X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.hpp;h=3a469f08cc52dc15ca51e13d9edf23f7a380a752;hb=ee27b6e01a979fdf832668eb87412b029f77e4d7;hp=3b688b43457d318c8f73471bb088d7ad5de1affb;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d;p=mothur.git

diff --git a/globaldata.hpp b/globaldata.hpp
index 3b688b4..3a469f0 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();
@@ -70,18 +75,31 @@ public:
 	string getStep();
 	string getForm();
 	string getSorted();
-	string getScaler();
+	string getEnds();
+	string getProcessors();
+
+	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();
@@ -96,8 +114,10 @@ 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, scaler;
+
+	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;
+
 
 	static GlobalData* _uniqueInstance;
 	GlobalData( const GlobalData& ); // Disable copy constructor