added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / secondarystructurecommand.h

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index a82cf4e5edd89a5536cfbecafb5def8f6a7e3ed4..dffb4cbd980ff504307465ae64a0f6645fe5e6a5 100644 (file)
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -39,7 +39,7 @@ class AlignCheckCommand : public Command {
                
        private:
                vector<int> structMap;
-               string mapfile, fastafile;
+               string mapfile, fastafile, outputDir;
                bool abort;
                int seqLength;