X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.cpp;h=86f8d013c59449b96009ba07859be7e0985cc141;hb=2e5ec5cbbd23637ed20da9bdd544d178a3b5d949;hp=474f732ef9b3c448e6bfe27753df7d59c4dec300;hpb=ed04a159be4f1fab2850fa4dd2f40bf51e94e974;p=mothur.git

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 474f732..86f8d01 100644
--- 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;
 			}
 		}