X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.hpp;h=59bbac5dc3c0bf0a4d99d6e671b083f9ed2dd954;hb=f0a594f6676ef5a52d1f122b6de70de2fda08c81;hp=a2b91738e15d29d02ccdc87559b3e4441c5349db;hpb=67b6343929b6dbed97c4b26c3bb849725d573f6d;p=mothur.git

diff --git a/globaldata.hpp b/globaldata.hpp
index a2b9173..59bbac5 100644
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -1,86 +1,105 @@
 #ifndef GLOBALDATA_HPP
 #define GLOBALDATA_HPP
-
-#include <string>
-#include <vector>
-#include <set>
+/*
+#include "mothur.h"
 #include "groupmap.h"
+#include "treemap.h"
+#include "rabundvector.hpp"
+#include "sabundvector.hpp"
+#include "listvector.hpp"
+#include "tree.h"
+#include "sparsematrix.hpp"
+#include "sequencedb.h"
+#include "nameassignment.hpp"
 
-using namespace std;
 
 class ListVector;
+class SharedListVector;
 class SparseMatrix;
+class FullMatrix;
+class Tree;
 class OrderVector;
 class InputData;
 class GroupMap;
+class TreeMap;
 class SAbundVector;
+class RAbundVector;
+class SequenceDB;
 
 class GlobalData {
 public:
 	static GlobalData* getInstance();
-	ListVector* getListVector();
-	SparseMatrix* getSparseMatrix();
+	/*ListVector* gListVector;
+	//SparseMatrix* gSparseMatrix;
 	InputData* ginput;
 	OrderVector* gorder;
 	ListVector* glist;
+	vector<Tree*> gTree;
+	SharedListVector* gSharedList;
 	SAbundVector* sabund;
-	GroupMap* gGroupmap;
-	string inputFileName, helpRequest, commandName;
-	bool allLines;
-	vector<string> singleEstimators, summaryEstimators, sharedEstimators, rareEstimators, sharedRareEstimators, sharedSummaryEstimators; //holds estimators to be used
-	set<int> lines; //hold lines to be used
-	set<string> labels; //holds labels to be used
+	RAbundVector* rabund;
+	//GroupMap* gGroupmap;
+	FullMatrix* gMatrix;
+	TreeMap* gTreemap;
+	SequenceDB* gSequenceDB;
+	NameAssignment* nameMap;
+	string argv; //inputFileName,
+	bool runParse, jumble, sim; //allLines, 
+	vector<string>  Estimators;//, Groups; //holds estimators to be used
+	//set<string> labels; //holds labels to be used
+	vector<string> Treenames;
+	map<string, string> names;
+	string saveNextLabel;
+	
 	
-	string getPhylipFile();
+	/*string getPhylipFile();
 	string getColumnFile();
 	string getListFile();
 	string getRabundFile();
 	string getSabundFile();
-	string getNameFile();
-	string getGroupFile();
+	string getNameFile();	//do we need this?
+	string getGroupFile();	//do we need this?
 	string getOrderFile();
-	string getFastaFile();
-	string getCutOff();
-	string getFormat();
-	string getPrecision();
-	string getMethod();
-	string getFileRoot();
-	string getIters();
-	string getJumble();
-	string getFreq();
+	string getOrderGroupFile();
+	string getTreeFile();
+	string getSharedFile();
+	string getRelAbundFile();
+	string getFormat();	//do we need this?
+
+
 	void setListFile(string);
+	void setTreeFile(string);
+	void setGroupFile(string);		//do we need this?
 	void setPhylipFile(string);
 	void setColumnFile(string);
-	void setNameFile(string);
+	void setNameFile(string);	//do we need this?
 	void setRabundFile(string);
 	void setSabundFile(string);
-	void setFormat(string);
-
+	void setSharedFile(string);
+	void setRelAbundFile(string);
+	void setOrderFile(string file);
+	void setOrderGroupFile(string file);
+	void setFormat(string);	//do we need this?*/
 	
-	void setListVector(ListVector*);
-	void setSparseMatrix(SparseMatrix*);
-	void clear(); 
 	
-	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>&);
 	
+	//void clear(); 
+	//void clearLabels();
+	//void clearAbund();
+	
+	//void newRead();
+	/*
 private:
-	string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile,line, label;
-	string cutoff, format, precision, method, fileroot, iters, jumble, freq, single, rarefaction, shared, summary, sharedsummary, sharedrarefaction;
+	MothurOut* m;
+	//string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format, distfile, ordergroup, relAbundfile;
+
 	static GlobalData* _uniqueInstance;
 	GlobalData( const GlobalData& ); // Disable copy constructor
 	void operator=( const GlobalData& ); // Disable assignment operator
 	GlobalData();
 	~GlobalData();
-	ListVector* gListVector;
-	SparseMatrix* gSparseMatrix;
 	
-};
-
-//**********************************************************************************************************************
+	
+};*/
 
 #endif