added cutoff change to mgcluster

[mothur.git] / venncommand.cpp

diff --git a/venncommand.cpp b/venncommand.cpp
index fb0560b38d6c5659fc7ae8b88af2160e6b479191..6d4c2a0616880aee92f5fec430f63df51606e929 100644 (file)
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -129,12 +129,12 @@ VennCommand::VennCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { listfile = ""; abort = true; }
                        else if (listfile == "not found") { listfile = ""; }
-                       else {  format = "list"; inputfile = listfile; }
+                       else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { sharedfile = ""; abort = true; }        
                        else if (sharedfile == "not found") { sharedfile = ""; }
-                       else {  format = "sharedfile"; inputfile = sharedfile; }
+                       else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
                        
                        if ((sharedfile == "") && (listfile == "")) { 
                                //is there are current file available for any of these?
@@ -183,6 +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"; }