added alignment code

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index 3a469f08cc52dc15ca51e13d9edf23f7a380a752..cb9aff67dfb4c07918891630c8729b61960451b5 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -77,7 +77,14 @@ public:
        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();
@@ -116,7 +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, 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;
+       string mismatch, gapopen, gapextend;
 
 
        static GlobalData* _uniqueInstance;