X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.hpp;h=c4bfe0519c8fb23c25304e5cbf936041d75da19a;hb=b22853b5cfbf5c47949ad2a084f2fad88b2e4be4;hp=801ca6013889e7300d99fa3763ab6701ec4bf530;hpb=3117b1c3109121dff476997d3c5db5b47a77729b;p=mothur.git

diff --git a/globaldata.hpp b/globaldata.hpp
index 801ca60..c4bfe05 100644
--- 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;