X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.hpp;h=aa68dc2c1dffd0fe90f82e8eabff554e0c8c0000;hb=a5a908953ab2ebb9386a895e5ddddf0135ad1f99;hp=be5b0087abdb7ee546e3d9f081a9091c95ee2b8c;hpb=51cf89e90eef8b300c2786eb1560dd89e6e83445;p=mothur.git

diff --git a/globaldata.hpp b/globaldata.hpp
index be5b008..aa68dc2 100644
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -23,6 +23,7 @@ class GroupMap;
 class TreeMap;
 class SAbundVector;
 class RAbundVector;
+class SequenceDB;
 
 class GlobalData {
 public:
@@ -35,10 +36,12 @@ public:
 	vector<Tree*> gTree;
 	SharedListVector* gSharedList;
 	SAbundVector* sabund;
+	RAbundVector* rabund;
 	GroupMap* gGroupmap;
 	FullMatrix* gMatrix;
 	TreeMap* gTreemap;
-	string inputFileName, helpRequest, commandName;
+	SequenceDB* gSequenceDB;
+	string inputFileName, helpRequest, commandName, vertical;
 	bool allLines;
 	vector<string>  Estimators, Groups; //holds estimators to be used
 	set<int> lines; //hold lines to be used
@@ -54,6 +57,8 @@ public:
 	string getGroupFile();
 	string getOrderFile();
 	string getFastaFile();
+	string getNexusFile();
+	string getClustalFile();
 	string getTreeFile();
 	string getSharedFile();
 	string getCutOff();
@@ -70,8 +75,15 @@ public:
 	string getStep();
 	string getForm();
 	string getSorted();
+
+	string getTrump();
+	string getSoft();
+	string getFilter();
+	
+
 	string getScale();
 
+
 	void setListFile(string);
 	void setPhylipFile(string);
 	void setColumnFile(string);
@@ -96,8 +108,10 @@ public:
 
 		
 private:
-	string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, line, label, randomtree, groups;
-	string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, scale;
+
+	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;
+
 
 	static GlobalData* _uniqueInstance;
 	GlobalData( const GlobalData& ); // Disable copy constructor