd986fc6022d6642179d58ed3b497c4f2166439..65f30ebc949f4945023fd295224d00d52827d82b 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -36,24 +36,23 @@ UnifracUnweightedCommand::UnifracUnweightedCommand() {
 /***********************************************************/
 int UnifracUnweightedCommand::execute() {
        try {
-       
+
                userData.resize(numComp,0);  //data[0] = unweightedscore 
                randomData.resize(numComp,0); //data[0] = unweightedscore
                //create new tree with same num nodes and leaves as users
-                               
+               
+               outSum << "Tree#" << '\t' << "Groups" << '\t'  <<  "UWScore" <<'\t' << "UWSig" <<  endl;
+               cout << "Tree#" << '\t' << "Groups" << '\t'  <<  "UWScore" << '\t' << "UWSig" <<  endl;
+               
                //get pscores for users trees
                for (int i = 0; i < T.size(); i++) {
                        counter = 0;
                        unweightedFile = globaldata->getTreeFile()  + toString(i+1) + ".unweighted";
                        unweightedFileout = globaldata->getTreeFile() + "temp." + toString(i+1) + ".unweighted";
                        
-                       //column headers
-//                     outSum << "Tree# " << i+1 << endl;
-                       outSum << "Tree#" << '\t' << "Groups" << '\t'  <<  "UWScore" <<'\t' << "UWSig" <<  endl;
-//                     cout << "Tree# " << i+1 << endl;
-                       cout << "Tree#" << '\t' << "Groups" << '\t'  <<  "UWScore" << '\t' << "UWSig" <<  endl;
-
-
+                       outSum << i+1 << '\t';
+                       cout << i+1 << '\t';
+                       
                        //get unweighted for users tree
                        rscoreFreq.resize(numComp);  
                        rCumul.resize(numComp);  
@@ -66,6 +65,7 @@ int UnifracUnweightedCommand::execute() {
                        for(int k = 0; k < numComp; k++) {
                                //saves users score
                                utreeScores[k].push_back(userData[k]);
+
                        }
                        
                        //get unweighted scores for random trees
@@ -85,6 +85,7 @@ int UnifracUnweightedCommand::execute() {
                                        //add randoms score to validscores
                                        validScores[randomData[k]] = randomData[k];
                                }
+                               
                        }
                
                for(int a = 0; a < numComp; a++) {
@@ -101,6 +102,8 @@ int UnifracUnweightedCommand::execute() {
                        UWScoreSig[a].push_back(rCumul[a][userData[a]]);
                }
                
+               
+               
                printUnweightedFile();
                printUWSummaryFile();
                
@@ -165,15 +168,14 @@ void UnifracUnweightedCommand::printUWSummaryFile() {
                outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
                        
                //print each line
-               for (int i = 0; i< T.size(); i++) {
-                       for(int a = 0; a < numComp; a++) {
-                               if (UWScoreSig[a][i] > (1/(float)iters)) {
-                                       outSum << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << utreeScores[a][i] << '\t' << UWScoreSig[a][i] << endl;
-                                       cout << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << utreeScores[a][i] << '\t' << UWScoreSig[a][i] << endl;
-                               }else {
-                                       outSum << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << utreeScores[a][i] << '\t' << "<" << (1/float(iters)) << endl;
-                                       cout << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << utreeScores[a][i] << '\t' << "<" << (1/float(iters)) << endl;
-                               }
+
+               for(int a = 0; a < numComp; a++) {
+                       if (UWScoreSig[a][0] > (1/(float)iters)) {
+                               outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << UWScoreSig[a][0] << endl;
+                               cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << UWScoreSig[a][0] << endl; 
+                       }else {
+                               outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl;
+                               cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl; 
                        }
                }
                
@@ -303,10 +305,10 @@ void UnifracUnweightedCommand::output(vector<double> data){
                        getline(inFile, inputBuffer);
 //                     out     <<  inputBuffer << setprecision(6) << '\t' << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << endl;
                
-                       out     <<  inputBuffer << setprecision(globaldata->getIters().length()-1) << '\t' << data[1] << '\t' << data[2] << endl;
+                       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()-1) << '\t' << data[1] << '\t' << data[2] << endl;
+                       out << setprecision(6) << data[0] << setprecision(globaldata->getIters().length())  << '\t' << data[1] << '\t' << data[2] << endl;
                }
 
        }