deleted read.shared command and added its functionality to read.otu.

[mothur.git] / rarefactsharedcommand.cpp

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 9bd8805f4867a6e445b42324d8b13d406471eace..58f73f34e45b61b30e5355ebd38cfa63f988448d 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -19,8 +19,6 @@ RareFactSharedCommand::RareFactSharedCommand(){
                fileNameRoot = getRootName(globaldata->inputFileName);
                format = globaldata->getFormat();
                validCalculator = new ValidCalculators();
-               
-               setGroups();
                                
                int i;
                for (i=0; i<globaldata->Estimators.size(); i++) {
@@ -80,6 +78,9 @@ int RareFactSharedCommand::execute(){
                        order = SharedList->getSharedOrderVector();
                }
                
+               //set users groups
+               setGroups();
+               
                while(order != NULL){
                
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){