fixed bug in read.tree updates help and validparameters strings, added ability for...

[mothur.git] / parsimonycommand.cpp

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 474f732ef9b3c448e6bfe27753df7d59c4dec300..86f8d013c59449b96009ba07859be7e0985cc141 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -28,8 +28,8 @@ ParsimonyCommand::ParsimonyCommand() {
                }else { //user wants random distribution
                        savetmap = globaldata->gTreemap;
                        getUserInput();
-                       parsFile = randomtree + ".rd_parsimony";
-                       openOutputFile(parsFile, out);
+                       parsFile = randomtree;
+                       parsFileout = globaldata->getTreeFile() + "temp";
                }
                
                //set users groups to analyze
@@ -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("");
@@ -226,8 +249,8 @@ void ParsimonyCommand::printParsimonyFile() {
 void ParsimonyCommand::printUSummaryFile() {
        try {
                //column headers
-               outSum << "Tree#" << '\t' << "Comb" << '\t'  <<  "ParsScore" << '\t' << '\t' << "ParsSig" <<  endl;
-               cout << "Tree#" << '\t' << "Comb" << '\t'  <<  "ParsScore" << '\t' << '\t' << "ParsSig" <<  endl;
+               outSum << "Tree#" << '\t' << "Groups" << '\t'  <<  "ParsScore" << '\t' << "ParsSig" <<  endl;
+               cout << "Tree#" << '\t' << "Groups" << '\t'  <<  "ParsScore" << '\t' << "ParsSig" <<  endl;
                
                //format output
                outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
@@ -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' << '\t' << userTreeScores[a][i] << '\t' << UScoreSig[a][i] << endl;
-                                       cout << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << '\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' << '\t' << userTreeScores[a][i] << '\t' << "<" << (1/float(iters)) << endl;
-                                       cout << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << '\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;
                
        }
@@ -327,9 +352,11 @@ void ParsimonyCommand::setGroups() {
                                if (globaldata->Groups.size() == 0) { 
                                        cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl; 
                                        for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
-                                               globaldata->Groups.push_back(tmap->namesOfGroups[i]);
-                                               numGroups++;
-                                               allGroups += tmap->namesOfGroups[i] + "-";
+                                               if (tmap->namesOfGroups[i] != "xxx") {
+                                                       allGroups += tmap->namesOfGroups[i] + "-";
+                                                       globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+                                                       numGroups++;
+                                               }
                                        }
                                        allGroups = allGroups.substr(0, allGroups.length()-1);
                                }else {
@@ -340,17 +367,22 @@ void ParsimonyCommand::setGroups() {
                                        allGroups = allGroups.substr(0, allGroups.length()-1);
                                }
                        }else{//user has enter "all" and wants the default groups
+                               globaldata->Groups.clear();
                                for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
-                                       globaldata->Groups.push_back(tmap->namesOfGroups[i]);
-                                       numGroups++;
-                                       allGroups += tmap->namesOfGroups[i] + "-";
+                                       if (tmap->namesOfGroups[i] != "xxx") {
+                                               globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+                                               numGroups++;
+                                               allGroups += tmap->namesOfGroups[i] + "-";
+                                       }
                                }
                                allGroups = allGroups.substr(0, allGroups.length()-1);
                                globaldata->setGroups("");
                        }
                }else {
                        for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
-                               allGroups += tmap->namesOfGroups[i] + "-";
+                               if (tmap->namesOfGroups[i] != "xxx") {
+                                       allGroups += tmap->namesOfGroups[i] + "-";
+                               }
                        }
                        allGroups = allGroups.substr(0, allGroups.length()-1);
                        numGroups = 1;
@@ -396,7 +428,7 @@ void ParsimonyCommand::initFile(string label){
                        if (randomtree == "") {
                                out <<  inputBuffer << '\t' << label + "Score" << '\t' << label + "UserFreq" << '\t' << label + "UserCumul" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
                        }else {
-                               out <<  inputBuffer << '\t' << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
+                               out <<  inputBuffer << '\t' << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
                        }
                }else{
                        openOutputFile(parsFileout, out);
@@ -404,7 +436,7 @@ void ParsimonyCommand::initFile(string label){
                        if (randomtree == "") {
                                out << label + "Score" << '\t' << label + "UserFreq" << '\t' << label + "UserCumul" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
                        }else {
-                               out << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
+                               out << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
                        }
                }
 
@@ -430,16 +462,16 @@ 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;
                        }
                }