X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=unifracunweightedcommand.cpp;h=9d170631592cc9faf9c54fbd5bde5c710efe05f6;hp=2b93df782bccc4d2dbc8533e7cdc38169059d6a7;hb=c5c7502f435e1413c19e373dab1dfebcaa67588d;hpb=2e5ec5cbbd23637ed20da9bdd544d178a3b5d949

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 2b93df7..9d17063 100644
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -19,7 +19,18 @@ UnifracUnweightedCommand::UnifracUnweightedCommand() {
 		sumFile = globaldata->getTreeFile() + ".uwsummary";
 		openOutputFile(sumFile, outSum);
 
-		setGroups(); //sets users groups to analyze
+		util = new SharedUtil();
+		util->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "unweighted");	//sets the groups the user wants to analyze
+		util->getCombos(groupComb, globaldata->Groups, numComp);
+		globaldata->setGroups("");
+		
+		//ABC
+		if (numComp != 1) {
+			groupComb.push_back(allGroups);
+			numComp++;
+		}
+
+		
 		convert(globaldata->getIters(), iters);  //how many random trees to generate
 		unweighted = new Unweighted(tmap);
 
@@ -114,7 +125,7 @@ int UnifracUnweightedCommand::execute() {
 		UWScoreSig.clear(); 
 	}
 		//reset groups parameter
-		globaldata->Groups.clear(); globaldata->setGroups("");
+		globaldata->Groups.clear(); 
 		outSum.close();
 		
 		return 0;
@@ -189,89 +200,6 @@ void UnifracUnweightedCommand::printUWSummaryFile() {
 		exit(1);
 	}
 }
-/***********************************************************/
-
-void UnifracUnweightedCommand::setGroups() {
-	try {
-		string allGroups = "";
-		numGroups = 0;
-		//if the user has not entered specific groups to analyze then do them all
-		if (globaldata->Groups.size() != 0) {
-			if (globaldata->Groups[0] != "all") {
-				//check that groups are valid
-				for (int i = 0; i < globaldata->Groups.size(); i++) {
-					if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
-						cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
-						// erase the invalid group from globaldata->Groups
-						globaldata->Groups.erase(globaldata->Groups.begin()+i);
-					}
-				}
-			
-				//if the user only entered invalid groups
-				if (globaldata->Groups.size() == 0) { 
-					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 < tmap->namesOfGroups.size(); i++) {
-						if (tmap->namesOfGroups[i] != "xxx") {
-							globaldata->Groups.push_back(tmap->namesOfGroups[i]);
-							numGroups++;
-							allGroups += tmap->namesOfGroups[i] + "-";
-						}
-					}
-					allGroups = allGroups.substr(0, allGroups.length()-1);
-				}else {
-					for (int i = 0; i < globaldata->Groups.size(); i++) {
-						allGroups += globaldata->Groups[i] + "-";
-						numGroups++;
-					}
-					allGroups = allGroups.substr(0, allGroups.length()-1);
-				}
-			}else{//user has enter "all" and wants the default groups
-				globaldata->Groups.clear();
-				for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
-					if (tmap->namesOfGroups[i] != "xxx") {
-						globaldata->Groups.push_back(tmap->namesOfGroups[i]);
-						numGroups++;
-						allGroups += tmap->namesOfGroups[i] + "-";
-					}
-				}
-				allGroups = allGroups.substr(0, allGroups.length()-1);
-				globaldata->setGroups("");
-			}
-		}else {
-			for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
-				if (tmap->namesOfGroups[i] != "xxx") {
-					allGroups += tmap->namesOfGroups[i] + "-";
-				}
-			}
-			allGroups = allGroups.substr(0, allGroups.length()-1);
-			numGroups = 1;
-		}
-		
-		//calculate number of comparsions
-		numComp = 0;
-		for (int r=0; r<numGroups; r++) { 
-			for (int l = r+1; l < numGroups; l++) {
-				groupComb.push_back(globaldata->Groups[r]+ "-" + globaldata->Groups[l]);
-				numComp++;
-			}
-		}
-		
-		//ABC
-		if (numComp != 1) {
-			groupComb.push_back(allGroups);
-			numComp++;
-		}
-	}
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the UnifracUnweightedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
-
-}
 /*****************************************************************/
 
 void UnifracUnweightedCommand::initFile(string label){