added alignment code

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index aa68dc2c1dffd0fe90f82e8eabff554e0c8c0000..cb9aff67dfb4c07918891630c8729b61960451b5 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -75,7 +75,16 @@ public:
        string getStep();
        string getForm();
        string getSorted();
-
+       string getEnds();
+       string getProcessors();
+       string getTemplateFile();
+       string getSearch();
+       string getKSize();
+       string getAlign();
+       string getMatch();
+       string getMismatch();
+       string getGapopen();
+       string getGapextend();
        string getTrump();
        string getSoft();
        string getFilter();
@@ -85,15 +94,19 @@ public:
 
 
        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);
        void setCalc(string);
+       void setEnds(string);
+       void setProcessors(string);
 
        void clear(); 
        void clearLabels();
@@ -110,7 +123,8 @@ 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;
+       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;
+       string mismatch, gapopen, gapextend;
 
 
        static GlobalData* _uniqueInstance;