added get.repseqs command, started matrix output command

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index 801ca6013889e7300d99fa3763ab6701ec4bf530..c4bfe0519c8fb23c25304e5cbf936041d75da19a 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -77,21 +77,29 @@ public:
        string getSorted();
        string getEnds();
        string getProcessors();
-
+       string getSize();
+       string getTemplateFile();
+       string getSearch();
+       string getKSize();
+       string getAlign();
+       string getMatch();
+       string getMismatch();
+       string getGapopen();
+       string getGapextend();
        string getTrump();
        string getSoft();
        string getFilter();
-       
-
        string getScale();
 
 
        void setListFile(string);
+       void setGroupFile(string file); 
        void setPhylipFile(string);
        void setColumnFile(string);
        void setNameFile(string);
        void setRabundFile(string);
        void setSabundFile(string);
+       void setSharedFile(string);
        void setFormat(string);
        void setRandomTree(string);
        void setGroups(string);
@@ -114,7 +122,8 @@ 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;
+       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 mismatch, gapopen, gapextend;
 
 
        static GlobalData* _uniqueInstance;