X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedutilities.cpp;h=f43bb8107f3ec05ef462bcbb491283706c6a9730;hb=1a1ed6dda1d655ff006459f15c712f057c93ddaf;hp=7d85c4cbbf3e989b4e92ac400b22ab274b60c548;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;p=mothur.git

diff --git a/sharedutilities.cpp b/sharedutilities.cpp
index 7d85c4c..f43bb81 100644
--- a/sharedutilities.cpp
+++ b/sharedutilities.cpp
@@ -49,7 +49,7 @@ void SharedUtil::getSharedVectors(vector<string> Groups, vector<SharedRAbundVect
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedUtil", "getSharedVectors");
+		m->errorOut(e, "SharedUtil", "getSharedVectors");
 		exit(1);
 	}
 }
@@ -93,7 +93,7 @@ void SharedUtil::getSharedVectorswithReplacement(vector<string> Groups, vector<S
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedUtil", "getSharedVectorswithReplacement");
+		m->errorOut(e, "SharedUtil", "getSharedVectorswithReplacement");
 		exit(1);
 	}
 }
@@ -107,7 +107,7 @@ 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 userGroups
 						userGroups.erase(userGroups.begin()+i);
 						i--;
@@ -116,7 +116,7 @@ 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 groupfile."); m->mothurOutEndLine();
 					for (int i = 0; i < allGroups.size(); i++) {
 						userGroups.push_back(allGroups[i]);
 					}
@@ -136,7 +136,7 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 			
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedUtil", "setGroups");
+		m->errorOut(e, "SharedUtil", "setGroups");
 		exit(1);
 	}
 }
@@ -149,7 +149,7 @@ 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 userGroups
 						userGroups.erase(userGroups.begin()+i);
 						i--;
@@ -171,7 +171,7 @@ 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 +180,7 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 	
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedUtil", "setGroups");
+		m->errorOut(e, "SharedUtil", "setGroups");
 		exit(1);
 	}
 }
@@ -199,7 +199,7 @@ 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 +226,7 @@ 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 +237,9 @@ 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 +252,7 @@ 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]);
@@ -263,7 +264,7 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedUtil", "setGroups");
+		m->errorOut(e, "SharedUtil", "setGroups");
 		exit(1);
 	}
 }
@@ -274,14 +275,18 @@ 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]);
+				}
 			}
 		} 
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedUtil", "getCombos");
+		m->errorOut(e, "SharedUtil", "getCombos");
 		exit(1);
 	}
 }
@@ -295,7 +300,7 @@ 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 +314,10 @@ void SharedUtil::updateGroupIndex(vector<string>& userGroups, map<string, int>&
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedUtil", "updateGroupIndex");
+		m->errorOut(e, "SharedUtil", "updateGroupIndex");
 		exit(1);
 	}
 }
+/**************************************************************************************/
+
+