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

[mothur.git] / mergegroupscommand.cpp

diff --git a/mergegroupscommand.cpp b/mergegroupscommand.cpp
index c54cd1c7dd8e578126b345c68ac0ac1d8f684e19..60b9c85481a2d455d53ab4b13a3bd46cfaf5a389 100644 (file)
--- a/mergegroupscommand.cpp
+++ b/mergegroupscommand.cpp
@@ -273,6 +273,14 @@ int MergeGroupsCommand::execute(){
                
                if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0;}
                
+               
+               //set shared file as new current sharedfile
+               string current = "";
+               itTypes = outputTypes.find("shared");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
+               }
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }