#ifndef GLOBALDATA_HPP
#define GLOBALDATA_HPP
-#include <string>
-#include <vector>
-#include <set>
-#include <iostream>
-#include <iomanip>
-#include <map>
-#include <sstream>
-#include <stdexcept>
-#include <exception>
-
+#include "mothur.h"
#include "groupmap.h"
#include "treemap.h"
class ListVector;
class SharedListVector;
class SparseMatrix;
+class FullMatrix;
class Tree;
class OrderVector;
class InputData;
class GlobalData {
public:
static GlobalData* getInstance();
- ListVector* getListVector();
- SparseMatrix* getSparseMatrix();
+ ListVector* gListVector;
+ SparseMatrix* gSparseMatrix;
InputData* ginput;
OrderVector* gorder;
ListVector* glist;
SharedListVector* gSharedList;
SAbundVector* sabund;
GroupMap* gGroupmap;
+ FullMatrix* gMatrix;
TreeMap* gTreemap;
string inputFileName, helpRequest, commandName;
bool allLines;
string getFreq();
string getAbund();
string getRandomTree();
+ string getGroups();
void setListFile(string);
void setPhylipFile(string);
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 operator=( const GlobalData& ); // Disable assignment operator
GlobalData();
~GlobalData();
- ListVector* gListVector;
- SparseMatrix* gSparseMatrix;
- void clear(); //clears all parameters
void reset(); //clears all non filename parameters