modified trim.seqs to account for primers of different lengths

[mothur.git] / mgclustercommand.h

diff --git a/mgclustercommand.h b/mgclustercommand.h
index 2ac80c91dd65fa7cf56f71331e4c4486c68c8b87..a1dac221b891a8551a36b7493d5bb7a603204cf5 100644 (file)
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -38,9 +38,10 @@ private:
        ListVector oldList;
        vector<seqDist> overlapMatrix;
        
-       string blastfile, method, namefile, overlapFile, distFile;
+       string blastfile, method, namefile, overlapFile, distFile, outputDir;
        ofstream sabundFile, rabundFile, listFile;
-       float cutoff, penalty;
+       double cutoff;
+       float penalty;
        int precision, length, precisionLength;
        bool abort, minWanted, hclusterWanted, merge;