X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedutilities.cpp;h=d9891db7966da9178ce0b0deaa177ddeb192fc79;hp=6dffee95e1c9a2e17bbda649424d0cb53402e513;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=257808d42702d889a85d0132abc6b8776fc57418

diff --git a/sharedutilities.cpp b/sharedutilities.cpp
index 6dffee9..d9891db 100644
--- a/sharedutilities.cpp
+++ b/sharedutilities.cpp
@@ -22,7 +22,9 @@ void SharedUtil::getSharedVectors(vector<string> Groups, vector<SharedRAbundVect
 		}
 		
 		lookup.clear();
-		
+        
+		sort(Groups.begin(), Groups.end());
+        
 		//create and initialize vector of sharedvectors, one for each group
 		for (int i = 0; i < Groups.size(); i++) { 
 			SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
@@ -102,6 +104,10 @@ 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
@@ -116,7 +122,7 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 				
 				//if the user only entered invalid groups
 				if (userGroups.size() == 0) { 
-					m->mothurOut("You provided no valid groups. I will run the command using all the groups in your groupfile."); m->mothurOutEndLine();
+					m->mothurOut("You provided no valid groups. I will run the command using all the groups in your file."); m->mothurOutEndLine();
 					for (int i = 0; i < allGroups.size(); i++) {
 						userGroups.push_back(allGroups[i]);
 					}
@@ -144,6 +150,10 @@ 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 +200,9 @@ 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 = "";
 
@@ -271,13 +284,18 @@ 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]);
+				}
 			}
 		} 
 	}
@@ -314,3 +332,6 @@ void SharedUtil::updateGroupIndex(vector<string>& userGroups, map<string, int>&
 		exit(1);
 	}
 }
+/**************************************************************************************/
+
+