merged pat's trim seqs edits with sarah's major overhaul of global data; also added...

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index a5477fff1d06b95aa35b6c1dc7d697bb0288246a..6515521768bfe2291775965e80eb94eac4d7a760 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -1,86 +1,98 @@
 #ifndef GLOBALDATA_HPP
 #define GLOBALDATA_HPP
 
-#include <string>
-#include <vector>
-#include <set>
+#include "mothur.h"
 #include "groupmap.h"
-
-using namespace std;
+#include "treemap.h"
+#include "rabundvector.hpp"
+#include "sabundvector.hpp"
+#include "listvector.hpp"
+#include "tree.h"
+#include "sparsematrix.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;
-       string inputFileName, helpRequest, commandName;
-       bool allLines;
-       vector<string> singleEstimators, summaryEstimators, sharedEstimators, rareEstimators, sharedRareEstimators, sharedSummaryEstimators; //holds estimators to be used
+       FullMatrix* gMatrix;
+       TreeMap* gTreemap;
+       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();
        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 getCutOff();
-       string getFormat();
-       string getPrecision();
-       string getMethod();
-       string getFileRoot();
-       string getIters();
-       string getJumble();
-       string getFreq();
+//     string getFastaFile();
+       string getTreeFile();
+       string getSharedFile();
+       string getFormat();     //do we need this?
+//     string getCandidateFile();
+//     string getTemplateFile();
+
        void setListFile(string);
+//     void setFastaFile(string);
+       void setTreeFile(string);
+//     void setCandidateFile(string);
+//     void setTemplateFile(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 setSharedFile(string);
+       void setOrderFile(string file);
+       void setFormat(string); //do we need this?
        
-       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>&);
+       void newRead();
        
 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, treefile, sharedfile, format;
+
        static GlobalData* _uniqueInstance;
        GlobalData( const GlobalData& ); // Disable copy constructor
        void operator=( const GlobalData& ); // Disable assignment operator
        GlobalData();
        ~GlobalData();
-       ListVector* gListVector;
-       SparseMatrix* gSparseMatrix;
-       void setReadFormat(string);
        
-       };
-
-//**********************************************************************************************************************
+       
+};
 
 #endif