added errorchecking and help info on new unifrac and treeclimber code

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index 5a1572c26f582a02ae82dcfb729d4be2068ec6f5..80891677d6e27d9f9e1e9671df4b128a962da116 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -5,15 +5,18 @@
 #include <vector>
 #include <set>
 #include "groupmap.h"
+#include "treemap.h"
 
 using namespace std;
 
 class ListVector;
 class SharedListVector;
 class SparseMatrix;
+class Tree;
 class OrderVector;
 class InputData;
 class GroupMap;
+class TreeMap;
 class SAbundVector;
 
 class GlobalData {
@@ -24,14 +27,17 @@ public:
        InputData* ginput;
        OrderVector* gorder;
        ListVector* glist;
+       vector<Tree*> gTree;
        SharedListVector* gSharedList;
        SAbundVector* sabund;
        GroupMap* gGroupmap;
+       TreeMap* gTreemap;
        string inputFileName, helpRequest, commandName;
        bool allLines;
        vector<string> singleEstimators, summaryEstimators, sharedEstimators, rareEstimators, sharedRareEstimators, sharedSummaryEstimators; //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();
@@ -42,6 +48,7 @@ public:
        string getGroupFile();
        string getOrderFile();
        string getFastaFile();
+       string getTreeFile();
        string getCutOff();
        string getFormat();
        string getPrecision();
@@ -50,6 +57,7 @@ public:
        string getIters();
        string getJumble();
        string getFreq();
+       string getRandomTree();
        void setListFile(string);
        void setPhylipFile(string);
        void setColumnFile(string);
@@ -57,6 +65,7 @@ public:
        void setRabundFile(string);
        void setSabundFile(string);
        void setFormat(string);
+       void setRandomTree(string);
 
        
        void setListVector(ListVector*);
@@ -71,7 +80,7 @@ public:
        void splitAtDash(string&, set<string>&);
        
 private:
-       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile,line, label;
+       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;
        static GlobalData* _uniqueInstance;
        GlobalData( const GlobalData& ); // Disable copy constructor
@@ -81,6 +90,7 @@ private:
        ListVector* gListVector;
        SparseMatrix* gSparseMatrix;
        
+       
 };
 
 //**********************************************************************************************************************