fixing minor bugs

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 36b0dc141406286b44130de699fea92f971d167f..6127c2d6da7717112fb2c7fdb5c82910f03f8323 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -44,6 +44,7 @@ CollectSharedCommand::CollectSharedCommand(string option){
                lines.clear();
                labels.clear();
                Estimators.clear();
+               Groups.clear();
                
                //allow user to run help
                if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
@@ -106,8 +107,8 @@ CollectSharedCommand::CollectSharedCommand(string option){
                        if (groups == "not found") { groups = ""; }
                        else { 
                                splitAtDash(groups, Groups);
-                               globaldata->Groups = Groups;
                        }
+                       globaldata->Groups = Groups;
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
@@ -242,16 +243,16 @@ int CollectSharedCommand::execute(){
                
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
                set<string> processedLabels;
-               set<string> userLabels = globaldata->labels;
-               set<int> userLines = globaldata->lines;
+               set<string> userLabels = labels;
+               set<int> userLines = lines;
                                
                //set users groups
                util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "collect");
                util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex);
 
-               while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+               while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 
-                       if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+                       if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){
                                
                                //create collectors curve
                                cCurve = new Collect(order, cDisplays);