added set.current and get.current commands and modified existing commands to update...

[mothur.git] / removeotuscommand.cpp

diff --git a/removeotuscommand.cpp b/removeotuscommand.cpp
index 347bb0870f3fde2ab71c86c5b67918fad4a4904c..f1ef4ac5a80c7e2782843349d1433680b38bda45 100644 (file)
--- a/removeotuscommand.cpp
+++ b/removeotuscommand.cpp
@@ -207,6 +207,18 @@ int RemoveOtusCommand::execute(){
                        m->mothurOut("Output File names: "); m->mothurOutEndLine();
                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
                        m->mothurOutEndLine();
+                       
+                       //set fasta file as new current fastafile
+                       string current = "";
+                       itTypes = outputTypes.find("group");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+                       }
+                       
+                       itTypes = outputTypes.find("list");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+                       }
                }
                
                return 0;