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

[mothur.git] / parsimonycommand.cpp

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index f718653e718a9918d25fd647f5df7984745c554d..190b7d6ce1b913c733e52b974451cb9b3d81664b 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -51,7 +51,9 @@ ParsimonyCommand::ParsimonyCommand() {
 /***********************************************************/
 int ParsimonyCommand::execute() {
        try {
-       
+               Progress* reading;
+               reading = new Progress("Comparing to random:", iters);
+               
                //get pscore for users tree
                userData.resize(numComp,0);  //data = AB, AC, BC, ABC.
                randomData.resize(numComp,0);  //data = AB, AC, BC, ABC.
@@ -66,9 +68,10 @@ int ParsimonyCommand::execute() {
                        //get pscores for users trees
                        for (int i = 0; i < T.size(); i++) {
                                userData = pars->getValues(T[i]);  //data = AB, AC, BC, ABC.
-                               
+
                                //output scores for each combination
                                for(int k = 0; k < numComp; k++) {
+
                                        //update uscoreFreq
                                        it = uscoreFreq[k].find(userData[k]);
                                        if (it == uscoreFreq[k].end()) {//new score
@@ -87,11 +90,13 @@ int ParsimonyCommand::execute() {
                        for (int j = 0; j < iters; j++) {
                                //create new tree with same num nodes and leaves as users
                                randT = new Tree();
+
                                //create random relationships between nodes
                                randT->assembleRandomTree();
+
                                //get pscore of random tree
                                randomData = pars->getValues(randT);
-                               
+                                       
                                for(int r = 0; r < numComp; r++) {
                                        //add trees pscore to map of scores
                                        it2 = rscoreFreq[r].find(randomData[r]);
@@ -105,18 +110,24 @@ int ParsimonyCommand::execute() {
                                        validScores[randomData[r]] = randomData[r];
                                }
                                
+                               //update progress bar
+                               reading->update(j);
+                               
                                delete randT;
                        }
+
                }else {
                        //get pscores for random trees
                        for (int j = 0; j < iters; j++) {
                                //create new tree with same num nodes and leaves as users
                                randT = new Tree();
                                //create random relationships between nodes
+
                                randT->assembleRandomTree();
+
                                //get pscore of random tree
                                randomData = pars->getValues(randT);
-                               
+                       
                                for(int r = 0; r < numComp; r++) {
                                        //add trees pscore to map of scores
                                        it2 = rscoreFreq[r].find(randomData[r]);
@@ -130,10 +141,13 @@ int ParsimonyCommand::execute() {
                                        validScores[randomData[r]] = randomData[r];
                                }
                                
+                               //update progress bar
+                               reading->update(j);
+                               
                                delete randT;
                        }
                }
-               
+
                for(int a = 0; a < numComp; a++) {
                        float rcumul = 0.0000;
                        float ucumul = 0.0000;
@@ -162,11 +176,20 @@ int ParsimonyCommand::execute() {
                        }
                }
                
+               //finish progress bar
+               reading->finish();
+               delete reading;
+
+               
                printParsimonyFile();
                if (randomtree == "") { printUSummaryFile(); }
                
                //reset globaldata's treemap if you just did random distrib
-               if (randomtree != "") { globaldata->gTreemap = savetmap; }
+               if (randomtree != "") {
+                       //memory leak prevention
+                       //if (globaldata->gTreemap != NULL) { delete globaldata->gTreemap;  }
+                       globaldata->gTreemap = savetmap;
+               }
                
                //reset randomTree parameter to ""
                globaldata->setRandomTree("");
@@ -237,11 +260,11 @@ void ParsimonyCommand::printUSummaryFile() {
                for (int i = 0; i< T.size(); i++) {
                        for(int a = 0; a < numComp; a++) {
                                if (UScoreSig[a][i] > (1/(float)iters)) {
-                                       outSum << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << '\t' << UScoreSig[a][i] << endl;
-                                       cout << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << '\t' << UScoreSig[a][i] << endl;
+                                       outSum << setprecision(6) << i+1 << '\t' << groupComb[a]  << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length()) << '\t' << UScoreSig[a][i] << endl;
+                                       cout << setprecision(6) << i+1 << '\t' << groupComb[a]  << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length()) << '\t' << UScoreSig[a][i] << endl;
                                }else {
-                                       outSum << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << '\t' << "<" << (1/float(iters)) << endl;
-                                       cout << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << '\t' << "<" << (1/float(iters)) << endl;
+                                       outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length())  << '\t' << "<" << (1/float(iters)) << endl;
+                                       cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length()) << '\t' << "<" << (1/float(iters)) << endl;
                                }
                        }
                }
@@ -293,6 +316,8 @@ void ParsimonyCommand::getUserInput() {
                getline(cin, s);
                
                //save tmap for later
+               //memory leak prevention
+               //if (globaldata->gTreemap != NULL) { delete globaldata->gTreemap;  }
                globaldata->gTreemap = tmap;
                
        }
@@ -431,16 +456,16 @@ void ParsimonyCommand::output(vector<double> data){
                        getline(inFile, inputBuffer);
                
                        if (randomtree == "") {
-                               out << inputBuffer << '\t' << setprecision(globaldata->getIters().length()) << data[0] << '\t' << data[1] << '\t' << data[2] << '\t' << data[3] << '\t' << data[4] << endl;
+                               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(globaldata->getIters().length()) << data[0] << '\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{
                        if (randomtree == "") {
-                               out << setprecision(globaldata->getIters().length()) << data[0] << '\t' << data[1] << '\t' << data[2] << '\t' << data[3] << '\t' << data[4] << endl;
+                               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(globaldata->getIters().length()) << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
+                               out << setprecision(6) << data[0] << setprecision(globaldata->getIters().length())  << '\t' << data[1] << '\t' << data[2] << endl;
                        }
                }