#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;
+ RAbundVector* rabund;
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
+ FullMatrix* gMatrix;
+ TreeMap* gTreemap;
+ SequenceDB* gSequenceDB;
+ string inputFileName, argv;
+ bool allLines, runParse, jumble;
+ vector<string> Estimators, Groups; //holds estimators to be used
set<string> labels; //holds labels to be used
+ vector<string> Treenames;
+
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 getTreeFile();
+ string getSharedFile();
+ 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 setOrderFile(string file);
+ void setFormat(string); //do we need this?
+
+ NameAssignment* nameMap;
- 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>&);
+ 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;
+
+ string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format, distfile;
+
static GlobalData* _uniqueInstance;
GlobalData( const GlobalData& ); // Disable copy constructor
void operator=( const GlobalData& ); // Disable assignment operator
GlobalData();
~GlobalData();
- ListVector* gListVector;
- SparseMatrix* gSparseMatrix;
+
};
-//**********************************************************************************************************************
-
#endif