X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.hpp;h=6070dd7b2cdd6122b78c5833359ce487497fd0e3;hb=1c2f1171eee8879de9dbe03a8a9d9093fc6a1f95;hp=80891677d6e27d9f9e1e9671df4b128a962da116;hpb=d037597badc8d18e235c59f0c1114180edb7f98f;p=mothur.git

diff --git a/globaldata.hpp b/globaldata.hpp
index 8089167..6070dd7 100644
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -1,9 +1,7 @@
 #ifndef GLOBALDATA_HPP
 #define GLOBALDATA_HPP
 
-#include <string>
-#include <vector>
-#include <set>
+#include "mothur.h"
 #include "groupmap.h"
 #include "treemap.h"
 
@@ -12,6 +10,7 @@ using namespace std;
 class ListVector;
 class SharedListVector;
 class SparseMatrix;
+class FullMatrix;
 class Tree;
 class OrderVector;
 class InputData;
@@ -22,8 +21,8 @@ class SAbundVector;
 class GlobalData {
 public:
 	static GlobalData* getInstance();
-	ListVector* getListVector();
-	SparseMatrix* getSparseMatrix();
+	ListVector* gListVector;
+	SparseMatrix* gSparseMatrix;
 	InputData* ginput;
 	OrderVector* gorder;
 	ListVector* glist;
@@ -31,13 +30,13 @@ public:
 	SharedListVector* gSharedList;
 	SAbundVector* sabund;
 	GroupMap* gGroupmap;
+	FullMatrix* gMatrix;
 	TreeMap* gTreemap;
 	string inputFileName, helpRequest, commandName;
 	bool allLines;
-	vector<string> singleEstimators, summaryEstimators, sharedEstimators, rareEstimators, sharedRareEstimators, sharedSummaryEstimators; //holds estimators to be used
+	vector<string>  Estimators, Groups; //holds estimators to be used
 	set<int> lines; //hold lines to be used
 	set<string> labels; //holds labels to be used
-	vector<string> Groups;
 	
 	string getPhylipFile();
 	string getColumnFile();
@@ -49,6 +48,7 @@ public:
 	string getOrderFile();
 	string getFastaFile();
 	string getTreeFile();
+	string getSharedFile();
 	string getCutOff();
 	string getFormat();
 	string getPrecision();
@@ -57,7 +57,10 @@ public:
 	string getIters();
 	string getJumble();
 	string getFreq();
+	string getAbund();
 	string getRandomTree();
+	string getGroups();
+
 	void setListFile(string);
 	void setPhylipFile(string);
 	void setColumnFile(string);
@@ -66,33 +69,28 @@ public:
 	void setSabundFile(string);
 	void setFormat(string);
 	void setRandomTree(string);
+	void setGroups(string);
+	void setCalc(string);
 
-	
-	void setListVector(ListVector*);
-	void setSparseMatrix(SparseMatrix*);
 	void clear(); 
+	void clearLabels();
+	void clearAbund();
 	
 	void parseGlobalData(string, string);
-	void splitAtEquals(string&, string&);
-	void splitAtComma(string&, string&);
-	void splitAtDash(string&, vector<string>&);
-	void splitAtDash(string&, set<int>&);
-	void splitAtDash(string&, set<string>&);
-	
+		
 private:
-	string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, line, label, randomtree, groups;
-	string cutoff, format, precision, method, fileroot, iters, jumble, freq, single, rarefaction, shared, summary, sharedsummary, sharedrarefaction;
+	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;
+
 	static GlobalData* _uniqueInstance;
 	GlobalData( const GlobalData& ); // Disable copy constructor
 	void operator=( const GlobalData& ); // Disable assignment operator
 	GlobalData();
 	~GlobalData();
-	ListVector* gListVector;
-	SparseMatrix* gSparseMatrix;
+	void reset();	//clears all non filename parameters
+	
 	
 	
 };
 
-//**********************************************************************************************************************
-
 #endif