X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.hpp;h=cb9aff67dfb4c07918891630c8729b61960451b5;hb=526a868606faa50caf86e7399f7554c0335b39e5;hp=aa68dc2c1dffd0fe90f82e8eabff554e0c8c0000;hpb=a5a908953ab2ebb9386a895e5ddddf0135ad1f99;p=mothur.git

diff --git a/globaldata.hpp b/globaldata.hpp
index aa68dc2..cb9aff6 100644
--- 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;