changed defaults for filter.seqs()

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index c4bfe0519c8fb23c25304e5cbf936041d75da19a..b3b0798cfd579c8c1b5e1a0cbbbca2eef0dc1473 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -41,7 +41,7 @@ public:
        FullMatrix* gMatrix;
        TreeMap* gTreemap;
        SequenceDB* gSequenceDB;
-       string inputFileName, helpRequest, commandName, vertical;
+       string inputFileName, helpRequest, commandName, vertical, argv;
        bool allLines;
        vector<string>  Estimators, Groups; //holds estimators to be used
        set<int> lines; //hold lines to be used
@@ -78,7 +78,7 @@ public:
        string getEnds();
        string getProcessors();
        string getSize();
-       string getTemplateFile();
+       string getCandidateFile();
        string getSearch();
        string getKSize();
        string getAlign();
@@ -122,7 +122,7 @@ 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, templatefile, search, ksize, align, match, size;
+       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 mismatch, gapopen, gapextend;