X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.cpp;h=c7340c7b1704c585b70e2677c0701aaf7edb4e33;hb=9651e8e7172d86707b34af15e95ec60ad4c3c3f9;hp=ee2125e99168553cb0e45de137d46211bdfc6421;hpb=f94ef0ca699bbb8f0d6dba8357c55f699a1ae29f;p=mothur.git

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index ee2125e..c7340c7 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";
-			parsFileout = globaldata->getTreeFile() + "temp" + ".rd_parsimony";
+			parsFile = randomtree;
+			parsFileout = globaldata->getTreeFile() + "temp";
 		}
 		
 		//set users groups to analyze
@@ -226,8 +226,8 @@ 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 +237,11 @@ 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' << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length()) << '\t' << UScoreSig[a][i] << endl;
+					cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << '\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;
 				}
 			}
 		}
@@ -340,6 +340,7 @@ 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++;
@@ -396,7 +397,7 @@ 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 +405,7 @@ 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 +431,16 @@ 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;
 			}
 		}