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

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 6fd4e04a0e562e5ee44fd0a05fc7df9b1bfae3d4..cb0b131f58e039f5eea76b784334715e1e7481e3 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -302,6 +302,12 @@ int FilterSeqsCommand::execute() {
                m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
                m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
                
+               //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();