X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.hpp;h=0c2548971555b599ea87eba61623fb2dfcf9a8ac;hb=36a8526766106bce1412e530e99f9c699dd59105;hp=3a469f08cc52dc15ca51e13d9edf23f7a380a752;hpb=ee27b6e01a979fdf832668eb87412b029f77e4d7;p=mothur.git

diff --git a/globaldata.hpp b/globaldata.hpp
index 3a469f0..0c25489 100644
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -41,7 +41,7 @@ public:
 	FullMatrix* gMatrix;
 	TreeMap* gTreemap;
 	SequenceDB* gSequenceDB;
-	string inputFileName, helpRequest, commandName, vertical;
+	string inputFileName, helpRequest, commandName, vertical, argv;
 	bool allLines;
 	vector<string>  Estimators, Groups; //holds estimators to be used
 	set<int> lines; //hold lines to be used
@@ -77,12 +77,18 @@ 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();
 
 
@@ -116,7 +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;