added name option to trim.seqs

[mothur.git] / venncommand.cpp

diff --git a/venncommand.cpp b/venncommand.cpp
index c6d534e1d8eaae7997c88cd95b700755b211ddb9..cae041704c52e7caf6c4368ca393d441a69065c9 100644 (file)
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -87,6 +87,7 @@ VennCommand::VennCommand(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();
@@ -182,6 +183,11 @@ VennCommand::VennCommand(string option)  {
                                }
                        }
                        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"; }