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

[mothur.git] / chimeraccodecommand.cpp

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index 8a4ccdedea59eb676ecf4f2161e9c1719db8f72a..457eaf314bf304fe3d7f9e5eec67509f07236a35 100644 (file)
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -435,6 +435,14 @@ int ChimeraCcodeCommand::execute(){
                        m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
                }
                
+               
+               //set accnos file as new current accnosfile
+               string current = "";
+               itTypes = outputTypes.find("accnos");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+               }
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }