made sorting optional but sort by default, in case the user wants to see the heatmap...

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index 31a63b67adad73bd7e46487a4849cee6135f6ede..f74619e29c792d28486447c919281f88b5d03ba0 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -1,16 +1,7 @@
 #ifndef GLOBALDATA_HPP
 #define GLOBALDATA_HPP
 
-#include <string>
-#include <vector>
-#include <set>
-#include <iostream>
-#include <iomanip>
-#include <map>
-#include <sstream>
-#include <stdexcept>
-#include <exception>
-
+#include "mothur.h"
 #include "groupmap.h"
 #include "treemap.h"
 
@@ -19,6 +10,7 @@ using namespace std;
 class ListVector;
 class SharedListVector;
 class SparseMatrix;
+class FullMatrix;
 class Tree;
 class OrderVector;
 class InputData;
@@ -29,8 +21,8 @@ class SAbundVector;
 class GlobalData {
 public:
        static GlobalData* getInstance();
-       ListVector* getListVector();
-       SparseMatrix* getSparseMatrix();
+       ListVector* gListVector;
+       SparseMatrix* gSparseMatrix;
        InputData* ginput;
        OrderVector* gorder;
        ListVector* glist;
@@ -38,6 +30,7 @@ public:
        SharedListVector* gSharedList;
        SAbundVector* sabund;
        GroupMap* gGroupmap;
+       FullMatrix* gMatrix;
        TreeMap* gTreemap;
        string inputFileName, helpRequest, commandName;
        bool allLines;
@@ -66,6 +59,10 @@ public:
        string getFreq();
        string getAbund();
        string getRandomTree();
+       string getGroups();
+       string getStep();
+       string getForm();
+       string getSorted();
 
        void setListFile(string);
        void setPhylipFile(string);
@@ -75,11 +72,9 @@ 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();
@@ -88,15 +83,13 @@ public:
                
 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 cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted;
 
        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