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

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 6592651d068fc12580043897898479bf858a2047..bf80ee8cb3ea18ed3d363816eda22d0a501e141f 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -330,6 +330,13 @@ int TrimFlowsCommand::execute(){
                outputTypes["flow.files"].push_back(flowFilesFileName);
                outputNames.push_back(flowFileName);
                
+               //set fasta file as new current fastafile
+               string current = "";
+               itTypes = outputTypes.find("fasta");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+               }
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }