working on pca

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index bb8d3863ea56b52dfea6c772dbf0beb397810849..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();    }
@@ -738,7 +745,7 @@ int TrimFlowsCommand::stripForward(Sequence& seq, int& group){
                
                string rawSequence = seq.getUnaligned();
                int success = pdiffs + 1;       //guilty until proven innocent
-               
+
                //can you find the primer
                for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
                        string oligo = it->first;