X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.hpp;h=b3b0798cfd579c8c1b5e1a0cbbbca2eef0dc1473;hb=6f9dc7ca71d7b8ed4aba2824f76ae6b29da89f3b;hp=40b87583aaa2e472f788b2102f5daea0628c2f9e;hpb=c196b6b4768ccb84955d773ff0f22e4994d1ba7b;p=mothur.git

diff --git a/globaldata.hpp b/globaldata.hpp
index 40b8758..b3b0798 100644
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -23,6 +23,7 @@ class GroupMap;
 class TreeMap;
 class SAbundVector;
 class RAbundVector;
+class SequenceDB;
 
 class GlobalData {
 public:
@@ -39,7 +40,8 @@ public:
 	GroupMap* gGroupmap;
 	FullMatrix* gMatrix;
 	TreeMap* gTreemap;
-	string inputFileName, helpRequest, commandName, vertical;
+	SequenceDB* gSequenceDB;
+	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
@@ -73,25 +75,37 @@ public:
 	string getStep();
 	string getForm();
 	string getSorted();
-
+	string getEnds();
+	string getProcessors();
+	string getSize();
+	string getCandidateFile();
+	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);
 	void setCalc(string);
+	void setEnds(string);
+	void setProcessors(string);
 
 	void clear(); 
 	void clearLabels();
@@ -108,7 +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;
+	string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, filter, scale, ends, processors, candidatefile, search, ksize, align, match, size;
+	string mismatch, gapopen, gapextend;
 
 
 	static GlobalData* _uniqueInstance;