X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedutilities.cpp;h=de627c643c9ff277854a1d8b8ffcb595004d0a85;hb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;hp=454b7d4073396f74c804ad1bba68cbea57ac5f57;hpb=9653c9f8c1b63ecb1a63b45e781c303713d5b5df;p=mothur.git

diff --git a/sharedutilities.cpp b/sharedutilities.cpp
index 454b7d4..de627c6 100644
--- a/sharedutilities.cpp
+++ b/sharedutilities.cpp
@@ -66,7 +66,6 @@ void SharedUtil::getSharedVectorswithReplacement(vector<string> Groups, vector<S
 		for (int j = 0; j < lookup.size(); j++) {
 			delete lookup[j];
 		}
-		
 		lookup.clear();
 		
 		//create and initialize vector of sharedvectors, one for each group
@@ -109,7 +108,7 @@ 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, string mode) {
+void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups) {
 	try {
 		if (userGroups.size() != 0) {
 			if (userGroups[0] != "all") {
@@ -122,6 +121,14 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 						i--;
 					}
 				}
+				
+				//if the user only entered invalid groups
+				if (userGroups.size() == 0) { 
+					cout << "You provided no valid groups. I will run the command using all the groups in your groupfile." << endl; 
+					for (int i = 0; i < allGroups.size(); i++) {
+						userGroups.push_back(allGroups[i]);
+					}
+				}
 
 			}else{//user has enter "all" and wants the default groups
 				userGroups.clear();
@@ -135,38 +142,46 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 			}
 		}
 			
-		if (mode == "venn")  {
-				//if the user only entered invalid groups
-				if (userGroups.size() == 0) { 
-					if (allGroups.size() > 4) {
-						cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using the first four groups in your groupfile." << endl; 
-						for (int i = 0; i < 4; i++) {
-							userGroups.push_back(allGroups[i]);
-						}
-					}else {
-						cout << "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." << endl; 
-						for (int i = 0; i < allGroups.size(); i++) {
-							userGroups.push_back(allGroups[i]);
-						}
-					}
-				}
-				
-				//check to make sure their are only 4 groups
-				if (userGroups.size() > 4) {
-					cout << "You may only use up to 4 groups at a time with this command.  I will choose the first four and disregard the rest." << endl;
-					for (int i = 4; i < userGroups.size(); i++) {
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the SharedUtil class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+
+}
+/**************************************************************************************************/
+//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 {
+		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) {
+						cout << userGroups[i] << " is not a valid group, and will be disregarded." << endl;
+						// erase the invalid group from userGroups
 						userGroups.erase(userGroups.begin()+i);
+						i--;
 					}
 				}
-		}else if (mode == "heat") {
-				//if the user only entered invalid groups
-				if (userGroups.size() == 0) { 
-					cout << "When using the groups parameter you must have at least 1 valid groups. I will run the command using all the groups in your groupfile." << endl; 
-					for (int i = 0; i < allGroups.size(); i++) {
-						userGroups.push_back(allGroups[i]);
-					}
+
+			}else{//user has enter "all" and wants the default groups
+				userGroups.clear();
+				for (int i = 0; i < allGroups.size(); i++) {
+					userGroups.push_back(allGroups[i]);
 				}
-		}else if ((mode == "collect") || (mode == "rarefact") || (mode == "summary") || (mode == "treegroup")) {
+			}
+		}else { //the user has not entered groups
+			for (int i = 0; i < allGroups.size(); i++) {
+				userGroups.push_back(allGroups[i]);
+			}
+		}
+			
+		if ((mode == "collect") || (mode == "rarefact") || (mode == "summary") || (mode == "treegroup")) {
 				//if the user only entered invalid groups
 				if ((userGroups.size() == 0) || (userGroups.size() == 1)) { 
 					cout << "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." << endl; 
@@ -188,12 +203,14 @@ 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 {
 		numGroups = 0;
 		label = "";
+
 		//if the user has not entered specific groups to analyze then do them all
 		if (userGroups.size() != 0) {
 			if (userGroups[0] != "all") {