changes to read.otu(list/shared) - took out substr calls

[mothur.git] / secondarystructurecommand.h

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index a82cf4e5edd89a5536cfbecafb5def8f6a7e3ed4..2e6191ca67f47f92f38bb8c030a8ad3e32920af6 100644 (file)
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -39,9 +39,9 @@ class AlignCheckCommand : public Command {
                
        private:
                vector<int> structMap;
-               string mapfile, fastafile;
+               string mapfile, fastafile, outputDir;
                bool abort;
-               int seqLength;
+               int seqLength, haderror;
                
                void readMap();
                statData getStats(string sequence);