added read.shared, broke up globaldata a bit

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index 80891677d6e27d9f9e1e9671df4b128a962da116..277d351062fd67726f0ba05d53647d8c98b2a53c 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -4,6 +4,13 @@
 #include <string>
 #include <vector>
 #include <set>
+#include <iostream>
+#include <iomanip>
+#include <map>
+#include <sstream>
+#include <stdexcept>
+#include <exception>
+
 #include "groupmap.h"
 #include "treemap.h"
 
@@ -34,7 +41,7 @@ public:
        TreeMap* gTreemap;
        string inputFileName, helpRequest, commandName;
        bool allLines;
-       vector<string> singleEstimators, summaryEstimators, sharedEstimators, rareEstimators, sharedRareEstimators, sharedSummaryEstimators; //holds estimators to be used
+       vector<string> Estimators; //holds estimators to be used
        set<int> lines; //hold lines to be used
        set<string> labels; //holds labels to be used
        vector<string> Groups;
@@ -49,6 +56,7 @@ public:
        string getOrderFile();
        string getFastaFile();
        string getTreeFile();
+       string getSharedFile();
        string getCutOff();
        string getFormat();
        string getPrecision();
@@ -66,22 +74,16 @@ public:
        void setSabundFile(string);
        void setFormat(string);
        void setRandomTree(string);
+       void setCalc(string);
 
        
        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>&);
-       
+               
 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;
        static GlobalData* _uniqueInstance;
        GlobalData( const GlobalData& ); // Disable copy constructor
        void operator=( const GlobalData& ); // Disable assignment operator
@@ -89,10 +91,11 @@ private:
        ~GlobalData();
        ListVector* gListVector;
        SparseMatrix* gSparseMatrix;
+       void clear();  //clears all parameters
+       void reset();   //clears all non filename parameters
+       
        
        
 };
 
-//**********************************************************************************************************************
-
 #endif