fixing minor bugs

[mothur.git] / rarefactsharedcommand.cpp

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index d0179be91a5b2eac505632797a8ebb3f74232282..fdc967856043fc8e191c9b3167fb83634f82ec0a 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -16,12 +16,14 @@
 RareFactSharedCommand::RareFactSharedCommand(string option){
        try {
                globaldata = GlobalData::getInstance();
+               
                abort = false;
                allLines = 1;
                lines.clear();
                labels.clear();
                Estimators.clear();
-               
+               Groups.clear();
+                               
                //allow user to run help
                if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
                
@@ -83,8 +85,8 @@ RareFactSharedCommand::RareFactSharedCommand(string option){
                        if (groups == "not found") { groups = ""; }
                        else { 
                                splitAtDash(groups, Groups);
-                               globaldata->Groups = Groups;
                        }
+                       globaldata->Groups = Groups;
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
@@ -176,7 +178,7 @@ int RareFactSharedCommand::execute(){
                input = globaldata->ginput;
                lookup = input->getSharedRAbundVectors();
                vector<SharedRAbundVector*> lastLookup = lookup;
-               
+
                if (lookup.size() < 2) { 
                        cout << "I cannot run the command without at least 2 valid groups."; 
                        for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }