added path search for lookup file in shhh.seqs

[mothur.git] / heatmapsimcommand.cpp

diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index 0d3bc33e2e406e1a811598fee620a92f3cedc3e2..92271d9dad6d3532e3463fd7e0be4ad9dcbf395c 100644 (file)
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -92,6 +92,7 @@ HeatMapSimCommand::HeatMapSimCommand(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 @@ HeatMapSimCommand::HeatMapSimCommand(string option)  {
                                if (calc == "default")  {  calc = "jest-thetayc";  }
                        }
                        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; } }
+                       }
                                
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }