removed line option

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index 6070dd7b2cdd6122b78c5833359ce487497fd0e3..e125e6f3d7032d78d2b1330dece6cf909a6bf320 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -4,8 +4,13 @@
 #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"
 
-using namespace std;
 
 class ListVector;
 class SharedListVector;
@@ -17,6 +22,8 @@ class InputData;
 class GroupMap;
 class TreeMap;
 class SAbundVector;
+class RAbundVector;
+class SequenceDB;
 
 class GlobalData {
 public:
@@ -29,66 +36,58 @@ public:
        vector<Tree*> gTree;
        SharedListVector* gSharedList;
        SAbundVector* sabund;
+       RAbundVector* rabund;
        GroupMap* gGroupmap;
        FullMatrix* gMatrix;
        TreeMap* gTreemap;
-       string inputFileName, helpRequest, commandName;
-       bool allLines;
+       SequenceDB* gSequenceDB;
+       string inputFileName, argv;
+       bool allLines, runParse, jumble;
        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
+       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 getTreeFile();
        string getSharedFile();
-       string getCutOff();
-       string getFormat();
-       string getPrecision();
-       string getMethod();
-       string getFileRoot();
-       string getIters();
-       string getJumble();
-       string getFreq();
-       string getAbund();
-       string getRandomTree();
-       string getGroups();
+       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 setRandomTree(string);
-       void setGroups(string);
-       void setCalc(string);
-
+       void setSharedFile(string);
+       void setOrderFile(string file);
+       void setFormat(string); //do we need this?
+       
        void clear(); 
        void clearLabels();
        void clearAbund();
        
-       void parseGlobalData(string, string);
-               
+       void newRead();
+       
 private:
-       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;
+
+       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format;
 
        static GlobalData* _uniqueInstance;
        GlobalData( const GlobalData& ); // Disable copy constructor
        void operator=( const GlobalData& ); // Disable assignment operator
        GlobalData();
        ~GlobalData();
-       void reset();   //clears all non filename parameters
-       
        
        
 };