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

[mothur.git] / getotuscommand.cpp

diff --git a/getotuscommand.cpp b/getotuscommand.cpp
index f10142bb74a67a9fa98bded8b8a2e0d48fa85358..15d2bcb8e46454809cdc4441574a469abfc6d6b2 100644 (file)
--- a/getotuscommand.cpp
+++ b/getotuscommand.cpp
@@ -207,6 +207,18 @@ int GetOtusCommand::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 list file as new current listfile
+                       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;