added mothur.h and fixed includes in many files

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index a5477fff1d06b95aa35b6c1dc7d697bb0288246a..1bccc34f58fa6fcaf136bab32cd74f5093babda7 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -1,18 +1,20 @@
 #ifndef GLOBALDATA_HPP
 #define GLOBALDATA_HPP
 
-#include <string>
-#include <vector>
-#include <set>
+#include "mothur.h"
 #include "groupmap.h"
+#include "treemap.h"
 
 using namespace std;
 
 class ListVector;
+class SharedListVector;
 class SparseMatrix;
+class Tree;
 class OrderVector;
 class InputData;
 class GroupMap;
+class TreeMap;
 class SAbundVector;
 
 class GlobalData {
@@ -23,11 +25,14 @@ public:
        InputData* ginput;
        OrderVector* gorder;
        ListVector* glist;
+       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
        
@@ -39,6 +44,9 @@ public:
        string getNameFile();
        string getGroupFile();
        string getOrderFile();
+       string getFastaFile();
+       string getTreeFile();
+       string getSharedFile();
        string getCutOff();
        string getFormat();
        string getPrecision();
@@ -47,6 +55,9 @@ public:
        string getIters();
        string getJumble();
        string getFreq();
+       string getAbund();
+       string getRandomTree();
+
        void setListFile(string);
        void setPhylipFile(string);
        void setColumnFile(string);
@@ -54,22 +65,22 @@ 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, 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
@@ -77,10 +88,10 @@ private:
        ~GlobalData();
        ListVector* gListVector;
        SparseMatrix* gSparseMatrix;
-       void setReadFormat(string);
+       void reset();   //clears all non filename parameters
        
-       };
-
-//**********************************************************************************************************************
+       
+       
+};
 
 #endif