This contains Pat's bug fixes and updates. It represents mothur v.1.3.0

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index b3b0798cfd579c8c1b5e1a0cbbbca2eef0dc1473..6d1b3f3c9dd9f2eb73f5abfd23829e63388f7e6e 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -75,7 +75,7 @@ public:
        string getStep();
        string getForm();
        string getSorted();
-       string getEnds();
+       string getCountEnds();
        string getProcessors();
        string getSize();
        string getCandidateFile();
@@ -86,9 +86,10 @@ public:
        string getMismatch();
        string getGapopen();
        string getGapextend();
+       string getVertical();
        string getTrump();
        string getSoft();
-       string getFilter();
+       string getHard();
        string getScale();
 
 
@@ -104,7 +105,7 @@ public:
        void setRandomTree(string);
        void setGroups(string);
        void setCalc(string);
-       void setEnds(string);
+       void setCountEnds(string);
        void setProcessors(string);
 
        void clear(); 
@@ -122,7 +123,7 @@ public:
 private:
 
        string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, nexusfile, clustalfile, treefile, sharedfile, line, label, randomtree, groups;
-       string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, filter, scale, ends, processors, candidatefile, search, ksize, align, match, size;
+       string 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;
        string mismatch, gapopen, gapextend;