X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.cpp;h=2b93df782bccc4d2dbc8533e7cdc38169059d6a7;hb=2e5ec5cbbd23637ed20da9bdd544d178a3b5d949;hp=cf1cbce05dfce301409d3b80d861f0fb9dc0a0bd;hpb=8fd4a602269974e6548f4a387dddd6bd80a999ab;p=mothur.git

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index cf1cbce..2b93df7 100644
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -36,7 +36,7 @@ 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
@@ -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();
 		
@@ -168,11 +171,11 @@ void UnifracUnweightedCommand::printUWSummaryFile() {
 
 		for(int a = 0; a < numComp; a++) {
 			if (UWScoreSig[a][0] > (1/(float)iters)) {
-				outSum << setprecision(6) << groupComb[a] << '\t' << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << UWScoreSig[a][0] << endl;
-				cout << setprecision(6)  << groupComb[a] << '\t' << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << UWScoreSig[a][0] << endl; 
+				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' << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl;
-				cout << setprecision(6)  << groupComb[a] << '\t' << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl; 
+				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; 
 			}
 		}
 		
@@ -208,9 +211,11 @@ void UnifracUnweightedCommand::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") {
+							globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+							numGroups++;
+							allGroups += tmap->namesOfGroups[i] + "-";
+						}
 					}
 					allGroups = allGroups.substr(0, allGroups.length()-1);
 				}else {
@@ -223,16 +228,20 @@ void UnifracUnweightedCommand::setGroups() {
 			}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;