Added get.line command.

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index f513d526c478e9b2160c51e42f9ce9bac6f58fdb..31a63b67adad73bd7e46487a4849cee6135f6ede 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"
 
@@ -27,14 +34,14 @@ public:
        InputData* ginput;
        OrderVector* gorder;
        ListVector* glist;
-       Tree* gTree;
+       vector<Tree*> gTree;
        SharedListVector* gSharedList;
        SAbundVector* sabund;
        GroupMap* gGroupmap;
        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
        
@@ -48,6 +55,7 @@ public:
        string getOrderFile();
        string getFastaFile();
        string getTreeFile();
+       string getSharedFile();
        string getCutOff();
        string getFormat();
        string getPrecision();
@@ -56,6 +64,9 @@ public:
        string getIters();
        string getJumble();
        string getFreq();
+       string getAbund();
+       string getRandomTree();
+
        void setListFile(string);
        void setPhylipFile(string);
        void setColumnFile(string);
@@ -63,22 +74,22 @@ public:
        void setRabundFile(string);
        void setSabundFile(string);
        void setFormat(string);
+       void setRandomTree(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;
-       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
@@ -86,10 +97,10 @@ private:
        ~GlobalData();
        ListVector* gListVector;
        SparseMatrix* gSparseMatrix;
+       void reset();   //clears all non filename parameters
+       
        
        
 };
 
-//**********************************************************************************************************************
-
 #endif