From: westcott <westcott>
Date: Thu, 23 Sep 2010 17:53:42 +0000 (+0000)
Subject: fixed order of unifrac commands so that it matches the summary commands
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=4745a956b3116a719f52f341d2a2db84df4817da;hp=61798fe609675abfedf511e542cc48c56a531199;p=mothur.git

fixed order of unifrac commands so that it matches the summary commands
---

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index a94c72c..7d1f4df 100644
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -177,7 +177,7 @@ int MetaStatsCommand::execute(){
 		
 		int numGroups = Sets.size();
 		for (int a=0; a<numGroups; a++) { 
-			for (int l = a+1; l < numGroups; l++) {	
+			for (int l = 0; l < a; l++) {	
 				vector<string> groups; groups.push_back(Sets[a]); groups.push_back(Sets[l]);
 				namesOfGroupCombos.push_back(groups);
 			}
diff --git a/mothur b/mothur
index 7bf5ba3..83351b2 100755
Binary files a/mothur and b/mothur differ
diff --git a/sharedutilities.cpp b/sharedutilities.cpp
index 6dffee9..d2a43ea 100644
--- a/sharedutilities.cpp
+++ b/sharedutilities.cpp
@@ -275,9 +275,13 @@ void SharedUtil::getCombos(vector<string>& groupComb, vector<string> userGroups,
 		numComp = 0;
 		for (int i=0; i< userGroups.size(); i++) { 
 			numComp += i; 
-			for (int l = i+1; l < userGroups.size(); l++) {
-				//set group comparison labels
-				groupComb.push_back(userGroups[i] + "-" + userGroups[l]);
+			for (int l = 0; l < i; l++) {
+				if (userGroups[i] > userGroups[l]) {
+					//set group comparison labels
+					groupComb.push_back(userGroups[l] + "-" + userGroups[i]);
+				}else{
+					groupComb.push_back(userGroups[i] + "-" + userGroups[l]);
+				}
 			}
 		} 
 	}
diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index e43c997..e6472a8 100644
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -231,7 +231,7 @@ int SummarySharedCommand::execute(){
 		input = globaldata->ginput;
 		lookup = input->getSharedRAbundVectors();
 		string lastLabel = lookup[0]->getLabel();
-		
+	
 		/******************************************************/
 		//output headings for files
 		/******************************************************/
@@ -412,7 +412,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
 				
 			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 				if(processors == 1){
-					driver(thisLookup, 0, numGroups, sumFileName, sumAllFileName);
+					driver(thisLookup, 0, numGroups, sumFileName+".temp", sumAllFileName+".temp");
 					m->appendFiles((sumFileName + ".temp"), sumFileName);
 					remove((sumFileName + ".temp").c_str());
 					if (mult) {
diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index 1417b5a..e4a0a9d 100644
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -158,7 +158,7 @@ int UnifracWeightedCommand::execute() {
 				//calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
 				vector< vector<string> > namesOfGroupCombos;
 				for (int a=0; a<numGroups; a++) { 
-					for (int l = a+1; l < numGroups; l++) {	
+					for (int l = 0; l < a; l++) {	
 						vector<string> groups; groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
 						namesOfGroupCombos.push_back(groups);
 					}
diff --git a/unweighted.cpp b/unweighted.cpp
index a9515d1..8103688 100644
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -24,7 +24,7 @@ EstOutput Unweighted::getValues(Tree* t, int p, string o) {
 		int numComp = 0;
 		vector< vector<string> > namesOfGroupCombos;
 		for (int r=0; r<numGroups; r++) { 
-			for (int l = r+1; l < numGroups; l++) {
+			for (int l = 0; l < r; l++) {
 				numComp++;
 				vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
 				namesOfGroupCombos.push_back(groups);
@@ -241,7 +241,7 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, st
 		int numComp = 0;
 		vector< vector<string> > namesOfGroupCombos;
 		for (int r=0; r<numGroups; r++) { 
-			for (int l = r+1; l < numGroups; l++) {
+			for (int l = 0; l < r; l++) {
 				numComp++;
 				vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
 				namesOfGroupCombos.push_back(groups);
diff --git a/weighted.cpp b/weighted.cpp
index fd7f854..52d90c8 100644
--- a/weighted.cpp
+++ b/weighted.cpp
@@ -30,7 +30,7 @@ EstOutput Weighted::getValues(Tree* t, int p, string o) {
 		//calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
 		vector< vector<string> > namesOfGroupCombos;
 		for (int i=0; i<numGroups; i++) { 
-			for (int l = i+1; l < numGroups; l++) {	
+			for (int l = 0; l < i; l++) {	
 				//initialize weighted scores
 				//WScore[globaldata->Groups[i]+globaldata->Groups[l]] = 0.0;
 				vector<string> groups; groups.push_back(globaldata->Groups[i]); groups.push_back(globaldata->Groups[l]);