fixed bug with trim.seqs allfiles=t

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 6f4bb454ba57c8fba0c4b501038679d5e48e6a61..4d71c07511d711ec10baad3b94ca724cbf1e320f 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -102,6 +102,7 @@ SummaryCommand::SummaryCommand(string option)  {
                                
                //allow user to run help
                if(option == "help") {  help();  abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -222,6 +223,11 @@ SummaryCommand::SummaryCommand(string option)  {
                                 if (calc == "default")  {  calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
                        }
                        m->splitAtDash(calc, Estimators);
+                       if (m->inUsersGroups("citation", Estimators)) { 
+                               ValidCalculators validCalc; validCalc.printCitations(Estimators); 
+                               //remove citation from list of calcs
+                               for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
+                       }
 
                        string temp;
                        temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }