added trim.seqs command

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index af5b3835ea67b52e6d16cfd0d37f323d95e4afd1..2a57310ccc301f490f007680a93e64ee1b0157cf 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -91,7 +91,12 @@ public:
        string getMaxHomoPolymer();
        string getMinLength();
        string getMaxLength();
-
+       string getFlip();
+       string getForwardMismatch();
+       string getReverseMismatch();
+       string getBarcodeMismatch();
+       string getOligosFile();
+       
        void setListFile(string);
        void setGroupFile(string file); 
        void setPhylipFile(string);
@@ -121,7 +126,7 @@ public:
                
 private:
 
-       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, line, label, randomtree, groups, cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, hard, scale, countends, processors, candidatefile, search, ksize, align, match, size, mismatch, gapopen, gapextend, minLength, maxLength, startPos, endPos, maxAmbig, maxHomoPolymer;
+       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, line, label, randomtree, groups, cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, hard, scale, countends, processors, candidatefile, search, ksize, align, match, size, mismatch, gapopen, gapextend, minLength, maxLength, startPos, endPos, maxAmbig, maxHomoPolymer, flip, forMismatch, revMismatch, barMismatch, oligoFile;
 
 
        static GlobalData* _uniqueInstance;