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

[mothur.git] / removerarecommand.cpp

diff --git a/removerarecommand.cpp b/removerarecommand.cpp
index 0c656a053a7293f4ef7fa3325edead27339c9196..bcb9af60d096a82b13c13efa35f4b74d54b0897b 100644 (file)
--- a/removerarecommand.cpp
+++ b/removerarecommand.cpp
@@ -243,6 +243,33 @@ int RemoveRareCommand::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 rabund file as new current rabundfile
+                       string current = "";
+                       itTypes = outputTypes.find("rabund");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+                       }
+                       
+                       itTypes = outputTypes.find("sabund");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(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); }
+                       }
+                       
+                       itTypes = outputTypes.find("shared");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
+                       }
                }
                
                return 0;