broke up globaldata and moved error checking and help into commands

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index 1bccc34f58fa6fcaf136bab32cd74f5093babda7..1d38d63afc4df198599b77cf725b734c531a33ac 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -4,37 +4,45 @@
 #include "mothur.h"
 #include "groupmap.h"
 #include "treemap.h"
-
-using namespace std;
+#include "rabundvector.hpp"
+#include "sabundvector.hpp"
+#include "listvector.hpp"
 
 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;
+       FullMatrix* gMatrix;
        TreeMap* gTreemap;
-       string inputFileName, helpRequest, commandName;
-       bool allLines;
+       SequenceDB* gSequenceDB;
+       string inputFileName, argv;
+       bool allLines, runParse;
        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();
@@ -47,49 +55,38 @@ public:
        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 getCandidateFile();
+               
        void setListFile(string);
+       void setFastaFile(string);
+       void setTreeFile(string);
+       void setCandidateFile(string);
+       void setGroupFile(string);      
        void setPhylipFile(string);
        void setColumnFile(string);
        void setNameFile(string);
        void setRabundFile(string);
        void setSabundFile(string);
+       void setSharedFile(string);
+       void setOrderFile(string file);
        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 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, fastafile, treefile, sharedfile, format, candidatefile;
 
        static GlobalData* _uniqueInstance;
        GlobalData( const GlobalData& ); // Disable copy constructor
        void operator=( const GlobalData& ); // Disable assignment operator
        GlobalData();
        ~GlobalData();
-       ListVector* gListVector;
-       SparseMatrix* gSparseMatrix;
-       void reset();   //clears all non filename parameters
-       
        
        
 };