fixed valid parameters to include shared parameter for read.shared command.

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index 80891677d6e27d9f9e1e9671df4b128a962da116..0dc4c348584989f101567c229c8246158f5ca70c 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -1,9 +1,7 @@
 #ifndef GLOBALDATA_HPP
 #define GLOBALDATA_HPP
 
-#include <string>
-#include <vector>
-#include <set>
+#include "mothur.h"
 #include "groupmap.h"
 #include "treemap.h"
 
@@ -12,6 +10,7 @@ using namespace std;
 class ListVector;
 class SharedListVector;
 class SparseMatrix;
+class FullMatrix;
 class Tree;
 class OrderVector;
 class InputData;
@@ -31,13 +30,13 @@ public:
        SharedListVector* gSharedList;
        SAbundVector* sabund;
        GroupMap* gGroupmap;
+       FullMatrix* gMatrix;
        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
-       vector<string> Groups;
        
        string getPhylipFile();
        string getColumnFile();
@@ -49,6 +48,7 @@ public:
        string getOrderFile();
        string getFastaFile();
        string getTreeFile();
+       string getSharedFile();
        string getCutOff();
        string getFormat();
        string getPrecision();
@@ -57,7 +57,10 @@ public:
        string getIters();
        string getJumble();
        string getFreq();
+       string getAbund();
        string getRandomTree();
+       string getGroups();
+
        void setListFile(string);
        void setPhylipFile(string);
        void setColumnFile(string);
@@ -66,22 +69,22 @@ public:
        void setSabundFile(string);
        void setFormat(string);
        void setRandomTree(string);
+       void setGroups(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, randomtree, groups;
-       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
@@ -89,10 +92,10 @@ private:
        ~GlobalData();
        ListVector* gListVector;
        SparseMatrix* gSparseMatrix;
+       void reset();   //clears all non filename parameters
+       
        
        
 };
 
-//**********************************************************************************************************************
-
 #endif