fixed bug with dist.shared subsampling. added mode parameter to dist.shared so...

[mothur.git] / splitabundcommand.cpp

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index 29ffdb44c16862994993566583393c0de9f6644a..8131fa9195f6b8d939b27891605dd862d618964b 100644 (file)
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -181,7 +181,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                        groups = validParameter.validFile(parameters, "groups", false);         
                        if (groups == "not found") { groups = ""; }
                        else if (groups == "all") { 
-                               if (groupfile != "") {  Groups = groupMap->namesOfGroups;  } 
+                               if (groupfile != "") {  Groups = groupMap->getNamesOfGroups();  } 
                                else {  m->mothurOut("You cannot select groups without a valid groupfile, I will disregard your groups selection. "); m->mothurOutEndLine(); groups = "";   }
                        }else { 
                                m->splitAtDash(groups, Groups);
@@ -213,10 +213,9 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                        accnos = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);                           if (temp == "not found") { temp = "0"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
 
                        if (cutoff == 0) {  m->mothurOut("You must provide a cutoff to qualify what is abundant for the split.abund command. "); m->mothurOutEndLine(); abort = true;  }
-
                }
 
        }