X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=collectsharedcommand.cpp;h=6c47f2d5a6b2e4ac178d61128e4e0739a7c41666;hp=ec35dd601e75abd3ea7b65e32aabcaa1c13b1c90;hb=c5c7502f435e1413c19e373dab1dfebcaa67588d;hpb=2e5ec5cbbd23637ed20da9bdd544d178a3b5d949

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index ec35dd6..6c47f2d 100644
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -41,6 +41,7 @@ CollectSharedCommand::CollectSharedCommand(){
 		fileNameRoot = getRootName(globaldata->inputFileName);
 		format = globaldata->getFormat();
 		validCalculator = new ValidCalculators();
+		util = new SharedUtil();
 		
 		int i;
 		for (i=0; i<globaldata->Estimators.size(); i++) {
@@ -113,6 +114,7 @@ CollectSharedCommand::~CollectSharedCommand(){
 	delete input;
 	delete cCurve;
 	delete read;
+	delete util;
 }
 
 //**********************************************************************************************************************
@@ -142,7 +144,8 @@ int CollectSharedCommand::execute(){
 		set<string> orderList;
 		
 		//set users groups
-		setGroups();
+		util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "collect");
+		util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex);
 
 		while(order != NULL){
 			orderList.insert(order->getLabel());
@@ -193,52 +196,5 @@ int CollectSharedCommand::execute(){
 	}	
 }
 
-
-//**********************************************************************************************************************
-void CollectSharedCommand::setGroups() {
-	try {
-		//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 (globaldata->gGroupmap->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) || (globaldata->Groups.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; 
-					for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
-						globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
-					}
-				}
-			}else{//user has enter "all" and wants the default groups
-				globaldata->Groups.clear();
-				for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
-					globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
-				}
-				globaldata->setGroups("");
-			}
-		}else {
-			for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
-				globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
-			}
-		}
-		
-	}
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the CollectSharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
-
-}
 /***********************************************************/