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

[mothur.git] / clearcutcommand.cpp

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index 767981de36e7c3da3063ea4a9b1df696040c0e4f..7fd8c134a0fdee4c6f93075f1d97e9f5ab98000a 100644 (file)
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -310,6 +310,14 @@ int ClearcutCommand::execute() {
                delete[] clearcutParameters; 
                
                if (!stdoutWanted) {    
+                       
+                       //set first tree file as new current treefile
+                       string currentTree = "";
+                       itTypes = outputTypes.find("tree");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { currentTree = (itTypes->second)[0]; m->setTreeFile(currentTree); }
+                       }
+                       
                        m->mothurOutEndLine();
                        m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }