X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedutilities.cpp;h=151b254c7ca983abe1568a962aba5eef0e2f5ead;hb=2009a1a1f47e7467094d844e7c07ab8ddf7bb447;hp=4339a254efbfd9af51796e5c1d473fffa9ffaefa;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/sharedutilities.cpp b/sharedutilities.cpp
index 4339a25..151b254 100644
--- a/sharedutilities.cpp
+++ b/sharedutilities.cpp
@@ -102,6 +102,10 @@ void SharedUtil::getSharedVectorswithReplacement(vector<string> Groups, vector<S
 //need to have mode because different commands require different number of valid groups
 void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups) {
 	try {
+		
+		sort(userGroups.begin(), userGroups.end());
+		sort(allGroups.begin(), allGroups.end());
+		
 		if (userGroups.size() != 0) {
 			if (userGroups[0] != "all") {
 				//check that groups are valid
@@ -144,6 +148,10 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 //need to have mode because different commands require different number of valid groups
 void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups, string mode) {
 	try {
+		
+		sort(userGroups.begin(), userGroups.end());
+		sort(allGroups.begin(), allGroups.end());
+		
 		if (userGroups.size() != 0) {
 			if (userGroups[0] != "all") {
 				//check that groups are valid
@@ -190,6 +198,9 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 //for parsimony and unifrac commands you set pairwise groups as well as an allgroups in calc
 void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups, string& label, int& numGroups, string mode){  //globaldata->Groups, your tree or group map, allgroups, mode
 	try {
+		sort(userGroups.begin(), userGroups.end());
+		sort(allGroups.begin(), allGroups.end());
+		
 		numGroups = 0;
 		label = "";
 
@@ -226,6 +237,7 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 			}
 			//rip extra - off allgroups 
 			label = label.substr(0, label.length()-1);
+			if ((mode != "weighted") && (allGroups.size() > 10)) {  label = "merged";  }
 		}
 		
 		if (mode == "weighted") {
@@ -270,13 +282,18 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 /**************************************************************************************/
 void SharedUtil::getCombos(vector<string>& groupComb, vector<string> userGroups, int& numComp) { //groupcomb, globaldata->Groups, numcomb
 	try {
+		sort(userGroups.begin(), userGroups.end());
 		//calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
 		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]);
+				}
 			}
 		} 
 	}
@@ -313,3 +330,6 @@ void SharedUtil::updateGroupIndex(vector<string>& userGroups, map<string, int>&
 		exit(1);
 	}
 }
+/**************************************************************************************/
+
+