X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedutilities.cpp;h=d9891db7966da9178ce0b0deaa177ddeb192fc79;hp=7d85c4cbbf3e989b4e92ac400b22ab274b60c548;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2

diff --git a/sharedutilities.cpp b/sharedutilities.cpp
index 7d85c4c..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());
@@ -49,7 +51,7 @@ void SharedUtil::getSharedVectors(vector<string> Groups, vector<SharedRAbundVect
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedUtil", "getSharedVectors");
+		m->errorOut(e, "SharedUtil", "getSharedVectors");
 		exit(1);
 	}
 }
@@ -93,7 +95,7 @@ void SharedUtil::getSharedVectorswithReplacement(vector<string> Groups, vector<S
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedUtil", "getSharedVectorswithReplacement");
+		m->errorOut(e, "SharedUtil", "getSharedVectorswithReplacement");
 		exit(1);
 	}
 }
@@ -102,12 +104,16 @@ 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
 				for (int i = 0; i < userGroups.size(); i++) {
 					if (isValidGroup(userGroups[i], allGroups) != true) {
-						mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); mothurOutEndLine();
+						m->mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
 						// erase the invalid group from userGroups
 						userGroups.erase(userGroups.begin()+i);
 						i--;
@@ -116,7 +122,7 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 				
 				//if the user only entered invalid groups
 				if (userGroups.size() == 0) { 
-					mothurOut("You provided no valid groups. I will run the command using all the groups in your groupfile."); 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]);
 					}
@@ -136,7 +142,7 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 			
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedUtil", "setGroups");
+		m->errorOut(e, "SharedUtil", "setGroups");
 		exit(1);
 	}
 }
@@ -144,12 +150,16 @@ 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
 				for (int i = 0; i < userGroups.size(); i++) {
 					if (isValidGroup(userGroups[i], allGroups) != true) {
-						mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); mothurOutEndLine();
+						m->mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
 						// erase the invalid group from userGroups
 						userGroups.erase(userGroups.begin()+i);
 						i--;
@@ -171,7 +181,7 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 		if ((mode == "collect") || (mode == "rarefact") || (mode == "summary") || (mode == "treegroup")) {
 				//if the user only entered invalid groups
 				if ((userGroups.size() == 0) || (userGroups.size() == 1)) { 
-					mothurOut("When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile."); mothurOutEndLine();
+					m->mothurOut("When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile."); m->mothurOutEndLine();
 					for (int i = 0; i < allGroups.size(); i++) {
 						userGroups.push_back(allGroups[i]);
 					}
@@ -180,7 +190,7 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 	
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedUtil", "setGroups");
+		m->errorOut(e, "SharedUtil", "setGroups");
 		exit(1);
 	}
 }
@@ -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 = "";
 
@@ -199,7 +212,7 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 				//check that groups are valid
 				for (int i = 0; i < userGroups.size(); i++) {
 					if (isValidGroup(userGroups[i], allGroups) != true) {
-						mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); mothurOutEndLine();
+						m->mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
 						// erase the invalid group from globaldata->Groups
 						userGroups.erase(userGroups.begin()+i);
 						i--;
@@ -226,6 +239,7 @@ 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") {
@@ -236,9 +250,9 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 						userGroups.push_back(allGroups[i]);
 					}
 				}
-				mothurOut("When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile."); mothurOutEndLine();
+				m->mothurOut("When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile."); m->mothurOutEndLine();
 			}else if (userGroups.size() == 1) { 
-				mothurOut("When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile."); mothurOutEndLine();
+				m->mothurOut("When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile."); m->mothurOutEndLine();
 				userGroups.clear();
 				for (int i=0; i < allGroups.size(); i++) { 
 					if (allGroups[i] != "xxx") {
@@ -251,7 +265,7 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 		}else if ((mode == "unweighted") || (mode == "parsimony")) {
 				//if the user only entered invalid groups
 				if ((userGroups.size() == 0) && (numGroups == 0)) { 
-					mothurOut("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."); mothurOutEndLine();
+					m->mothurOut("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."); m->mothurOutEndLine();
 					for (int i = 0; i < allGroups.size(); i++) {
 						if (allGroups[i] != "xxx") {
 							userGroups.push_back(allGroups[i]);
@@ -263,25 +277,30 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedUtil", "setGroups");
+		m->errorOut(e, "SharedUtil", "setGroups");
 		exit(1);
 	}
 }
 /**************************************************************************************/
 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]);
+				}
 			}
 		} 
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedUtil", "getCombos");
+		m->errorOut(e, "SharedUtil", "getCombos");
 		exit(1);
 	}
 }
@@ -295,7 +314,7 @@ bool SharedUtil::isValidGroup(string groupname, vector<string> groups) {
 		return false;
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedUtil", "isValidGroup");
+		m->errorOut(e, "SharedUtil", "isValidGroup");
 		exit(1);
 	}
 }
@@ -309,7 +328,10 @@ void SharedUtil::updateGroupIndex(vector<string>& userGroups, map<string, int>&
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedUtil", "updateGroupIndex");
+		m->errorOut(e, "SharedUtil", "updateGroupIndex");
 		exit(1);
 	}
 }
+/**************************************************************************************/
+
+