From: westcott <westcott>
Date: Tue, 21 Apr 2009 13:33:41 +0000 (+0000)
Subject: fixed bug with parsimony(groups=all) and unifrac.unweighted(groups=all)
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=9653c9f8c1b63ecb1a63b45e781c303713d5b5df;p=mothur.git

fixed bug with parsimony(groups=all) and unifrac.unweighted(groups=all)
---

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index b5c59e8..56305e2 100644
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -36,12 +36,8 @@ ParsimonyCommand::ParsimonyCommand() {
 		util->getCombos(groupComb, globaldata->Groups, numComp);
 		globaldata->setGroups("");
 		
-		//ABC
-		if (numComp != 1) {
-			groupComb.push_back(allGroups);
-			numComp++;
-		}
-
+		if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
+		
 		convert(globaldata->getIters(), iters);  //how many random trees to generate
 		pars = new Parsimony(tmap);
 		counter = 0;
diff --git a/sharedutilities.cpp b/sharedutilities.cpp
index edd16c7..454b7d4 100644
--- a/sharedutilities.cpp
+++ b/sharedutilities.cpp
@@ -211,24 +211,24 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 				for (int i=0; i < allGroups.size(); i++) { 
 					if (allGroups[i] != "xxx") {
 						userGroups.push_back(allGroups[i]);
-						label += allGroups[i] + "-";
 					}
 				}
 			}
 		}else { //the user has not entered groups
 			for (int i=0; i < allGroups.size(); i++) { 
 				if (allGroups[i] != "xxx") {
-					label += allGroups[i] + "-";
 					if (mode == "weighted") {
 						userGroups.push_back(allGroups[i]);
 					}else {
 						numGroups = 1;
+						label += allGroups[i] + "-";
 					}
 				}
 			}
+			//rip extra - off allgroups 
+			label = label.substr(0, label.length()-1);
 		}
 		
-		
 		if (mode == "weighted") {
 			//if the user only entered invalid groups
 			if (userGroups.size() == 0) { 
@@ -256,20 +256,11 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 					for (int i = 0; i < allGroups.size(); i++) {
 						if (allGroups[i] != "xxx") {
 							userGroups.push_back(allGroups[i]);
-							label += allGroups[i] + "-";
 						}
 					}
-				}else {
-					for (int i = 0; i < userGroups.size(); i++) {
-						label += userGroups[i] + "-";
-					}
 				}
 				
-				//rip extra - off allgroups 
-				label = label.substr(0, label.length()-1);
-				
 				if (numGroups != 1) { numGroups = userGroups.size(); }
-		
 		}
 	}
 	catch(exception& e) {
diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index a9b46bf..fcff253 100644
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -24,13 +24,8 @@ UnifracUnweightedCommand::UnifracUnweightedCommand() {
 		util->getCombos(groupComb, globaldata->Groups, numComp);
 		globaldata->setGroups("");
 		
-		//ABC
-		if (numComp != 1) {
-			groupComb.push_back(allGroups);
-			numComp++;
-		}
-
-		
+		if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
+				
 		convert(globaldata->getIters(), iters);  //how many random trees to generate
 		unweighted = new Unweighted(tmap);
 
@@ -61,9 +56,6 @@ int UnifracUnweightedCommand::execute() {
 			
 			output = new ColumnFile(globaldata->getTreeFile()  + toString(i+1) + ".unweighted");
 			
-			outSum << i+1 << '\t';
-			cout << i+1 << '\t';
-			
 			//get unweighted for users tree
 			rscoreFreq.resize(numComp);  
 			rCumul.resize(numComp);  
@@ -116,7 +108,7 @@ int UnifracUnweightedCommand::execute() {
 		
 		
 			printUnweightedFile();
-			printUWSummaryFile();
+			printUWSummaryFile(i);
 			
 			delete output;
 			rscoreFreq.clear(); 
@@ -171,7 +163,7 @@ void UnifracUnweightedCommand::printUnweightedFile() {
 }
 
 /***********************************************************/
-void UnifracUnweightedCommand::printUWSummaryFile() {
+void UnifracUnweightedCommand::printUWSummaryFile(int i) {
 	try {
 				
 		//format output
@@ -180,6 +172,9 @@ void UnifracUnweightedCommand::printUWSummaryFile() {
 		//print each line
 
 		for(int a = 0; a < numComp; a++) {
+			outSum << i+1 << '\t';
+			cout << i+1 << '\t';
+			
 			if (UWScoreSig[a][0] > (1/(float)iters)) {
 				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; 
diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index d9991e8..e900af4 100644
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -51,7 +51,7 @@ class UnifracUnweightedCommand : public Command {
 		ofstream outSum, out;
 		ifstream inFile;
 		
-		void printUWSummaryFile();
+		void printUWSummaryFile(int);
 		void printUnweightedFile();