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

[mothur.git] / degapseqscommand.cpp

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index 5df61889747833ef27f5929d227c849ea7245769..7fd2803a4ec6c5e578d7b180a9e08fda1af33385 100644 (file)
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -219,6 +219,13 @@ int DegapSeqsCommand::execute(){
                        if (m->control_pressed) {  outputTypes.clear(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) {       remove(outputNames[j].c_str()); } return 0; }
                }
                
+               //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 Name: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }